• This record comes from PubMed

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1

. 2021 Jan ; 17 (1) : 1-382. [epub] 20210208

Language English Country United States Media print-electronic

Document type Guideline, Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.

Persistent link   https://www.medvik.cz/link/pmid33634751

Grant support
U01 AR076092 NIAMS NIH HHS - United States
R01 DK015658 NIDDK NIH HHS - United States
R01 AI083387 NIAID NIH HHS - United States
R01 DK108835 NIDDK NIH HHS - United States
MRF_C0483 MRF - United Kingdom CEP Register
K08 CA230151 NCI NIH HHS - United States
R01 CA211070 NCI NIH HHS - United States
R15 GM122035 NIGMS NIH HHS - United States
R35 GM127029 NIGMS NIH HHS - United States
R35 GM130331 NIGMS NIH HHS - United States
R01 DK114401 NIDDK NIH HHS - United States
R01 NS105971 NINDS NIH HHS - United States
R35 HL135736 NHLBI NIH HHS - United States
P01 CA140043 NCI NIH HHS - United States
R21 DE028256 NIDCR NIH HHS - United States
R01 HL126933 NHLBI NIH HHS - United States
MR/M00869X/2 Medical Research Council - United Kingdom
R01 ES029092 NIEHS NIH HHS - United States
K08 AI102971 NIAID NIH HHS - United States
R01 HL088256 NHLBI NIH HHS - United States
MR/T002220/1 Medical Research Council - United Kingdom
R01 DK057993 NIDDK NIH HHS - United States
R01 DK110162 NIDDK NIH HHS - United States
R01 AI130454 NIAID NIH HHS - United States
R01 CA140964 NCI NIH HHS - United States
R01 DK125513 NIDDK NIH HHS - United States
R01 CA229275 NCI NIH HHS - United States
R35 GM131681 NIGMS NIH HHS - United States
R01 AR077440 NIAMS NIH HHS - United States
29800 Cancer Research UK - United Kingdom
R35 GM131919 NIGMS NIH HHS - United States
T32 DK007745 NIDDK NIH HHS - United States
R01 DK093668 NIDDK NIH HHS - United States
L30 AI091018 NIAID NIH HHS - United States
R01 AI087682 NIAID NIH HHS - United States
T32 HL134621 NHLBI NIH HHS - United States
RF1 NS083704 NINDS NIH HHS - United States
R01 AG049780 NIA NIH HHS - United States
R01 AG061447 NIA NIH HHS - United States
R15 NS075684 NINDS NIH HHS - United States
R01 HL107594 NHLBI NIH HHS - United States
16337 Cancer Research UK - United Kingdom
R01 CA252707 NCI NIH HHS - United States
I01 BX004444 BLRD VA - United States
R01 NS095634 NINDS NIH HHS - United States
P01 DK098108 NIDDK NIH HHS - United States
P30 ES006694 NIEHS NIH HHS - United States
R21 CA209345 NCI NIH HHS - United States
R01 NS103981 NINDS NIH HHS - United States
R01 AI136921 NIAID NIH HHS - United States
R01 AG057509 NIA NIH HHS - United States
BBS/E/B/000C0413 Biotechnology and Biological Sciences Research Council - United Kingdom
MR/N022696/1 Medical Research Council - United Kingdom
R35 CA232113 NCI NIH HHS - United States
MR/R009732/1 Medical Research Council - United Kingdom
R01 HL133545 NHLBI NIH HHS - United States
K08 AG050808 NIA NIH HHS - United States
G0501003 Medical Research Council - United Kingdom
R01 EY026885 NEI NIH HHS - United States
MC_UU_00018/2 Medical Research Council - United Kingdom
R01 GM118660 NIGMS NIH HHS - United States
R01 DK124308 NIDDK NIH HHS - United States
MR/R025096/1 Medical Research Council - United Kingdom
R01 HL077328 NHLBI NIH HHS - United States
P30 ES005022 NIEHS NIH HHS - United States
R15 GM102846 NIGMS NIH HHS - United States
R01 DK130879 NIDDK NIH HHS - United States
R01 NS115403 NINDS NIH HHS - United States
R01 DK112698 NIDDK NIH HHS - United States
P30 AG024824 NIA NIH HHS - United States
R01 GM115517 NIGMS NIH HHS - United States
R01 DK124901 NIDDK NIH HHS - United States
R01 DK123447 NIDDK NIH HHS - United States
I01 BX004306 BLRD VA - United States
R01 CA160417 NCI NIH HHS - United States
R01 CA184137 NCI NIH HHS - United States
R35 HL145241 NHLBI NIH HHS - United States
R01 EY018341 NEI NIH HHS - United States
R01 CA238457 NCI NIH HHS - United States
R01 NS042023 NINDS NIH HHS - United States
R01 EY019643 NEI NIH HHS - United States
R56 AG063820 NIA NIH HHS - United States
R01 AI139046 NIAID NIH HHS - United States
R35 GM136325 NIGMS NIH HHS - United States
P30 DK089503 NIDDK NIH HHS - United States
R01 HL141759 NHLBI NIH HHS - United States
R01 HL085629 NHLBI NIH HHS - United States
R15 NS104857 NINDS NIH HHS - United States
24453 Cancer Research UK - United Kingdom
R01 HL118558 NHLBI NIH HHS - United States
R01 HL153614 NHLBI NIH HHS - United States
P20 GM121176 NIGMS NIH HHS - United States
R35 GM131689 NIGMS NIH HHS - United States
R01 ES031253 NIEHS NIH HHS - United States
R01 HL132318 NHLBI NIH HHS - United States
I01 BX001516 BLRD VA - United States
R01 DK108921 NIDDK NIH HHS - United States
U54 GM104942 NIGMS NIH HHS - United States
R37 AI042999 NIAID NIH HHS - United States
R01 HL154147 NHLBI NIH HHS - United States
R01 GM101972 NIGMS NIH HHS - United States
MR/S009426/1 Medical Research Council - United Kingdom
R01 AI111935 NIAID NIH HHS - United States
R01 CA244144 NCI NIH HHS - United States
R01 AI113919 NIAID NIH HHS - United States
R01 NS094154 NINDS NIH HHS - United States
MC_U105184308 Medical Research Council - United Kingdom
IK6 BX005793 BLRD VA - United States
R01 AG064892 NIA NIH HHS - United States
R01 GM119160 NIGMS NIH HHS - United States
R01 CA227838 NCI NIH HHS - United States
R01 AR070837 NIAMS NIH HHS - United States
MC_U105170648 Medical Research Council - United Kingdom
R35 GM119571 NIGMS NIH HHS - United States
R01 CA247992 NCI NIH HHS - United States
MR/S032304/1 Medical Research Council - United Kingdom
R01 AA019730 NIAAA NIH HHS - United States
R01 GM102297 NIGMS NIH HHS - United States
R01 NS089737 NINDS NIH HHS - United States
R21 NS102780 NINDS NIH HHS - United States
BBS/E/F/000PR10355 Biotechnology and Biological Sciences Research Council - United Kingdom
R01 NS115876 NINDS NIH HHS - United States
15816 Cancer Research UK - United Kingdom
R01 HL153599 NHLBI NIH HHS - United States
R01 EY027733 NEI NIH HHS - United States
R01 NS110943 NINDS NIH HHS - United States
UKDRI-2002 Medical Research Council - United Kingdom
R01 DK121545 NIDDK NIH HHS - United States
R01 CA181196 NCI NIH HHS - United States
R01 GM111295 NIGMS NIH HHS - United States
R01 AI122176 NIAID NIH HHS - United States
R01 NS093362 NINDS NIH HHS - United States
P30 EY001583 NEI NIH HHS - United States
R01 AG062475 NIA NIH HHS - United States
R01 DK117965 NIDDK NIH HHS - United States
P30 CA014236 NCI NIH HHS - United States
R01 NS118146 NINDS NIH HHS - United States
29576 Cancer Research UK - United Kingdom
R01 NS083704 NINDS NIH HHS - United States
R01 NS093843 NINDS NIH HHS - United States
P50 AA011999 NIAAA NIH HHS - United States
R01 NS110716 NINDS NIH HHS - United States
R01 CA190370 NCI NIH HHS - United States
RF1 AG058476 NIA NIH HHS - United States
206444/Z/17/Z Wellcome Trust - United Kingdom
R01 CA237536 NCI NIH HHS - United States
P30 DK020572 NIDDK NIH HHS - United States
R01 DK099558 NIDDK NIH HHS - United States
R25 NS070682 NINDS NIH HHS - United States
P30 DK084567 NIDDK NIH HHS - United States
I01 BX004235 BLRD VA - United States
R01 AI072648 NIAID NIH HHS - United States
R35 GM122536 NIGMS NIH HHS - United States
R01 DK113170 NIDDK NIH HHS - United States
R01 HL072166 NHLBI NIH HHS - United States
R01 DK024031 NIDDK NIH HHS - United States
R01 CA197398 NCI NIH HHS - United States
29754 Cancer Research UK - United Kingdom
R01 CA200310 NCI NIH HHS - United States
R01 GM127791 NIGMS NIH HHS - United States
R01 DK107220 NIDDK NIH HHS - United States
R01 CA233794 NCI NIH HHS - United States
PG/17/14/32867 British Heart Foundation - United Kingdom
MC_EX_G0800785 Medical Research Council - United Kingdom
P01 AG054407 NIA NIH HHS - United States
I01 BX000774 BLRD VA - United States
R01 AG062375 NIA NIH HHS - United States
R01 AG067664 NIA NIH HHS - United States
R01 DK121759 NIDDK NIH HHS - United States
R01 AI132697 NIAID NIH HHS - United States
P01 AG031782 NIA NIH HHS - United States
R41 CA271967 NCI NIH HHS - United States
I01 BX003803 BLRD VA - United States
R01 AI124121 NIAID NIH HHS - United States
R01 AI054476 NIAID NIH HHS - United States
R01 AR061370 NIAMS NIH HHS - United States
R01 HL142879 NHLBI NIH HHS - United States
R01 EY029675 NEI NIH HHS - United States
R00 GM117218 NIGMS NIH HHS - United States
R01 HL123340 NHLBI NIH HHS - United States

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

1st Affiliated Hospital of Nanjing Medical University Department of Neurosurgery Nanjing China; Jiangsu Province Hospital Department of Neurosurgery Nanjing China

1st Affiliated Hospital of Nanjing Medical University Jiangsu Province Hospital Nanjing China

1st Affiliated Hospital of Xi'an Jiaotong University School of Medicine Center for Translational Medicine Xi'an Shaanxi China

2nd Affiliated Hospital of Zhejiang University School of Medicine Department of Respiratory and Critical Care Medicine Hangzhou China

3 Department of Medicine University Medical Center Hamburg Eppendorf Hamburg Germany

3rd Department of Internal Medicine University of Occupational and Environmental Health Kitakyushu Japan

3rd Military Medical University College of Pharmacy Department of Pharmacology Chongqing China

3rd Military Medical University Department of Occupational Health Chongqing China

3rd Military Medical University of China Xinqiao Hospital Institute of Respiratory Diseases Chongqing China

3rd Military Medical University Southwest Hospital Institute of Pathology and Southwest Cancer Centre Chongqing China

4th Medical Center of the Chinese PLA General Hospital Trauma Research Center Beijing China

4th Military Medical University College of Stomatology Department of Oral Anatomy and Physiology and TMD Xi'an China

4th Military Medical University School of Aerospace Medicine Xi'an China

A 5 Zhirmunsky National Scientific Center of Marine Biology Laboratory of Pharmacology Far Eastern Branch Russian Academy of Sciences Vladivostok Russian Federation

Aarhus University Department of Biomedicine Aarhus Denmark

Aarhus University Department of Molecular Biology and Genetics Aarhus C Denmark

Aarhus University Hospital Steno Diabetes Center Aarhus Aarhus Denmark

Aarhus University Hospital Steno Diabetes Center Aarhus Aarhus Denmark; Aarhus University Department of Clinical Medicine Research Laboratory for Biochemical Pathology Aarhus Denmark

Academia Sinica Institute of Biological Chemistry Taipei Taiwan

Academia Sinica Institute of Cellular and Organismic Biology Taipei Taiwan

Academic Decency MeTooSTEM Nashville TN USA

Achucarro Basque Center for Neuroscience Department of Neurosciences University of the Basque Country EHU UPV Leioa Bizkaia Spain

Achucarro Basque Center for Neuroscience Department of Pharmacology University of the Basque Country EHU UPV Leioa Bizkaia Spain

Adam Mickiewicz University Faculty of Biology Institute of Experimental Biology Department of General Botany Poznan Poland

Affiliated Cancer Hospital and Institute of Guangzhou Medical University Guangzhou China

Affiliated Hospital of GuangDong Medical University Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City Zhanjiang Guangdong China

Affiliated Union Hospital of Fujian Medical University Fuzhou Fujian China

Agricultural Biotechnology Research Institute of Iran Department of Systems Biology Karaj Iran

Ain Shams University Faculty of Medicine Department of Medical Biochemistry and Molecular Biology Cairo Egypt

Air Force Medical University Xijing Hospital and School of Basic Medicine Department of Pathology State Key Laboratory of Cancer Biology Xi'an China

Air Force Medical University Xijing Hospital Department of Clinical Laboratory Xi'an China

Air Force Medical University Xijing Hospital Department of Plastic and Reconstructive Surgery Xi'an China

Aix Marseille Univ CNRS LISM Institut de Microbiologie de la Méditerranée Marseille France

Aix Marseille Université CNRS INSERM CIML 13288 Marseille cedex 9 France; Institute for Research in Biomedicine and Ilidio Pinho Foundation Department of Medical Sciences University of Aveiro 3810 193 Aveiro Portugal; Shanghai Institute of Immunology Department of Microbiology and Immunology Shanghai Jiao Tong University School of Medicine Shanghai 200025 PR China

Ajou University College of Pharmacy and Research Institute of Pharmaceutical Science and Technology Suwon Korea

Ajou University Graduate School of Medicine Department of Biomedical Sciences Suwon Gyeonggi Korea

Akita University Graduate School of Medicine Department of Ophthalmology Akita Japan

Albert Einstein College of Medicine Department of Developmental and Molecular Biology and Department of Genetics New York NY USA

Albert Einstein College of Medicine Department of Developmental and Molecular Biology Bronx NY USA

Albert Einstein College of Medicine Department of Developmental and Molecular Biology Bronx NY USA; Albert Einstein College of Medicine Institute for Aging Studies Bronx NY USA

Albert Einstein College of Medicine Department of Genetics Bronx NY USA

Albert Einstein College of Medicine Department of Medicine Bronx NY USA

Albert Einstein College of Medicine Department of Molecular Pharmacology Bronx NY USA

Albert Einstein College of Medicine Department of Pathology Bronx NY USA

Albert Einstein College of Medicine Departments of Medicine and Cell Biology and Wilf Family Cardiovascular Research Institute Bronx NY USA

Albert Einstein College of Medicine Departments of Molecular Pharmacology and Biochemistry Bronx NY USA

Albert Einstein College of Medicine Institute for Aging Studies Department of Developmental and Molecular Biology Bronx NY USA

Albert Einstein College of Medicine Radiation Oncology Bronx NY USA

Albert Ludwigs University of Freiburg Faculty of Medicine Institute of Molecular Medicine and Cell Research Freiburg Germany

All India Institute of Medical Sciences Department of Biotechnology New Delhi India

Alpert Medical School of Brown University Rhode Island Hospital Division of Cardiothoracic Surgery Providence RI USA

Amgen Inc South San Francisco CA USA

Amrita Vishwa Vidyapeetham School of Biotechnology Kollam Kerala India

Amsterdam University Medical Centers Location AMC Tytgat Institute for Intestinal Research Department of Gastroenterology and Hepatology Amsterdam The Netherlands

Amsterdam University Medical Centers location VUmc Department of Clinical Genetics Amsterdam The Netherlands

Anhui Province Key Laboratory of Medical Physics and Technology Center of Medical Physics and Technology Hefei Institutes of Physical Science Chinese Academy of Sciences Hefei Anhui China; University of Science and Technology of China Anhui China

Anhui University of Science and Technology Department of Medical Immunology Huainan China

Applied Biotechnology Research Center Baqiyatallah University of Medical Sciences Tehran P O Box 19395 5487 Iran

Arizona State University Phoenix AZ USA

Army Medical University Daping Hospital Center of Bone Metabolism and Repair State Key Laboratory of Trauma Burns and Combined Injury Trauma Center Research Institute of Surgery Laboratory for the Prevention and Rehabilitation of Military Training Related Injuries Chongqing China

Army Medical University Daping Hospital Center of Bone Metabolism and Repair State Key Laboratory of Trauma Burns and Combined Injury Trauma Center Research Institute of Surgery Laboratory for the Prevention and Rehabilitation of Training Related Injuries Chongqing China

Army Medical University Department of Bichemistry and Molecular Biology Chongqing Chongqing China

Asahikawa Medical University Department of Ophthalmology Hokkaido Japan

AstraZeneca Bioscience Oncology R and D Cambridge UK

Australian Regenerative Medicine Institute Monash University Clayton Victoria Australia

Autophagy Research Center Health Policy Research Center Institute of Health Shiraz University of Medical Sciences Shiraz Iran

Babraham Institute Babraham Cambridge UK

Babraham Institute Cambridge UK

Babraham Institute Signalling ISP Cambridge UK

Banaras Hindu University Institute of Science Department of Zoology Lanka Varanasi Uttar Pradesh India

Bar Ilan University Azrieli Faculty of Medicine Safed Israel

Barcelona Institute of Science and Technology Barcelona Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas Barcelona Spain; Universitat de Barcelona Facultat de Biologia Departament de Bioquimica i Biomedicina Molecular Barcelona Spain

Barkatullah University Department of Biochemistry and Genetics Bhopal India

Barts Cancer Institute Queen Mary University of London Centre for Biotherapeutics and Biomarkers London UK

Baruch S Blumberg Institute Pennsylvania Cancer and Regenerative Medicine Research Center Wynnewood PA USA; Xavier University School of Medicine Woodbury NY USA

Baylor College of Medicine Department of Biochemistry and Molecular Biology Houston TX USA

Baylor College of Medicine Department of Medicine Houston TX USA

Baylor College of Medicine Department of Molecular and Human Genetics Houston TX USA

Baylor College of Medicine Department of Molecular Physiology and Biophysics Houston TX USA

Baylor College of Medicine Jan and Dan Duncan Neurological Research Institute and Department of Molecular and Human Genetics Houston TX USA

BC Cancer Michael Smith Genome Sciences Centre Vancouver BC Canada

BC Cancer Research Centre Department of Experimental Therapeutics Vancouver BC Canada

BC Cancer Trev and Joyce Deeley Research Centre Victoria BC Canada; University of Victoria Department of Biochemistry and Microbiology Victoria BC Canada

Beckman Research Institute at City of Hope Department of Systems Biology Monrovia CA USA

Beijing Academy of Agriculture and Forestry Sciences Institute of Plant and Environment Protection Beijing China

Beijing Institute of Basic Medical Sciences Beijing China

Beijing Institute of Genomics Chinese Academy of Sciences Beijing China

Bellvitge Biomedical Research Institute IDIBELL Oncobell Program L'Hospitalet de Llobregat Barcelona Spain

Ben Gurion University of the Negev Department of Chemistry Be'er Sheva Israel

Ben Gurion University of the Negev Faculty of Health Sciences Department of Clinical Biochemistry and Pharmacology Beer Sheva Israel

Ben May Department for Cancer Research University of Chicago Chicago IL USA

Beth Israel Deaconess Medical Center Harvard Medical School Boston MA USA

Biodonostia Health Research Institute group of Cellular Oncology; IKERBASQUE; CIBERfes Spain

Biomedical Research Foundation Academy of Athens Center of Clinical Experimental Surgery and Translational Research Athens Greece

Biomedical Research Foundation of the Academy of Athens Center of Clinical Experimental Surgery and Translational Research Athens Greece

Biomedical Research Foundation of the Academy of Athens Laboratory of Neurodegenerative Diseases Athens Greece; National and Kapodistrian University of Athens Medical School 1st Department of Neurology Athens Greece

Biomedical Research Institute of Murcia IMIB Arrixaca Telomerase Cancer and Aging Group Surgical Department Murcia Spain

Biomedical Research Institute of New Mexico VA Healthcare System Albuquerque NM USA

Bispebjerg Hospital Institute of Sports Medicine Copenhagen Copenhagen Denmark; UniCamillus Saint Camillus International University of Health Sciences Rome Italy

Bogazici University Department of Molecular Biology and Genetics Bebek Istanbul Turkey

Boston Children's Hospital and Harvard Medical School Boston MA USA

Boston Children's Hospital Harvard Medical School Departments of Urology and Surgery Boston MA USA

Boston University Department of Biology Boston MA USA

Boston University Department of Biomedical Engineering Boston MA USA

Boston University Department of Pathology and Laboratory Medicine Boston MA USA

Boston University Departments of Biomedical Engineering Chemistry and Medicine Boston MA USA

Boston University Metcalf Science Center Boston MA USA

Boston University School of Medicine Division of Hematology and Medical Oncology Department of Pharmacology and Experimental Therapeutics Boston MA USA

Botucatu Medical School São Paulo State University Botucatu SP Brazil

Brandeis University Department of Biology and Rosenstiel Basic Medical Sciences Research Center Waltham MA USA

Brigham and Women's Hospital Harvard Medical School Center for Nanomedicine and Department of Anesthesiology Boston MA USA

Bristol Medical School University of Bristol Bristol UK

Buchmann Institute and Institute of Biochemistry 2 Medical Faculty Goethe University Frankfurt Germany

Buenos Aires University Biochemistry and Pharmacy School Deparment of Microbiology Immunology Biotechnology and Genetic IDEHU CABA Argentina

Bulgarian Academy of Sciences Institute of Biology and Immunology of Reproduction Acad Kiril Bratanov Sofia Bulgaria

Burnet Institute Melbourne Australia

CABD CSIC Universidad Pablo de Olavide Departamento de Fisiología Anatomía y Biología Celular Sevilla Spain

CAESAR Research Center Bonn Germany

Cajal Institute CSIC and CIBERNED ISCIII Madrid Spain

California Institute of Technology Division of Biology and Biological Engineering Pasadena CA USA

Cancer Drug Resistance and Stem Cell Program University of Sydney NSW Australia

Cancer Institute of the 2nd Affiliated Hospital and Institute of Translational Medicine Zhejiang University School of Medicine Hangzhou Zhejiang China

Cancer Research Center of Toulouse INSERM U1037 CNRS ERL5294 University of Toulouse Toulouse France

Cancer Research Center of Toulouse UMR 1037 Inserm university of Toulouse Toulouse France

Cancer Research UK Beatson Institute Glasgow UK

Cancer Research UK Beatson Institute Glasgow UK; University of Glasgow Institute of Cancer Sciences Glasgow UK

Cancer Research UK Cancer Therapeutics Unit The Institute of Cancer Research London Sutton UK

Capital Medical University Beijing Ditan Hospital Liver Disease Center Beijing China

Capital Medical University Beijing Institute for Brain Disorders Beijing China

Capital Medical University School of Basic Medical Sceinces Department of Neurobiology Beijing China

Cardiff University Division of Cancer and Genetics Heath Park Cardiff UK

Cardiff University Division of Cancer and Genetics Heath Park Way Cardiff UK

Carité Universitaetsmedizin Berlin Campus Mitte Institut für Integrative Neuroanatomie Berlin Germany

Carl von Ossietzky University Oldenburg School of Medicine and Health Sciences Department for Neuroscience Oldenburg Germany

CAS Center for Excellence in Nanoscience CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology Zhongguancun Beijing China

CAS Key Laboratory of Regenerative Biology Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences Guangzhou China

Case Western Reserve University Comprehensive Cancer Center Cleveland OH USA

Case Western Reserve University School of Medicine Department of Pediatrics Cleveland OH USA; InterRayBio LLC Baltimore MD USA

Case Western Reserve University School of Medicine Departments of Medicine and Pathology Cleveland OH USA

Cedars Sinai Medical Center Department of Medicine Division of Digestive and Liver Diseases Los Angeles CA USA

Cedars Sinai Medical Center Smidt Heart Institute Los Angeles CA USA

Cell and Developmental Biology Center National Heart Lung and Blood Institute National Institutes of Health Bethesda MD USA

Cell Death Research and Therapy Lab Department of Cellular and Molecular Medicine Center for Cancer Biology VIB KU Leuven Leuven Belgium

Cellular and Molecular Signaling New York NY USA

Cellular Microbiology and Physics of Infection Group Center for Infection and Immunity of Lille Institut Pasteur de Lille CNRS INSERM CHU Lille University of Lille Lille Cedex France

Centenary Institute The University of Sydney Newtown New South Wales Australia; Faculty of Medicine and Health The University of Sydney Newtown New South Wales Australia

Center for gender specific medicine Italian National Health Institute Rome Italy

Center for Global Health Catholic University of the Sacred Heart Rome Italy

Center for Molecular Biology of Heidelberg University DKFZ ZMBH Alliance Heidelberg Germany

Center for Molecular Medicine Maine Medical Center Research Institute Scarborough ME USA

Center for Systems and Therapeutics Gladstone Institutes; Departments of Neurology and Physiology University of California San Francisco San Francisco CA USA

Center of Toxins Immune response and Cell Signaling Instituto Butantan São Paulo Brazil

Center of Translational Immunlogy University Medical Center Utrecht Utrecht The Netherlands

Central China Normal University College of Life Sciences Wuhan Hubei Province China

Central Michigan University Department of Psychology and Neuroscience Program Mt Pleasant MI USA

Central South University School of Life Sciences Molecular Biology Research Center Changsha Hunan China

Central South University The 2nd Xiang Ya Hospital National Clinical Research Center for Metabolic Diseases Department of Metabolism and Endocrinology Changsha Hunan China

Central South University The 2nd Xiangya Hospital Department of Nephrology Changsha Hunan China

Central University of Tamil Nadu Thiruvarur Tamil Nadu India

Centre de Recherche des Cordeliers INSERM UMRS 1138 Sorbonne Université Université de Paris Equipe 11 labellisée par la Ligue contre le Cancer 75006 Paris France; Metabolomics and Cell Biology Platforms Institut Gustave Roussy 94805 Villejuif France

Centre de Recherche des Cordeliers INSERM Université de Paris Sorbonne Université Paris France

Centre de Recherche en Cancérologie de Marseille INSERM U1068 CNRS UMR 7258 Aix Marseille Université and Institut Paoli Calmettes Parc Scientifique et Technologique de Luminy Marseille France

Centre de Recherche en Cancérologie de Marseille INSERM U1068 CNRS UMR7258 Aix Marseille Université U105 Institut Paoli Calmettes Parc Scientifique et Technologique de Luminy Marseille France

Centre des Sciences du Goût et de l'Alimentation AgroSup Dijon CNRS INRAE University of Bourgogne Franche Comté Eye and Nutrition Research Group Dijon France

Centre for Cancer Biology University of South Australia Adelaide Australia

Centre for Genomic Regulation Department of Cell and Developmental Biology Barcelona España

Centre for Innovative Biomedicine and Biotechnology University of Coimbra Coimbra Portugal

Centre for Research in Agricultural Genomics CSIC IRTA UAB UB Campus UAB Bellaterra Barcelona Spain

Centre International de Recherche en Infectiologie University Lyon Inserm U1111 Université Claude Bernard Lyon 1 CNRS UMR5308 ENS Lyon Lyon France

Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER Consejo Superior de Investigaciones Científicas Universidad de Sevilla Universidad Pablo de Olavide Seville Spain

Centro de Biología Molecular Severo Ochoa Consejo Superior de Investigaciones Científicas Universidad Autónoma de Madrid Madrid Spain; Department of Cell Biology and Immunology Campus de Cantoblanco Madrid Spain

Centro de Biología Molecular Severo Ochoa Madrid Spain

Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Instituto de Investigaciones Biomédicas Alberto Sols UAM CSIC Madrid Spain; Universidad Autónoma de Madrid School of Medicine Department of Biochemistry Madrid Spain

Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco AC Unidad de Biotecnología Médica y Farmacéutica Guadalajara Jalisco México

Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Department of Molecular Biomedicine Laboratory of Cell Death and Cancer Therapy Madrid Spain

Centro de Investigaciones Biológicas CSIC Department of Cellular and Molecular Biology Madrid Spain

Centro de Investigaciones Biológicas Margarita Salas CIB CSIC Madrid Spain

Centro de Investigaciones Biológicas Margarita Salas CSIC Madrid Spain

Centro di Riferimento Oncologico CRO IRCCS Molecular Oncology Unit Aviano Italy

Centro di Riferimento Oncologico di Aviano IRCCS Immunopathology and Cancer Biomarkers Aviano Italy

Centro Nacional de Biotecnología CNB CSIC Madrid Spain

Chang Gung Memorial Hospital Liver Research Center Linkou Taoyuan Taiwan; Chang Gung University College of Medicine Graduate Institute of Biomedical Sciences Taoyuan Taiwan; Chang Gung University of Science and Technology College of Human Ecology Research Center for Chinese Herbal Medicine Taoyuan Taiwan

Chang Gung University College of Medicine and Chang Gung Memorial Hospital Department of Cardiology Taoyuan City Taiwan; National Health Research Institutes Institute of Cellular and System Medicine Zhunan Taiwan

Chang Gung University Department of Biochemistry and Molecular Biology Taoyuan Taiwan Republic of China

Changhua Christian Hospital Department of Otorhinolaryngology Head and Neck Surgery Changhua Taiwan

Charité Universitätsmedizin Berlin Department of Anesthesiology and Intensive Care Medicine Campus Charité Mitte and Campus Virchow Klinikum Berlin Germany

Charité University Medicine Berlin Department of Hepatology and Gastroenterology Berlin Germany

Charles University Faculty of Medicine in Hradec Kralove Department of Medical Biology and Genetics Hradec Kralove Czech Republic

Chengdu Medical College Department of Anatomy and Histology and Embryology Development and Regeneration Key Lab of Sichuan Province Chengdu China

Chiba University Department of Biology Chiba Japan

Chiba University Graduate School of Medicine Department of General Medical Science Chiba Japan

Children's Cancer Hospital Egypt 57357 Tumor Biology Research Program Cairo Egypt

Children's Hospital Medical Center Division of Experimental Hematology and Cancer Biology Cincinnati OH USA

Children's Hospital of Soochow University Institute of Pediatric Research Suzhou China

Childrens' Hospital Hannover Medical School Hannover Germany

China Academy of Chinese Medical Sciences Artemisinin Research Center and the Institute of Chinese Materia Medica Beijing China

China Agricultural University College of Biological Sciences State Key Laboratory of Agro Biotechnology and MOA Key Laboratory of Soil Microbiology Beijing China

China National Rice Research Institute State Key Laboratory of Rice Biology Hangzhou China

China Pharmaceutical University School of Basic Medicine and Clinical Pharmacy State Key Laboratory of Natural Medicines Jiangsu Key Laboratory of Carcinogenesis and Intervention Nanjing China

China Pharmaceutical University School of Life Science and Technology Nanjing Jiangsu China

China Pharmaceutical University State Key Laboratory of Natural Medicines Nanjing Jiangsu China

Chinese Academy of Agricultural Sciences Institute of Plant Protection State Key Laboratory for Biology of Plant Diseases and Insect Pests Beijing China

Chinese Academy of Agriculture Sciences Lanzhou Veterinary Research Institute State Key Laboratory of Veterinary Etiological Biology Lanzhou Gansu China

Chinese Academy of Medical Sciences and Peking Union Medical College Institute of Blood Transfusion Chengdu China

Chinese Academy of Medical Sciences and Peking Union Medical College Institute of Dermatology Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs Nanjing Jiangsu China

Chinese Academy of Medical Sciences and Peking Union Medical College Institute of Materia Medica State Key Laboratory of Bioactive Substance and Function of Natural Medicines Molecular Immunology and Cancer Pharmacology Group Beijing China

Chinese Academy of Medical Sciences and Peking Union Medical College Institute of Medicinal Biotechnology Beijing China

Chinese Academy of Sciences Center for Biosafety Mega Science Institute of Microbiology CAS Key Laboratory of Pathogenic Microbiology and Immunology Chaoyang District Beijing China

Chinese Academy of Sciences Center for Excellence in Molecular and Cellular Sciences Shanghai Institute of Biochemistry and Cell Biology Shanghai China

Chinese Academy of Sciences Guangzhou Institutes of Biomedicine and Health CAS Key Laboratory of Regenerative Biology Guangzhou China

Chinese Academy of Sciences Hefei Institutes of Physical Science High Magnetic Field Laboratory Hefei Anhui Province China

Chinese Academy of Sciences Institute of Biophysics Beijing China

Chinese Academy of Sciences Institute of Biophysics National Laboratory of Biomacromolecules Beijing China

Chinese Academy of Sciences Institute of Modern Physics Lanzhou China

Chinese Academy of Sciences Institute of Zoology State Key Laboratory of Stem cell and Reproductive Biology Beijing China

Chinese Academy of Sciences Kunming Institute of Zoology Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences Kunming Yunnan China

Chinese Academy of Sciences Shanghai Institute of Nutrition and Health CAS Key Laboratory of Tissue Microenvironment and Tumor Laboratory of Molecular Cardiology Shanghai China

Chinese People's Liberation Army General Hospital Department of Cardiology Beijing China

Chinese University of Hong Kong School of Biomedical Sciences Hong Kong China

Chonbuk National University Department of VeterinaryMedicine Iksan Korea

Chongqing University School of Medicine Center for Neurointelligence Chongqing China

Chonnam National University The Future Life and Society Research Center Gwangju Korea

Chosun University School of Medicine Gwangju Korea

Christian Albrechts University Kiel Biochemical Institute Kiel Germany

CHU Clermont Ferrand Chirurgie Gynécologique Clermont Ferrand France; Université Clermont Auvergne Institut Pascal UMR6602 CNRS UCA SIGMA Clermont Ferrand France

Chulalongkorn University Faculty of Allied Health Sciences Age Related Inflammation and Degeneration Research Unit Department of Clinical Chemistry Bangkok Thailand

Chung Shan Medical University Institute of Medicine Taichung Taiwan

Chung Shan Medical University Institute of Medicine Taiwan

Chungbuk National University Department of Biology Education Seowon Gu Cheongju Chungbuk Korea

Chungnam National University Graduate School of Analytical Science and Technology Daejeon 305 764 Republic of Korea

Chungnam National University School of Medicine Infection Control Convergence Research Center Daejeon Korea

City of Hope Comprehensive Cancer Center Beckman Research Institute Department of Diabetes Complications and Metabolism Duarte CA USA

City University of Hong Kong Department of Biomedical Sciences Hong Kong China

Clermont Auvergne University INRAE Human Nutrition Unit F 63000 Clermont Ferrand France

Cleveland Clinic Department of Cancer Biology Cleveland OH USA

Cleveland Clinic Department of Cardiovascular Medicine Heart and Vascular Institute Cleveland OH USA

Cleveland Clinic Department of Gastroenterology Hepatology and Nutrition Cleveland OH USA

Cleveland Clinic Lerner Research Institute Department of Inflammation and Immunity Cleveland OH USA

Clinic of Neonatology Department of Women Mother and Child University Hospital Center of Vaud Lausanne Switzerland

Clínica Universidad de Navarra Metabolic Research Laboratory CIBEROBN IdiSNA Pamplona Spain

CNC Center for Neuroscience and Cell Biology Coimbra IIIUC Instituto de Investigação Interdisciplinar University of Coimbra Coimbra Portugal

CNRS Biotechnology and cell signaling Ecole Supérieure de Biotechnologie de Strasbourg Strasbourg University Laboratory of excellence Medalis; University of Strasbourg Institute for Advanced Study Strasbourg France

CNRS Institut Curie Paris France

CNRS Université de Bordeaux Laboratoire de Biogenèse Membranaire UMR5200 33140 Villenave d'Ornon Bordeaux France; Université de Bordeaux CNRS Laboratoire de Biogenèse Membranaire UMR5200 Villenave d'Ornon Bordeaux France

Colby College Department of Biology Waterville ME USA

College of Life Science and Technology Jinan University Guangzhou China

College of Life Sciences Nankai University Tianjin China

College of Respiratory and Critical Care Medicine Chinese PLA General Hospital Beijing China

Columbia University Department of Medicine New York NY USA

Columbia University Department of Neurology and Pathology and Cell Biology New York NY USA

Columbia University Department of Pathology and Cell Biology New York NY USA

Columbia University Naomi Berrie Diabetes Center Department of Pathology and Cell Biology College of Physicians and Surgeons New York NY USA

Columbia University New York NY USA

Columbia University Vagelos College of Physicians and Surgeons Department of Pathology and Cell Biology New York NY USA

Comenius University Department of Biochemistry Bratislava Slovakia

Commonwealth Scientific and Industrial Research Organization Agriculture and Food Brisbane Queensland Australia

Complutense University Instituto de Investigaciones Sanitarias San Carlos Department of Biochemistry and Molecular Biology School of Biology Madrid Spain

CONACYT Centro de Investigación Biomédica de Oriente Instituto Mexicano del Seguro Social Puebla Mexico

Concordia University Department of Biology Montreal Quebec Canada

Concordia University Department of Biology Montreal Quebec Canada; McGill University Department of Anatomy and Cell Biology Montreal Quebec Canada

CONICET Universidad Nacional de Cuyo Instituto de Histología y Embriología de Mendoza Mendoza Argentina

Consejo Superior de Investigaciones Científicas Instituto de Bioquímica Vegetal y Fotosíntesis Sevilla Spain

Consejo Superior de Investigaciones Científicas Universidad de Salamanca Campus Unamuno Salamanca Spain

Consiglio Nazionale delle Ricerche Istituto di Biochimica e Biologia Cellulare Monterotondo scalo Italy

Cornell University Department of Entomology Ithaca NY USA

CSIC Universidad de Sevilla Instituto de Bioquímica Vegetal y Fotosíntesis Sevilla Spain

CSIR Central Drug Research Institute Lucknow India

CSIR Indian Institute of Chemical Biology Kolkata India

CSIR Indian Institute of Integrative Medicine Department of Cancer Pharmacology Sanat Nagar Srinagar Jammu and Kashmir India

CSIR Institute of Genomics and Integrative Biology South Campus New Delhi India

CSIR National Physical Laboratory Dr K S Krishnan Marg New Delhi India

CURML University Center of Legal Medicine Lausanne University Hospital Lausanne Switzerland

D'Youville College School of Pharmacy Department of Pharmaceutical Social and Administrative Sciences Buffalo NY USA

Daegu Gyeongbuk Institute of Science and Technology Department of Brain and Cognitive Sciences Daegu Korea

Dalhousie University Department of Biochemistry and Molecular Biology Dalhousie Medicine New Brunswick Saint John NB Canada

Dalhousie University Faculty of Medicine Departments of Pathology Biology and Microbiology and Immunology Halifax NS Canada

Dalian Medical University College of Basic Medical Sciences Dalian China

Damietta University Faculty of Science Biochemistry Department Damietta Egypt

Dana Farber Cancer Institute Division of Genomic Stability and DNA Repair Department of Radiation Oncology Boston MA USA

Danish Cancer Society Research Center Cell Stress and Survival Unit Center for Autophagy Recycling and Disease Copenhagen Denmark

Danish Cancer Society Research Center Center for Autophagy Recycling and Disease Cell Death and Metabolism Unit Copenhagen Denmark; University of Copenhagen Department of Cellular and Molecular Medicine Copenhagen Denmark

Danish Cancer Society Research Center Center for Autophagy Recycling and Disease Cell Stress and Survival Unit Copenhagen Denmark; IRCCS Bambino Gesù Children's Hospital Department of Pediatric Hemato Oncology and Cell and Gene therapy Rome Italy; University of Rome Tor Vergata Department of Biology Rome Italy

Danish Cancer Society Research Center Computational Biology Laboratory Copenhagen Denmark

Danish Cancer Society Research Center Copenhagen Denmark

Danish Cancer Society Research Center Redox Signaling and Oxidative Stress Group Copenhagen Denmark

Danish Cancer Society Research Center RNA and Autophagy Group Copenhagen Denmark

Danish Cancer Society Research Center Unit for Cell Death and Metabolism Center for Autophagy Recycling and Disease Copenhagen Denmark; University of Copenhagen Department of Cellular and Molecular Medicine Faculty of Health Sciences Copenhagen N Denmark

Dankook University College of Dentistry Cheonan Korea

Dankook University College of Medicine Department of Pharmacology Cheonan Chungnam Korea

Danube Private University Department of Medicine Dental Medicine Krems Donau Austria

Dartmouth College Department of Chemistry Hanover NH USA

David Geffen School of Medicine at UCLA Department of Medicine Los Angeles CA USA

David Geffen School of Medicine at UCLA Department of Microbiology Immunology and Molecular Genetics Los Angeles CA USA

David Geffen School of Medicine at UCLA Department of Neurology Los Angeles CA USA

David Geffen School of Medicine at University of California Los Angeles Department of Medicine Division of Dermatology Los Angeles CA USA

Deakin University School of Medicine Faculty of Health Victoria Australia

Delft University of Technology Kavli Institute of Nanoscience Department of Bionanoscience Delft The Netherlands

Democritus University of Thrace 1st Department of Internal Medicine and Laboratory of Molecular Hematology Alexandroupolis Greece

Democritus University of Thrace Department of Radiotherapy Oncology Alexandroupolis Greece

Democritus University of Thrace Medical School Department of Pathology Alexandroupolis Greece

Department of Anatomy Cell and Developmental Biology Eötvös Loránd University Budapest Hungary

Department of Anatomy Faculty of Medicine Helsinki Finland

Department of Biochemistry and Molecular Biology Institute for Human Infection and Immunity University of Texas Medical Branch at Galveston Galveston TX USA

Department of Bioinformatics School of Basic Medical Sciences Southern Medical University Guangzhou China

Department of Biological Sciences and Biotechnology Faculty of Sciences Islamic University of Gaza Gaza 108 Palestine

Department of Biological Sciences University of Denver Denver CO USA

Department of Biomedical Sciences College of Medicine Florida State University Tallahassee FL USA

Department of Biomedical Sciences College of Veterinary Medicine Iowa State University Ames IA USA

Department of Biophysics Post Graduate Institute of Medical Education and Research Chandigarh India

Department of Cell Biology and Histology Faculty of Biology University of Murcia IMIB Arrixaca Murcia Spain

Department of Cell Death and Proliferation Institute of Biomedical Research of Barcelona ; Liver Unit Hospital Clinic i Provincial de Barcelona IDIBAPS CIBEREHD Barcelona Spain

Department of Clinical Psychopharmacology and Neurotoxicology National Institute of Mental Health and Neurosciences Bengaluru 560029 Karnataka India

Department of Emergency Medicine Thomas Jefferson University Philadelphia PA USA

Department of Experimental and Health Sciences Pompeu Fabra University E 08003 Barcelona Spain

Department of Experimental Pathology Institute of Biomedical Research of Barcelona Spanish Research Council ; IDIBAPS and CIBEREHD Barcelona Spain

Department of Fundamental Neurosciences University of Lausanne Lausanne Switzerland

Department of Human Anatomy and Cell Science Max Rady College of Medicine Rady Faculty of Health Sciences University of Manitoba Winnipeg Canada

Department of Human Genetics Genentech Inc South San Francisco CA USA

Department of Immunology Duke University Medical Center Durham NC USA

Department of Internal Medicine University of Michigan Ann Arbor MI USA

Department of Medical and Surgical Sciences and Biotechnologies Sapienza University of Rome Italy; IRCCS Neuromed Pozzilli Italy

Department of Medicine and Surgery University of Perugia Perugia Italy

Department of Microbiology and Immunology Dalhousie University Halifax Nova Scotia Canada

Department of Molecular Cellular and Developmental Biology University of Michigan Ann Arbor MI USA

Department of Molecular Medicine Sapienza University of Rome Rome Italy

Department of Molecular Microbiology Washington University School of Medicine St Louis MO USA

Department of Molecular Signal Processing Leibniz Institute of Plant Biochemistry Halle Germany

Department of Neurology Boston Children's Hospital Boston MA USA

Department of Neurology University of Michigan School of Medicine Ann Arbor MI USA

Department of Neurophysiology Institute for Biological Research Siniša Stanković National Institute of Republic of Serbia University of Belgrade Belgrade Serbia

Department of Obstetrics and Gynecology Weill Cornell Medicine 1300 York Avenue Box 35 New York NY United States

Department of Oncology Pathology Cancer Center Karolinska Karolinska Institute Stockholm Sweden

Department of Pathology and Experimental Therapeutics and Institute of Biomedicine of the University of Barcelona Bellvitge University Hospital IDIBELL Hospitalet de Llobregat; University of Brescia Department of Molecular and Translational Medicine Brescia BS Italy

Department of Pathophysiology and Transplantation University of Milan Milan Italy; Institute of Molecular Bioimaging and Physiology CNR Milan Italy

Department of Pharmacology and Experimental Neuroscience University of Nebraska Medical Center Omaha NE USA

Department of Pharmacology and Toxicology Faculty of Pharmacy Ain Shams University Cairo Egypt; Department of Experimental Oncology IEO European Institute of Oncology IRCCS Milan Italy

Department of Physiology Department of Obstetrics Gynecology Wayne State University Detroit MI USA

Departmento de Biología Celular e Histología Facultad de Biología Universidad de Murcia Instituto Murciano de Investigación Biosanitaria Arrixaca Murcia Spain

Departments of Pharmacology and Microbiology University of Maryland School of Medicine Baltimore MD USA; Stanford University School of Medicine Stanford CA USA

Departments of Pharmacology and Toxicology and Neurology The University of Alabama at Birmingham Birmingham AL USA

DGIST Department of Brain and Cognitive Sciences Daegu Korea

Diabetes and Metabolism Research Institute Department of Molecular and Cellular Endocrinology; City of Hope Medical Center Beckman Research Institute Comprehensive Cancer Center Duarte CA USA

Ditmanson Medical Foundation Chia Yi Christian Hospital Translational Medicine Research Center Chiayi City Taiwan

Division of Brain Disease Research Korea National Institute of Health Cheongju si Republic of Korea

Division of Developmental Biology National Institute of Child Health and Human Development National Institutes of Health Bethesda MD USA

Division of Gastroenterology and Hepatology Department of Internal Medicine E Da Hospital Kaohsiung Taiwan; 1 Shou University College of Medicine School of Medicine Kaohsiung Taiwan

Division of Medical Genetics Fondazione IRCCS Casa Sollievo della Sofferenza San Giovanni Rotondo Italy

Division of Stem Cell and Gene Therapy Research Institute of Nuclear Medicine and Allied Sciences Timar Pur New Delhi India

Dokuz Eylul University Izmir International Biomedicine and Genome Institute Izmir Turkey

Dong A University College of Medicine Department of Anatomy and Cell Biology Busan Korea

Dong A University College of Medicine Department of Molecular Neuroscience Peripheral Neuropathy Research Center Busan Korea

Dong A University Medical School Department of Molecular Neuroscience Busan Korea

Doshisha University Graduate School of Brain Science Laboratory of Structural Neuropathology Kyoto Japan

Doshisha Women's College of Liberal Arts Faculty of Pharmaceutical Sciences Kyotanabe Kyoto Japan

Dresden University Medical Center Department of Neurology Dresden Germany

Duke NUS Medical School Cardiovascular and Metabolic Disorders Program Singapore Singapore

Duke University Department of Biology and Howard Hughes Medical Institute Durham NC USA

Duke University Department of Medicine Durham NC USA

Duke University Department of Medicine; Duke University Department of Molecular Genetics and Microbiology; Duke University Department of Immunology Durham NC USA; Geriatric Research Education and Clinical Center VA Health Care Center Durham NC USA

Duke University Department of Molecular Genetics and Microbiology Durham NC USA

Duke University Department of Ophthalmology Durham NC USA

Duke University School of Medicine Duke Center for Virology Department of Molecular Genetics and Microbiology Durham NC USA

Durham University Department of Biosciences Durham UK

EA 3842 Limoges University Faculty of Medicine Limoges cedex France

Earlham Institute Norwich UK

East China Normal University Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education Shanghai China

East China Normal University School of Life Sciences Shanghai China

East Tennessee State University Quillen College of Medicine Center of Excellence for Inflammation Infectious Diseases and Immunity Department of Medicine Johnson City TN USA

Eastern Michigan University Department of Chemistry Ypsilanti MI USA

Eberhard Karls University Tübingen Interfaculty Institute of Cell Biology Tübingen Germany

Ecole Polytechnique Fédérale de Lausanne Departments of Oncology and Laboratory Medicine Hematology Service Lausanne Switzerland

Edinburgh Cancer Research UK Centre MRC Institute of Genetics and Molecular Medicine University of Edinburgh Edinburgh UK

Edinburgh Napier University School of Applied Sciences Edinburgh UK

Ege University Faculty of Medicine Department of Medical Biology Izmir Turkey

Ehime University Department of Aquatic Life Sciences Ainan Ehime Japan

Ehime University Graduate School of Medicine Department of Cardiology Pulmonology Hypertension and Nephrology Shitsukawa Toon Ehime Japan

Emory University Department of Pharmacology and Chemical Biology School of Medicine Atlanta GA USA

Emory University School of Medicine Department of Medicine Atlanta GA USA

Emory University School of Medicine Department of Pharmacology and Chemical Biology Atlanta GA USA

Emory University School of Medicine Department of Psychiatry and Behavioral Sciences Atlanta GA USA

Emory University School of Medicine Division of Endocrinology Metabolism and Lipids Atlanta GA USA

Eötvös Loránd University Department of Genetics Budapest Hungary

Erasmus University Medical Center Department of Epidemiology; Division of Pharmacology Department of Internal Medicine Rotterdam The Netherlands

Ernst Ruska Centre for Microscopy and Spectroscopy with Electrons Forschungszentrum Jülich Jülich Germany

ETH Zürich Institute of Biochemistry Zürich Switzerland

Eurac Research Institute for Biomedicine Bolzano Italy

European Institute of Oncology IRCCS Department of Experimental Oncology Milan Italy

European Institute of Oncology IRCCS Department of Experimental Oncology Milan Italy; University of Milano Department of Oncology and Hemato Oncology Milan Italy

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge UK

European Molecular Biology Laboratory Heidelberg Germany

European Neuroscience Institute A Joint Initiative of the University Medical Center Göttingen and the Max Planck Society Göttingen Germany

Evelina Children's Hospital Guy's and St Thomas' NHS Foundation Trust Children's Neuroscience Centre London UK; King's College London Muscle Signalling Section Randall Division of Cell and Molecular Biophysics London UK; King's College London Institute of Psychiatry Psychology and Neuroscience Department of Basic and Clinical Neuroscience London UK

Ewha Womans University Department of Biochemistry College of Medicine Seoul Korea

Ewha Womans University Department of Life Science Immune and Vascular Cell Network Research Center National Creative Initiatives Seoul Korea

Experimental Physiopathology Department of Sciences Experimental Physiopatholgy Medical School University of São Paulo Brazil

Faculdade de Medicina e Ciências Biomédicas Universidade do Algarve Faro Portugal; ABC RI Algarve Biomedical Center Research Institute Faro Portugal; Centre for Biomedical Research Faro Portugal

Faculty of Engineering and Natural Sciences Sabanci University Orta Mahalle Üniversite Caddesi No 27 Orhanlı Tuzla 34956 Istanbul Turkey; Sabanci University Nanotechnology Research and Application Center Tuzla 34956 Istanbul Turkey

Far Eastern Federal University School of Natural Sciences Vladivostok Russian Federation

Federal University of ABC Santo André SP Brazil

Federal University of Ceara Drug Research and Development Center Fortaleza CE Brazil

Federal University of Rio de Janeiro Institute of Microbiology Department of Immunology Rio de Janeiro Brazil

Federal University of São Carlos Department of Gerontology São Carlos SP Brazil

Federal University of São Paulo Department of Medicine Nephrology Division Laboratory of Clinical and Experimental Immunology São Paulo SP Brazil

Federal University of São Paulo Department of Pharmacology Paulista School of Medicine São Paulo Brazil

Federal University of Sergipe Department of Pharmacy São José SE Brazil

Feinstein Institutes for Medical Research Center for Immunology and Inflammation Manhasset NY USA

Flinders University College of Medicine and Public Health Adelaide Australia

Flinders University Flinders Health and Medical Research Institute Adelaide Australia

Florida Atlantic University Charles E Schmidt College of Medicine Department of Biomedical Science Boca Raton FL USA

Florida International University Department of Immunology and Nano Medicine Miami FL USA

Florida State University Department of Nutrition Food and Exercise Sciences Tallahassee FL USA

Folkhälsan Research Center Helsinki Finland

Fondazione G Pascale Istituto Nazionale Tumori IRCCS Cell Biology and Biotherapy Unit Naples Italy

Fondazione IRCCS Casa Sollievo della Sofferenza Poliambulatorio Giovanni Paolo 2 Division of Medical Genetics San Giovanni Rotondo Italy

Fondazione IRCCS Istituto Neurologico Carlo Besta Neuromuscular Disease and Immunology Unit Milan Italy; University of Brescia Unit of Biology and Genetics Department of Molecular and Translation Medicine Brescia Italy

Fondazione IRCCS Istituto Neurologico Carlo Besta Neuromuscular Diseases and Neuroimmunology Unit Milano Italy

Fondazione IRCCS Ospedale San Raffaele Division of Neuroscience Milan Italy

Fondazione Istituto di Ricerca Pediatrica Città della Speranza Neuroblastoma Laboratory Padua Italy

Fondazione Policlinico Universitario Agostino Gemelli IRCCS Rome Italy

Forschungszentrum Jülich Institute of Biological Information Processing IBI 7 Jülich Germany

Foundation for Research and Technology Hellas Institute of Molecular Biology and Biotechnology Heraklion Crete Greece; University of Crete Medical School Heraklion Crete Greece

Fralin Biomedical Research Institute at VTC Roanoke VA USA

Francis Crick Institute London UK; UCL Royal Free Hospital London UK

Free University of Berlin Department of Biology Chemistry and Pharmacy Berlin Germany

Freie Universitaet Berlin Department of Veterinary Medicine Institute of Veterinary Biochemistry Berlin Germany

Friedrich Alexander Universität Erlangen Nürnberg Department of Immune Modulation University Hospital Erlangen Erlangen Germany

Friedrich Alexander Universität Erlangen Nürnberg Department of Stem Cell Biology Erlangen Germany

Friedrich Alexander University Erlangen Nürnberg and Universitätsklinikum Erlangen Department of Internal Medicine 3 Rheumatology and Immunology Erlangen Germany

Friedrich Alexander University Erlangen Nürnberg University Hospital Erlangen Department of Molecular Neurology Erlangen Germany

Friedrich Baur Institute Department of Neurology University of Munich Munich Germany

Friedrich Loeffler Institut Insitute of Immunology Greifswald Insel Riem Germany

Friedrich Schiller University Jena University Hospital Jena Institute of Human Genetics Jena Germany

Fudan University Hospital of Obstetrics and Gynecology Institute of Obstetrics and Gynecology Laboratory for Reproductive Immunology Shanghai China

Fudan University School of Pharmacy Department of Biological Medicines Shanghai China

Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences Shanghai China

Fudan University Zhongshan Hospital Liver Cancer Institute Department of Liver Surgery and Transplantation Shanghai China

Fukuoka University Faculty of Pharmaceutical Sciences Department of Biochemistry Fukuoka Japan

Fukushima Medical University School of Medicine Department of Anatomy and Histology Fukushima Japan

Functional Genomics of Cardiomyopathies Institute of Experimental Pharmacology and Toxicology University Medical Center Hamburg Eppendorf 20246 Hamburg Germany

Fundación Instituto Leloir and IIBBA CONICET Buenos Aires Argentina; Laboratorio de Glicobiología Celular y Genética Aplicada de Levaduras Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Argentina

Garvan Institute of Medical Research St Vincent's Medical School Faculty of Medicine UNSW Sydney Australia

Geisel School of Medicine at Dartmouth Department of Biochemistry and Cell Biology Hanover NH USA

Genentech Inc Department of Cancer Immunology South San Francisco CA USA

Georg August Universität Göttingen Institute for Microbiology and Genetics Department of Molecular Microbiology and Genetics Göttingen Germany

Georg August University Göttingen Institute of Microbiology and Genetics Department of Genetics of Eukaryotic Microorganisms Göttingen Germany

Georgetown University Department of Biology Washington DC USA

Georgia State University Department of Biology Atlanta GA USA

Georgia State University The Center for Molecular and Translation Medicine Atlanta GA USA

German Center for Neurodegenerative Diseases Bonn Germany

German Center for Neurodegenerative Diseases Bonn Germany; CAESAR Research Center Bonn Germany

German Center for Neurodegenerative Diseases Bonn Germany; Max Planck Institute for Metabolism Research Hamburg Outstation Hamburg Germany; Shanghai Qiangrui Biotech Co Ltd Fengxian District Shanghai China

German Center for Neurodegenerative Diseases DZNE Bonn Germany and Department of Neurodegenerative Diseases and Geriatric Psychiatry University Bonn Bonn Germany

German Institute of Human Nutrition Department of Molecular Toxicology Nuthetal Germany

German Institute of Human Nutrition Potsdam Rehbruecke Department of Molecular Toxicology Nuthetal Germany

Ghent University Translational Nuclear Receptor Research VIB Center for Medical Biotechnology Department of Biomolecular Medicine Ghent Belgium

Ghent University VIB Center for Inflammation Research Ghent Belgium

Gifu University Graduate School of Medicine Department of Cardioligy Gifu Japan

Gladstone Institute of Neurological Disease and University of California San Francisco Department of Neurology San Francisco CA USA

Goethe University Faculty of Medicine Department of Clinical Pharmacology Frankfurt Germany

Goethe University Frankfurt Buchmann Institute for Molecular Life Sciences Frankfurt am Main Germany

Goethe University Frankfurt Institute for Experimental Cancer Research in Pediatrics Frankfurt Germany

Goethe University Frankfurt Institute of Pharmaceutical Chemistry Frankfurt am Main Germany

Goethe University Hospital Frankfurt Neuroscience Center Experimental Neurosurgery Frankfurt Main Germany

Goethe University Institute for Experimental Cancer Research in Pediatrics Frankfurt am Main Germany

Goethe University Institute for Molecular Biosciences Frankfurt Main Germany

Goethe University Institute of Biochemistry 2 Faculty of Medicine Frankfurt am Main Germany

Goethe University Institute of Biophysical Chemistry Frankfurt Germany

Goethe University Institute of Pharmacology and Toxicology Frankfurt Germany

Goethe University University Hospital University Cancer Center Frankfurt Department of Medicine Hematology Oncology Frankfurt Germany

Graduate Institute of Medical Sciences College of Medicine Taipei Medical University Taipei Taiwan; Department of Microbiology and Immunology School of Medicine College of Medicine Taipei Medical University Taipei Taiwan

Graduate School of Dong A University College of Medicine Department of Translational Biomedical Sciences Busan Korea

Gregor Mendel Institute Vienna Biocenter Vienna Austria

Guangdong Medical University Institute of Nephrology and Zhanjiang Key Laboratory of Prevention and Management of Chronic Kidney Disease Zhanjiang Guangdong China

Guangxi Medical University School of Preclinical Medicine Department of Physiology Nanning China

Guangzhou Medical University Department of Histology and Embryology Guangzhou China

Guangzhou Medical University School of Basic Medical Sciences State Key Laboratory of Respiratory Disease Guangzhou China

Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation School of Basic Medical Sciences Affiliated Cancer Hospital and Institute of Guangzhou Medical University Guangzhou China

Guangzhou University of Chinese Medicine Medical College of Acupuncture Moxibustion and Rehabilitation Guangzhou China; Hong Kong Baptist University School of Chinese Medicine Mr and Mrs Ko Chi Ming Centre for Parkinson's Disease Research Hong Kong SAR China

Gwangju Institute of Science and Technology School of Life Sciences Gwangju South Korea

Gyeongsang National University School of Medicine Department of Biochemistry and Convergence Medical Sciences and Institude of Health Sciences Jinju Republic of Korea

Hacettepe University Faculty of Medicine Department of Medical Biology Ankara Turkey

Hampton University School of Pharmacy Department of Pharmaceutical Sciences Hampton VA USA

Hangzhou Normal University Affiliated Hospital of Hangzhou Normal University College of Medicine Holistic Integrative Pharmacy Institutes and Comprehensive Cancer Diagnosis and Treatment Center Hangzhou Zhejiang China

Hangzhou Normal University School of Medicine College of Pharmacy Hangzhou Zhejiang China

Hannam University Department of Biological Sciences and Biotechnology Daejeon South Korea

Hannover Medical School Department for Clinical Immunology and Rheumatology Hannover Germany

Hannover Medical School Department of Nephrology and Hypertension Hannover Germany

Hannover Medical School Institute for Molecular and Therapeutic Strategies Hannover Germany

Hanyang University College of Pharmacy Ansan Gyeonggido Korea

Harbin Institute of Technology the HIT Center for Life Sciences School of Life Sciences and Technology Harbin China

Harvard Medical School and Brigham and Women's Hospital Precision Neurology Program and APDA Center for Advanced Parkinson Research Boston MA USA

Harvard Medical School Boston Children's Hospital F M Kirby Neurobiology Center Translational Neuroscience Center Department of Neurology Boston MA USA

Harvard Medical School Brigham and Women's Hospital Department of Neurology Boston MA USA

Harvard Medical School Department of Biological Chemistry and Molecular Pharmacology Boston MA USA

Harvard Medical School Department of Dermatology Cutaneous Biology Research Center Massachusetts General Hospital Boston MA USA

Harvard Medical School Department of Microbiology; Brigham and Women's Hospital Division of Infectious Diseases Boston MA USA

Harvard Medical School Massachusetts General Hospital Cutaneous Biology Research Center Charlestown MA USA

Harvard Medical School Massachusetts General Hospital Gastrointestinal Unit Medicine Boston MA USA

Harvard Medical School Ophthalmology Boston MA USA

Hasselt University Biomedical Research Institute Diepenbeek Belgium

Health and Medical University Potsdam Germany

Health Research Institute Germans Trias i Pujol Innate Immunity Group Badalona Barcelona Spain

Health Sciences University of Hokkaido College of Rehabilitation Sciences Department of Physical Therapy Ishikari Tobetsu Hokkaido Japan

Hebrew University of Jerusalem Department of Biochemistry and Food Science Rehovot Israel

Heinrich Heine Universität Düsseldorf Institut für Physikalische Biologie Düsseldorf Germany

Heinrich Heine University Düsseldorf Medical faculty Institute of Biochemistry and Molecular Biology 1 Düsseldorf Germany

Heinrich Heine University Medical Faculty Institute of Molecular Medicine 1 Düsseldorf Germany

Helmholtz Centre for Infection Research Braunschweig Germany

Henan Academy of Agricultural Sciences Institute of Plant Nutrition Agricultural Resources and Environmental Science Jinshui District Zhengzhou Henan China

Henan University of Technology College of Bioengineering Zhengzhou China

Hepatobiliary Section Department of Internal Medicine Kaohsiung Medical University Hospital and Hepatitis Research Center College of Medicine Kaohsiung Medical University Kaohsiung Taiwan

Hirosaki University Graduate School of Medicine Institute of Brain Science Department of Neuropathology Hirosaki Japan; UCL Queen Square Institute of Neurology Queen Square Brain Bank for Neurological Disorders London UK

Hiroshima University Graduate School of Biomedical and Health Sciences Hiroshima Japan

Hokkaido University Department of Rheumatology Endocrinology and Nephrology Sapporo Japan

Hollings Cancer Center Department of Biochemistry and Molecular Biology Charleston SC USA

Hong Kong Baptist University Faculty of Science Department of Biology Hong Kong China; Hong Kong Baptist University Golden Meditech Centre for NeuroRegeneration Sciences Hong Kong China

Hong Kong Baptist University Mr and Mrs Ko Chi Ming Centre for Parkinson's Disease Research School of Chinese Medicine Hong Kong China

Hong Kong Baptist University School of Chinese Medicine Hong Kong China

Hong Kong Baptist University School of Chinese Medicine Hong Kong lxChina

Hopp Children's Cancer Center Heidelberg Clinical Cooperation Unit Pediatric Oncology Im Neuenheimer Feld Heidelberg Germany

Hopwood Centre for Neurobiology Lifelong Health Theme South Australian Health and Medical Research Institute Adelaide Australia

Hospital for Sick Children Cell Biology Program Toronto ON Canada

Hospital for Sick Children Program in Cell Biology Department Toronto Canada; University of Toronto Department of Biochemistry Toronto Canada

Hospital Universitari de Tarragona Joan XXIII Institut d'Investigació Sanitària Pere Virgili Madrid Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas Instituto de Salud Carlos 3 Madrid Spain

Hospital Universitari de Tarragona Joan XXIII Institut d'Investigació Santitària Pere Virgili

Hospital Universitario de Canarias Research Unit; CIBERNED and Universidad de La Laguna ITB Santa Cruz de Tenerife Spain

Houston Methodist Research Institute Weill Cornell Medicine Houston TX USA

Howard University College of Medicine Department of Anatomy Washington D C USA

Huazhong Agricultural University College of Horticulture and Forestry Science Key Laboratory of Horticultural Plant Biology Wuhan China

Huazhong Agricultural University College of Veterinary Medicine State Key Laboratory of Agricultural Microbiology Wuhan China

Huazhong Agricultural University Laboratory of Molecular Nutrition for Aquatic Economic Animals Fishery College Wuhan China

Huazhong Agricultural University National Key Laboratory of Crop Genetic Improvement Wuhan China

Huazhong Agricultural University School of Veterinary Medicine Biomedical Center Hongshan Wuhan China

Huazhong University of Science and Technology College of Life Science and Technology Hubei Bioinformatics and Molecular Imaging Key Laboratory Key Laboratory of Molecular Biophysics of Ministry of Education Wuhan Hubei China

Huazhong University of Science and Technology College of Life Science and Technology Key Laboratory of Molecular Biophysics of Ministry of Education Wuhan Hubei China

Huazhong University of Science and Technology Liyuan hospital of Tongji Medical College Department of Endocrinology Wuhan Hubei China

Huazhong University of Science and Technology School of Basic Medicine Wuhan HuBei China

Huazhong University of Science and Technology Tongji Medical College School of Pharmacy Wuhan Hubei China

Hubei Key Laboratory of Cell Homeostasis College of Life Sciences Wuhan University Wuhan Hubei China

Hubei University of Technology National 111 Center for Cellular Regulation and Molecular Pharmaceutics Wuhan China

Hunan Key Laboratory of Medical Epigenomics Department of Dermatology 2nd Xiangya Hospital Central South University Changsha China

Hungarian Academy of Sciences Budapest Hungary; Department of Anatomy Cell and Developmental Biology Eötvös Loránd University Budapest Hungary

Hwa Chong Institution Singapore Singapore

Hyogo College of Medicine Department of Genetics Hyogo Japan

Icahn School of Medicine at Mount Sinai Department of Geriatrics and Palliative Medicine New York NY USA

Icahn School of Medicine at Mount Sinai Department of Medicine Division of Liver Diseases New York NY USA

Icahn School of Medicine at Mount Sinai Department of Medicine New York NY USA

Icahn School of Medicine at Mount Sinai Departments of Neurology and Neuroscience New York NY USA

ICAR Indian Veterinary Research Institute FMD Vaccine Research Laboratory Bengaluru India

ICAR Indian Veterinary Research Institute FMD VP Laboratory Bengaluru India

ICMR Vector Control Research Center Unit of Microbiology and Immunology Puducherry India

ICREA Pompeu Fabra University Madrid Spain

IEO European Institute of Oncology IRCCS IFOM IEO Campus Department of Experimental Oncology Milan Italy

IFOM The FIRC Institute of Molecular Oncology Milan Italy

Ifremer RBE Département Ressources La Tremblade France

Ifremer SG2M LGPMM Laboratoire de Génétique et Pathologie des Mollusques Marins La Tremblade France

IGBMC Inserm U1258 Cnrs UMR7104 Strasbourg University Illkirch France

Imperial College London Department of Life Sciences and MRC Centre for Molecular Bacteriology and Infection London UK

Imperial College London Department of Life Sciences London UK

Imperial College London Faculty of Medicine London UK

Imperial College London MRC Centre for Molecular Bacteriolgy and Infection Department of Microbiology London UK

Imperial College London Section of Paediatric Infectious Disease and Virology London UK

Incheon National University College of Life Sciences and Bioengineering Division of Life Sciences Incheon Korea

Incheon National University Division of Life Sciences College of Life Sciences and Bioengineering Incheon Korea

Indian Council of Medical Research National AIDS Research Institute Division of Molecular Virology Pune MH India

Indian Institute of Science Centre for BioSystems Science and Engineering Bangalore India

Indian Institute of Science Department of Biochemistry Bangalore India

Indian Institute of Science Department of Microbiology and Cell Biology Bangalore KA India

Indian Institute of Technology Delhi Kusuma School of Biological Sciences New Delhi India

Indian Institute of Technology Guwahati Department of Biosciences and Bioengineering Guwahati Assam India

Indian Institute of Technology Indore Discipline of Biosciences and Biomedical Engineering Indore Madhya Pradesh India

Indian Institute of Technology Jodhpur Cellular and Molecular Neurobiology Unit Jodhpur Rajasthan India

Indian Institute of Technology Ropar India

Indiana University Purdue University Department of Pathology and Laboratory Medicine Indianapolis IN USA

Indiana University School of Medicine Department of Biochemistry and Molecular Biology Indianapolis IN USA

Indiana University School of Medicine Department of Microbiology and Immunology Indianapolis IN USA

Indiana University School of Medicine Department of Pathology and Laboratory Medicine Indianapolis IN USA

Indiana University School of Medicine Department of Pediatrics and Center for Diabetes and Metabolic Diseases Indianapolis IN USA

Indiana University School of Medicine Department of Pediatrics Indianapolis IN USA

Indiana University School of Medicine Indianapolis IN USA

Inflammation Research Center San Diego CA USA

INMG INSERM CNRS University of Lyon Lyon France

iNOVA4Health Chronic Diseases Research Center Faculdade de Ciências Médicas Universidade Nova de Lisboa Lisboa Portugal

INRA UR1037 Laboratory of Fish Physiology and Genomics Campus de Beaulieu Rennes France; Hunan Normal University College of Life Sciences State Key Laboratory of Developmental Biology of Freshwater Fish Changsha Hunan China

INRS INRS Institut Armand Frappier Montréal QC Canada

INRS Institut Armand Frappier Laval QC Canada

INSERM Institute of Metabolic and Cardiovascular Diseases Université de Toulouse Toulouse France

INSERM U1065 Centre Méditerranéen de Médecine Moléculaire Nice France; Université de Nice Sophia Antipolis UFR de Médecine Nice France

Inserm U1138 Centre de Recherche des Cordeliers Sorbonne Université Université de Paris Paris France

INSERM U1151 Institut Necker Enfants Malades Team 8 Université Paris Descartes Sorbonne Paris Cité Paris France

INSERM U1231 Dijon France

INSERM U1242 University of Rennes Rennes France; Centre de Lutte Contre le Cancer Eugène Marquis Rennes France

INSERM U955 Team Virus Hepatology Cancers Créteil France; Université Paris Est UMR S955 UPEC Créteil France

INSERM UMR1037 CRCT Toulouse France; Université Toulouse 3 Paul Sabatier UMR1037 CRCT Toulouse France; CNRS ERL5294 CRCT Toulouse France

INSERM UMR1163 Laboratory of Epithelial Biology and Disease Imagine Institute Paris Descartes University Sorbonne Paris Cité Hôpital Necker Enfants Malades Paris France

Inserm Unit 1195 University of Paris Saclay Le Kremlin Bicetre France

Insight Institute of Neurosurgery and Neuroscience Department of Research Flint MI USA

Institut d'Investigacions Biomèdiques de Barcelona Barcelona Spain

Institut de Biologie Moléculaire des Plantes Centre National de la Recherche Scientifique Unité Propre de Recherche 2357 Conventionné avec l'Université de Strasbourg Strasbourg France

Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch France

Institut de Génétique et de Biologie Moléculaire et Cellulaire INSERM U964 CNRS UMR7104 University of Strasbourg Illkirch France

Institut de Pharmacologie et de Biologie Structurale Université de Toulouse CNRS Université Paul Sabatier Toulouse France

Institut Hospital del Mar d'Investigacions Mèdiques Barcelona Spain

Institut Jean Pierre Bourgin INRA AgroParisTech CNRS Université Paris Saclay Versailles France

Institut Jean Pierre Bourgin INRAE AgroParisTech Université Paris Saclay 78000 Versailles France

Institut National de la Recherche Scientifique Centre Armand Frappier Santé Biotechnologie Laval QC Canada

Institut National de la Santé et de la Recherche Médicale Centre de Recherche des Cordeliers Sorbonne Université Université de Paris Paris France

Institut National de la Santé et de la Recherche Médicale Sorbonne Université Université de Paris Centre de Recherche des Cordeliers Paris France

Institut National de la Santé et de la Recherche Médicale Université de Paris Paris Cardiovascular Center PARCC Paris France

Institut Necker Enfants Malades INSERM U1151 CNRS UMR 8253 Université de Paris Paris France

Institut Pasteur Biologie des Bactéries Intracellulaires and CNRS UMR 3525 Paris France

Institut Pasteur Membrane Biochemistry and Transport Paris France

Institute for Advanced Chemistry of Catalonia Barcelona Spain

Institute for Animal Developmental and Molecular Biology Heinrich Heine University Düsseldorf Düsseldorf Germany

Institute for Research and Technology in Food and Agriculture Animal Breeding and Genetics Programme Caldes de Montbui Spain

Institute for Research in Biomedicine Cellular Plasticity and Disease Group Barcelona Spain

Institute for Research in Biomedicine Instituto de Salud Carlos 3 Madrid Spain

Institute for Stem Cell Science and Regenerative Medicine Bangalore Karnataka India

Institute for Systems Analysis and Computer Science A Ruberti National Research Council IRCCS Fondazione Santa Lucia Rome Italy

Institute of Biochemistry and Biophysics Polish Academy of Sciences Warsaw Poland

Institute of Biomedical Research of Barcelona CSIC Barcelona Spain; Liver Unit Hospital Clinic i Provincial de Barcelona IDIBAPS and CIBEREHD Barcelona Spain; Research Center for ALPD Keck School of Medicine University of Southern California Los Angeles CA USA

Institute of Biomedicine of Valencia Spanish Research Council Valencia Spain

Institute of Cancer Research Cancer Research UK Cancer Imaging Centre Division of Radiotherapy and Imaging London UK

Institute of Experimental Medicine CAS Department of Neuroregeneration Prague Czech Republic

Institute of Life Sciences Bhubaneswar Odisha India

Institute of Life Sciences Chongqing Medical University Chongqing PR China

Institute of Life Sciences School of Medicine Swansea University Swansea Wales UK

Institute of Microbial Technology Department of Molecular Biology Chandigarh India

Institute of Molecular Biology and Pathology National Research Council Fondazione Santa Lucia Laboratory of Cell Signaling Rome Italy

Institute of Neuroscience of Soochow University Suzhou China

Institute of Neurosciences and Department of Neurology of the 2nd Affiliated Hospital of Guangzhou Medical University Guangzhou China

Institute of Psychiatry and Neurology 1st Department of Neurology Warsaw Poland

Institute of Science and Technology Austria Klosterneuburg Austria

Institute of Translational Pharmacology National Research Council Rome Italy; European Center for Brain Research Laboratory of Resolution of Neuroinflammation IRCCS Santa Lucia Foundation Rome Italy

Institute of Virology University Hospital Essen Essen Germany

Instituto Cajal Consejo Superior de Investigaciones Científicas and CIBERFES Madrid Spain

Instituto de Biofisica da UFRJ Rio de Janeiro Brazil

Instituto de Biomedicina de Valencia CSIC Valencia Spain

Instituto de Fisiologia Celular UNAM Department of Biochemistry and Structural Biology Mexico City Mexico

Instituto de Histología y Embriología Universidad Nacional de Cuyo CONICET Facultad de Ciencias Médicas Mendoza Argentina

Instituto de Investigación Biomédica de A Coruña A Coruña Spain

Instituto de Investigación Sanitaria de Navarra Fundación Miguel Servet Biomedical Research Center of Navarre Navarrabiomed Immunomodulation Group Pamplona Spain

Instituto de Investigaciones Biomédicas Alberto Sols C S 1 C U A M Madrid Spain

Instituto de Investigaciones Biomédicas Alberto Sols CSIC UAM Madrid Spain

Instituto de Investigaciones Biomedicas Alberto Sols Instituto de Salud Carlos 3 Madrid Spain

Instituto de Investigaciones Biomedicas Alberto Sols Madrid Spain

Instituto de Investigaciones Biomedicas en Retrovirus y Sida Universidad de Buenos Aires CONICET Argentina

Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Universidad de Buenos Aires CONICET Argentina

Instituto de Investigaciones en Ingeniería Genética y Biología Molecular Dr Héctor N Torres Laboratorio de señalización y mecanismos adaptativos en Tripanosomátidos Buenos Aires Argentina; Universidad de Buenos Aires Departamento de Fisiología Biología Molecular y Celular Facultad de Ciencias Exactas y Naturales Buenos Aires Argentina

Instituto de Investigaciones en Ingeniería Genética y Biología Molecular Dr Héctor N Torres Laboratorio de Señalización y Mecanismos Adaptativos en Tripanosomátidos Buenos Aires Argentina; Universidad de Buenos Aires Departamento de Fisiología Biología Molecular y Celular Facultad de Ciencias Exactas y Naturales Buenos Aires Argentina

Instituto de Investigaciones en Ingeniería Genética y Biología Molecular Dr Héctor N Torres Laboratorio de señalización y mecanismos adaptativos en Tripanosomátidos Buenos Aires Argentina; Universidad de Buenos Aires Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales Buenos Aires Argentina

Instituto de Investigaciones Marinas CSIC Department of Biotechnology and Aquaculture Immunology and Genomics Vigo Spain

Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran Unidad de Bioquimica Mexico City Mexico

Instituto Nacional de Enfermedades Respiratorias Isamel Cosío Villegas Departamento de Investigación en Microbiología Ciudad de México México

Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria Department of Biotechnology Madrid Spain

Instituto Oswaldo Cruz LITEB IOC Fundação Oswaldo Cruz FIOCRUZ Rio de Janeiro Brazil

Interdisciplinary Research Center on Biology and Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences 201203 Shanghai China; Department of Cell Biology Harvard Medical School Boston MA USA

Internal Medicine 1 Brandenburg Hospital Faculty of Health Sciences Joint Faculty of the Brandenburg University of Technology Cottbus Senftenberg the Brandenburg Medical School Theodor Fontane and the University of Potsdam Brandenburg Germany

International Centre for Genetic Engineering and Biotechnology Cellular Immunology Group Aruna Asaf Ali Marg New Delhi India

International Centre for Genetic Engineering and Biotechnology New Delhi India

International Clinical Research Center St'Anne University Hospital Brno Czech Republic; Institute of Molecular Biology and Biophysics Federal Research Center of Fundamental and Translational Medicine Novosibirsk Siberia Russia

Iowa State University Animal Science Department Ames IA USA

Iowa State University Department of Biomedical Sciences Ames IA USA

Iowa State University Department of Genetics Development and Cell Biology Ames IA USA

Iowa State University Department of Genetics Development and Cell Biology Roy J Carver Co Laboratory Ames IA USA

Iowa State University Department of Kinesiology Ames IA USA

Iowa State University Roy J Carver Department of Biochemistry Biophysics and Molecular Biology Ames IA USA

IRBLleida University of Lleida Department of Experimental Medicine Lleida Spain

IRCCS Bambino Gesù Children's Hospital Department of Pediatric Hemato Oncology and Cell and Gene Therapy Rome Italy

IRCCS Casa Sollievo della Sofferenza Opera di Padre Pio da Pietrelcina Division of Internal Medicine and Chronobiology Unit Department of Medical Sciences San Giovanni Rotondo Italy

IRCCS Fondazione Santa Lucia Rome Italy

IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico Dino Ferrari Center Neuroscience Section University of Milan Department of Pathophysiology and Transplantation Milan Italy

IRCCS San Raffaele Scientific Institute Division of Genetics and Cell Biology Milan Italy

IRCM Institut de Recherche en Cancérologie de Montpellier Tumor Microenvironment and Resistance to Treatment Laboratory INSERM U1194 Université de Montpellier Institut régional du Cancer de Montpellier Montpellier France

IRIM University of Montpellier CNRS Montpellier France

Islamic University of Gaza Department of Medical Laboratory Sciences Faculty of Health Sciences Gaza Palestine

Istanbul University Cerrahpasa Cerrahpasa Faculty of Medicine Medical Biology Department Istanbul Turkey

Istituto Dermopatico dell'Immacolata IDI IRCCS Rome Italy

Istituto di Fisiologia Clinica Consiglio Nazionale delle Ricerche Siena Italy; Core Research Laboratory Istituto per lo Studio la Prevenzione e la Rete Oncologica Siena Italy

Istituto Superiore di Sanità Department of Environment and Health Section of Mechanisms Biomarkers and Models Rome Italy

Istituto Superiore di Sanità Department of Infectious Diseases Rome Italy

Istituto Superiore di Sanità Department of Oncology and Molecular Medicine Rome Italy

Istituto Superiore di Sanità Department of Oncology and Molecular Medicine Rome Italy; Fondazione Umberto Veronesi Milan Italy

Italian Institute for Genomic Medicine Italy

Italian Liver Foundation Trieste Italy

Jadavpur University Department of Life Science and Biotechnology Kolkata India

Jadavpur University Department of Mathematics Centre for Mathematical Biology and Ecology Kolkata India

Jagiellonian University Department of Evolutionary Immunology Faculty of Biology Krakow Poland

Jawaharlal Nehru Centre for Advanced Scientific Research Molecular Biology and Genetics Unit and Neuroscience Unit Autophagy Laboratory Jakkur Bangalore India

Jawaharlal Nehru University School of Life Sciences New Delhi India

Jena University Hospital Department of Anesthesiology and Intensive Care Medicine Center for Molecular Biomedicine Jena Germany

Jiangsu University School of Medicine Zhenjiang Jiangsu China

Jikei University School of Medicine Research Center for Medical Sciences Division of Gene Therapy Tokyo Japan

Jinan University College of Life Science and Technology Department of Biology Guangzhou China

Jinan University College of Life Science and Technology Guangzhou China

Jinan University College of Pharmacy Guangzhou China

Jinan University Medical College Key Laboratory for Regenerative Medicine of the Ministry of Education Division of Histology and Embryology Guangzhou China

Jinshan Branch of Shanghai Sixth People's Hospital Department of Laboratory Medicine Shanghai China

Johann Wolfgang Goethe University Frankfurt am Main Faculty of Computer Science and Mathematics Institute of Computer Science Frankfurt am Main Germany

Johann Wolfgang Goethe University Institute of Anatomy 3 'Cellular and Molecular Anatomy' Frankfurt Germany

Johannes Gutenberg University Institute of Pharmaceutical and Biomedical Sciences Department of Pharmaceutical Biology Mainz Germany

Johannes Gutenberg University Mainz Institute of Developmental Biology and Neurobiology Mainz Germany

Johannes Kepler University Linz Institute of Biophysics Linz Austria

Johannes Kepler University Linz Kepler University Hospital GmbH Institute of Pathology and Molecular Pathology Linz Austria

Johns Hopkins University Bloomberg School of Public Health Biochemistry and Molecular Biology Department Baltimore MD USA

Johns Hopkins University Bloomberg School of Public Health W Harry Feinstone Department of Molecular Microbiology and Immunology Baltimore MD USA

Johns Hopkins University Department of Biochemistry and Molecular Biology Baltimore MD USA

Johns Hopkins University Department of Molecular Microbiology and Immunology Baltimore MD USA

Johns Hopkins University Department of Oncology Sidney Kimmel Comprehensive Cancer Center Baltimore MD USA

Johns Hopkins University School of Medicine Department of Cell Biology Baltimore MD USA

Johns Hopkins University School of Medicine Department of Neuroscience Baltimore MD USA

Johns Hopkins University School of Medicine Department of Otolaryngology Head and Neck Surgery Head and Neck Cancer Research Division Baltimore MD USA

Johns Hopkins University School of Medicine Department of Pharmacology and Molecular Sciences and Department of Medicine Baltimore MD USA

Josep Carreras Leukaemia Research Institute Barcelona Spain

Jožef Stefan Institute Department of Biochemistry and Molecular and Structural Biology Ljubljana Slovenia

Julius L Chambers Biomedical Biotechnology Research Institute and North Carolina Central University Department of Pharmaceutical Sciences Durham NC USA

Juntendo University Graduate School of Medicine Department of Cell Biology and Neuroscience Hongo Bunkyo ku Tokyo Japan

Juntendo University Graduate School of Medicine Department of Cellular and Molecular Neuropathology Tokyo Japan

Juntendo University Graduate School of Medicine Department of Metabolism and Endocrinology Bunkyo ku Tokyo Japan

Juntendo University Graduate School of Medicine Department of Neurology Bunkyo ku Tokyo Japan

Juntendo University Graduate School of Medicine Department of Physiology Tokyo Japan

Juntendo University Graduate School of Medicine Department of Research for Parkinson's Disease Tokyo Japan

Juntendo University Graduate School of Medicine Department of Treatment and Research in Multiple Sclerosis and Neuro intractable Disease Bunkyo ku Tokyo Japan

Juntendo University Juntendo University Graduate School of Medicine Division for Development of Autophagy Modulating Drugs Tokyo Japan

Juntendo University School of Medicine Department of Gastroenterology Bunkyo ku Tokyo Japan

Juntendo University School of Medicine Department of Physiology Bunkyo ku Tokyo Japan

Justus Liebig University Department of Internal Medicine Giessen Germany

Justus Liebig University Department of Internal Medicine Universities of Giessen and Marburg Lung Center Giessen Germany

Justus Liebig University Giessen Institute of Medical Microbiology Giessen Germany

Justus Liebig University University Hospital Giessen and Marburg GmbH Departement of Ophthalmology Giessen Germany

KAIST Department of Biological Sciences Daejon Korea

Kalinga institute of industrial technology School of Biotechnology Campus 11 Patia Bhubaneswar Odisha India

Kanazawa Medical University Department of Diabetology and Endocrinology Uchinadacho Ishikawa Japan

Kanazawa University WPI Nano Life Science Institute Kanazawa Ishikawa Japan

Kansas City University of Medicine and Biosciences Department of Basic Science Kansas City MO USA

Kaohsiung Medical University Department of Pathology Kaohsiung City Taiwan

Kaohsiung Medical University Graduate Institute of Medicine and Department of Biochemistry Faculty of Medicine College of Medicine Kaohsiung Taiwan

Kaohsiung Medical University Graduate Institute of Medicine Kaohsiung Taiwan

Kaohsiung Medical University School of Dentistry College of Dental Medicine Kaohsiung Taiwan

Karolinska Institute Department of Cell and Molecular Biology Stockholm Sweden

Karolinska Institute Department of Physiology and Pharmacology Stockholm Sweden

Karolinska Institutet Biomedicum Department of Cell and Molecular Biology Stockholm Sweden

Karolinska Institutet Department of Biosciences and Nutrition Huddinge Sweden

Karolinska Institutet Department of Laboratory Medicine Division of Clinical Microbiology Stockholm Sweden

Karolinska Institutet Department of Neurobiology Care Sciences and Society Division of Neurogeriatrics Solna Stockholm Sweden

Karolinska Institutet Department of Oncology Pathology Stockholm Sweden

Karolinska Institutet Department of Physiology and Pharmacology Stockholm Sweden

Karolinska Institutet Department of Women's and Children's Health Stockholm Sweden AND Karolinska University Hospital Pediatric Oncology Stockholm Sweden

Karolinska Institutet Department of Women's and Children's Health Stockholm Sweden; Astrid Lindgren Children's Hospital Karolinska University Hospital Solna Sweden

Karolinska Institutet Division of Toxicology Institute of Environmental Medicine Stockholm Sweden; Lomonosov Moscow State University Faculty of Basic Medicine Moscow Russia

Karolinska Institutet Institute of Environmental Medicine Stockholm Sweden

Kashan University of Medical Sciences Research Center for Biochemistry and Nutrition in Metabolic Disease Kashan Iran

Keimyung University School of Medicine Department of Immunology Daegu Korea

Keio University School of Medicine Department of Neurology Tokyo Japan

Kerman University of Medical Sciences Institute of Neuropharmacology Neuroscience Research Center Kerman Iran

Kerman University of Medical Sciences Institute of Neuropharmacology Pharmaceutics Research Center Kerman Iran

Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education Department of Pathophysiology Shanghai Jiao Tong University School of Medicine Shanghai China

Key Laboratory of Oral Biomedicine Ministry of Education School and Hospital of Stomatology Wuhan University Wuhan Hubei China

Kiel University and University Hospital Schleswig Holstein Campus Kiel Institute of Clinical Molecular Biology Kiel SH Germany

Kindai University Pharmaceutical Research and Technology Institute Higashi Osaka Osaka Japan

King's College London Department of Basic and Clinical Neuroscience London United Kingdom; Institut du Cerveau et de la Moelle épinière Paris France

King's College London GKT School of Medical Education London UK

King's College London Institute of Psychiatry Psychology and Neuroscience Department of Basic and Clinical Neuroscience Maurice Wohl Clinical Neuroscience Institute London UK

King's College London School of Cardiovascular Medicine and Sciences London UK

King's College London School of Cardiovascular Medicine and Sciences The Rayne Institute St Thomas' Hospital London UK

Kobe University Graduate School of Medicine Center for Infectious Diseases Division of Infectious Disease Control Kobe Japan

Koç University School of Medicine Department of Molecular Biology and Genetics and KUTTAM Research Center for Translational Medicine Istanbul Turkey

Kogakuin University Research Institute for Science and Technology Hachioji Tokyo Japan

Kolling Institute Department of Neurogenetics University of Sydney and Royal North Shore Hospital St Leonards NSW Australia

Komarov Botanical Institute RAS Laboratory of Molecular and Ecological Physiology Saint Petersburg Russian Federation

Konkuk University Department of Bioscience and Biotechnology Seoul Korea

Konkuk University Department of Stem Cell and Regenerative Biotechnology Seoul Korea

Konkuk University Department of Veterinary Medicine Seoul Korea

Konkuk University School of Medicine Department of Anatomy Seoul Korea

Konkuk University School of Medicine Department of Ophthalmology Seoul Korea

Korea Advanced Institute of Science and Technology Graduate School of Medical Science and Engineering Daejeon Korea

Korea Food Research Institute Research Group of Natural Material and Metabolism Jeollabuk do Korea

Korea Research Institute of Bioscience and Biotechnology Cell Factory Research Center Daejeon Korea; University of Science and Technology KRIBB School of Biotechnology Department of Environmental Biotechnology Daejeon Korea

Korea Research Institute of Chemical Technology Center for Convergent Research of Emerging Virus Infection Daejeon Korea

Korea University Department of Life Sciences Seoul Korea

KU Leuven Clinical Division and Laboratory of Intensive Care Medicine Department of Cellular and Molecular Medicine Leuven Belgium

KU Leuven Department of Cellular and Molecular Medicine and Leuven Kanker Instituut Leuven Belgium

KU Leuven Department of Cellular and Molecular Medicine Campus Gasthuisberg Leuven Belgium

KU Leuven Department of cellular and Molecular Medicine Laboratory of cellular transport systems Leuven Belgium

KU Leuven Department of Cellular and Molecular Medicine Leuven Belgium

KU Leuven Department of Development and Regenaration Laboratory of Pediatrics PKD Research Group Leuven Belgium

KU Leuven Department of Imaging and Pathology Leuven Belgium

KU Leuven Department of Public Health and Primary Care Centre Environment and Health Leuven Belgium

Kunming Institute of Zoology Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province Kunming Yunnan China

Kunming University of Science and Technology Medical School Kunming Yunnan China

Kyoto Institute of Technology Department of Applied Biology Matsugasaki Sakyo ku Kyoto Japan

Kyoto Prefectural University of Medicine Department of Anatomy and Neurobiology Kyoto Japan

Kyoto Prefectural University of Medicine Graduate School of Medical Science Department of Cardiovascular Medicine Kyoto Japan

Kyoto University Department of Microbiology Graduate School of Medicine Kyoto Japan

Kyoto University Graduate School of Agriculture Division of Applied Life Sciences Kyoto Japan

Kyoto University of Advanced Science Faculty of Bioenvironmental Science Kameoka Kyoto Japan

Kyung Hee University Department of Oral Biochemistry and Molecular Biology School of Dentistry Seoul Korea

Kyungpook National University Department of Life Science Deagu Korea

Kyungpook National University School of Medicine Department of Biochemistry and Cell Biology Cell and Matrix Research Institute Daegu Korea

Kyungpook National University School of Medicine Department of Physiology Daegu Korea

Kyushu University Depatment of Bioscience and Biotechnology Nishi ku Fukuoka Japan

Kyushu University Medical Institute of Bioregulation Fukuoka Japan

L N C 1 B Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie AREA Science Park Trieste Italy

La Jolla Institute for Immunology and University of California San Diego Laboratory of Inflammation Biology La Jolla CA USA

La Trobe Institute for Molecular Science La Trobe University Melbourne Victoria Australia; Olivia Newton John Cancer Research Institute Heidelberg Victoria Australia; School of Cancer Medicine La Trobe University Melbourne Victoria Australia

Laboratoire d'Optique et Biosciences Ecole Polytechnique CNRS Inserm Institut Polytechnique de Paris Palaiseau France

Laboratorio de Genética Bioquímica Instituto Carlos 3 Zaragoza Spain

Laboratory of Cell Biology Oswaldo Cruz Institute Oswaldo Cruz Foundation Rio de Janeiro Brazil

Laboratory of Host Pathogen Dynamics National Heart Lung and Blood Institute National Institutes of Health Bethesda MD USA

Laboratory of Immunoendocrinology Department of Clinical and Toxicological Analyses University of São Paulo São Paulo Brazil

Laboratory of Immunosenescence and Stem Cell Metabolism Department of Oncology Ludwig Cancer Institute University of Lausanne 1066 Epalinges Switzerland

Laboratory of Neurodevelopment Neurogenetics and Molecular Neurobiology IRCCS Fondazione Santa Lucia Rome Italy

Laboratory of Pain and Signaling Butantan Institute Sao Paulo SP Brazil; Stanford University Department of Anesthesiology Perioperative and Pain Medicine Stanford CA USA

Laboratory of Sex gender Medicine National Institute of Biostructures and Biosystems Sassari Italy

Lanzhou University School of Life Sciences Lanzhou China

Lanzhou University School of Public Health Lanzhou Gansu China

Leibniz Forschungsinstitut für Molekulare Pharmakologie Department of Molecular Pharmacology and Cell Biology Berlin Germany

Leiden University Institute of Biology Leiden Leiden The Netherlands; The City University of New York Queens College The Graduate Center of the City University of New York Department of Biology Flushing NY USA

Leiden University Medical Center Department of Cell and Chemical Biology and Oncode Institute Leiden The Netherlands

Lewis Katz School of Medicine at Temple University Center for Translational Medicine Philadelphia PA USA

Lewis Katz School of Medicine at Temple University Philadelphia PA USA

Life and Health Sciences Research Institute School of Medicine University of Minho Braga Portugal and ICVS 3B's PT Government Associate Laboratory Braga Guimarães Portugal

Life Sciences Institute and Department of Cell and Developmental Biology University of Michigan Ann Arbor MI USA

Life Sciences Institute and Department of Molecular Cellular and Developmental Biology University of Michigan Ann Arbor MI USA

Lifelong Health South Australian Health and Medical Research Institute North Terrace Adelaide Australia

Linköping University Department of Biomedical and Clinical Sciences Faculty of Medicine and Health Sciences Linköping Sweden

Lomonosov Moscow State University A N Belozersky Institute of Physico Chemical Biology Moscow Russia

Lomonosov Moscow State University Chemistry Department Moscow Russia

Lomonosov Moscow State University Department of Biology Moscow Russia

London School of Hygiene and Tropical Medicine Department of Infection Biology London UK

Long Beach VA and University of California Irvine Irvine CA USA

Louisiana State University Health Sciences Center Shreveport Department of Pathology and Translational Pathobiology Shreveport LA USA

Lovelace Respiratory Research Institute Molecular Biology and Lung Cancer Program Albuquerque NM USA

Loyola University Stritch School of Medicine Department of Microbiology and Immunology Chicago IL USA

Ludwig Institute for Cancer Research; University of California San Diego Department of Cellular and Molecular Medicine La Jolla CA USA

Ludwig Maximilians Universität München Munich Cluster for Systems Neurology München Germany

Lund University Department of Experimental Medical Science Cell Death Lysosomes and Artificial Intelligence Group Lund Sweden

Lund University Department of Experimental Medical Science Laboratory of Molecular Neurogenetics Wallenberg Neuroscience Center and Lund Stem Cell Center Lund Sweden

Luxembourg Institute of Health Department of Oncology NorLux Neuro Oncology Laboratory Luxembourg Luxembourg

Luxembourg Institute of Health Tumor Immunotherapy and Microenvironment group Department of Oncology Luxembourg City Luxembourg

Maastricht University Medical Center CARIM School for Cardiovascular Diseases Department of Pathology Maastricht The Netherlands

Maastricht University Medical Center GROW School for Oncology Department of Radiotherapy Maastricht| The Netherlands

Maastricht University Medical Center School for Cardiovascular disease Department of Pathology Maastricht The Netherlands; University of Edinburgh Centre for Cardiovascular Science Edinburgh UK

Macau University of Science and Technology State Key Laboratory of Quality Research in Chinese Medicine Taipa Macau China

Mackay Memorial Hospital Department of Pediatrics Taipei Taiwan; Mackay Medical College Department of Medicine New Taipei Taiwan

Mackay Memorial Hospital Department of Radiation Oncology Taipei Taiwan

Macquarie University Faculty of Medicine and Health Sciences New South Wales Australia

Macquarie University Faculty of Medicine Health and Human Sciences Department of Biomedical Science Centre for Motor Neuron Disease Research Sydney NSW Australia

Macquarie University Faculty of Medicine Health and Human Sciences New South Wales Australia

MACS Agharkar Research Institute Developmental Biology Group Pune India; Savitribai Phule Pune University Ganeshkhind Pune Maharashtra India

Magna Graecia University Department of Health Sciences Catanzaro Italy

Mahidol University Department of Microbiology Faculty of Science Ratchathewi Bangkok Thailand

Mannheim University of Applied Sciences Faculty of Biotechnology Mannheim Germany

Masaryk University Faculty of Medicine Department of Biology Brno Czech Republic

Mashhad University of Medical Sciences Pharmaceutical Technology Institute Biotechnology Research Center Mashhad Iran

Massachusetts General Hospital and Harvard Medical School Department of Medicine Endocrine Division Boston MA USA

Massachusetts General Hospital Department of Medicine Diabetes Unit and Center for Genomic Medicine Boston MA USA; Harvard Medical School Department of Medicine Boston MA USA

Massachusetts General Hospital Department of Molecular Biology Boston MA USA

Mater Research Institute University of Queensland Brisbane Australia

Max Delbrück Center for Molecular Medicine Department of Crystallography Berlin Germany

Max Perutz Labs University of Vienna Vienna Biocenter Vienna Austria

Max Planck Institut für Molekulare Pflanzenphysiologie Potsdam Germany

Max Planck Institute for Biology of Ageing and CECAD University of Cologne Germany

Max Planck Institute for Biology of Ageing Cologne Germany

Max Planck Institute for Biology of Ageing Cologne Germany; University of Cologne Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases Cologne Germany

Max Planck Institute for Infection Biology Berlin Germany

Max Planck Institute for the Biology of Ageing Cologne Germany

Max Planck Institute of Biophysical Chemistry Biochemistry of Signal Dynamics Göttingen Germany

Max Planck Institute of Biophysics Department of Theoretical Biophysics Frankfurt am Main Germany

Max Planck Institute of Molecular Plant Physiology Potsdam Golm Germany

Max Planck Institute of Psychiatry Translational Research in Psychiatry Munich Germany

Mayo Clinic College of Medicine Department of Experimental Pathology Rochester MN USA

Mayo Clinic Department of Biochemistry and Molecular Biology Division of Gastroenterology and Hepatology Rochester MN USA

Mayo Clinic Department of Biochemistry and Molecular Biology Rochester MN USA

Mayo Clinic Department of Medicine Division of Gastroenterology and Hepatology Rochester MN USA

Mayo Clinic Department of Molecular Medicine Rochester MN USA

Mayo Clinic Department of Physiology and Biomedical Engineering Rochester MN USA

Mayo Clinic Division of Gastroenterology and Hepatology Rochester MN USA

Mayo Clinic Rochester MN USA

McGill University Departments of Medicine and Oncology and Segal Cancer Centre Montreal Quebec Canada

McGill University Health Center Department of Medicine Cancer Research Program Montreal QC Canada

McGill University Health Centre Montréal QC Canada

MD Anderson Cancer Center Department of Gynecologic Oncology and Reproductive Medicine Houston TX USA

Medical College of Wisconsin Department of Biochemistry Milwaukee WI USA

Medical College of Wisconsin Department of Medicine and Cardiovascular Center Milwaukee WI USA

Medical Research Institute Wuhan University Wuhan China

Medical School of Zhejiang University Sir Run Run Shaw Hospital Key lab of Biotherapy in Zhejiang Laboratory of Cancer Biology Hangzhou China

Medical University Innsbruck Department of Medicine 1 Innsbruck Austria

Medical University of Bialystok Department of Pharmaceutical Biochemistry Bialystok Poland

Medical University of Graz Division of Cardiology Graz Austria

Medical University of Graz Division of Cell Biology Histology and Embryology Gottfried Schatz Research Center Graz Austria

Medical University of Graz Gottfried Schatz Research Center for Cell Signaling Metabolism and Aging Molecular Biology and Biochemistry Graz Austria

Medical University of Graz Gottfried Schatz research center Graz Austria

Medical University of Innsbruck Institute for Cell Biology Innsbruck Austria

Medical University of Lodz Department of Laboratory Diagnostics Lodz Poland

Medical University of Lublin Department of Pathophysiology Lublin Poland

Medical University of South Carolina Charleston SC 29425 USA

Medical University of South Carolina Department of Medicine Division of Rheumatology and Immunology Charleston SC USA

Medical University of Vienna Department of Dermatology Division for Biology and Pathobiology of the Skin Vienna Austria

Medical University of Vienna Department of Pathology Vienna Austria

Medical University of Warsaw Department of Immunology Warsaw Poland

Meir Medical Center Translational Hemato Oncology Laboratory Kfar Saba Israel; Tel Aviv University Department of Human Molecular Genetics and Biochemistry Sackler School of Medicine Tel Aviv Israel

Melbourne Dementia Research Centre The Florey Institute of Neuroscience and Mental Health The University of Melbourne Parkville VIC Australia

Memorial Sloan Kettering Cancer Center New York NY USA

Metabolism and Cancer Laboratory Molecular Mechanisms and Experimental Therapy in Oncology Program Institut d'Investigació Biomèdica de Bellvitge IDIBELL L'Hospitalet de Llobregat Barcelona Spain

Metabolomics and Cell Biology Platforms Gustave Roussy Comprehensive Cancer Institute Villejuif France; Equipe 11 labellisée Ligue contre le Cancer Centre de Recherche des Cordeliers INSERM U 1138 Paris France

MFP CNRS UMR 5234 University of Bordeaux Bordeaux France

Michigan State University College of Human Medicine Grand Rapids MI USA

Michigan Technological University Department of Chemistry Houghton MI USA

Middle East Technical University Department of Biological Sciences Ankara Turkey

Middlesex University Department of Natural Sciences London UK

Mie University Graduate School of Bioresources Tsu Japan

Model Animal Research Center of Nanjing University Nanjing Jiangsu China

Molecular Biology and Genetics Unit Jawaharlal Nehru Centre for Advanced Scientific Research Bangalore India

Molecular Physiology and Cell Signaling Institute of Systems Molecular and Integrative Biology University of Liverpool Liverpool UK

Monash Biomedicine Discovery Institute and Monash University Department of Anatomy and Developmental Biology Melbourne Victoria Australia

Monash University Cancer Program Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology VIC Australia; Peter MacCallum Cancer Centre Prostate Cancer Translational Research Laboratory Melbourne Victoria Australia; University of Melbourne Sir Peter MacCallum Department of Oncology Parkville VIC Australia

Monash University School of Biological Sciences Melbourne Victoria Australia

Monash University School of Clinical Sciences at Monash Health Centre for Inflammatory Diseases Rheumatology Group Clayton Victoria Australia

Montana BioAg Inc Missoula MT USA

Montreal Neurological Institute Department of Neurology and Neurosurgery McGill University Montreal Quebec Canada

Mortimer B Zuckerman Mind Brain and Behavior Institute Columbia University New York NY USA

Moscow State University A N Belozersky Institute of Physico Chemical Biology Department of Functional Biochemistry of Biopolymers Moscow Russia

Moscow State University A N Belozersky Institute of Physico Chemical Biology Laboratory of Structure and function of mitochondria Moscow Russia

MRC Laboratory of Molecular Biology Cambridge UK

MRC Laboratory of Molecular Biology Division of Protein and Nucleic Acid Chemistry Cambridge UK

MRC Protein Phosphorylation and Ubiquitylation Unit School of Life Sciences University of Dundee UK

MVR Cancer Hospital and Research Institute Molecular Oncology Cancer Genomics Proteomics Kerala India

N N Blokhin National medical research center of oncology Department of biomarkers and mechanisms of tumor angiogenesis Moscow Russia

Nagasaki University Graduate School of Biomedical Sciences Department of Infectious Diseases Nagasaki Japan

Nagasaki University Institute of Biomedical Sciences Department of Clinical Research Pharmacy Nagasaki Japan

Nagoya City University Graduate School of Medical Sciences Department of Nephro urology Nagoya Aichi Japan

Nagoya University Graduate School of Medicine Department of Pathology and Biological Responses Nagoya Japan

Nanjing Agricultural University College of Animal Science and Technology Nanjing Jiangsu China

Nanjing Agricultural University College of Horticulture Weigang NO 1 Nanjing China

Nanjing Agricultural University College of Life Sciences Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs Nanjing China

Nanjing Agricultural University College of Plant Protection Department of Plant Pathology Nanjing China

Nanjing Medical University Department of Physiology Nanjing Jiangsu China

Nanjing Medical University Nanjing 1st Hospital Department of Neurology Nanjing China

Nanjing University Medical School Division of Immunology Nanjing Jiangsu China

Nanjing University of Chinese Medicine Nanjing China

Nankai University Department of Microbiology Tianjin China

Naples University Department of Veterinary Medicine and Animal Productions Naples Italy

Nasonova Research Institute of Rheumatology Moscow Russia

Nathan Kline Institute for Psychiatric Research Center for Dementia Research Orangeburg NY; New York University Langone Health Department of Psychiatry New York NY USA

Nathan S Kline Institute Center for Dementia Research Orangeburg NY USA

National and Kapodistrian University of Athens Department of Biology Panepistimioupolis Athens Greece

National and Kapodistrian University of Athens Faculty of Biology Department of Cell Biology and Biophysics Panepistimiopolis Athens Greece

National and Kapodistrian University of Athens Medical School Division of Molecular Oncology Department of Biological Chemistry Athens Greece

National Autonomous University of Mexico Department of Neurodevelopment and Physiology Institute of Cellular Physiology Mexico City Mexico

National Autonomous University of Mexico Faculty of Chemistry Department of Biology Mexico city Mexico

National Cancer Center Korea Goyang Gyeonggi Korea

National Center for Biotechnology CSIC Laboratory of Intracellular Bacterial Pathogens Madrid Spain

National Center for Cell Science Pune India

National Center of Biomedical Analysis Beijing China

National Cheng Kung University College of Medicine Department of Microbiology and Immunology Tainan Taiwan

National Cheng Kung University College of Medicine Department of Pharmacology Tainan Taiwan

National Cheng Kung University College of Medicine Department of Physiology Tainan City Taiwan

National Cheng Kung University Department of Biochemistry and Molecular Biology Tainan Taiwan

National Chiao Tung University Department of Applied Chemistry and Institute of Molecular Science Hsinchu Taiwan

National Chung Hsing University Institute of Biomedical Sciences Taichung City Taiwan

National Health Research Institutes Institute of Biomedical Engineering and Nanomedicine Zhunan Miaoli Taiwan

National Hospital for Paraplagics Research Unit Molecular Neuroprotection Group Toledo Spain

National Hospital for Paraplegics Research Unit Molecular Neuroprotection Group Toledo Spain

National Institute for Infectious Diseases L Spallanzani IRCCS Rome Italy

National Institute of Biological Sciences Beijing China

National Institute of Biomedical Innovation Health and Nutrition Center for Rare Disease Research Ibaraki Osaka Japan

National Institute of Child Health and Human Development National Institutes of Health Cell Biology and Neurobiology Branch Bethesda MD USA

National Institute of Genetic Engineering and Biotechnology Institute of Medical Biotechnology Molecular Medicine Department Tehran Iran

National Institute of Infectious Diseases Department of Bacteriology 1 Toyama Tokyo Japan

National Institute of Mental Health and Neurosciences Department of Neurochemistry Bengaluru Karnataka India

National Institute of Neuroscience National Center of Neurology and Psychiatry Department of Degenerative Neurological Diseases Kodaira Tokyo Japan

National Institute of Neuroscience National Center of Neurology and Psychiatry Department of Peripheral Nervous System Research Kodaira Tokyo Japan

National Institute of Technology Rourkela Department of Life Science Cancer and Cell Death Laboratory Rourkela Odisha India

National Institutes of Health Eunice Kennedy Shriver National Institute of Child Health and Human Development Bethesda MD USA

National Institutes of Health Eunice Kennedy Shriver National Institute of Child Health and Human Development Neurosciences and Cellular and Structural Biology Division Bethesda MD USA

National Institutes of Health Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases Bethesda MD USA

National Institutes of Health Laboratory of Virology Innate Immunity and Pathogenesis Section Hamilton MT USA

National Institutes of Health National Eye Institute Ophthalmic Genetics and Visual Function Branch Ophthalmic Molecular Genetics Section Bethesda MD USA

National Institutes of Health National Eye institute Protein Structure and Function Section Bethesda MD USA

National Institutes of Health National Institute of Allergy and Infectious Disease Vaccine Research Center Bethesda MD USA

National Institutes of Health National Institute of Allergy and Infectious Diseases Laboratory of Immunoregulation Bethesda MD USA

National Institutes of Health National Institute of Arthritis and Musculoskeletal and Skin Diseases Pediatric Translational Research Branch Bethesda MD USA

National Institutes of Health National Institute of Environmental Health Sciences Research Triangle Park NC USA

National Institutes of Health National Institute of Neurological Disorders and Stroke Bethesda MD USA

National Institutes of Health National Institute on Aging Laboratory of Neurogenetics Bethesda MD USA

National Institutes of Health National Institutes of Neurological Disorders and Stroke Bethesda MD USA

National Institutes of Health NIAMS Lymphocyte Nuclear Biology Bethesda MD USA

National Institutes of Health NIEHS RTP Durham NC USA

National Jewish Health and the University of Colorado Denver CO USA

National Jewish Health Department of Academic Affairs Denver CO USA

National Jewish Health Department of Medicine Division of Allergy and Immunology and Division of Pulmonary and Critical Care Medicine Denver CO USA

National Medicines Institute Department of Drug Biotechnology and Bioinformatics Warszawa Poland

National Neuroscience Institute Duke NUS Medical School Singapore

National Research Council Institute of Food Sciences Avellino Italy

National Research Council Institute of Molecular Genetics Pavia Italy

National Research Council of Italy Neuroscience Institute Padua Italy

National Sun Yat sen University Institute of Biopharmaceutical Sciences Kaohsiung Taiwan

National Taipei University of Nursing and Health Sciences School of Nursing Taipei Taiwan

National Tsing Hua University Department of Chemical Engineering and Frontier Research Center on Fundamental and Applied Sciences of Matters Hsinchu Taiwan

National University of Córdoba Clinical Biochemistry Department CIBICI CONICET Córdoba Argentina

National University of Singapore Department of Medicine Cardiovascular Research Institute Singapore

National University of Singapore Department of Physiology Singapore

National University of Singapore Faculty of Sciences Department of Pharmacy Singapore

National University of Singapore Yong Loo Lin School of Medicine Department of Biochemistry Singapore

National University of Singapore Yong Loo Lin School of Medicine Department of Physiology Mitochondrial Physiology and Metabolism Lab Singapore; National University of Singapore NUHS Centre for Healthy Ageing Singapore

National University of Singapore Yong Loo Lin School of Medicine Department of Physiology Singapore

National University of Singapore Yong Loo Lin School of Medicine Department of Physiology; National University of Singapore LSI Neurobiology Programme; National University of Singapore Institute for Health Innovation and Technology; National University Hospital Singapore Centre for Healthy Longevity; Institute of Molecular and Cell Biology Agency for Science Technology and Research Singapore

National University of Singapore Yong Loo Lin School of Medicine Healthy Longevity Translational Research Program Singapore; National University Health System Centre for Healthy Longevity Singapore

National University of Singapore Yong Loo Lin School of Medicine Strategic Research Programme in Precision Medicine Singapore

National Yang Ming University Department of Life Sciences and Institute of Genome Sciences Taipei Taiwan

NCR Biotech Science Cluster Translational Health Science and Technology Institute Complex Analysis Group Faridabad India

Nelson Mandela University Department of Biochemistry and Microbiology Port Elizabeth South Africa

Nencki Institute of Experimental Biology of Polish Academy of Sciences Neurobiology Center Laboratory of Molecular Neurobiology Warsaw Poland

New York Institute of Technology College of Osteopathic Medicine Department of Biomedical Sciences Old Westbury NY USA

New York University Abu Dhabi Saadiyat Island Campus Division of Science Cell Death Signaling Laboratory Abu Dhabi UAE

New York University Medical School Laura and Isaac Perlmutter Cancer Center Department of Radiation Oncology New York NY USA

New York University School of Medicine Department of Environmental Medicine Urology Biochemistry and Molecular Pharmacology New York NY USA

New York University School of Medicine Department of Radiation Oncology Perlmutter Cancer Center New York NY USA

New York University School of Medicine Departments of Psychiatry and Cell Biology and the Nathan Kline Institute Orangeburg NY USA

New York University School of Medicine Skirball Institute and Department of Microbiology New York NY USA

Newcastle University Ageing Research Laboratories Institute for Cell and Molecular Biosciences Newcastle upon Tyne UK

Newcastle University Biosciences Institute Newcastle Upon Tyne UK

Newcastle University Institute of Translation and Clinical Studies Precision Medicine The Medical School Newcastle upon Tyne UK

NHRI Institute of Cellular and System Medicine Zhunan Taiwan

Nihon Pharmaceutical University Department of Pharmaceutical and Medical Business Sciences Bunkyoku Tokyo Japan

Nihon University College of Bioresource Sciences Fujisawa Kanagawa Japan

Niigata University Brain Research Institute Department of Neurosurgery Niigata Japan

Niigata University Graduate School of Medical and Dental Sciences Department of Cellular Physiology Niigata Japan

Normandie University UNIROUEN INSERM U1239 DC2N Rouen France; Institute for Research and Innovation in Biomedicine Rouen France

Normandy University UNICAEN INSERM UMR S U1237 Physiopathology and Imaging of Neurological Disorders GIP Cyceron Caen FRANCE

North Dakota State University Department of Chemistry and Biochemistry Fargo ND USA

Northeast Ohio Medical university Department of Anatomy and Neurobiology Rootstown OH USA

Northwest A and F University College of Life Sciences Yangling Shaanxi China

Northwest A and F University College of Veterinary Medicine Shaanxi Centre of Stem Cells Engineering and Technology Yangling Shaanxi China

Northwestern University Feinberg School of Medicine Department of Cell and Developmental Biology Chicago IL USA

Northwestern University Feinberg School of Medicine Department of Neurology and Lou and Jean Malnati Brain Tumor Institute Chicago IL USA

Northwestern University Feinberg School of Medicine Department of Neurology Chicago IL USA

Northwestern University Feinberg School of Medicine Department of Pathology Chicago IL USA

Norwegian University of Science and Technology Department of Biomedical Laboratory Science Trondheim Norway

Norwegian University of Science and Technology Department of Clinical and Molecular Medicine Centre for Molecular Inflammation Research Trondheim Norway

Norwegian University of Science and Technology Trondheim Norway

Nottingham Trent University School of Science and Technology Nottingham UK

NYU School of Medicine Department of Medicine New York NY USA

Ohio Musculoskeletal and Neurological Institute and Department of Biomedical Sciences Heritage College of Osteopathic Medicine Ohio University Athens OH USA

Ohio State University Department of Microbial Infection and Immunity and the Infectious Disease Research Institute Columbus OH USA

Old Dominion University Frank Reidy Research Center for Bioelectrics Norfolk VA USA

Oncogenetic Laboratory Meir Medical Center Kfar Saba and Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel

OncoRay National Center for Radiation Research in Oncology Faculty of Medicine and University Hospital Carl Gustav Carus Technische Universität Dresden Germany; Helmholtz Zentrum Dresden Rossendorf Institute of Radiooncology OncoRay Dresden Germany; German Cancer Consortium Heidelberg Germany

OncoRay National Center for Radiation Research in Oncology Faculty of Medicine Technische Universität Dresden Dresden Germany

Oregon Health and Science University Casey Eye Institute Portland OR USA

Oregon Health and Science University Knight Cardiovascular Institute Portland OR USA

Oregon State University College of Pharmacy Department of Pharmaceutical Sciences Portland OR USA

Osaka International Cancer Institute Department of Molecular and Cellular Biology Osaka Japan

Osaka University Graduate School of Dentistry Osaka Japan

Osaka University Graduate School of Medicine Department of Genetics Suita Osaka Japan

Osaka University Laboratory of Mitochondrial Dynamics Graduate School of Frontier Biosciences Osaka Japan

Oslo University Hospital and University of Oslo Department of Pathology Tumor Immunology Lab Oslo Norway

Oslo University Hospital Institute for Cancer Research Department of Molecular Cell Biology Montebello Oslo Norway

Oslo University Hospital Institute for Cancer Research Department of Molecular Cell Biology Oslo Norway

Oslo University Hospital Institute for Cancer Research Department of Tumor Biology Montebello Oslo Norway

Ospedale San Raffaele and Vita Salute San Raffaele University Division of Genetics and Cell Biology Milano Italy

Oswaldo Cruz Foundation Oswaldo Cruz Institute Leprosy Laboratory Rio de Janeiro Brazil

Part overlaps with Costanza Montagna Danish Cancer Society Research Center Computational Biology Laboratory Copenhagen Denmark; Danish Cancer Society Research Center Computational Biology Laboratory Copenhagen Denmark

Pasteur institute of Iran Department of Hepatitis and HIV Tehran Iran

Peking Union Medical College and Chinese Academy of Medical Sciences Peking Union Medical College Hospital Department of Critical Care Medicine Beijing China

Peking University 1st Hospital Renal Division Xi Cheng District Beijing China

Peking University Health Sciences Center Department of Biochemistry and Molecular Biology Beijing China

Peking University School of Basic Medical Science Department of Immunology Beijing China

Penn State College Medicine Department of Cellular and Molecular Physiology Hershey PA USA

Penn State College of Medicine Department of Cellular and Molecular Physiology Hershey PA USA

Penn State University College of Medicine Department of Cellular and Molecular Physiology Hershey PA USA

Penn State University College of Medicine Department of Pediatrics Hershey PA USA

Pennsylvania State University Department of Biochemistry and Molecular Biology University Park PA USA

People's Hospital of Hangzhou Medical College Zhejiang Provincial People's Hospital Department of Oncology Hangzhou China; Zhejiang Provincial People's Hospital Clinical Research Institute Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province Hangzhou China

Perelman School of Medicine at the University of Pennsylvania Department of Medicine Philadelphia PA USA

Perelman School of Medicine at the University of Pennsylvania Department of Neuroscience Philadelphia PA USA

Pfizer Inc DSRD La Jolla CA USA

Pfizer Oncology Research and Development Pearl River NY USA

Pharmaceutical Sciences Department College of Pharmacy Gulf Medical University Ajman United Arab Emirates

Philipps University and University Hospital of Marburg Department of Neuropathology Marburg Germany

Philipps University of Marburg Department of Cytobiology and Cytopathology Marburg Germany

Philipps University of Marburg Department of Visceral Thoracic and Vascular Surgery Marburg Germany

PK PD Toxicology and Formulation Division CSIR Indian Institute of Integrative Medicine Jammu India

Plymouth University Peninsula School of Medicine and Dentistry Plymouth UK

Polish Academy of Sciences Mossakowski Medical Research Centre Laboratory of Ischemic and Neurodegenerative Brain Research Warsaw Poland

Polytechnic University of Marche Department of Life and Environmental Sciences Ancona Italy

Pontificia Universidad Católica de Chile Escuela de Medicina and Centro Interdisciplinario de Neurociencias Facultad de Medicina Departamento de Neurología Santiago Chile

Pontificia Universidad Católica de Chile Faculty of Biological Sciences Department of Physiology Santiago de Chile Chile

Post Graduate Institute of Medical Education and Research Department of Urology Chandigarh India

Poznan University of Medical Sciences Department of Clinical Chemistry and Molecular Diagnostics Poznan Poland

Presidio San Paolo Polo Universitario Dipartimento di Scienze della Salute San Paolo Milano Italy

Protein Metabolism Medical Research Center and Department of Biomedical Sciences Seoul National University School of Medicine Seoul Korea

PSL Research University Equipe labelisée par la Ligue Contre le Cancer Institut Curie Inserm U830 Stress and Cancer laboratory Paris France

Pulmonology Department Hospital del Mar IMIM Pompeu Fabra University CIBERES Barcelona Spain

Purdue University Department of Botany and Plant Pathology West Lafayette IN USA

Purdue University Department of Nutrition Science West Lafayette IN USA

QIMR Berghofer Medical Research Institute Herston Queensland Australia

Qingdao Agricultural University College of Plant Health and Medicine Qingdao Shandong China

Qingdao University Institute of Brain Science and Disease Qingdao Shandong China

Quadram Institute Bioscience Department of Gut Microbes and Health Norwich UK

Quadram Institute Bioscience Norwich Research Park Norwich Norfolk UK

Queen Mary University Blizard Institute Flow Cytometry Core Facility London UK

Queen Mary University of London Barts Cancer Institute London UK

Queen Mary University of London Blizard Institute Centre for Cell Biology and Cutaneous Research London UK

Queen's University Department of Biomedical and Molecular Sciences Kingston Ontario Canada

Queen's University of Belfast Wellcome Wolfson Institute for Experimental Medicine Belfast UK

Queensland University of Technology Centre for Tropical Crops and Biocommodities Science and Engineering Faculty Brisbane Queensland Australia

Queensland University of Technology Institute of Health and Biomedical Innovation Brisbane QLD Australia

Queensland University of Technology Institute of Health and Biomedical Innovation Kelvin Grove Brisbane Queensland Australia

Radboud University Medical Center Department of Internal Medicine Nijmegen The Netherlands

Radboud University Medical Center Nijmegen The Netherlands

Radboud University Medical Centre Department of Internal Medicine Nijmegen The Netherlands

Redox Signaling and Oxidative Stress group Danish Cancer Society Research Center Copenhagen Denmark

Regional Centre for Biotechnology NCR Biotech Science Cluster Faridabad India

Reseach Center Borstel Leibniz Lung Center Priority Research Area Infections Junior Research Group Coinfection Borstel Germany

Research Center Borstel Cellular Microbiology Borstel Germany

Research Center Borstel Leibniz Lung Center Priority Area Infections Division Cellular Microbiology Borstel Germany

Research Center Principe Felipe Cellular Pathology Laboratory Valencia Spain

Research Department National Neuroscience Institute Singapore

Research Institute in Oncology and Hematology CancerCare Manitoba Winnipeg Manitoba Canada

Research Institute of the McGill University Health Centre Meakins Christie Laboratories and Translational Research in Respiratory Diseases Program Montréal Québec Canada; McGill University Department of Critical Care and Division of Experimental Medicine Montréal Québec Canada; UQAM Faculté des Sciences Département des Sciences de l'activité physique Montréal Canada

Rheinische Friedrich Wilhelms Universität Institut für Biochemie und Molekularbiologie Bonn Germany

Rice University Department of Bioengineering Houston TX USA

Rice University Department of Biosciences Houston TX USA

RIKEN Center for Brain Science Laboratory for Protein Conformation Diseases Wako Saitama Japan

RIKEN Center for Sustainable Resource Science Wako Saitama Japan

RIKEN Laboratory for Retinal Regeneration Kobe Hyogo Japan

Royal College of Surgeons in Ireland Department of Physiology and Medical Physics Dublin 2 Ireland

Royal Holloway University of London Centre for Biomedical Sciences Egham Surrey UK

Royal Veterinary College London UK; UCL Queen Square Institute of Neurology Department of Neurodegenerative Disease London UK

Rudolf Virchow Center University of Würzburg Würzburg Germany

Ruhr Universität Bochum Medizinische Fakultät Biochemie Intrazellulärer Transportprozesse Bochum Germany

Ruhr University Bochum Department of Molecular Immunology Bochum Germany

Ruprecht Karls University of Heidelberg Women's Hospital Department of Gynecological Endocrinology and Fertility Disorders Heidelberg Germany

Rutgers Biomedical and Health Sciences Rutgers University Robert Wood Johnson Medical School Department of Pharmacology New Brunswick NJ USA

Rutgers New Jersey Medical School Department of Cell Biology and Molecular Medicine Newark NJ USA

Rutgers Robert Wood Johnson Medical School Department of Neuroscience and Cell Biology Piscataway NJ USA

Rutgers University Center for Advanced Biotechnology and Medicine Piscataway NJ USA

Rutgers University Department of Biological Sciences Newark NJ USA

Rutgers University Department of Chemical Biology Ernest Mario School of Pharmacy Piscataway NJ USA

Rutgers University Department of Surgery New Brunswick NJ USA

Rutgers University New Jersey Medical School and Public Health Research Institute Newark NJ USA

Rutgers University The State University of New Jersey Department of Cell Biology and Neuroscience Piscataway NJ USA

RWTH Aachen University Medical School Institute of Biochemistry and Molecular Biology Aachen Germany

S and J Kishi Research Corporation Jupiter FL USA

Saarland University Department of Neurology Homburg Germany

Sabanci University Nanotechnology Research and Application Center Tuzla Istanbul Turkey

Sage Therapeutics Cambridge MA USA

Saha Institute of Nuclear Physics Biophysics and Structural Genomics Division HBNI Kolkata India

Saint Louis University Department of Biology Saint Louis MO USA

Saitama University Department of Regulatory Biology Saitama Japan

Saitama University Graduate School of Science and Engineering Saitama Japan

San Raffaele Open University and IRCCS San Raffaele Pisana Laboratorio di Patologia Cellulare e Molecolare Rome Italy

Sanford Burnham Prebys Medical Discovery Institute Program of Development Aging and Regeneration La Jolla CA USA

Sanford Burnham Prebys Medical Discovery Research Institute La Jolla CA USA

Sanjay Gandhi Postgraduate Institute of Medical Sciences Department of Endocrinology Lucknow India

Sanofi Biologics Research 49 New York Ave Framingham MA USA

Sanofi Vitry Sur Seine France

São Paulo State University Botucatu Medical School Center for Evaluation of Environmental Impact on Human Health Department of Pathology Botucatu SP Brazil

São Paulo State University College of Agronomy Sciences Department of Bioprocesses and Biotechnology Center for Evaluation of Environmental Impact on Human Health Botucatu SP Brazil

Sapienza University of Rome DAHFMO Section of Anatomy Rome Italy

Sapienza University of Rome Department of Anatomy Histology Forensic Medicine and Orthopedics Histology and Medical Embryology Section Rome Italy

Sapienza University of Rome Department of Anatomy Histology Forensic Medicine and Orthopedics Rome Italy

Sapienza University of Rome Department of Biochemical Sciences A Rossi Fanelli Rome Italy

Sapienza University of Rome Department of Biology and Biotechnology C Darwin Rome Italy

Sapienza University of Rome Department of Clinical and Molecular Medicine Laboratory affiliated to Istituto Pasteur Italia Fondazione Cenci Bolognetti Rome Italy

Sapienza University of Rome Department of Clinical Internal Anesthesiological and Cardiovascular Sciences Rome Italy

Sapienza University of Rome Department of Experimental Medicine Rome Italy

Sapienza University of Rome Department of Radiotherapy Policlinico Umberto 1 Rome Italy

Sapienza University of Rome Ospedale Sant'Andrea Rome Italy

Sapporo Higashi Tokushukai Hospital Advanced Surgery Center Sapporo Hokkaido Japan

Sapporo Medical University Department of Cardiovascular Renal and Metabolic Medicine Sapporo Japan

Save as Ravi Manjithaya

School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China

School of Biochemistry Faculty of Life Sciences University of Bristol Bristol UK

School of Biochemistry University of Bristol Bristol UK

School of Medicine Jiangsu University Zhenjiang Jiangsu China

School of Medicine Shenzhen University Shenzhen China

School of Medicine the Southern University of Science and Technology Shenzhen China

School of Pharmacy Complutense University Madrid Spain; Centro de Investigación Biomédica en Red Madrid Spain

School of Pharmacy Jeonbuk National University Jeollabuk do Republic of Korea

School of Radiation Medicine and Protection and State Key Laboratory of Radiation Medicine and Protection Soochow University Suzhou China

Scientific Institute IRCCS E Medea Laboratory of Molecular Biology Bosisio Parini Lecco Italy

Scripps Research Institute La Jolla CA USA

Sechenov 1st Moscow State Medical University Institute for Regenerative Medicine Moscow Russia

Section on Eukaryotic DNA Replication National Institute of Child Health and Human Development National Institutes of Health Bethesda MD USA

Semmelweis University Budapest Hungary

Seoul National University College of Medicine Department of Biochemistry and Molecular Biology Seoul Korea

Seoul National University College of Medicine Department of Biomedical Sciences and Ophthalmology Seoul Korea

Seoul National University College of Medicine Department of Biomedical Sciences Neuroscience Research Institute Seoul Korea

Seoul National University College of Pharmacy Seoul Korea

Seoul National University Department of Biological Sciences Seoul South Korea

Seoul National University School of Biological Science Seoul Korea

Seoul National University School of Biological Sciences Seoul Korea

Service of Endocrinology University Hospital Doctor Peset Foundation for the Promotion of Health and Biomedical Research in the Valencian Region Department of Physiology University of Valencia Valencia Spain

Shandong Agricultural University College of Plant Protection Shandong China

Shandong Cancer Hospital and Institute Cancer Research Center Jinan Shandong Province China

Shandong Normal University Shandong Provincial Key Laboratory of Plant Stress College of Life Sciences Jinan Shandong China

Shandong University School of Life Science Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology Qingdao China

Shandong University School of Life Sciences Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology Qingdao China

Shandong University School of public health Department of Toxicology and nutrition Jinan Shandong China

Shanghai Institute of Nutrition and Health Chinese Academy of Sciences Shanghai China

Shanghai Institute of Organic Chemistry Chinese Academy of Science Interdisciplinary Research Center on Biology and Chemistry Shanghai China; University of Chinese Academy of Sciences Beijing China

Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai China

Shanghai Jiao Tong University Bio 10 Institutes Shanghai China

Shanghai Jiao Tong University School of Life Sciences and Biotechnology Shanghai China

Shanghai Jiao Tong University School of Medicine Department of Hypertension Ruijin Hospital Shanghai China

Shanghai Jiao Tong University School of Medicine Ren Ji Hospital Center for Reproductive Medicine Shanghai China

Shanghai Jiao Tong University School of Medicine Ruijin Hospital Department of Otolaryngology and Head and Neck Surgery Shanghai China

Shanghai Jiao Tong University School of Medicine Shanghai General Hospital Department of Orthopedics Shanghai China; Shanghai Bone Tumor Institution Shanghai China

Shanghai Jiao Tong University School of Medicine Shanghai Institute of Immunology and Department of Immunology and Microbiology Shanghai China

Shanghai Ninth People's Hospital National Clinical Research Center for Oral Disease Shanghai Jiao Tong Univeristy School of Medicine Shanghai China

Shanghai Proton and Heavy Ion Center Department of Research and Development Pudong Shanghai China

Shanghai Sixth People's Hospital Department of Cardiovascular Medicine and Shanghai Jiaotong University School of Medicine Shanghai Institute of Immunology Shanghai China

Shanghai University of Traditional Chinese Medicine Longhua Hospital Cancer Institute Shanghai China

ShanghaiTech University School of Life Science and Technology Shanghai China

Shanxi Agricultural University Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine Taigu Shanxi China

Shenyang Pharmaceutical University Department of Pharmacology Shenyang China

Shenzhen University College of Medicine Shenzhen Guangdong China

Shenzhen University Health Science Center School of Dentistry Shenzhen Guangdong Province China

Shenzhen University Health Science Center School of Pharmaceutical Sciences Shenzhen Guangdong China

Shenzhen University Medical School Department of Biochemistry and Molecular Biology Shenzhen China

Shiga University of Medical Science Department of Medicine Otsu Shiga Japan

Shimane University Faculty of Medicine Internal Medicine 1 Izumo Shimane Japan

Sichuan Academy of Medical Science and Provincial Hospital Medical School of UESTC Chengdu China

Sichuan University and Collaborative Innovation Center for Biotherapy West China Hospital West China School of Basic Medical Sciences and Forensic Medicine and State Key Laboratory of Biotherapy and Cancer Center Chengdu China

Sichuan University West China Hospital Centre of Geriatrics and Gerontology Chengdu China

Sichuan University West China Hospital State key laboratory of biotherapy Chengdu Sichuan China

Sichuan University West China School of Basic Medical Sciences and Forensic Medicine Chengdu China

Sichuan University West China School of Pharmacy Key Laboratory of Drug Targeting and Drug Delivery System of the Education Ministry Chengdu China

Simon Fraser University Department of Chemistry Department of Molecular Biology and Biochemistry Burnaby British Columbia Canada

Smidt Heart Institute Cedars Sinai Medical Center Los Angeles CA USA

Soochow University Center for Circadian Clocks; School of Biology and Basic Medical Sciences Medical College Suzhou Jiangsu China

Soochow University College of Pharmaceutical Sciences Department of Pharmacology and Laboratory of Aging and Nervous Diseases Suzhou China

Soochow University College of Pharmaceutical Sciences Department of Pharmacology Suzhou Jiangsu China

Soochow University Department of Pathogenic Biology Suzhou Jiangsu Province China

Soochow University Department of Pharmacology and Laboratory of Cerebrovascular Pharmacology College of Pharmaceutical Science Suzhou Jiangsu China

Soochow University Hematology Center of Cyrus Tang Hematology Institute School of Medicine Suzhou China

Soochow University Institute of Neuroscience Jiangsu Key Laboratory of Translational Research and Therapy for Neuro Psycho Diseases Suzhou Jiangsu China

Soochow University Institute of Neuroscience Suzhou Jiangsu Province China

Soochow University Institutes for Translational Medicine Suzhou Jiangsu China

Soochow University Laboratory Animal Center Suzhou Jiangsu Province China

Sookmyung Women's University Department of Biological Sciences Seoul Korea

Sorbonne Université CNRS UMR8226 Institut de Biologie Physico Chimique Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes Paris France

Sorbonne Université Developmental Biology Laboratory CNRS Institut de Biologie Paris Seine IBPS UMR7622 Paris France

Soroka University Medical Center Institute of Hematology and Ben Gurion University of the Negev Faculty of Health Sciences Department of Clinical Biochemistry and Pharmacology Beer Sheva Israel

South Australian Health and Medical Research Institute Hopwood Centre for Neurobiology Lifelong Health Theme Adelaide South Australia Australia

South China Agricultural University College of Veterinary Medicine Guangzhou Guangdong China

South China Agricultural University Guangdong Provincial Key Laboratory of Agro animal Genomics and Molecular Breeding Guangdong Provincial Sericulture and Mulberry Engineering Research Center College of Animal Science Guangzhou China

South China Normal University School of Life Sciences Institute of Insect Science and Technology Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology Guangzhou China

South China University of Technology School of Medicine and Institute for Life Sciences GuangZhou China

Southeast University School of Medicine Department of Physiology Nanjing Jiangsu China

Southern Medical University Shenzhen Hospital Department of Gastroenterology Shenzhen Guangdong

Southern Medical University Shenzhen Hospital Department of Pathology Bao'an District Shenzhen Guangdong China

Southern University of Science and Technology Department of Biology Shenzhen China

Southwest Hospital 3rd Military Medical University Key Laboratory of Hepatobiliary and Pancreatic Surgery Institute of Hepatobiliary Surgery Chongqing China

Southwest Medical University Department of Medical Cellular Biology Luzhou Sichuan China

Southwest Medical University Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica Jiangyang District Luzhou China

Spencer Center for Vision Research Byers Eye Institute Stanford University School of Medicine Stanford CA USA

Sprott Centre for Stem Cell Research Ottawa Hospital Research Institute and University of Ottawa Department of Medicine Ottawa ON Canada

St Boniface Hospital Albrechtsen Research Centre Departments of Physiology and Pathophysiology and Pharmacology and Therapeutics Max Rady College of Medicine; Rady Faculty of Health Sciences University of Manitoba Winnipeg Manitoba Canada

St Jude Children's Research Hospital Department of Cell and Molecular Biology Memphis TN USA

St Jude Children's Research Hospital Department of Immunology Memphis TN USA

St Jude Children's Research Hospital Department of Pathology Memphis TN USA

St Marianna University Graduate School of Medicine Department of Molecular Neuroscience Kanagawa Japan

Stanford University Department of Chemical and Systems Biology Stanford CA USA

Stanford University Department of Gastroenterology and Hepatology Stanford CA USA

Stanford University School of Medicine Department of Neurosurgery Palo Alto CA USA

Stanford University School of Medicine Department of Pathology CA USA

Stanford University School of Medicine Department of Pathology Stanford CA USA

State Key Laboratory of Medicinal Chemical Biology Tianjin Key Laboratory of Protein Science College of Life Sciences Nankai University Tianjin China

State Key Laboratory of Membrane Biology Institute of Zoology Institute for Stem Cell and Regeneration Chinese Academy of Sciences University of Chinese Academy of Sciences Beijing China

State University of New York at Buffalo Buffalo NY USA

State University of New York Downstate Health Sciences University Department of Surgery and Cell Biology Brooklyn NY USA

State University of New York University at Buffalo Jacobs School of Medicine and Biomedical Sciences Departments of Ophthalmology Biochemistry and Neuroscience Program Buffalo NY USA

State University of New York Upstate Medical University Departments of Medicine Microbiology and Immunology Biochemistry and Molecular Biology Syracuse NY USA

Stazione Zoologica Anton Dohrn Napoli Italy

Stellenbosch University Department of Physiological Sciences Stellenbosch Western Cape South Africa

Stockholm University Department of Biochemistry and Biophysics Stockholm Sweden

Stockholm University The Wenner Gren Institute Department of Molecular Biosciences Stockholm Sweden

Stony Brook University Department of Pathology Stony Brook NY USA

Suez Canal University Faculty of Veterinary Medicine Ismailia Egypt

Sun Yat sen University School of Life Science Guangzhou China

Sun Yat sen University School of Life Sciences Guangdong Provincial Key Laboratory of Plant Resources State Key Laboratory of Biocontrol Guangzhou China

Sun Yat sen University School of Life Sciences MOE Key Laboratory of Gene Function and Regulation Guangzhou Guangdong China

Sun Yat Sen University School of Pharmaceutical Sciences Guangzhou China

Sun Yat Sen University Sun Yat sen Memorial Hospital Department of Neurology Guangzhou City Guangdong China

Sun Yat sen University Sun Yat sen Memorial Hospital Department of Pathology Guangzhou Guangdong Province China

Sun Yat sen University The 3rd Affiliated Hospital of Sun Yat sen University Vaccine Research Institute Guangzhou China

Swansea University Medical School Molecular Neurobiology group Swansea United Kingdom

Swedish Agricultural University Department of Plant Biology Uppsala Sweden

Swedish University of Agricultural Sciences and Linnean Center for Plant Biology Department of Molecular Sciences Uppsala BioCenter Uppsala Sweden; Heidelberg University Center for Organismal Studies Neuenheimer Feld Heidelberg Germany

Swedish University of Agricultural Sciences and Linnean Center for Plant Biology Uppsala BioCenter Department of Molecular Sciences Uppsala Sweden

Swedish University of Agricultural Sciences and Linnean Center for Plant Biology Uppsala BioCenter Department of Plant Biology Uppsala Sweden

Swedish University of Agricultural Sciences Department of Forest Mycology and Plant Pathology Uppsala Sweden

Swedish University of Agricultural Sciences The Linnean Centre of Plant Biology in Uppsala Department of Plant Biology Uppsala Sweden

Tabriz University of Medical Sciences Faculty of Advanced Medical Sciences Department of Medical Nanotechnology Tabriz Iran

Tabriz University of Medical Sciences Molecular Medicine Research Center Tabriz Iran

Taipei Medical University College of Medical Science and Technology Graduate Institute of Cancer Biology and Drug Discovery Taipei Taiwan

Taipei Veterans Generals Hospital Department of Medical Research Taipei Taiwan

Technical University Dresden Center for Molecular and Cellular Bioengineering Department of Cellular Biochemistry Dresden Germany

Technical University of Munich School of Medicine Klinikum rechts der Isar Department of Neurology Munich Germany

Technische Universität Dresden Center for Regenerative Therapies Dresden Dresden Germany

Technische Universität Dresden Institute for Physiological Chemistry Dresden Germany

Technische Universität Dresden Medical Clinic 1 University Hospital Carl Gustav Carus Dresden Germany; Technische Universität Dresden Faculty of Medicine Institute for Clinical Chemistry and Laboratory Medicine Dresden Germany; Institute of Molecular Genetics of the ASCR Department of Cancer Cell Biology Prague Czech Republic

Technische Universität München Klinikum rechts der Isar Comprehensive Cancer Center München München Germany

Tehran University of Medical Sciences Cancer Biology Research Center Tehran Iran

Tehran University of Medical Sciences School of Medicine Department of Medical Immunology Tehran Iran

Tel Aviv University Sackler Faculty of Medicine and Sagol School of Neuroscience Department of Human Molecular Genetics and Biochemistry Tel Aviv Israel

Tel Aviv University School of Neurobiology Biochemistry and Biophysics Tel Aviv Israel

Telethon Institute of Genetics and Medicine Naples Italy; Baylor College of Medicine Houston TX USA

Telethon Institute of Genetics and Medicine Pozzuoli Naples Italy

Temple University Alzheimer's Center at Temple Philadelphia PA USA

Temple University Center for Metabolic Disease Research and Department of Physiology Philadelphia PA USA

Temple University Lewis Katz School of Medicine Cardiovascular Research Center and Department of Physiology Philadelphia PA USA

Texas A and M College of Dentistry Department of Endodontics Dallas TX USA

Texas A and M University Institute of Biosciences and Technology Houston TX USA

Texas Biomedical Research Institute Host Pathogen Interactions Program San Antonio TX USA

Texas Tech University Department of Nutritional Sciences and Obesity Research Institute Lubbock TX USA

Texas Tech University Health Sciences Center Department of Pharmaceutical Sciences Amarillo TX USA

The 1st Affiliated Hospital Jinan University Guangzhou China

The 1st Affiliated Hospital of Guangzhou University of Chinese Medicine Guangzhou China

The 1st Affiliated Hospital of Nanjing Medical University Department of Neurosurgery Nanjing Jiangsu China

The 1st Hospital of Jilin University Cancer Center Department of Hematology Changchun Jilin China

The 1st Hospital of Jilin University Department of Ear Nose and Throat Changchun Jilin China

The 1st Hospital of Jilin University Department of Neurology Changchun China

The 1st Hospital of Jilin University Laboratory of Cancer Precision Medicine Changchun Jilin China

The 2nd Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University Department of Orthopaedics Wenzhou Zhejiang China

The 2nd Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University Department of Orthopaedics Wenzhou Zhejiang Province China

The 2nd Affiliated Hospital of Xi'an Jiaotong University Department of Radiation Oncology Xi'an Shaan Xi China

The 4th Military Medical University National Key Discipline of Cell Biology Department of Physiology and Pathophysiology Xi'an Shaanxi China

The 4th Military Medical University Tangdu Hospital Department of Experimental Surgery Xi'an Shaanxi China

The 4th Military Medical University Tangdu Hospital Department of Neurosurgery Xi'an Shaanxi China

The 4th Military Medical University Xijing Hospital Department of Orthopaedics Xi'an China

The 5th Affiliated Hospital of Guangzhou Medical University Guangzhou China

The Abigail Wexner Research Institute at Nationwide Children's Hospital Center for Microbial Pathogenesis Columbus OH USA

The Broad Institute of Harvard and MIT Massachusetts General Hospital Harvard Medical School Department of Molecular Biology Cambridge MA USA

The Catholic University of Korea Seoul St Mary's Hospital Department of Ophthalmology and Visual Science Seoul Kor

The Children's Hospital of Philadelphia Center for Applied Genomics Philadelphia PA USA

The Chinese University of Hong Kong Department of Anaesthesia and Intensive Care Hong Kong China

The Chinese University of Hong Kong Department of Medicine and Therapeutics and Department of Anaesthesia and Intensive Care Hong Kong China

The Chinese University of Hong Kong Faculty of Medicine School of Biomedical Sciences Shatin New Territories Hong Kong

The Chinese University of Hong Kong Lui Che Woo Institute of Innovative Medicine Centre for Cardiovascular Genomics and Medicine Joint Laboratory of Bioresources and Molecular Research of Common Diseases Kunming Yunnan China

The Chinese University of Hong Kong School of Biomedical Sciences Hong Kong China

The Chinese University of Hong Kong School of Biomedical Sciences Hong Kong China; The Chinese University of Hong Kong Department of Obstetrics and Gynecology Hong Kong China

The Chinese University of Hong Kong School of Life Sciences Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology Shatin New Territories Hong Kong China

The Chinese University of Hong Kong School of Life Sciences Shatin N T Hong Kong China

The Chinese University of Hong Kong School of Public Health and Primary Care Hong Kong China

The Chinese University of Hong Kong State Key Laboratory of Digestive Disease Department of Medicine and Therapeutics Hong Kong China

The Chinese University of Hong Kong The Prince of Wales Hospital The Faculty of Medicine Department of Orthopaedics and Traumatology New Territories Shatin Hong Kong China

The Connecticut Agricultural Experiment Station Center for Vector Biology and Zoonotic Diseases Department of Environmental Sciences New Haven CT USA

The Francis Crick Institute Molecular Cell Biology of Autophagy London UK

The Hebrew University of Jerusalem Alexander Silberman Institute of Life Sciences Department of Plant and Environmental Sciences Edmond Safra Campus Jerusalem Israel

The Hebrew University of Jerusalem The Institute for Medical Research Israel Canada Department of Biochemistry and Molecular Biology Ein Karem Jerusalem Israel

The Henry M Jackson Foundation Inc Bethesda MD USA

The Hong Kong Polytechnic University Department of Applied Biology and Chemical Technology Hong Kong China

The Hong Kong Polytechnic University Department of Health Technology and Informatics Hong Kong China

The Hong Kong Polytechnic University Faculty of Health and Social Sciences Department of Health Technology and Informatics Hunghom Hong Kong

The Hospital for Sick Children Translational Medicine Program Toronto Canada

The Institute of Cancer Research Cancer Therapeutics Unit Sutton UK

The Institute of Genetics and Animal Biotechnology Polish Academy of Sciences Magdalenka Poland; Ludwig Boltzmann Institute for Digital Health and Patient Safety Medical University of Vienna Vienna Austria; Institute of Neurobiology Bulgarian Academy of Sciences Sofia Bulgaria; Department of Pharmacognosy University of Vienna Vienna Austria

The Jikei University School of Medicine Department of Biochemistry Minato ku Tokyo Japan

The Jikei University School of Medicine Division of Respiratory Disease Departent of Internal Medicine Tokyo Japan

The Norwegian Radium Hospital Institute for Cancer Research Department of Molecular Cell Biology Montebello Oslo Norway; University of Oslo Faculty of Mathematics and Natural Sciences The Department of Biosciences Oslo Norway

The Norwegian Radium Hospital Institute for Cancer Research Department of Molecular Cell Biology Montebello Oslo Norway; University of Oslo Faculty of Medicine Institute of Clinical Medicine Centre for Cancer Cell Reprogramming Oslo Norway

The Ohio State University College of Veterinary Medicine Department of Veterinary Biosciences Columbus OH USA

The Ohio State University Department of Cancer Biology and Genetics Columbus OH USA

The Ohio State University Department of Surgery Columbus OH USA

The Ohio State University Wexner Medical Center Department of Surgery Columbus OH USA

The Open University School of Life Health and Chemical Sciences Faculty of Science Technology Engineering and Mathematics Milton Keynes UK

The Rockefeller University Laboratory of Cellular and Molecular Neuroscience New York NY USA

The Scripps Research Institute Department of Molecular Medicine La Jolla CA USA

The State Key Laboratory Breeding Base of Basic Science of Stomatology Wuhan University School and Hospital of Stomatology Department of Oral Medicine Wuhan Hubei China

The University of British Columbia Department of Biochemistry and Molecular Biology Vancouver BC Canada

The University of Chicago Department of Microbiology Chicago IL USA

The University of Chicago Department of Pathology Chicago IL USA; present address VIR Biotechnology San Francisco CA USA

The University of Hong Kong Department of Anesthesiology Queen Mary Hospital Hong Kong China

The University of Hong Kong Li Ka Shing Faculty of Medicine Department of Obstetrics and Gynecology Hong Kong China

The University of Hong Kong Queen Mary Hospital Department of Paediatrics and Adolescent Medicine Pokfulam Hong Kong China

The University of Hong Kong School of Chinese Medicine Hong Kong China

The University of Hong Kong School of Chinese Medicine Li Ka Shing Faculty of Medicine Hong Kong China

The University of Illinois at Chicago College of Medicine Department of Pharmacology Chicago IL USA

The University of Kansas Cancer Center Division of Hematologic Malignancies and Cellular Therapeutics Kansas City KS USA

The University of Queensland Queensland Brain Institute Clem Jones Centre for Ageing Dementia Research Brisbane Australia

The University of Queensland School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre St Lucia Brisbane Queensland Australia

The University of Sheffield Department of Biomedical Science Firth Court Western Bank Sheffield UK

The University of Suwon Department of Health Science Hwaseong Gyeonggi Korea

The University of Sydney Kolling Institute Renal Medicine Sydney New South Wales Australia

The University of Texas Health Science Center at Houston Department of Integrative Biology and Pharmacology Houston TX USA

The University of Texas Health Science Center at Houston McGovern Medical School Department of Internal Medicine Cardiology Houston TX USA

The University of Texas Health Science Center at Houston McGovern Medical School The Brown Foundation Institute of Molecular Medicine Department of Neurobiology and Anatomy Programs in Human and Molecular Genetics and Neuroscience of the MD Anderson UTHealth GSBS Houston TX USA

The University of Texas M D Anderson Cancer Center Department of Experimental Therapeutics Houston TX USA

The University of Texas McGovern Medical School at Houston Department of Neurology Houston TX USA

The University of Texas MD Anderson Cancer Center Department of Leukemia Houston TX USA

The University of Texas MD Anderson Cancer Center Institute for Applied Cancer Science Houston TX USA

The University of Tokyo Department of Biochemistry and Molecular Biology Graduate School of Medicine Tokyo Japan

The University of Tokyo Graduate School of Medicine Department of Biochemistry and Molecular Biology Tokyo Japan

The University of Tokyo Institute for Quantitative Biosciences Laboratory of RNA Function Tokyo Japan; Albert Einstein College of Medicine Department of Anatomy and Structural Biology Bronx NY USA

The Wilmer Eye Institute Johns Hopkins University School of Medicine Baltimore MD USA

The Wistar Institute Molecular and Cellular Oncogenesis Program Philadelphia PA USA

The Wistar Institute Philadelphia PA USA

Theoretical Division Los Alamos National Laboratory Los Alamos NM USA

Thomas Jefferson University Center for Translational Medicine Philadelphia PA USA

Thomas Jefferson University Department of Orthopaedic Surgery and Graduate Program in Cell Biology and Regenerative Medicine Philadelphia PA USA

Thomas Jefferson University Department of Pathology Anatomy and Cell Biology Philadelphia PA USA

Thomas Jefferson University Vickie and Jack Farber Institute for Neuroscience Hospital for Neuroscience Philadelphia PA USA

Tianjin Medical University Department of Biochemistry and Molecular Biology; School of Basic Medical Sciences Tianjin Key Laboratory of Medical Epigenetics Tianjin China

Tianjin Medical University Department of Immunology School of Basic Medical Sciences Tianjin China

Tianjin University of Traditional Chinese Medicine Tianjin State Key Laboratory of Modern Chinese Medicine Tianjin China

Tohoku University Graduate School fo Life Sciences Sendai Miyagi Japan

Tohoku University Graduate School of Agricultural Science Sendai Japan

Tohoku University Graduate School of Life Sciences Department of Integrative Life Sciences Sendai Miyagi Japan

Tohoku University Graduate School of Medicine Division of Neurology Department of Neuroscience and Sensory Organs Sendai Japan

Tokai University School of Medicine Department of Molecular Life Sciences Isehara Kanagawa Japan

Tokai University School of Medicine Division of Gastroenterology and Hepatology Department of Internal Medicine Isehara Kanagawa Japan

Tokyo Institute of Technology Institute of Innovative Research Cell Biology Center Yokohama Japan

Tokyo Institute of Technology School of Life Science and Technology Yokohama Japan

Tokyo Medical and Dental University Department of Cardiovascular Medicine Tokyo Japan

Tokyo Medical and Dental University Department of Pathological Cell Biology Tokyo Japan

Tokyo Medical and Dental University Institute of Biomaterials and Bioengineering Tokyo Japan

Tokyo Medical and Dental University Medical Hospital Department of Gastroenterology and Hepatology Bunkyo ku Tokyo Japan

Tokyo Medical and Dental University Tokyo Japan

Tokyo Medical University Department of Biochemistry Tokyo Japan

Tokyo University of Pharmacy and Life Sciences School of Life Sciences Hachioji Horinouchi Tokyo Japan

Tokyo University of Science Department of Applied Biological Science Noda Chiba Japan

Tongji University School of Medicine Shanghai Tenth People's Hospital Department of Gastroenterology Shanghai China

Tongren Hospital Shanghai Jiaotong University School of Medicine Department of Neurology Shanghai China

Total Toxicology Labs Southfield MI USA

Toulouse University CNRS UPS Center for Integrative Biology Toulouse France

Translational Genomics Group Incliva Health Research Institute Burjasot Valencia Spain; Interdisciplinary Research Structure for Biotechnology and Biomedicine University of Valencia Burjasot Valencia Spain

Translational Stem Cell Biology Metabolism Program Research Programs Unit University of Helsinki Helsinki Finland

Trev and Joyce Deeley Research Centre BC Cancer Victoria British Columbia Canada

Trinity College Dublin Department of Clinical Medicine Trinity Centre for Health Sciences Dublin Ireland

Trinity College Dublin School of Medicine Trinity Translational Medicine Institute Dublin Ireland

Trinity College Dublin Trinity Translational Medicine Institute Dublin Ireland

Tsinghua University School of Life Sciences Beijing China

Tsinghua University School of Life Sciences Tsinghua University Peking University Joint Center for Life Sciences State Key Laboratory of Membrane Biology Beijing China

Tsinghua Unversity School of Life Sciences Beijing China

Tufts University USDA Human Nutrition Research Center on Aging Laboratory for Nutrition and Vision Research Boston MA USA

Tulane Health Sciences Center Department of Pathology and Laboratory Sciences New Orleans LA USA

Tulane University Department of Microbiology and Immunology New Orleans LA USA

Tulane University Health Sciences Center Department of Pathology and Laboratory Medicine New Orleans LA USA

Tulane University School of Medicine Department of Pharmacology New Orleans LA USA

Tuscia University Department of Ecological and Biological Sciences Viterbo Italy

UCL Institute of Ophthalmology London UK

UCL Queen Square Institute of Neurology Department of Clinical and Movement Neurosciences London UK

UCL Queen Square Institute of Neurology London UK

UCL Queen Square Institute of Neurology Reta Lila Weston Institute London UK

UiT The Arctic University of Norway Department of Pharmacy Pharmacology Research Group Tromso Norway

Ulm University Institute of Biochemistry and Molecular Biology Faculty of Medicine Ulm Germany

Ulsan National Institute of Science and Technology Department of Biological Sciences Ulsan Korea

UMBC Department of Chemical Biochemical and Environmental Engineering Baltimore MD USA

Umeå University Department of Chemistry Umeå Sweden

Umeå University Umeå Centre for Microbial Research Department of Chemistry Umeå Sweden

UMR 7242 Biotechnology and cellular signaling CNRS Illkirch France

UMR7242 CNRS Université de Strasbourg Strasbourg France

United Arab Emirates University College of Medicine and Health Sciences Department of Anatomy Al Ain UAE

Univ of Pittsburgh and Pittsburgh VA HealthSystem Department of Pathology Pittsburgh PA USA

Universidad Autónoma de Madrid Centro de Biología Molecular Severo Ochoa Madrid Spain

Universidad Autónoma de Madrid Departamento de Biología Molecular Madrid Spain

Universidad Autónoma de Madrid Departamento de Biología Molecular Madrid Spain and Centro de Biología Molecular Severo Ochoa Madrid Spain

Universidad Autónoma de Madrid Department of Biology Madrid Spain

Universidad Autónoma de Madrid Facultad de Medicina Departamento de Anatomía Histología y Neurociencia Madrid Spain

Universidad Autonoma de Madrid School of Medicine Department of Pharmacology Madrid Spain

Universidad Autonoma de Nuevo Leon School of Medicine Department of Histology Monterrey Nuevo Leon Mexico

Universidad Cardenal Herrera CEU CEU Universities School of Health Sciences Department of Biomedical Sciences Moncada Spain

Universidad Castilla La Mancha Departmento Ciencias Medicas Albacete Spain

Universidad Castilla La Mancha Facultad de Farmacia Área Tecnología Farmacéutica Albacete Spain

Universidad de Buenos Aires Consejo Nacional de Investigaciones Científicas y Técnicas Facultad de Ciencias Exactas y Naturales Departamento de Química Biológica Laboratorio de Disfunción Celular en Enfermedades Neurodegenerativas y Nanomedicina Buenos Aires Argentina

Universidad de Buenos Aires Consejo Nacional de Investigaciones Científicas y Técnicas Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales Buenos Aires Argentina

Universidad de Buenos Aires Facultad de Farmacia y Bioquímica Departamento de Microbiología Inmunología y Biotecnología Cátedra de Inmunología Buenos Aires Argentina; Universidad de Buenos Aires CONICET Instituto de Estudios de la Inmunidad Humoral Buenos Aires Argentina

Universidad de Chile Facultad de Odontología Advanced Center for Chronic Diseases Santiago Chile

Universidad de Chile Facultad de Odontología Autophagy Research Center Santiago Chile

Universidad de Chile Instituto de Nutrición y Tecnología de los Alimentos Santiago Chile

Universidad de Chile School of Medicine Instituto de Ciencias Biomédicas Santiago de Chile Chile

Universidad de Concepción Department of Biochemistry and Molecular Biology Concepción Chile

Universidad de La Laguna Departamento de Ciencias Médicas Básicas Tenerife Spain

Universidad de la República Facultad de Agronomía Departamento de Biología Vegetal Montevideo Uruguay

Universidad de Salamanca Institute of Functional Biology and Genomics Salamanca Spain

Universidad de Santiago de Chile Faculty of Chemistry and Biology Department of Biology Santiago Chile

Universidad de Sevilla Departamento de Psicología Experimental Facultad de Psicología Sevilla Spain

Universidad de Valparaíso Centro Interdisciplinario de Neurociencia de Valparaíso Laboratory of Molecular Sensors Valparaíso Chile

Universidad de Zaragoza IA2 IIS Laboratorio de Genética Bioquímica Zaragoza Spain; Universidad de Zaragoza IA2 IIS Centro de Encefalopatías y Enfermedades Transmisibles Emergentes Zaragoza Spain

Universidad del País Vasco Instituto Biofisika and Departamento de Bioquímica y Biología Molecular Bilbao Spain

Universidad Francisco de Vitoria Madrid Spain

Universidad Mayor Center for Integrative Biology and Geroscience Center for Brain Health and Metabolism Santiago Chile

Universidad Mayor Center for Integrative Biology and Geroscience for Brain Health and Metabolism Santiago Chile

Universidad Mayor Center for Integrative Biology Santiago Chile

Universidad Miguel Hernández Elche Spain

Universidad Nacional Autónoma de México Faculty of Sciences Department of Cell Biology Fibrosis Lab Mexico City Mexico

Universidad Nacional Autónoma de México Institute of Biotechnology Plant Molecular Biology Department Cuernavaca Morelos México

Universidad Nacional Autónoma de México Instituto de Biotecnología Departamento de Medicina Molecular y Bioprocesos Laboratorio de Neuroinmunobiología Cuernavaca Morelos México

Universidad Nacional Autónoma de México Instituto de Fisiologia Celular Ciudad Universitaria Ciudad de México México

Universidad Nacional Autónoma de México Instituto de Fisiología Celular División de Neurociencias Departamento de Neuropatología Molecular Mexico DF Mexico

Universidad Nacional de Cordoba Laboratorio de Oncohematología Hospital Nacional de Clínicas CONICET Córdoba Argentina

Universidad Nacional de Cuyo Facultad de Ciencias Médicas Laboratorio de Biología Celular y Molecular IHEM CONICET Mendoza Argentina

Universidad San Sebastián Centro de Biología Celular y Biomedicina Facultad de Medicina y Ciencia Santiago Chile

Universidade Anhanguera de São Paulo Programa de Pós graduação Stricto sensu e Pesquisa São Paulo Brazil

Universidade de Lisboa Faculty of Pharmacy Research Institute for Medicines Lisboa Portugal

Universidade de São Paulo Department of Biochemistry Institute of Chemistry Sao Paulo Brazil

Universidade do Porto i3S Instituto de Investigação e Inovação em Saúde Porto Portugal; IPATIMUP Institute of Molecular Pathology and Immunology of the University of Porto Cancer Drug Resistance Group Porto Portugal; FFUP Faculty of Pharmacy of the University of Porto Department of Biological Sciences Porto Portugal

Universidade Federal de São Carlos Department of Genetics and Evolution São Carlos Brazil

Universidade Federal de São Paulo Department of Morphology and Genetics São Paulo SP Brazil

Universidade Federal de São Paulo Paulista School of Medicine Departament of Pharmacology São Paulo Brazil

Universidade Federal de Viçosa Departamento de Biologia Vegetal Viçosa MG Brazil

Universidade Federal do Rio de Janeiro Institute of Biophysics Carlos Chagas Filho Immunobiology Program Rio de Janeiro RJ Brazil

Universidade Federal do Rio Grande do Sul Center of Biotechnology and Department of Biophysics Porto Alegre RS Brazil

Universidade Federal do Rio Grande do Sul Morphological Sciences Department Porto Alegre RS Brazil; Clinicas Hospital of Porto Alegre Porto Alegre RS Brazil

Universidade NOVA de Lisboa CEDOC NOVA Medical School Faculdade de Ciências Médicas Lisboa Portugal

Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia Departamento Ciências da Vida UCIBIO Caparica Portugal

Universidade Nove de Julho Faculty of Pharmacy São Paulo SP Brazil

Università Cattolica del Sacro Cuore Department of Life Science and Public Health Section of Histology and Embryology Rome Italy

Università Cattolica del Sacro Cuore Rome Italy

Università degli Studi di Catania Dipartimento di Chirurgia Generale e Specialità Medico Chirurgiche Catania Italy

Università degli Studi di Milano Department of Biomedical and Clinical Sciences L Sacco Milan Italy

Università degli Studi di Milano Department of Medical Biotechnology and Translational Medicine Milano Italy

Università degli Studi di Milano Dipartimento di Scienze della Salute Milano Italy

Università degli Studi di Milano Dipartimento di Scienze Farmacologiche e Biomolecolari Centro di Eccellenza per lo studio delle Malattie Neurodegenerative Milano Italy

Università degli Studi di Sassari Dipartimento di Scienze Biomediche Sassari Italy

Università degli Studi Sapienza di Roma SAIMLAL Department Roma Italy

Università del Piemonte Orientale Department of Health Sciences Laboratory of Molecular Pathology Novara Italy

Università della Svizzera italiana Faculty of Biomedical Sciences Institute for Research in Biomedicine Bellinzona Switzerland; School of Life Sciences École Polytechnique Fédérale de Lausanne Lausanne Switzerland

Università di Milano Department of Biomedical and Clinical Sciences L Sacco Milan Italy

Università di Sassari Dipartimento di Scienze Biomediche Sassari Italy

Universitat Autonoma de Barcelona Departament of Biochemistry and Institut Neurosciences Faculty of Medicine Bellaterra Barcelona Spain

Universitat Autònoma de Barcelona Institute of Neuroscience Barcelona Spain

Universitat de Lleida Department of Experimental Medicine IRBLleida Lleida Spain

Universität zu Köln CECAD Forschungszentrum Institut für Genetik Köln Germany

Universitätsklinikum Essen Institute for Cell Biology Essen Germany

Université Côte D'Azur CNRS Inserm Institut de Biologie Valrose Nice France

Université Côte d'Azur INSERM C3M Nice France

Université Côte d'Azur INSERM CNRS IPMC team labeled Laboratory of Excellence Distalz Valbonne France

Université Côte d'Azur OncoAge Nice France

Université Côte d'Azur Université Nice Sophia Antipolis CEA DRF BIAM Faculté de Médecine UMR E 4320 TIRO MATOs Nice France

Université Côte d'Azur Université Nice Sophia Antipolis CEA DRF Institut Frédéric Joliot Faculté de Médecine UMR E 4320 TIRO MATOs Nice France

Université de Bordeaux Institut des Maladies Neurodégénératives CNRS UMR 5293 Bordeaux France

Université de Lyon ENSL UCBL CNRS LBMC UMS 3444 Biosciences Lyon Gerland Lyon France

Universite de Moncton Department of Chemistry and Biochemistry Moncton NB Canada

Université de Paris Centre de Recherche des Cordeliers Paris France

Université de Paris Centre de Recherche sur l'Inflammation Inserm UMR1149 Paris France

Université de Paris Centre de recherche sur l'inflammation Team Gut Inflammation Inserm U1149 CNRS ERL8252 Paris France

Université de Paris PARCC INSERM Paris France

Université de Paris Sorbonne Université Centre de Recherche des Cordeliers INSERM U1138 Paris France

Université de Paris Sorbonne Université Centre de Recherche des Cordeliers INSERM U1138 Team Metabolism Cancer and Immunity Paris France; Gustave Roussy Cancer Campus Metabolomics and Cell Biology Platforms Villejuif France

Université de Paris Sorbonne Université INSERM U1138 Centre de Recherche des Cordeliers Equipe labellisée par la Ligue contre le cancer Paris France; Institut Gustave Roussy Metabolomics and Cell Biology Platforms Villejuif France; Hôpital Européen Georges Pompidou AP HP Pôle de Biologie Paris France; Chinese Academy of Medical Sciences Suzhou Institute for Systems Medicine Suzhou China; Karolinska Institute Karolinska University Hospital Department of Women's and Children's Health Stockholm Sweden

Université de Pau et des Pays de l'Adour E2S UPPA INRAE NUMEA 64310 Saint Pée sur Nivelle France

Université de Pau et des Pays de l'Adour E2S UPPA INRAE UMR1419 Nutrition Métabolisme et Aquaculture F 64310 Saint Pée sur Nivelle France

Université de Sherbrooke Département d'immunologie et de biologie cellulaire Sherbrooke Québec Canada

Université de Strasbourg CNRS UPR 3572 Institut de Biologie Moléculaire et Cellulaire Strasbourg France

Université du Québec à Trois Rivières Département de Biologie Médicale Trois Rivières Québec Canada

Université Lyon Université Claude Bernard Lyon 1 CNRS UMR 5310 INSERM U1217 Institut NeuroMyoGène Lyon France

Université Paris Descartes Institut Cochin INSERM U1016 CNRS UMR8104 Paris France

Université Paris Saclay CEA 1035 CNRS Institute for Integrative Biology of the Cell INSERM U1280 Gif sur Yvette France

Université Paris Saclay Inserm U1185 Le Kremlin Bicêtre France

Université Paris Saclay INSERM UMR S 1193 Châtenay Malabry France

Université Paris Saclay INSERM UMR1195 Hôpital Le Kremlin Bicêtre 80 rue du Général Leclerc 94276 Kremlin Bicêtre France

Université Paris Saclay Institut des Neurosciences Paris Saclay CNRS UMR 9197 Orsay France

Université Toulouse 3 Toulouse France

University at Buffalo The State University of New York Department of Physiology and Biophysics Buffalo NY USA

University Bourgogne Franche Comté AgroSup Dijon PAM UMR A 02 102 Dijon France

University California San Diego Division of Biological Sciences Section of Molecular Biology CA USA

University Campus Bio Medico Department of Medicine Rome Italy

University Children's Hospital Zurich Children's Research Center and Department of Oncology Zurich Switzerland

University Clinic Freiburg Institute for Microbiology and Hygiene University of Freiburg Faculty of Medicine Freiburg Germany

University College Cork Department of Cancer Research Cork Ireland

University College Cork Department of Pharmacology and Therapeutics County Cork Ireland

University College London Cancer Institute London UK

University College London Department of Neuroscience Physiology and Pharmacology London UK

University College London Institute of Healthy Ageing Department of Genetics Evolution and Environment London UK

University College London MRC Laboratory for Molecular Cell Biology London UK

University College London School of Pharmacy Department of Pharmacology London United Kingdom

University Côte d'Azur FHU OncoAge Department of Pathology Nice France

University Côte d'Azur U1081 Nice France

University Duisburg Essen Essen University Hospital Department of Gastroenterology and Hepatology Essen Germany; Department of Gastroenterology Hepatology and Endocrinology Hannover Medical School Hannover Germany

University Federico 2 of Naples Department of Molecular Medicine and Medical Biotechnology Naples Italy

University G D'Annunzio Department of Medical Sciences DSMOB Chieti Italy; Regina Elena National Cancer Institute Department of Research Rome Italy

University Grenoble Alpes and Inserm U1055 Laboratory of Fundamental and Applied Bioenergetics Grenoble France

University Hospital and University of Zürich Department of Gastroenterology and Hepatology Zürich Switzerland

University Hospital Basel Department of Biomedicine Ocular Pharmacology and Physiology Basel Switzerland

University Hospital Erlangen Department of Molecular Neurology Erlangen Germany

University Hospital Jena Institute of Human Genetics Jena Thuringia Germany

University Hospital La Paz Research Institute Cancer and Human Molecular Genetics Area Oto Neurosurgery Research Group Madrid Spain

University Hospital Münster Institute of Musculoskeletal Medicine Münster Germany

University Hospital of Bonn Institute of Reconstructive Neurobiology Bonn Germany

University Hospital of Lausanne Central Laboratory of Hematology Lausanne Switzerland

University Hospital of North Norway The Heart and Lung Clinic; University of Tromso The Artic University of Norway Department of Clinical Medicine Tromso Norway

University Hospital of Regensburg Institute of Clinical Microbiology and Hygiene Regensburg Germany

University Hospital RWTH Aachen Institute of Molecular Pathobiochemistry Experimental Gene Therapy and Clinical Chemistry Aachen Germany

University Hospitals Leuven Department of Neurology Leuven Belgium; KU Leuven Department of Neurosciences Leuven Belgium

University Magna Graecia of Catanzaro Department of Health Sciences Catanzaro Italy

University Medical Center Eppendorf Institute for Medical Microbiology Hamburg Germany

University Medical Center Göttingen Center for Biostructural Imaging of Neurodegeneration Department of Experimental Neurodegeneration Göttingen Germany; Max Planck Institute for Experimental Medicine Göttingen Germany; Newcastle University The Medical School Institute of Neuroscience Newcastle upon Tyne UK

University Medical Center Gottingen Department of Experimental Neurodegeneration Gottingen Germany

University Medical Center Göttingen Institute of Cellular Biochemistry Göttingen Germany

University Medical Center Hamburg Eppendorf Children's Hospital University Children's Hamburg Germany

University Medical Center Hamburg Eppendorf Department of Oncology Hematology and Bone Marrow Transplantation with Section Pneumology Hamburg Germany

University Medical Center of Johannes Gutenberg University Institute for Virology Mainz Germany

University Medical Center of the Johannes Gutenberg University Institute of Pathobiochemistry Mainz Germany

University Medical Center Utrecht Center for Molecular Medicine Utrecht The Netherlands; Regenerative Medicine Center Utrecht The Netherlands

University Medicine Goettingen Neurology Department of Translational Neurodegeneration Center for Biostructural Imaging of Neurodegeneration Goettingen Germany

University Medicine Göttingen Clinic for Neurology Göttingen Germany

University Monastir Faculty of Medicine LR12ES05 Lab NAFS 'Nutrition Functional Food and Vascular Health' Monastir Tunisia

University of Alabama at Birmingham Cardiac Aging and Redox Signaling Laboratory Molecular and Cellular Pathology Department of Pathology Birmingham AL USA

University of Alabama at Birmingham Center for Neurodegeneration and Experimental Therapeutics Department of Neurology Birmingham AL USA

University of Alabama at Birmingham Department of Medicine Division of Cardiovascular Disease Birmingham AL USA

University of Alabama at Birmingham Department of Medicine Pulmonary Allergy and Critical Care Medicine Birmingham VA Medical Center Birmingham AL USA

University of Alabama at Birmingham Department of Ophthalmology and Visual Sciences Birmingham AL USA

University of Alabama at Birmingham Department of Optometry and Vision Science Birmingham AL USA

University of Alabama at Birmingham Department of Pathology Birmingham AL USA

University of Alabama at Birmingham Department of Pharmacology and Toxicology Birmingham AL USA

University of Alabama at Birmingham Division of Cardiovascular Disease Department of Medicine Birmingham AL USA

University of Alabama at Birmingham Division of Nephrology and Birmingham VA Medical Center Birmingham AL USA

University of Alabama Department of Biological Sciences Tuscaloosa AL USA

University of Alberta Department of Biochemistry Edmonton Alberta Canada

University of Alberta Department of Biochemistry Edmonton Canada

University of Alberta Department of Laboratory Medicine and Pathology Edmonton AB Canada

University of Alcalá Deparment of Systems Biology Biochemistry and Molecular Biology Alcalá de Henares Madrid Spain

University of Amsterdam Medical Biochemistry Amsterdam UMC Amsterdam The Netherlands

University of Antwerp Department of Biomedical Sciences Peripheral Neuropathy Research Group Antwerp Belgium

University of Antwerp Laboratory of Physiopharmacology Antwerp Belgium

University of Arizona Cancer Center Tucson AZ USA

University of Arizona College of Medicine Department of Basic Medical Sciences Phoenix AZ USA

University of Arizona Department of Medicine Tucson AZ USA

University of Arizona Department of Molecular and Cellular Biology Tucson AZ USA

University of Arizona Department of Pharmacology and Toxicology Tucson AZ USA

University of Arkansas Center of Excellence for Poultry Science Fayetteville AR USA

University of Arkansas for Medical Sciences and Central Arkansas Veterans Healthcare System Little Rock AR USA

University of Arkansas for Medical Sciences Department of Geriatrics Little Rock AR USA

University of Arkansas for Medical Sciences Fay W Boozman College of Public Health Department of Environmental and Occupational Health Little Rock AR USA

University of Arkansas for Medical Sciences Little Rock AR USA

University of Auckland School of Biological Sciences Auckland New Zealand

University of Barcelona Barcelona Hepatic Hemodynamic Unit Liver Unit Hospital Clinic Hospital Clínic Institut d'Investigacions Biomèdiques Barcelona Spain

University of Barcelona Department of Biochemistry and Molecular Biomedicine and Network Center for Biomedical Research in Pathophysiology of Obesity and Nutrition Barcelona Spain

University of Barcelona Faculty of Pharmacy Department of Biochemistry and Physiology Barcelona Spain

University of Barcelona School of Medicine Unit of Anatomy Department of Pathology and Experimental Therapeutics Barcelona Spain; L'Hospitalet de Llobregat Institut d'Investigació Biomèdica de Bellvitge IDIBELL Molecular Mechanisms and Experimental Therapy in Oncology Program Barcelona Spain

University of Belgrade Faculty of Medicine Institute of Microbiology and Immunology Belgrade Serbia

University of Belgrade Institute for Biological Research Sinisa Stankovic National Institute of Republic of Serbia Department of Neurobiology Belgrade Serbia

University of Belgrade Institute for the Application of Nuclear Energy Belgrade Serbia

University of Belgrade Institute of Molecular Genetics and Genetic Engineering Belgrade Serbia

University of Bergen Department of Biomedicine Centre for Cancer Biomarkers Bergen Norway

University of Bern Institute of Cell Biology Bern Switzerland

University of Bern Institute of Pathology Bern Switzerland; TRANSAUTOPHAGY European network for multidisciplinary research and translation of autophagy knowledge COST Action CA15138

University of Bern Institute of Pathology Division of Experimental Pathology Bern Switzerland

University of Bern Institute of Pharmacology Bern Switzerland; Sechenov University Department of Clinical Immunology and Allergology Moscow Russia

University of Birmingham College of Medical and Dental Sciences Institute of Inflammation and Ageing Birmingham UK

University of Birmingham Institute of Biomedical Research Institute of Cancer and Genomic Sciences College of Medical and Dental Sciences Edgbaston Birmingham UK

University of Birmingham Institute of Cancer and Genomic Sciences Birmingham UK

University of Birmingham Institute of Metabolism and Systems Research Birmingham UK

University of Bologna Department of Biomedical and Neuromotor Sciences Bologna Italy

University of Bologna Department of Medical and Surgical Sciences; Rizzoli Orthopaedics Institute Laboratory of Immunorheumatology and Tissue Regeneration Bologna Italy

University of Bologna Department of Pharmacy and Biotechnology Bologna Italy

University of Bonn Clinical Centre Department of Psychiatry Neurohomeostasis Group Bonn Germany

University of Bonn Department of Neurology Molecular Cell Biology Unit Bonn Germany

University of Bonn Department of Pharmaceutical and Cellbiological Chemistry Bonn Germany

University of Bonn LIMES Institute Bonn Germany

University of Bonn Pharmaceutical Institute Section Pharmacology and Toxicology Bonn Germany

University of Bordeaux CNRS IBGC UMR 5095 Bordeaux France

University of Bordeaux CNRS IMN UMR 5293 Bordeaux France

University of Bourgogne Franche Comté Team 'Biochemistry of the Peroxisome Inflammation and Lipid Metabolism Inserm Faculty of Sciences Gabriel Dijon France

University of Brescia Department of Molecular and Translational Medicine Brescia Italy

University of British Columbia Centre for Heart Lung Innovation Department of Pathology and Laboratory Medicine Vancouver BC Canada

University of British Columbia Department of Ophthalmology and Visual Sciences Vancouver British Columbia Canada

University of British Columbia Department of Urologic Sciences Vancouver BC Canada

University of Buenos Aires Faculty of Pharmacy and Biochemistry Institute of Immunology Genetics and Metabolism CONICET Buenos Aires Argentina

University of Buenos Aires Institute of Biochemistry and Molecular Medicine Pathophysiology Department School of Pharmacy and Biochemistry CONICET Buenos Aires Argentina

University of Burgundy Centre Georges François Leclerc Department of Medical Oncology Dijon France

University of Calabria Department of Biology Ecology and Earth Sciences Centre for Microscopy and Microanalysis Calabria Italy

University of Calabria Department of Farmacy Health and Nutritional Sciences Rende Italy

University of Calabria Department of Pharmacy Health and Nutritional Sciences Arcavacata di Rende Italy

University of Calabria Department of Pharmacy Health and Nutritional Sciences Cosenza Italy

University of Calabria Department of Pharmacy Health Science and Nutrition Section of Preclinical and Translational Pharmacology Cosenza Italy

University of Calcutta Department of Biotechnology and Dr B C Guha Centre for Genetic Engineering and Biotechnology Kolkata India

University of Calgary Cumming School of Medicine Departments of Medical Genetics and Biochemistry and Molecular Biology Calgary Alberta Canada

University of Calgary Cumming School of Medicine Libin Cardiovascular Institute of Alberta Departments of Biochemistry and Molecular Biology and Physiology and Pharmacology Calgary Alberta Canada

University of Calgary Department of Comparative Biology and Experimental Medicine Calgary AB Canada

University of California Berkeley Department of Molecular and Cell Biology Berkeley CA USA

University of California Berkeley Department of Molecular Biology and Cell Biology Berkeley CA USA; University of California Berkeley California Institute for Quantitative Biosciences Berkeley CA USA

University of California Berkeley Departments of Molecular and Cell Biology and Nutritional Sciences and Toxicology Berkeley CA USA; Chan Zuckerberg Biohub San Francisco CA USA

University of California Davis and MIND Institute School of Veterinary Medicine Dept Molecular Biosciences Davis CA USA

University of California Davis Department of Dermatology Sacramento CA USA

University of California Davis Department of Molecular and Cellular Biology Davis CA USA

University of California Davis Department of Pathology and Laboratory Medicine Shriners Hospitals for Children Institute for Pediatric Regenerative Medicine Sacramento CA USA

University of California Davis Division of Rheumatology Allergy and Clinical Immunology School of Medicine Sacramento CA USA

University of California Davis School of Medicine Department of Pharmacology Davis CA USA

University of California Irvine Department of Psychiatry and Human Behavior Irvine CA USA

University of California Irvine School of Medicine Irvine CA USA

University of California Los Angeles David Geffen School of Medicine Department of Human Genetics Los Angeles CA USA

University of California Los Angeles Department of Integrative Biology and Physiology Los Angeles CA USA

University of California Los Angeles Department of Neurology Molecular and Medical Pharmacology David Geffen School of Medicine Los Angeles CA USA

University of California Los Angeles School of Dentistry Division of Oral Biology and Medicine Los Angeles CA USA

University of California San Diego Department of Cellular and Molecular Medicine La Jolla CA USA

University of California San Diego Department of Neurosciences La Jolla CA USA

University of California San Diego Department of Pharmacology La Jolla CA US

University of California San Diego La Jolla CA USA; Rady Children's Hospital San Diego San Diego CA USA

University of California San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences La Jolla CA USA

University of California San Diego UCSD Moores Cancer Center La Jolla CA USA

University of California San Diego; Section of Cell and Developmental Biology La Jolla CA USA

University of California San Francisco Department of Medicine Zuckerberg San Francisco General Hospital and TraumaCenter San Francisco CA USA

University of California San Francisco Department of Ophthalmology San Francisco CA USA

University of California San Francisco Department of Pathology San Francisco CA USA

University of California San Francisco San Francisco CA USA

University of California San Francisco UCSF Diabetes Center Department of Cell and Tissue Biology San Francisco CA USA

University of Cambridge Cambridge Institute for Medical Research UK Dementia Research Institute and Department of Medical Genetics Cambridge UK

University of Cambridge Cancer Research UK Cambridge Institute Cambridge UK

University of Cambridge MRC Mitochondrial Biology Unit Cambridge UK

University of Camerino Department of Biosciences and Biotechnology Camerino Italy

University of Camerino School of Biosciences and Veterinary Medicine Camerino Italy

University of Camerino School of Pharmacy Camerino MC Italy

University of Camerino School of Pharmacy Experimental Medicine Section Camerino Italy

University of Campania L Vanvitelli Department of Precision Medicine Naples Italy; Institute of Genetic Research Biogem scarl Laboratory of Molecular and Precision Oncology Ariano Irpino Italy

University of Campania L Vanvitelli Dipartimento di Scienze Mediche Traslazionali Naples Italy

University of Campania Luigi Vanvitelli Department of Precision Medicine Naples Italy

University of Campinas School of Applied Science Department of Sport Sciences Limeira Brazil

University of Canterbury Biomolecular Interaction Centre School of Biological Sciences Christchurch New Zealand

University of Chicago Department of Medicine Section of Dermatology Chicago IL USA

University of Chieti Pescara Department of Medical Oral and Biotechnological Science Chieti Italy

University of Chile Biomedical Neuroscience Institute Faculty of Medicine Santiago Chile; FONDAP Center for Geroscience Brain Health and Metabolism Santiago Chile; University of Chile Institute of Biomedical Science Program of Cellular and Molecular Biology Santiago Chile; Buck Institute for Research on Aging Novato CA USA

University of Chile Faculty of Chemical and Pharmaceutical Sciences Advanced Center for Chronic Diseases Santiago Chile

University of Chile Faculty of Chemical and Pharmaceutical Sciences Department of Chemical Pharmacology and Toxicology Santiago de Chile Chile

University of Chile Institute of Nutrition and Food Technology Santiago Chile

University of Cincinnati College of Medicine Cincinnati Children's Research Foundation Division of Pulmonary Biology Department of Pediatrics Cincinnati OH USA

University of Cincinnati College of Medicine Department of Cancer Biology Cincinnati OH USA

University of Cincinnati Department of Cancer Biology Cincinnati OH USA

University of Cincinnati Division of Hematology Oncology Cincinnati OH USA

University of Clermont Auvergne M2iSH UMR 1071 Inserm INRA USC 2018 CRNH Clermont Ferrand France

University of Coimbra CNC Center for Neuroscience and Cell Biology and Faculty of Medicine and CIBB Center for Innovative Biomedicine and Biotechnology Coimbra Portugal

University of Coimbra Coimbra Institute for Clinical and Biomedical Research Faculty of Medicine Coimbra Portugal; University of Coimbra Center for Innovative Biomedicine and Biotechnology Coimbra Portugal

University of Coimbra Faculty of Medicine and CNC Center for Neuroscience and Cell Biology Coimbra Portugal

University of Coimbra Institute of Physiology Faculty of Medicine Coimbra Portugal and CNC Center for Neuroscience and Cell Biology Coimbra Portugal

University of Coimbra Portugal CNC Center for Neuroscience and Cell Biology and Faculty of Pharmacy Coimbra Portugal

University of Colima University Center for Biomedical Research Colima Mexico

University of Cologne and University Hospital Cologne Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases Cologne Germany; Center for Molecular Medicine Cologne Germany

University of Cologne Center for Biochemistry Cologne Germany

University of Cologne Centre for Biochemistry Institute of Biochemistry 1 Medical Faculty Cologne Germany

University of Cologne Faculty of Medicine and University Hospital Cologne Department of Pediatrics Cologne Germany

University of Cologne Faculty of Medicine and University Hospital Cologne Department of Pediatrics Cologne Germany; University of Cologne Faculty of Medicine and University Hospital Cologne Center for Molecular Medicine Cologne Germany

University of Cologne Faculty of Medicine and University Hospital Cologne Institute for Medical Microbiology Immunology and Hygiene Cologne Germany

University of Cologne Institute for Genetics and CECAD Research Center Cologne Germany

University of Colorado AMC Department of Pharmacology Aurora CO USA

University of Colorado Anschutz Medical Campus Department of Biochemistry and Molecular Genetics Aurora CO USA

University of Colorado Anschutz Medical Campus Department of Pharmacology Aurora CO USA

University of Colorado Anschutz Medical Campus Division of Cardiology Aurora CO USA

University of Colorado Anschutz Medical Campus Division of Renal diseases Aurora CO USA

University of Colorado at Boulder Department of Biochemistry Boulder CO USA

University of Colorado Denver Children's Hospital Colorado Morgan Adams Foundation Pediatric Brain Tumor Research Program Aurora CO

University of Colorado Denver Department of Medicine Aurora CO USA

University of Colorado School of Medicine Department of Pharmacology Aurora CO USA

University of Copenhagen Biotech Research and Innovation Centre Copenhagen Denmark

University of Copenhagen Copenhagen Biocentre Faculty of Health and Medical Sciences Biotech Research and Innovation Centre Neuroinflammation Unit Copenhagen N Denmark

University of Copenhagen Department of Biology Copenhagen Denmark

University of Copenhagen Department of Biology Denmark

University of Copenhagen Department of Neuroscience Copenhagen Denmark

University of Copenhagen Department of Nutrition Exercise and Sports Section of Molecular Physiology Copenhagen Denmark

University of Copenhagen Novo Nordisk Foundation Center for Basic Metabolic Research Copenhagen Denmark

University of Cordoba Department of Cell Biology Physiology and Immunology Córdoba Spain

University of Crete School of Medicine Laboratory of Clinical Microbiology and Microbial Pathogenesis Voutes Heraklion Crete Greece

University of Crete School of Medicine Laboratory of Clinical Microbiology and Microbial Pathogenesis Voutes Heraklion Crete Greece; Foundation for Research and Technology Institute of Molecular Biology and Biotechnology Heraklion Crete Greece

University of Cyprus Department of Biological Sciences Bioinformatics Research Laboratory Nicosia Cyprus

University of Defense Faculty of Military Health Sciences Department of Radiobiology Hradec Kralove Czech Republic

University of Delhi South Campus Department of Genetics New Delhi India

University of Duisburg Essen Centre for Medical Biotechnology Faculty of Biology Essen Germany

University of Dundee School of Life Sciences MRC Protein Phosphorylation and Ubiquitylation Unit Dundee UK

University of Dundee School of Medicine Division of Cellular Medicine Dundee Scotland UK

University of East Anglia School of Biological Sciences Norwich Research Park UK

University of Eastern Finland A 1 Virtanen Institute for Molecular Sciences Kuopio Finland

University of Eastern Finland and Kuopio University Hospital Department of Ophthalmology Kuopio Finland

University of Eastern Finland Department of Ophthalmology Kuopio Finland

University of Eastern Finland Faculty of Health Sciences School of Pharmacy Kuopio Finland

University of Eastern Finland School of Pharmacy Kuopio Finland

University of Edinburgh Cancer Research UK Edinburgh Centre Institute of Genetics and Molecular Medicine Edinburgh UK

University of Edinburgh MRC Institute of Genetics and Molecular Medicine Scotland UK

University of Electronic Science and Technology of China School of Medicine Chengdu China; Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital Department of Pharmacy Chengdu Sichuan China

University of Exeter Medical School European Centre for Environment and Human Health Plymouth UK; University of Plymouth School of Biological and Marine Sciences Plymouth UK

University of Extremadura Centro de Investigación Biomedica en Red de Enfermedades Neurodegenerativas Department of Biochemistry Molecular Biology and Genetics Faculty of Nursing and Occupational Therapy Cáceres Spain

University of Ferrara Department of Chemical and Pharmaceutical Sciences Ferrara Italy

University of Ferrara Department of Morphology Surgery and Experimental Medicine Ferrara Italy

University of Ferrara Department of Translational Medicine Ferrara Italy

University of Florida Department of Physical Therapy Gainesville FL USA

University of Florida Food Science and Human Nutrition Department Gainesville FL USA

University of Freiburg Institute of Biochemistry and Molecular Biology ZBMZ Faculty of Medicine Freiburg Germany; University of Freiburg CIBSS Centre for Integrative Biological Signalling Studies Freiburg Germany

University of Fribourg Department of Biology Fribourg Switzerland

University of Gdansk Department of Medical Biology and Genetics Gdansk Poland

University of Gdansk Department of Molecular Biology Gdansk Poland

University of Gdansk Faculty of Chemistry Gdansk Poland

University of Geneva Department of Biochemistry Faculty of Science Switzerland

University of Genoa Department of Earth Environment and Life Sciences Genoa Italy

University of Genoa DIMES Department of Experimental Medicine Human Anatomy Genoa Italy

University of Genova Department of Internal Medicine and IRCCS Policlinico San Martino Genova Italy

University of Genova Department of Internal Medicine Genova Italy

University of Georgia Department of Kinesiology Athens GA USA

University of Glasgow Institute of Cancer Sciences Glasgow UK

University of Glasgow Institute of Molecular Cell and Systems Biology Glasgow Scotland United Kingdom

University of Glasgow Wolfson Wohl Cancer Research Centre Institute of Cancer Sciences Glasgow UK

University of Granada Faculty of Pharmacy Department of Physical Chemistry Granada Spain

University of Graz Institute of Molecular Biosciences BioTechMed Graz BioHealth Graz Austria

University of Graz Institute of Molecular Biosciences BioTechMed Graz Graz Austria

University of Graz Institute of Molecular Biosciences NAWI Graz Graz Austria

University of Graz NAWI Graz Institute of Molecular Biosciences Graz Austria; BioTechMed Graz Graz Austria; University of Graz Field of Excellence BioHealth Graz Austria

University of Greifswald Institute of Pharmacy Greifswald Germany

University of Groningen University Medical Center Groningen Department of Hematology Groningen The Netherlands

University of Groningen University Medical Center of Groningen Department of Biomedical Sciences of Cells and Systems Groningen The Netherlands

University of Guelph Department of Food Science Guelph Canada

University of Helsinki and Helsinki University Hospital Department of Virology Helsinki Finland

University of Helsinki Faculty of Pharmacy Division of Pharmacology and Pharmacotherapy Drug Research Program Helsinki Finland

University of Helsinki Institute of Biotechnology Cell and Tissue Dynamics Programme and Electron Microscopy Unit Helsinki Finland

University of Helsinki Institute of Biotechnology Electron Microscopy Unit Helsinki Finland

University of Helsinki Medicum Biochemistry and Developmental Biology Helsinki Finland

University of Helsinki Molecular and Integrative Biosciences Research Programme Helsinki Finland

University of Hong Kong Cardiology Division Department of Medicine Hong Kong China

University of Hong Kong Department of Medicine Division of Neurology Pokfulam Hong Kong China

University of Houston College of Pharmacy Department of Pharmacological and Pharmaceutical Sciences Houston TX USA

University of Houston Department of Pharmacological and Pharmaceutical Sciences Houston TX USA

University of Iceland Faculty of Medicine Biomedical center Reykjavik Iceland

University of Illinois at Chicago College of Medicine Department of Biochemistry and Molecular Genetics Chicago IL USA

University of Illinois at Chicago Department of Medicine Chicago IL USA

University of Illinois at Chicago Department of Pathology College of Medicine Chicago IL USA

University of Illinois at Urbana Champaign Department of Molecular and Integrative Physiology Urbana IL USA

University of Illinois Department of Anesthesiology Chicago IL USA

University of Indonesia Faculty of Medicine Department of Obstetric and Gynecology Jakarta Indonesia

University of Innsbruck Division of Cell Metabolism and Differentiation Research Research Institute for Biomedical Aging Research Innsbruck Austria

University of Innsbruck Institute for Biomedical Aging Research Department of Molecular Biology Innsbruck Austria

University of Innsbruck Institute of Biochemistry and Center for Molecular Biosciences Innsbruck Innsbruck Austria; University Medical Center Groningen University of Groningen Section Systems Medicine of Metabolism and Signaling Laboratory of Pediatrics Groningen The Netherlands

University of Insubria Department of Biotechnology and Life Sciences Varese Italy

University of Iowa Carver College of Medicine Fraternal Order of Eagles Diabetes Research Center Department of Anatomy and Cell Biology Iowa City IA USA

University of Iowa Department of Biology Aging Mind and Brain Initiative Iowa City IA USA

University of Iowa Departments of Pediatrics and Microbiology Iowa City IA USA

University of Iowa Fraternal Order of Eagles Diabetes Research Center Obesity Research and Education Initiative Abboud Cardiovascular Research Center Department of Health and Human Physiology Iowa City IA USA

University of Iowa Iowa City IA USA

University of Kaiserslautern Department of Biology Plant Physiology Kaiserslautern Germany

University of Kaiserslautern Phytopathology Kaiserslautern Germany

University of Kansas Department of Molecular Biosciences and University of Kansas Medical School University of Kansas Cancer Center Department of Radiation Oncology Lawrence KS USA

University of Kansas Medical Center Department of Biochemistry and Molecular Biology Kansas City KS USA

University of Kansas Medical Center Department of Microbiology Molecular Genetics and Immunology Kansas City KS USA

University of Kansas Medical Center Department of Otolaryngology Kansas City KS USA

University of Kansas Medical Center Department of Pharmacology Toxicology and Therapeutics Kansas City KS USA

University of Kansas Medical Center Department of Pharmacology Toxicology and Thereapeutics Kansas City KS USA

University of Kansas School of Medicine Department of Anatomy and Cell Biology Kansas City KS USA

University of Kentucky College of Medicine Department of Molecular and Cellular Biochemistry Lexington KY USA

University of Kentucky College of Medicine Markey Cancer Center Lexington KY USA

University of Kentucky Department of Cancer Biology and Toxicology Lexington KY USA

University of Kentucky Department of Ophthalmology and Visual Sciences Lexington KY USA

University of Kentucky Department of Toxicology and Cancer Biology Lexington KY USA

University of La Laguna Institute of Biomedical Technologies Department of Basic Medical Sciences La Laguna Tenerife Spain

University of Las Palmas de Gran Canaria Department of Physical Education and Research Institute of Biomedical and Health Sciences Las Palmas de Gran Canaria Spain

University of Las Palmas de Gran Canaria Department of Physical Education and Research Institute of Biomedical and Health Sciences Las Palmas de Gran Canaria Spain; Norwegian School of Sport Sciences Department of Physical Performance Oslo Norway

University of Lausanne Hospital and Lausanne University Institute of Pathology Department of Laboratory Medicine and Pathology Lausanne Switzerland

University of León Institute of Biomedicine León Spain

University of Limerick Department of Biological Sciences Limerick Ireland; University of Limerick Health Research Institute Limerick Ireland

University of Liverpool Department of Cellular and Molecular Physiology Liverpool UK

University of Liverpool Institute of Translational Research Cellular and Molecular Physiology Liverpool UK

University of Lleida Department of Basic Medical Sciences IRBLleida Lleida Spain

University of Lodz Faculty of Biology and Environmental Protection Lodz Poland

University of London The Royal Veterinary College Department of Comparative Biomedical Sciences UCL Consortium for Mitochondrial Research London UK

University of Louisville Pediatric Research Institute Department of Pediatrics Louisville KY USA

University of Louvain Louvain Institute of Biomolecular Science and Technology Louvain la Neuve Belgium

University of Luxembourg Department of Life Sciences and Medicine Molecular Disease Mechanisms Group Belval Luxembourg

University of Luxembourg Luxembourg Centre for Systems Biomedicine Esch sur Alzette Luxembourg

University of Macau Faculty of Health Sciences Macau China

University of Macau Institute of Chinese Medical Sciences State Key Laboratory of Quality Research in Chinese Medicine Taipa Macao China

University of Madras Department of Biochemistry Guindy Campus Chennai India

University of Malaga Department of Molecular Biology and Biochemistry Malaga Spain

University of Malaya Institute of Biological Sciences Kuala Lumpur Malaysia

University of Malta Department of Physiology and Biochemistry Msida Malta

University of Manitoba Department of Medical Microbiology and Infectious Diseases Winnipeg Manitoba Canada

University of Manitoba Department of Physiology and Pathophysiology Regenerative Medicine Program Winnipeg Manitoba Canada

University of Manitoba Departments of Biochemistry and Medical Genetics Winnipeg Canada

University of Manitoba Institute of Cardiovascular Sciences Department of Physiology and Pathophysiology Winnipeg Manitoba Canada

University of Mar del Plata Department of Biology and Chemestry Mar del Plata BA Argentina

University of Maribor Faculty of Medicine Maribor Slovenia; University of Maribor Faculty of Natural Sciences and Mathematics Department of Biology Maribor Slovenia; University of Maribor Faculty of Chemistry and Chemical Engineering Maribor Slovenia; Medical University of Graz Division of Cell Biology Histology and Embryology Gottfried Schatz Research Center Graz Austria

University of Maryland Molecular Virology Laboratory VA MD College of Veterinary Medicine College Park MD USA

University of Maryland School of Medicine Center for Biomedical Engineering and Technology Baltimore MD USA

University of Maryland School of Medicine Center for Shock Trauma and Anesthesiology Research Departments of Anesthesiology Anatomy and Neurobiology Baltimore MD USA

University of Maryland School of Medicine Department of Anesthesiology Baltimore MD USA

University of Maryland School of Medicine Department of Anesthesiology Shock Trauma and Anesthesiology Research Center Baltimore MD USA

University of Maryland School of Medicine Department of Microbiology and Immunology Baltimore MD USA

University of Maryland School of Medicine Departments of Otorhinolaryngology Head and Neck Surgery Ophthalmology and Visual Science Baltimore MD USA

University of Massachusetts Medical School Department of Microbiology and Physiological Systems Worcester MA USA

University of Massachusetts Medical School Department of Molecular Cell and Cancer Biology Worcester MA USA

University of Massachusetts Medical School Molecular Cell and Cancer Biology Worcester MA USA

University of Massachusetts Medical School Program in Molecular Medicine Worcester MA USA

University of Medicine and Pharmacy of Craiova Department of Medical Genetics Craiova Romania

University of Melbourne Bio21 Molecular Science and Biotechnology Institute Parkville Victoria Australia

University of Melbourne Department of Pharmacology and Therapeutics Melbourne Victoria Australia

University of Melbourne Florey Institute of Neuroscience and Mental Health Melbourne VIC Australia

University of Melbourne School of Biomedical Sciences Melbourne Victoria Australia

University of Messina Department of Human Pathology in Adult and Developmental Age Gaetano Barresi Section of Pathology Messina Italy

University of Messina Sicily Italy

University of Miami Department of Surgery and Sylvester Comprehensive Cancer Center Miami FL USA

University of Miami Department of Surgery Miami FL USA

University of Michigan Department of Biological Chemistry Ann Arbor MI USA

University of Michigan Department of Internal Medicine Division of Hematology and Oncology Ann Arbor MI USA

University of Michigan Department of Molecular and Integrative Physiology Ann Arbor MI USA

University of Michigan Department of Neurology Ann Arbor MI USA

University of Michigan Department of Ophthalmology and Visual Sciences Ann Arbor MI USA

University of Michigan Departments of Surgery and Pathology Ann Arbor MI USA

University of Michigan Kellogg Eye Center Department of Ophthalmology and Visual Sciences Ann Arbor MI USA

University of Michigan Life Sciences Institute Ann Arbor MI USA

University of Michigan Life Sciences Institute Department of Molecular and Integrative Physiology Ann Arbor MI USA

University of Michigan Medical School Department of Neurology Ann Arbor MI USA

University of Michigan Rogel Cancer Center Department of Periodontics and Oral Medicine Department of Otolaryngology Head and Neck Surgery Ann Arbor MI USA

University of Milan Department of Biosciences Milan Italy

University of Milan Department of Health Sciences Milano Italy

University of Milan Department of Pharmacological and Biomolecular Sciences Milan Italy

University of Milano Bicocca Department of Biotechnology and Biosciences Milan Italy

University of Milano Department of Biomedical Sciences for Health Milan Italy

University of Minho School of Medicine Life and Health Sciences Research Institute Braga Portugal

University of Minho School of Medicine Life and Health Sciences Research Institute Braga Portugal; ICVS 3B's PT Government Associate Laboratory Braga Guimarães Portugal

University of Minnesota Department of Biochemistry Molecular Biology and Biophysics and Department of Medicine Minneapolis MN USA

University of Minnesota Department of Biochemistry Molecular Biology and Biophysics Minneapolis MN USA

University of Minnesota Department of Genetics Cell Biology and Development Minneapolis MN USA

University of Minnesota Hormel Institute Austin MN USA

University of Minnesota Institute for Translational Neuroscience Department of Neuroscience Minneapolis MN USA

University of Minnesota Medical School Department of Laboratory Medicine and Pathology Minneapolis MN USA

University of Missouri Division of Animal Science and Department of Obstetrics Gynecology and Women's Health Columbia MO USA

University of Modena and Reggio Emilia Department of Biomedical Metabolic and Neural Sciences Modena Italy

University of Modena and Reggio Emilia Department of Life Sciences Modena Italy

University of Montpellier CNRS UMR5235 LPHI Montpellier France

University of Montpellier UMR 5235 Montpellier France

University of Montreal Faculty of Medicine Microbiology Infectious diseases and Immunology Department CRCHUM Montréal QC Canada

University of Münster Institute of Medical Microbiology Münster Germany

University of Münster University Hospital Department of Neurology with Institute of Translational Neurology Münster Germany

University of Murcia Department of Biochemistry Molecular Biology B and Immunology; Biomedical Research Institute of Murcia Unit of Autophagy Immunity and Cancer Murcia Spain

University of Naples Federico 2 Department of Biology Naples Italy

University of Naples Federico 2 Department of Chemical Materials and Industrial Production Engineering Naples Italy

University of Naples Federico 2 Department of Molecular Medicine and Medical Biotechnology Naples Italy

University of Naples Federico 2 Department of Pharmacy Naples Italy

University of Naples Federico 2 Department of Translational Medical Sciences Naples Italy

University of Natural Resources and Life Sciences Department of Applied Genetics and Cell Biology Vienna Austria

University of Nebraska Lincoln Department of Agronomy and Horticulture Center for Plant Science Innovation Lincoln NE USA

University of Nebraska Lincoln Department of Plant Pathology Lincoln NE USA

University of Nebraska Lincoln Redox Biology Center Lincoln NE USA

University of Nebraska Medical Center Department of Cellular and Integrative Physiology Omaha NE USA

University of Nebraska Medical Center Department of Pharmacology and Experimental Neuroscience Omaha NE USA

University of Nebraska Medical Center Departments of Internal Medicine and Biochemistry and Molecular Biology Omaha NE USA

University of Nevada Reno School of Medicine Department of Pharmacology Reno NV USA

University of New Mexico Clinical and Translational Sciences Center Albuquerque NM USA

University of New Mexico Department of Molecular Genetics and Microbiology Department of Neurology Albuquerque NM USA

University of New Mexico Health Sciences Center Autophagy Inflamamtion and Metabolism Center Albuquerque NM USA

University of New Mexico Health Sciences Center Department of Biochemistry and Molecular Biology Albuquerque NM USA

University of New Mexico Health Sciences Center Division of Gastroenterology and Hepatology Department of Internal Medicine Albuquerque NM USA

University of Newcastle School of Biomedical Sciences and Pharmacy NSW Australia

University of Nice Mediterranean Center for Molecular Medicine Inserm U1065 Nice France

University of North Carolina at Chapel Hill Department of Pharmacology Chapel Hill NC USA

University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center Chapel Hill NC USA

University of North Carolina at Charlotte Department of Biological Sciences Charlotte NC USA

University of North Carolina Department of Pathology Chapel Hill NC USA

University of North Dakota Biology School of Medicine and Health Sciences Department of Biomedical Sciences Grand Forks ND USA

University of North Texas Health Science Center Department of Microbiology Immunology and Genetics Fort Worth TX USA

University of North Texas Health Science Center North Texas Eye Research Institute and Department of Pharmaceutical Sciences Fort Worth TX USA

University of Notre Dame Department of Biological Sciences Notre Dame IN USA

University of Nottingham School of Life Sciences Nottingham UK

University of Nottingham School of Life Sciences Queen's Medical Centre Nottingham UK

University of Oklahoma Health Sciences Center Department of Obstetrics and Gynecology Oklahoma City OK USA

University of Oklahoma Health Sciences Center Stephenson Cancer Center Department of Obstetrics and Gynecology Section of Gynecologic Oncology Oklahoma City OK USA

University of Oslo and Akershus University Hospital Department of Clinical Molecular Biology Lørenskog Norway; The Norwegian Centre on Healthy Ageing Oslo Norway

University of Oslo Centre for Cancer Cell Reprogramming Institute of Clinical Medicine Faculty of Medicine Montebello Norway; Oslo University Hospital Department of Molecular Cell Biology Institute for Cancer Research Montebello Norway

University of Oslo Centre for Molecular Medicine Norway Oslo Norway

University of Oslo Department of Neuro Pathology Oslo Norway

University of Oslo Faculty of Medicine Institute of Basic Medical Sciences Department of Molecular Medicine Oslo Norway; University of Oslo Faculty of Medicine Institute of Clinical Medicine Centre for Cancer Cell Reprogramming Oslo Norway

University of Oslo Institute of Basic Medical Sciences Oslo Norway

University of Oslo Oslo University Hospital and Institute for Clinical Medicine Department of Ophthalmology Center for Eye Research Oslo Norway

University of Osnabrück Department of Biology Chemistry and Center of Cellular Nanoanalytics Osnabrück Osnabrück Germany

University of Otago Department of Physiology HeartOtago Dunedin Otago New Zealand

University of Otago School of Biomedical Sciences and Brain Health Research Centre Department of Biochemistry Dunedin New Zealand

University of Ottawa Department of Cellular and Molecular Medicine Ottawa ON Canada

University of Ottawa Department of Cellular and Molecular Medicine Ottawa Ontario Canada

University of Ottawa Department of Chemistry and Biomolecular Sciences and Department of Biochemistry Microbiology and Immunology Host Microbe Interactions Laboratory Ottawa ON Canada

University of Oviedo Department of Functional Biology Physiology Oviedo Asturias Spain

University of Oviedo Department of Morphology and Cell Biology Oviedo Spain

University of Oviedo Principality of Asturias Institute for Biomedical Research Department of Functional Biology Oviedo Spain

University of Oxford John Radcliffe Hospital Translational Gastroenterology Unit and Department of Paediatrics Oxford and Oxford NIHR Biomedical Research Centre Oxford UK

University of Oxford Kennedy Institute of Rheumatology Oxford UK

University of Oxford Nuffield Department of Clinical Neurosciences Oxford UK

University of Oxford Nuffield Department of Women's and Reproductive Health Oxford UK

University of Oxford Oxford Parkinson's Disease Centre Department of Physiology Anatomy and Genetics Oxford UK

University of Oxford Sir William Dunn School of Pathology Oxford UK

University of Padova Biology Department Padova Italy

University of Padova Department of Biology Padova Italy

University of Padova Department of Biomedical Sciences Padova Italy

University of Padova Department of Molecular Medicine Padova Italy

University of Padua Department of Biomedical Sciences Padua Italy

University of Padua Department of Biomedical Sciences Padua Italy; Italian National Research Council Neuroscience Institute Padua Italy

University of Palermo Department of Biological Chemical and and Pharmaceutical Sciences and Technologies Palermo Italy

University of Palermo Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche Palermo Italy

University of Pavia Department of Biology and Biotechnology L Spallanzani Pavia Italy

University of Pavia Department of Drug Sciences Pharmacology Unit Pavia Italy

University of Pavia Department of Molecular Medicine Biochemistry Unit Pavia Italy

University of Pennsylvania Abramson Cancer Center Department of Medicine PA USA

University of Pennsylvania Department of Anesthesiology Philadelphia PA USA

University of Pennsylvania Department of Basic and Translational Sciences Philadelphia PA USA

University of Pennsylvania Department of Pathology and Laboratory Medicine Philadelphia PA USA

University of Pennsylvania Perelman School of Medicine and Division of Neurology The Children's Hospital of Philadelphia Department of Neurology Philadelphia PA USA

University of Pennsylvania Perelman School of Medicine Department of Medicine Philadelphia PA USA

University of Pennsylvania Perelman School of Medicine PENN Center for Pulmonary Biology Lung Epithelial Biology Laboratories Philadelphia PA USA

University of Perugia Department of Chemistry Biology and Biotechnology Perugia Italy

University of Perugia Department of Medicine and Surgery Perugia Italy

University of Piemonte Orientale Department of Translational Medicine Novara Italy

University of Pisa Department of Translational Medicine and New Technologies in Medicine and Surgery Pisa Italy; 1 R C C S Neuromed Pozzilli Pozzilli Italy

University of Pisa Department of Translational Research and New Technologies in Medicine and Surgery Pisa Italy

University of Pisa Interdepartmental Research Centre on Biology and Pathology of Aging Pisa Italy

University of Pittsburgh Aging Institute Department of Medicine Pittsburgh PA USA

University of Pittsburgh Department of Biological Sciences Pittsburgh PA USA

University of Pittsburgh Department of Medicine Aging Institute Pittsburgh PA USA

University of Pittsburgh Department of Pathology Pittsburgh PA USA

University of Pittsburgh Department of Pathology; University of Pittsburgh Cancer Institute Pittsburgh PA USA

University of Pittsburgh Department of Pharmacology and Chemical Biology Pittsburgh PA USA

University of Pittsburgh Department of Surgery Pittsburgh PA USA

University of Pittsburgh Medical Center Department of Critical Care Medicine Department of Pediatrics Safar Center for Resuscitation Research and the Children's Hospital of Pittsburgh Pittsburgh PA USA

University of Pittsburgh Medical Center Department of Pediatrics Pittsburgh PA USA

University of Pittsburgh Medical Center Pittsburgh PA USA

University of Pittsburgh School of Medicine Department of Pathology Pittsburgh PA USA

University of Pittsburgh School of Medicine Department of Surgery Pittsburgh PA USA

University of Pittsburgh School of Medicine Departments of Ophthalmology Cell Biology and Developmental Biology Pittsburgh PA USA

University of Pittsburgh School of Medicine Hillman Cancer Center and Department of Microbiology and Molecular Genetics Pittsburgh PA USA

University of Plymouth Faculty of Health Medicine Dentistry and Human Sciences Peninsula Dental School Plymouth Devon UK

University of Porto Faculty of Pharmacy UCIBIO REQUIMTE Porto Portugal

University of Porto REQUIMTE UCIBIO Faculty of Pharmacy Porto Portugal

University of Pretoria School of Medicine Faculty of Health Sciences Department of Physiology Pretoria South Africa

University of Prince Edward Island Charlottetown Prince Edward Island Canada

University of Rajshahi Department of Pharmacy Rajshahi Bangladesh

University of Rochester Department of Anesthesiology and Perioperative Medicine Rochester NY USA

University of Rochester Medical Center Microbiology and Immunology Rochester NY USA

University of Rome La Sapienza Department of Biology and Biotechnology C Darwin Rome Italy

University of Rome La Sapienza Rome Italy

University of Rome Sapienza Department of Clinical and Molecular Medicine Laboratory affiliated to Istituto Pasteur Italia Fondazione Cenci Bolognetti Rome Italy

University of Rome Sapienza Department of Experimental Medicine Rome Italy

University of Rome Tor Vergata Department of Biology Rome Italy

University of Rome Tor Vergata Department of Biology Rome Italy; Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia Laboratory of Cell Signaling Rome Italy

University of Rome Tor Vergata Department of Clinical Sciences and Translational Medicine Rome Italy

University of Rzeszow Institute of Biology and Biotechnology Department of Biotechnology Rzeszow Poland

University of Sadat City Department of Molecular Biology Genetic Engineering and Biotechnology Research Institute Sadat City Egypt

University of Salento Department of Biological and Environmental Sciences and Technologies Lecce Italy

University of Salento Dept of Biological and Environmental Sciences and Technologies Lecce Italy

University of Salerno Department of Medicine Surgery and Dentistry Scuola Medica Salernitana Baronissi SA Italy

University of São Paulo Department of Immunology Laboratory of Transplantation Immunobiology São Paulo SP Brazil

University of São Paulo Department of Parasitology São Paulo Brazil

University of São Paulo Faculty of Pharmaceutical Sciences Department of Pathophysiology Sao Paulo Brazil

University of São Paulo Institute of Biomedical Sciences Department of Anatomy Laboratory of Functional Neuroanatomy of Pain São Paulo Brazil

University of Sao Paulo Institute of Biomedical Sciences Sao Paulo SP Brazil

University of Sao Paulo Institute of Biosciences Sao Paulo SP Brazil

University of São Paulo Ribeirão Preto Medical School Department of Genetics Ribeirão Preto SP Brazil

University of São Paulo School of Pharmaceutical Sciences of Ribeirão Preto Department of Clinical Analyses Toxicology and Food Sciences Ribeirão Preto SP Brazil

University of Sao Paulo School of Physical Education and Sport Cellular and Molecular Exercise Physiology Laboratory Sao Paulo SP Brazil

University of Science and Technology of China School of Life Sciences Hefei Anhui China

University of Seoul Department of Life Science Seoul Korea

University of Seville Department of Genetics Seville Spain

University of Seville Faculty of Pharmacy Department of Physiology Seville Spain

University of Seville School of Pharmacy Instituto de Biomedicina de Sevilla Sevilla Spain

University of Sheffield Department of Biomedical Science Firth Court Western Bank Sheffield UK

University of Sheffield Department of Infection Immunity and Cardiovascular Disease and the Bateson Centre Sheffield UK

University of Sheffield The Bateson Centre Department of Infection Immunity and Cardiovascular Disease Sheffield South Yorkshire UK

University of Sherbrooke Division of Rheumatology Department of Medicine Sherbrooke QC Canada

University of Siena Department of Life Sciences Siena Italy

University of Singapore Department of Biological Sciences Singapore

University of South Carolina Department of Drug Discovery and Biomedical Sciences Columbia SC USA

University of South Carolina School of Medicine Department of Cell Biology and Anatomy Columbia SC USA

University of South Carolina School of Medicine Department of Pathology Microbiology and Immunology Columbia SC USA

University of South Carolina Upstate Spartanburg SC USA

University of South Dakota Division of Basic Biomedical Sciences Vermillion SD USA

University of South Florida Department of Cell Biology Microbiology and Molecular Biology Tampa FL USA

University of South Florida Morsani College of Medicine Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute Tampa FL USA; Institute for Biological Instrumentation of Russian Academy of Sciences Laboratory of New Methods in Biology Pushchino Moscow region Russia

University of South Florida Morsani College of Medicine Department of Molecular Medicine Tampa FL USA

University of Southampton Biological Sciences Faculty of Environmental and Life Sciences Highfield Southampton UK

University of Southampton Clinical and Experimental Sciences Faculty of Medicine UK

University of Southampton Faculty of Environmental and Life Sciences Biological Sciences and the Institute for Life Sciences Southampton UK

University of Southeast School of Medicine Department of Pharmacology Nanjing JiangSu China

University of Southern California Center for Craniofacial Molecular Biology Los Angeles CA USA

University of Southern California Keck School of Medicine Department of Molecular Microbiology and Immunology Los Angeles CA USA

University of Split School of Medicine Split Croatia

University of St Andrews School of Medicine North Haugh St Andrews UK

University of Surrey School of Bioscience and Medicine Department of Microbial Sciences Stag Hill Campus Guildford Surrey UK

University of Sussex School of Life Sciences Department of Biochemistry and Biomedicine Brighton UK

University of Sydney Department of Pathology and Bosch Institute Sydney NSW Australia

University of Sydney Kolling Institute Renal Research Lab Sydney New South Wales Australia

University of Sydney Northern Clinical School Kolling Institute of Medical Research Sydney NSW Australia

University of Sydney Sydney Medical School Renal Medicine St Leonards NSW Australia

University of Sydney Westmead Institute for Medical Research Centre for Transplant and Renal Research Sydney NSW Australia

University of Szeged Department of Medical Microbiology and Immunobiology Szeged Hungary

University of Technology Department of applied science Division of Biotechnology Baghdad Iraq

University of Tennessee Department of Chemical and Biomolecular Engineering Knoxville TN USA

University of Tennessee Health Science Center Department of Physiology Memphis TN USA

University of Teramo Faculty of Veterinary Medicine Teramo Italy

University of Texas Health San Antonio Department of Medicine San Antonio TX USA

University of Texas Health Science Center at Houston Center for Stem Cell and Regenerative Disease Institute of Molecular Medicine Houston TX USA

University of Texas Health Science Center at San Antonio Department of Cell Systems and Anatomy San Antonio TX USA

University of Texas M D Anderson Cancer Center Department of Leukemia Houston TX USA

University of Texas MD Anderson Cancer Center Department of Cancer Systems Imaging Houston TX USA

University of Texas MD Anderson Cancer Center Department of Experimental Radiation Oncology Houston TX USA

University of Texas MD Anderson Cancer Center Department of Sarcoma Medical Oncology Houston TX USA

University of Texas Medical Branch Department of Pathology Galveston TX USA

University of Texas Medical Branch Mitchell Center for Neurodegenerative Diseases Department of Neurology Galveston TX USA

University of Texas Southwestern Medical Center Center for Autophagy Research Department of Internal Medicine and Howard Hughes Medical Institute Dallas TX USA

University of Texas Southwestern Medical Center Dallas TX USA

University of Texas Southwestern Medical Center Department of Internal Medicine Center for Autophagy Research Dallas TX USA

University of Texas Southwestern Medical Center Department of Internal Medicine Charles and Jane Center for Mineral Metabolism and Clinical Research Dallas TX USA

University of Texas Southwestern Medical Center Department of Internal Medicine Dallas TX USA

University of Texas Southwestern Medical Center Department of Molecular Biology Dallas Texas USA

University of Texas Southwestern Medical Center Department of Molecular Biology Dallas TX USA

University of Texas Southwestern Medical Center Department of Surgery Dallas TX USA

University of the Basque Country Instituto Biofisika and Department of Biochemistry and Molecular Biology Leioa Spain

University of the West of England Department of Applied Sciences Bristol UK

University of Torino Department of Molecular Biotechnology and Health Sciences Torino Italy

University of Toronto Centre for Addiction and Mental Health Toronto Ontario Canada

University of Toronto Department of Biochemistry Toronto Ontario Canada

University of Toronto Department of Laboratory Medicine and Pathobiology Toronto Ontario Canada

University of Toronto Department of Medicine Toronto Ontario Canada

University of Toronto Faculty of Medicine Department of Immunology Toronto ON Canada

University of Toronto Sinai Health System Lunenfeld Tanenbaum Research Institute Toronto Ontario Canada

University of Toulouse Institute of Metabolic and cardiovascular Diseases INSERM UMR 1048 Toulouse France

University of Toyama Sugitani Toyama Japan

University of Tromsø The Arctic University of Norway Department of Medical Biology Tromsø Norway

University of Tübingen Center for Plant Molecular Biology Tübingen Germany

University of Turin Department of Clinical and Biological Sciences Turin Italy

University of Turin Department of Veterinary Sciences Grugliasco Italy

University of Turku Institute of Biomedicine Turku Finland

University of Tuscia Department for Innovation in Biological Agro food and Forest systems Viterbo Italy

University of Ulm Department of Internal Medicine 2 Molecular Cardiology Ulm Germany

University of Ulsan College of Medicine Asan Medical Center Department of Psychiatry Seoul Korea

University of Urbino Carlo Bo Department of Biomolecular Sciences Unit of Pharmacology and Public Health Urbino Italy

University of Urbino Carlo Bo Department of Biomolecular Sciences Urbino Italy

University of Utah Department of Nutrition and Integrative Physiology; Division of Endocrinology Metabolism and Diabetes; Investigator Molecular Medicine Program Salt Lake City UT USA

University of Utah Huntsman Cancer Institute and Department of Oncological Sciences Salt Lake City UT USA

University of Utah Huntsman Cancer Institute Salt Lake City UT USA; University of Utah School of Medicine Division of Oncology Department of Internal Medicine Salt Lake City UT USA

University of Valencia Faculty of Medicine Department of Pharmacology Valencia Spain; CIBERehd Valencia Spain

University of Valencia Faculty of Medicine Department of Physiology Valencia Spain; CIBERehd Valencia Spain

University of Verona Azienda Ospedaliera Universitaria Integrata Verona Department of Medicine Verona; Italy

University of Verona Department of Neurosciences Biomedicine and Movement Sciences Biological Chemistry Section Verona Italy

University of Vienna Cell Imaging and Ultrastructure Research Vienna Austria

University of Vienna Max Perutz Labs Department of Biochemistry and Cell Biology Vienna BioCenter Vienna Austria

University of Virginia Department of Biology Charlottesville VA USA

University of Virginia Department of Cell Biology Charlottesville VA USA

University of Virginia Department of Neuroscience Charlottesville VA USA

University of Virginia Departments of Medicine Pharmacology Molecular Physiology and Biological Physics Center for Skeletal Muscle Research at Robert M Berne Cardiovascular Research Center University of Virginia School of Medicine Charlottesville VA USA

University of Virginia School of Medicine Department of Surgery Charlottesville VA USA

University of Warwick School of Life Sciences Coventry UK

University of Washington Department of Laboratory Medicine Seattle WA USA

University of Washington Department of Medicine Seattle WA USA; VA Puget Sound Health Care System Seattle WA USA

University of Washington Departments of Medicine Microbiology and Genome Sciences Seattle WA USA

University of Washington School of Medicine Department of Biochemistry Seattle WA USA

University of Waterloo Department of Kinesiology Waterloo Ontario Canada

University of Waterloo School of Pharmacy Kitchener ON Canada

University of West Florida Department of Movement Sciences and Health Pensacola FL USA

University of Western Ontario Department of Physiology and Pharmacology London Ontario Canada

University of Wisconsin Department of Surgery Madison WI USA

University of Wisconsin Madison Center for Quantitative Cell Imaging and Department of Botany Madison WI USA

University of Wisconsin Madison Department of Medicine and Neuroscience Madison WI USA

University of Wisconsin Madison Department of Surgery Madison WI USA

University of Wuerzburg Department of Vegetative Physiology Wuerzburg Germany

University of Würzburg Institute of Clinical Neurobiology Würzburg Germany

University of Würzburg Institute of Pathology Würzburg Germany

University of Wyoming College of Health Sciences Laramie WY USA

University of York Department of Biology Heslington UK

University of Zagreb School of Medicine Croatian Institute for Brain Research Zagreb Croatia

University of Zagreb School of Medicine Department of Physiology and Croatian Institute for Brain Research Zagreb Croatia

University of Zaragoza Faculty of Veterinary IIS Aragón IA2 CITA CIBERNED Laboratory of Genetics and Biochemistry Zaragoza Spain

University of Zurich Institute of Experimental Immunology Switzerland Zurich

University of Zürich Institute of Experimental Immunology Viral Immunobiology Zürich Switzerland

University of Zurich Institute of Physiology Zurich Switzerland

University of Zürich Schlieren Campus Center for Molecular Cardiology Schlieren Switzerland

University Paris 13 UMR_S942 Inserm; University of Paris Bobigny France

University Roma Tre Department of Science LIME Rome Italy

University Santiago de Compostela Department of Pharmacology Veterinary Faculty Lugo Spain

University Tartu Department of Pharmacology Tartu Estonia

USC Norris Comprehensive Cancer Center Los Angeles CA USA

UT Southwestern Medical Center Department of Surgery Dallas Texas USA

UT Southwestern Medical Center Departments of Medicine and Molecular Biology Dallas TX USA

VA San Diego Healthcare Systems and University of California San Diego Department of Anesthesiology La Jolla CA USA

Vall d'Hebron Research Institute Barcelona Spain

Vall d'Hebron research Institute UAB Neurodegenerative Diseases Group Barcelona Spain

Vall d´Hebron Research Institute Barcelona Spain

Van Andel Institute Center for Epigenetics Grand Rapids MI USA

Vanderbilt University Medical Center Vanderbilt Eye Institute Nashville TN USA

Vanderbilt University School of Medicine Department of Pathology Microbiology and Immunology Nashville TN USA

Vascular Biology Center Medical College of Georgia Augusta University Augusta GA USA; South China University of Technology Guangzhou 1st People's Hospital School of Medicine and Institutes for Life Sciences Guangzhou Guangdong China

Vavilov Institute of General Genetics RAS Department of Epigenetics Moscow Russia

VIB KU Leuven Center for Brain and Disease Research Leuven Belgium; KU Leuven Department of Neurosciences Leuven Brain Institute Leuven Belgium

Virginia Commonwealth University Departement of Pharmacology and Toxicology Richmond VA USA

Virginia Commonwealth University Department of Biochemistry and Molecular Biology Richmond VA USA

Virginia Commonwealth University Department of Computer Science Richmond VA USA

Virginia Commonwealth University Departments of Pharmacology Toxicology and Medicine and Massey Cancer Center Richmond VA USA

Virginia Commonwealth University School of Medicine Department of Human and Molecular Genetics Richmond VA USA; Virginia Commonwealth University VCU Institute of Molecular Medicine Richmond VA USA; Columbia University College of Physicians and Surgeons Departments of Pathology Neurosurgery and Urology New York NY USA

Virginia Commonwealth University School of Medicine VCU Institute of Molecular Medicine Massey Cancer Center Department of Microbiology and Immunology Richmond VA USA

Virginia Polytechnic Institute and State University School of Neuroscience Blacksburg VA USA

Virginia Polytechnic Institute Department of Biological Sciences Blacksburg VA USA

VIT University School of Biosciences and Technology Vellore Tamilnadu India

Vita Salute San Raffaele University and IRCCS San Raffaele Scientific Institute Division of Immunology Transplantation and Infectious Diseases Milano Italy

Wake Forest Baptist Comprehensive Cancer Center Department of Cancer Biology Winston Salem NC USA

Waksman Institute Department of Genetics Rutgers University Piscataway NJ USA

Walter and Eliza Hall Institute of Medical Research Ubiquitin Signalling Division Melbourne Australia; University of Melbourne Department of Medical Biology Melbourne Australia

Washington State University Department of Veterinary Microbiology and Pathology College of Veterinary Medicine Pullman WA USA

Washington State University Institute of Biological Chemistry Pullman WA USA

Washington University Division of Infectious Diseases Department of Medicine and Molecular Microbiology St Louis MO USA

Washington University in Saint Louis School of Medicine Department of Psychiatry Saint Louis MO USA

Washington University in St Louis Department of Biology St Louis MO USA

Washington University in St Louis Department of Cell Biology and Physiology St Louis MO USA

Washington University in St Louis Department of Medicine St Louis MO USA

Washington University in St Louis Department of Ophthalmology and Visual Sciences St Louis MO USA

Washington University in St Louis Professor of Obstetrics and Gynecology St Louis MO USA

Washington University in St Louis School of Medicine Department of Internal Medicine St Louis MO USA

Washington University School of Medicine and John Cochran VA Medical Center Department of Medicine St Louis MO USA

Washington University School of Medicine Department of Medicine Cardiovascular Division l and John Cochran VA Medical Center St Louis MO USA

Washington University School of Medicine Department of Medicine Saint Louis MO USA

Washington University School of Medicine Department of Neurology St Louis MO USA

Washington University School of Medicine Department of Obstetrics and Gynecology and Department of Pathology and Immunology St Louis MO USA

Washington University School of Medicine Departments of Pediatrics and Cell Biology and Physiology St Louis MO USA

Washington University School of Medicine Division of Pulmonary and Critical Care Medicine St Louis MO USA

Wayne State University School of Medicine Department of Ophthalmology Visual and Anatomical Sciences Detroit MI USA

Wayne State University School of Medicine Department of Pharmacology Detroit MI USA

Weill Cornell Englander Institute of Precision Medicine Department of Radiation Oncology New York NY USA

Weill Cornell Medical College Department of Radiation Oncology New York NY USA; Sandra and Edward Meyer Cancer Center New York NY USA; Caryl and Israel Englander Institute for Precision Medicine New York NY USA; Yale School of Medicine Department of Dermatology New Haven CT USA; Université de Paris Paris France

Weill Cornell Medicine Brain and Mind Research Institute Burke Neurological Institute White Plains NY USA

Weill Cornell Medicine Department of Medicine New York NY USA

Weill Cornell Medicine Department of Pathology and Laboratory Medicine New York NY USA

Weill Cornell Medicine Departments of Pediatrics and Cell and Developmental Biology New York NY USA

Weill Cornell Medicine Division of Nephrology and Hypertension Joan and Sanford 1 Weill Department of Medicine New York NY USA

Weill Cornell Medicine Feil Family Brain and Mind Research Institute New York NY USA

Weill Cornell Medicine Rockefeller University Campus Department of Pathology and Laboratory Medicine New York NY USA

Weizmann Institute of Science Department of Molecular Genetics Rehovot Israel

Weizmann Institute of Science Department of Plant and Environmental Sciences Rehovot Israel

Wenzhou Medical University Key Laboratory of Biotechnology and Pharmaceutical Engineering School of Pharmaceutical Sciences Wenzhou China

Wenzhou Medical University School of Laboratory Medicine and Life Sciences Wenzhou Zhejiang Province China

Wenzhou Medical University School of Pharmaceutical Sciences Wenzhou China

Wenzhou Medical University State Key Laboratory of Ophthalmology Optometry and Visual Science School of Optometry and Ophthalmology and the Eye Hospital Wenzhou China

West Virginia University Department of Surgery Morgantown WV USA

West Virginia University School of Medicine Department of Physiology and Pharmacology Morgantown WV USA

Western University Department of Physiology and Pharmacology London ON Canada

Women and Infants Hospital of Rhode Island Warren Alpert Medical School of Brown University Department of Pediatrics Providence RI USA

Wonkwang University School of Medicine Department of Microbiology Iksan Jeonbuk Korea

Wonkwang University School of Medicine Zoonosis Research Center Iksan Jeonbuk Korea

Wonkwang Univesity Department of Biological Sciences Iksan Chunbuk Korea

Wright State University Department of Biochemistry and Molecular Biology Dayton OH USA

Wuhan Sports University College of Health Science Tianjiu Research and Development Center for Exercise Nutrition and Foods Hubei Key Laboratory of Exercise Training and Monitoring Wuhan Hubei China

Wuhan University College of Life Sciences Wuhan Hubei China

Wuhan University Department of Cell Biology College of Life Sciences Wuhan Hubei China

Wuhan University Hubei Key laboratory of Cell Homeostasis College of Life Sciences Wuhan China

Wuhan University Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan China

Wuhan University School and Hospital of Stomatology Key Lab of Oral Biomedicine of Ministry of Education Wuhan Hubei China

Wuhan University School of Pharmaceutical Sciences Zhongnan Hospital Wuhan China

Xi'an Jiaotong University Department of Public Health Xi'an Shaanxi China

Xi'an Jiaotong University School of Medicine the 1st Affiliated Hospital Department of Nephrology Xi'an City Shaanxi Province China

Xiamen University School of Medicine Fujian Provincial Key Laboratory of Reproductive Health Research Xiang'an Xiamen China

Xuzhou Medical University Department of Anesthesiology Xuzhou Jiangsu China

Yale School of Medicine Department of Cell Biology New Haven CT USA

Yale University Department of Cellular and Molecular Physiology New Haven CT USA

Yale University Department of Molecular Biophysics and Biochemistry New Haven CT USA

Yale University School of Medicine Department of Comparative Medicine and Department of Cellular and Molecular Physiology New Haven CT USA

Yale University School of Medicine Department of Neuroscience and Department of Cell Biology New Haven CT USA

Yamaguchi University Joint Faculty of Veterinary Medicine Laboratory of Veterinary Pharmacology Yoshida Yamaguchi Japan

Yangzhou University College of Veterinary Medicine Jiangsu Province China

Yonsei University College of Medicine Department of Internal Medicine Seoul Korea

Yonsei University College of Medicine Department of Pharmacology Seoul Korea

Yonsei University College of Medicine Severance Biomedical Science Institute and Department of Internal Medicine Seoul Korea

Yonsei University College of Medicine Severance Biomedical Science Institute Seoul Korea

Yonsei University Department of Biotechnology Seodaemun gu Seoul Korea

Yonsei University Division of Biological Science and Technology Wonju Korea

Yonsei University Wonju Korea

York College The City University of New York Department of Biology Jamaica NY USA

York University Department of Biology Toronto Canada

Zhejiang Academy of Agricultural Sciences Institute of Plant Protection and Microbiology State Key Laboratory for Managing Biotic and Chemical Treatments to the Quality and Safety of Agro products Hangzhou China; Zhejiang University Institute of Biotechnology Hangzhou China

Zhejiang Provincial People's Hospital Department of Endocrinology Hangzhou China

Zhejiang University Biotechnology Institute State Key Laboratory for Rice Biology Hangzhou China

Zhejiang University College of Medicine The 1st Affiliated Hospital Malignant Lymphoma Diagnosis and Therapy Center Hangzhou Zhejiang China

Zhejiang University College of Pharmaceutical Sciences Hangzhou China

Zhejiang University College of Pharmaceutical Sciences Institute of Pharmacology and Toxicology Hangzhou Zhejiang China

Zhejiang University Department of Biochemistry in School of Medicine Hangzhou Zhejiang Province China

Zhejiang University Department of Horticulture Hangzhou China

Zhejiang University Life Sciences Institute and Innovation Center for Cell Signaling Network Hangzhou China

Zhejiang University MOA Key Laboratory of Animal Virology Hangzhou Zhejiang China

Zhejiang University School of Medicine Department of Biochemistry and Department of Cardiology of the 2nd Affiliated Hospital Hangzhou Zhejiang China

Zhejiang University School of Medicine Department of Biochemistry and Department of Hepatobiliary and Pancreatic Surgery of the 1st Affiliated Hospital Hangzhou China

Zhejiang University School of Medicine Department of Biochemistry Hangzhou Zhejiang China

Zhejiang University School of Medicine Department of Cell Biology Hangzhou Zhejiang Province China

Zhejiang University School of Medicine Department of Environmental Medicine Hangzhou Zhejiang Province China

Zhejiang University School of Medicine Department of Microbiology and Parasitology Hangzhou China

Zhejiang University School of Medicine Department of Pathology Hangzhou China

Zhejiang University School of Medicine Department of Toxicology of School of Public Health and Department of Gynecologic Oncology of Women's Hospital Hangzhou China

Zhejiang University School of Medicine The 1st Affiliated Hospital Zhejiang Provincial Key Laboratory of Pancreatic Disease Hangzhou Zhejiang China

Zhejiang University School of Medicine Women's Hospital Hangzhou Zhejiang China

Zhejiang University Sir Run Run Shaw Hospital College of Medicine Department of Medical Oncology Zhejiang Hangzhou China

Zhejiang University the 1st Affiliated Hospital Hangzhou Zhejiang China

ZhejiangUniversity Sir Run Run Shaw Hospital School of Medicine Key Lab of Biotherapy in Zhejiang Province Hangzhou China

Zhengzhou University 3rd Affiliated Hospital and Institute of Neuroscience Henan Key Laboratory of Child Brain Injury Zhengzhou China; Gothenburg University Institute of Neuroscience and Physiology Gothenburg Sweden

Zhujiang Hospital of Southern Medical University Department of Neurology Guangzhou Guangdong Province China

See more in PubMed

Klionsky DJ, Abdalla FC, Abeliovich H, et al. Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy. 2012. Apr;8(4):445–544. PubMed PMID: 22966490; PubMed Central PMCID: PMC3404883. PubMed PMC

Klionsky DJ, Abdelmohsen K, Abe A, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy. 2016;12(1):1–222. PubMed PMID: 26799652; PubMed Central PMCID: PMCPMC4835977. doi:10.1080/15548627.2015.1100356. PubMed DOI PMC

Klionsky DJ, Abeliovich H, Agostinis P, et al. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy. 2008. Feb;4(2):151–75. PubMed PMID: 18188003; PubMed Central PMCID: PMC2654259. eng. PubMed PMC

Klionsky DJ, Cuervo AM, Seglen PO.. Methods for monitoring autophagy from yeast to human. Autophagy. 2007. May-Jun;3(3):181–206. PubMed PMID: 17224625; eng. PubMed

Xia HG, Najafov A, Geng J, et al. Degradation of HK2 by chaperone-mediated autophagy promotes metabolic catastrophe and cell death. J Cell Biol. 2015. Aug 31;210(5):705–16. PubMed PMID: 26323688; PubMed Central PMCID: PMC4555813. doi:10.1083/jcb.201503044. PubMed DOI PMC

Eskelinen E-L, Reggiori F, Baba M, et al. Seeing is believing: the impact of electron microscopy on autophagy research. Autophagy. 2011. Sep 1;7(9):935–56. PubMed PMID: 21566462; Eng. PubMed

Klionsky DJ. The autophagosome is overrated! [Editorial]. Autophagy. 2011. Apr;7(4):353–4. PubMed PMID: 21258205; eng. PubMed PMC

Seglen PO. Regulation of autophagic protein degradation in isolated liver cells. In: Glaumann H, Ballard FJ, editors. Lysosomes: their role in protein breakdown. London: Academic Press; 1987. p. 369–414.

Knorr RL, Lipowsky R, Dimova R.. Autophagosome closure requires membrane scission. Autophagy. 2015. Nov 2;11(11):2134–2137. PubMed PMID: 26466816; PubMed Central PMCID: PMCPMC4824592. doi:10.1080/15548627.2015.1091552. PubMed DOI PMC

Knorr RL, Mizushima N, Dimova R.. Fusion and scission of membranes: Ubiquitous topological transformations in cells. Traffic. 2017. Nov;18(11):758–761. PubMed PMID: 28799689. doi:10.1111/tra.12509. PubMed DOI

Gordon PB, Seglen PO.. Prelysosomal convergence of autophagic and endocytic pathways. Biochem Biophys Res Commun. 1988. Feb 29;151(1):40–7. PubMed PMID: 3126737; eng. PubMed

Lucocq JM, Hacker C.. Cutting a fine figure: on the use of thin sections in electron microscopy to quantify autophagy. Autophagy. 2013. Sep;9(9):1443–8. PubMed PMID: 23881027. doi:10.4161/auto.25570. PubMed DOI

Kovács J, Fellinger E, Karpati AP, et al. Morphometric evaluation of the turnover of autophagic vacuoles after treatment with Triton X-100 and vinblastine in murine pancreatic acinar and seminal vesicle epithelial cells. Virchows Arch B Cell Pathol Incl Mol Pathol. 1987;53(3):183–90. PubMed PMID: 2888237; eng. PubMed

Kovács J, Fellinger E, Karpati PA, et al. The turnover of autophagic vacuoles: evaluation by quantitative electron microscopy. Biomed Biochim Acta. 1986;45(11–12):1543–7. PubMed PMID: 3579875; eng. PubMed

Kovács J, Laszlo L, Kovács AL.. Regression of autophagic vacuoles in pancreatic acinar, seminal vesicle epithelial, and liver parenchymal cells: a comparative morphometric study of the effect of vinblastine and leupeptin followed by cycloheximide treatment. Exp Cell Res. 1988. Jan;174(1):244–51. PubMed PMID: 3335225; eng. PubMed

Chu CT. Autophagic stress in neuronal injury and disease. J Neuropathol Exp Neurol. 2006. May;65(5):423–32. PubMed PMID: 16772866; eng. PubMed PMC

Fass E, Shvets E, Degani I, et al. Microtubules support production of starvation-induced autophagosomes but not their targeting and fusion with lysosomes. J Biol Chem. 2006. Nov 24;281(47):36303–16. PubMed PMID: 16963441; eng. PubMed

Kovács AL, Reith A, Seglen PO.. Accumulation of autophagosomes after inhibition of hepatocytic protein degradation by vinblastine, leupeptin or a lysosomotropic amine. Exp Cell Res. 1982. Jan;137(1):191–201. PubMed PMID: 7056284; eng. PubMed

Bestebroer J, V’Kovski P, Mauthe M, et al. Hidden behind autophagy: the unconventional roles of ATG proteins. Traffic. 2013. Oct;14(10):1029–41. PubMed PMID: 23837619. doi:10.1111/tra.12091. PubMed DOI PMC

Luo SM, Ge ZJ, Wang ZW, et al. Unique insights into maternal mitochondrial inheritance in mice. Proc Natl Acad Sci U S A. 2013. Aug 6;110(32):13038–43. PubMed PMID: 23878233; PubMed Central PMCID: PMC3740871. doi:10.1073/pnas.1303231110. PubMed DOI PMC

Politi Y, Gal L, Kalifa Y, et al. Paternal mitochondrial destruction after fertilization is mediated by a common endocytic and autophagic pathway in Drosophila. Dev Cell. 2014. May 12;29(3):305–20. PubMed PMID: 24823375. doi:10.1016/j.devcel.2014.04.005. PubMed DOI

Toth S, Nagy K, Palfia Z, et al. Cellular autophagic capacity changes during azaserine-induced tumour progression in the rat pancreas. Up-regulation in all premalignant stages and down-regulation with loss of cycloheximide sensitivity of segregation along with malignant transformation. Cell Tissue Res. 2002. Sep;309(3):409–16. PubMed PMID: 12195297; eng. doi:10.1007/s00441-001-0506-7. PubMed DOI

Loos B, Engelbrecht AM.. Cell death: a dynamic response concept. Autophagy. 2009. Jul;5(5):590–603. PubMed PMID: 19363298; eng. PubMed

Seglen PO, Gordon PB, Grinde B, et al. Inhibitors and pathways of hepatocytic protein degradation. Acta Biol Med Ger. 1981;40(10–11):1587–98. PubMed PMID: 7342604. PubMed

Luhr M, Saetre F, Engedal N.. The long-lived protein degradation assay: an efficient method for quantitative determination of the autophagic flux of endogenous proteins in adherent cell lines. bio-protocol. 2018;8(9). doi:10.21769/BioProtoc.2836. PubMed DOI PMC

Ktistakis NT, Andrews S, Long J.. What is the advantage of a transient precursor in autophagosome biogenesis?. Autophagy. 2011. Jan;7(1):118–22. PubMed PMID: 20935487; eng. doi:10.1083/jcb.200803137. PubMed DOI

Beugnet A, Tee AR, Taylor PM, et al. Regulation of targets of mTOR (mammalian target of rapamycin) signalling by intracellular amino acid availability. Biochem J. 2003. Jun1;372(Pt 2):555–66. PubMed PMID: 12611592; PubMed Central PMCID: PMC1223408. eng. doi:10.1042/BJ20021266. PubMed DOI PMC

Kovács AL, Réz G, Pálfia Z, et al. Autophagy in the epithelial cells of murine seminal vesicle in vitro. Formation of large sheets of nascent isolation membranes, sequestration of the nucleus and inhibition by wortmannin and 3-methyladenine. Cell Tissue Res. 2000. Nov;302(2):253–61. PubMed PMID: 11131136. PubMed

Stavoe AK, Hill SE, Hall DH, et al. KIF1A/UNC-104 Transports ATG-9 to regulate neurodevelopment and autophagy at synapses. Dev Cell. 2016. Jul 25;38(2):171–85. PubMed PMID: 27396362; PubMed Central PMCID: PMCPMC4961624. doi:10.1016/j.devcel.2016.06.012. PubMed DOI PMC

Mizushima N, Yoshimori T.. How to interpret LC3 immunoblotting. Autophagy. 2007. Nov-Dec;3(6):542–5. PubMed PMID: 17611390; eng. PubMed

Nishida Y, Arakawa S, Fujitani K, et al. Discovery of Atg5/Atg7-independent alternative macroautophagy. Nature. 2009. Oct 1;461(7264):654–8. doi:10.1038/nature08455. PubMed PMID: 19794493; eng. PubMed DOI

Szalai P, Hagen LK, Saetre F, et al. Autophagic bulk sequestration of cytosolic cargo is independent of LC3, but requires GABARAPs. Exp Cell Res. 2015. Apr 10;333(1):21–38. PubMed PMID: 25684710. doi:10.1016/j.yexcr.2015.02.003. PubMed DOI

Engedal N, Seglen PO.. Autophagy of cytoplasmic bulk cargo does not require LC3. Autophagy. 2016;12(2):439–41. PubMed PMID: 26237084; PubMed Central PMCID: PMCPMC4836025. doi:10.1080/15548627.2015.1076606. PubMed DOI PMC

Nguyen TN, Padman BS, Usher J, et al. Atg8 family LC3/GABARAP proteins are crucial for autophagosome-lysosome fusion but not autophagosome formation during PINK1/Parkin mitophagy and starvation. J Cell Biol. 2016. Dec 19;215(6):857–874. PubMed PMID: 27864321; PubMed Central PMCID: PMCPMC5166504. doi:10.1083/jcb.201607039. PubMed DOI PMC

Vaites LP, Paulo JA, Huttlin EL, et al. Systematic analysis of human cells lacking ATG8 proteins uncovers roles for GABARAPs and the CCZ1/MON1 regulator C18orf8/RMC1 in macroautophagic and selective autophagic flux. Mol Cell Biol. 2018. Jan 1;38(1). PubMed PMID: 29038162; PubMed Central PMCID: PMCPMC5730722. doi:10.1128/MCB.00392-17. PubMed DOI PMC

Galluzzi L, Pietrocola F, Levine B, et al. Metabolic control of autophagy. Cell. 2014. Dec 4;159(6):1263–1276. PubMed PMID: 25480292. doi:10.1016/j.cell.2014.11.006. PubMed DOI PMC

Loos B, Engelbrecht AM, Lockshin RA, et al. The variability of autophagy and cell death susceptibility: Unanswered questions. Autophagy. 2013. Sep;9(9):1270–85. PubMed PMID: 23846383; PubMed Central PMCID: PMC4026026. doi:10.4161/auto.25560. PubMed DOI PMC

McWilliams TG, Prescott AR, Allen GF, et al. mito-QC illuminates mitophagy and mitochondrial architecture in vivo. J Cell Biol. 2016. Aug 1;214(3):333–45. PubMed PMID: 27458135; PubMed Central PMCID: PMCPMC4970326. doi:10.1083/jcb.201603039. PubMed DOI PMC

Hombrebueno JR, Cairns L, Dutton LR, et al. Uncoupled turnover disrupts mitochondrial quality control in diabetic retinopathy. JCI Insight. 2019. Dec 5;4(23). PubMed PMID: 31661466. doi: 10.1172/jci.insight.129760. PubMed DOI PMC

Calvo-Garrido J, Carilla-Latorre S, Mesquita A, et al. A proteolytic cleavage assay to monitor autophagy in Dictyostelium discoideum. Autophagy. 2011. Sep 1;7(9):1063–8. PubMed PMID: 21876387; eng. doi:10.4161/auto.7.9.16629. PubMed DOI

Chu CT, Plowey ED, Dagda RK, et al. Autophagy in neurite injury and neurodegeneration: in vitro and in vivo models. Methods Enzymol. 2009;453:217–49. PubMed PMID: 19216909; PubMed Central PMCID: PMC2669321. eng. doi:10.1016/S0076-6879(08)04011-1. PubMed DOI PMC

Geng J, Klionsky DJ.. Determining Atg protein stoichiometry at the phagophore assembly site by fluorescence microscopy. Autophagy. 2010. Jan;6(1):144–7. PubMed PMID: 20131413; PubMed Central PMCID: PMC2841983. eng. PubMed PMC

Grander D, Kharaziha P, Laane E, et al. Autophagy as the main means of cytotoxicity by glucocorticoids in hematological malignancies. Autophagy. 2009. Nov;5(8):1198–200. PubMed PMID: 19855186; eng. PubMed

He C, Klionsky DJ.. Analyzing autophagy in zebrafish. Autophagy. 2010. Jul 19;6(5). PubMed PMID: 20495344; Eng. PubMed PMC

Kanki T, Kang D, Klionsky DJ.. Monitoring mitophagy in yeast: the Om45-GFP processing assay. Autophagy. 2009. Nov;5(8):1186–9. PubMed PMID: 19806021; PubMed Central PMCID: PMC2850110. eng. PubMed PMC

Klionsky DJ. Autophagy: lower eukaryotes and non-mammalian systems, part A. In: Klionsky DJ, editor. Methods enzymol. Vol. 451. Amsterdam: Academic Press/Elsevier; 2008. 2009 2 3 eng.

Klionsky DJ. Autophagy in disease and clinical applications, Part C. In: Klionsky DJ, editor. Methods enzymol Vol. 453. Amsterdam: Academic Press/Elsevier; 2008.

Klionsky DJ. Autophagy in mammalian systems, part B. In: Klionsky DJ, editor. Methods enzymol. Vol. 452. Amsterdam: Academic Press/Elsevier; 2008.

Raju D, Jones NL.. Methods to monitor autophagy in H. pylori vacuolating cytotoxin A (VacA)-treated cells [Review]. Autophagy. 2010. Jan;6(1):138–43. PubMed PMID: 19875940; eng. PubMed

Seglen PO, Brinchmann MF.. Purification of autophagosomes from rat hepatocytes. Autophagy. 2010. May 21;6(4):542–7. PubMed PMID: 20505360; Eng. PubMed

Swanlund JM, Kregel KC, Oberley TD.. Investigating autophagy: quantitative morphometric analysis using electron microscopy. Autophagy. 2010. Feb;6(2):270–7. PubMed PMID: 19923921; eng. PubMed PMC

Welter E, Thumm M, Krick R.. Quantification of nonselective bulk autophagy in S. cerevisiae using Pgk1-GFP. Autophagy. 2010. Aug;6(6):794–7. PubMed PMID: 20523132; eng. PubMed

Xu F, Liu XH, Zhuang FL, et al. Analyzing autophagy in Magnaporthe oryzae. Autophagy. 2011. May;7(5):525–30. PubMed PMID: 21317549; eng. PubMed

Zhang J, Ney PA.. Reticulocyte mitophagy: monitoring mitochondrial clearance in a mammalian model. Autophagy. 2010. Apr;6(3):405–8. PubMed PMID: 20200480; eng. PubMed

Zhu J, Dagda RK, Chu CT.. Monitoring mitophagy in neuronal cell cultures. Methods Mol Biol. 2011;793:325–39. doi:10.1007/978-1-61779-328-8_21. PubMed PMID: 21913110; eng. PubMed DOI PMC

Luhr M, Szalai P, Engedal N.. The Lactate dehydrogenase sequestration assay - a simple and reliable method to determine bulk autophagic sequestration activity in mammalian cells. J vis exp. 2018. Jul;27(137). PubMed PMID: 30102280; PubMed Central PMCID: PMCPMC6126555. doi:10.3791/57971. PubMed DOI PMC

Klionsky DJ, Bruford EA, Cherry JM, et al. In the beginning there was babble. Autophagy. 2012. Aug;8(8):1165–7. PubMed PMID: 22836666; PubMed Central PMCID: PMC3625114. doi:10.4161/auto.20665. PubMed DOI PMC

Kotoulas OB, Kalamidas SA, Kondomerkos DJ.. Glycogen autophagy. Microsc Res Tech. 2004. May 1;64(1):10–20. PubMed PMID: 15287014. doi:10.1002/jemt.20046. PubMed DOI

Kotoulas OB, Kalamidas SA, Kondomerkos DJ.. Glycogen autophagy in glucose homeostasis. Pathol Res Pract. 2006;202(9):631–8. PubMed PMID: 16781826. doi:10.1016/j.prp.2006.04.001. PubMed DOI

Singh PK, Singh S.. Changing shapes of glycogen-autophagy nexus in neurons: perspective from a rare epilepsy. Front Neurol. 2015;6:14. PubMed PMID: 25699013; PubMed Central PMCID: PMC4316721. doi:10.3389/fneur.2015.00014. PubMed DOI PMC

Lincoln C, Long J, Yamaguchi J, et al. A knotted1-like homeobox gene in Arabidopsis is expressed in the vegetative meristem and dramatically alters leaf morphology when overexpressed in transgenic plants. Plant Cell. 1994. Dec;6(12):1859–76. PubMed PMID: 7866029; PubMed Central PMCID: PMCPMC160567. doi:10.1105/tpc.6.12.1859. PubMed DOI PMC

Cui Y, Cao W, He Y, et al. A whole-cell electron tomography model of vacuole biogenesis in arabidopsis root cells. Nat Plants. 2019. Jan;5(1):95–105. PubMed PMID: 30559414. doi:10.1038/s41477-018-0328-1. PubMed DOI

Yla-Anttila P, Vihinen H, Jokitalo E, et al. Monitoring autophagy by electron microscopy in Mammalian cells. Methods Enzymol. 2009;452:143–64. PubMed PMID: 19200881; eng. doi:10.1016/S0076-6879(08)03610-0. PubMed DOI

Cardenal-Munoz E, Arafah S, Lopez-Jimenez AT, et al. Mycobacterium marinum antagonistically induces an autophagic response while repressing the autophagic flux in a TORC1- and ESX-1-dependent manner. PLoS Pathog. 2017. Apr;13(4):e1006344. PubMed PMID: 28414774; PubMed Central PMCID: PMCPMC5407849. doi:10.1371/journal.ppat.1006344. PubMed DOI PMC

Eskelinen E-L. Maturation of autophagic vacuoles in mammalian cells. Autophagy. 2005. Apr;1(1):1–10. PubMed PMID: 16874026; eng. PubMed

Eskelinen E-L. To be or not to be? Examples of incorrect identification of autophagic compartments in conventional transmission electron microscopy of mammalian cells [Evaluation Studies Research Support, Non-U.S. Gov’t]. Autophagy. 2008. Feb;4(2):257–60. PubMed PMID: 17986849; eng. PubMed

Eskelinen E-L, Kovacs AL.. Double membranes vs. lipid bilayers, and their significance for correct identification of macroautophagic structures. Autophagy. 2011. Sep 1;7(9):931–2. PubMed PMID: 21642767; Eng. PubMed

Biazik J, Yla-Anttila P, Vihinen H, et al. Ultrastructural relationship of the phagophore with surrounding organelles. Autophagy. 2015;11(3):439–51. PubMed PMID: 25714487; PubMed Central PMCID: PMC4502653. doi:10.1080/15548627.2015.1017178. PubMed DOI PMC

Berg TO, Fengsrud M, Stromhaug PE, et al. Isolation and characterization of rat liver amphisomes. Evidence for fusion of autophagosomes with both early and late endosomes. J Biol Chem. 1998. Aug 21;273(34):21883–92. PubMed PMID: 9705327; eng. PubMed

Eskelinen E-L. Macroautophagy in mammalian cells. In: Saftig P, editor. Lysosomes. Georgetown, TX: LandesBioscience/Eurekah.com; 2005.

Turturici G, Tinnirello R, Sconzo G, et al. Extracellular membrane vesicles as a mechanism of cell-to-cell communication: advantages and disadvantages. Am J Physiol Cell Physiol. 2014. Apr 1;306(7):C621–33. PubMed PMID: 24452373. doi:10.1152/ajpcell.00228.2013. PubMed DOI

Eskelinen E-L. Fine structure of the autophagosome. In: Deretic V, editor. Autophagosome and phagosome. Methods in molecular biology. Vol. 445. Totowa, NJ: Humana Press; 2008. p. 11–28. PubMed

Di Rienzo M, Antonioli M, Fusco C, et al. Autophagy induction in atrophic muscle cells requires ULK1 activation by TRIM32 through unanchored K63-linked polyubiquitin chains. Sci Adv. 2019. May;5(5):eaau8857. PubMed PMID: 31123703; PubMed Central PMCID: PMCPMC6527439. doi:10.1126/sciadv.aau8857. PubMed DOI PMC

Khaminets A, Heinrich T, Mari M, et al. Regulation of endoplasmic reticulum turnover by selective autophagy. Nature. 2015. Jun 18;522(7556):354–8. PubMed PMID: 26040720. doi: 10.1038/nature14498. PubMed DOI

Zielke S, Meyer N, Mari M, et al. Loperamide, pimozide, and STF-62247 trigger autophagy-dependent cell death in glioblastoma cells. Cell Death Dis. 2018. Sep 24;9(10):994. PubMed PMID: 30250198; PubMed Central PMCID: PMCPMC6155211. doi:10.1038/s41419-018-1003-1. PubMed DOI PMC

Yang DS, Lee JH, Nixon RA.. Monitoring autophagy in Alzheimer’s disease and related neurodegenerative diseases. Methods Enzymol. 2009;453:111–44. PubMed PMID: 19216904. doi:10.1016/S0076-6879(08)04006-8. PubMed DOI

Yokota S, Himeno M, Kato K.. Immunocytochemical localization of acid phosphatase in rat liver. Cell Struct Funct. 1989. Apr;14(2):163–71. PubMed PMID: 2743419. PubMed

Boland B, Kumar A, Lee S, et al. Autophagy induction and autophagosome clearance in neurons: relationship to autophagic pathology in Alzheimer’s disease. J Neurosci. 2008. Jul 2;28(27):6926–37. PubMed PMID: 18596167; PubMed Central PMCID: PMC2676733. doi:10.1523/JNEUROSCI.0800-08.2008. PubMed DOI PMC

Nixon RA, Wegiel J, Kumar A, et al. Extensive involvement of autophagy in Alzheimer disease:an immuno-electron microscopy study. J Neuropathol Exp Neurol. 2005. Feb;64(2):113–22. PubMed PMID: 15751225; eng. PubMed

Lee JH, McBrayer MK, Wolfe DM, et al. Presenilin 1 maintains lysosomal Ca homeostasis via TRPML1 by regulating vATpase-mediated lysosome acidification. Cell Rep. 2015. Aug 19. PubMed PMID: 26299959. doi:10.1016/j.celrep.2015.07.050. PubMed DOI PMC

Lee JH, Yu WH, Kumar A, et al. Lysosomal proteolysis and autophagy require presenilin 1 and are disrupted by Alzheimer-related PS1 mutations. Cell. 2010. Jun 25;141(7):1146–58. PubMed PMID: 20541250; eng. doi:10.1016/j.cell.2010.05.008. PubMed DOI PMC

Chu CT. A pivotal role for PINK1 and autophagy in mitochondrial quality control: implications for Parkinson disease. Hum Mol Genet. 2010. Apr 15;19(R1):R28–37. PubMed PMID: 20385539; PubMed Central PMCID: PMC2875056. eng. doi:10.1093/hmg/ddq143. PubMed DOI PMC

Lee S, Sato Y, Nixon RA.. Lysosomal proteolysis inhibition selectively disrupts axonal transport of degradative organelles and causes an Alzheimer’s-like axonal dystrophy. J Neurosci. 2011. May 25;31(21):7817–30. PubMed PMID: 21613495; PubMed Central PMCID: PMC3351137. doi:10.1523/JNEUROSCI.6412-10.2011. PubMed DOI PMC

Maday S, Wallace KE, Holzbaur EL.. Autophagosomes initiate distally and mature during transport toward the cell soma in primary neurons. J Cell Biol. 2012. Feb 20;196(4):407–17. PubMed PMID: 22331844; PubMed Central PMCID: PMCPMC3283992. doi:10.1083/jcb.201106120. PubMed DOI PMC

Largeau C, Legouis R.. Correlative Light and Electron Microscopy to Analyze LC3 Proteins in Caenorhabditis elegans Embryo. Methods Mol Biol. 2019;1880:281–293. PubMed PMID: 30610704. doi: 10.1007/978-1-4939-8873-0_18. PubMed DOI

Zhan L, Chen S, Li K, et al. Autophagosome maturation mediated by Rab7 contributes to neuroprotection of hypoxic preconditioning against global cerebral ischemia in rats. Cell Death Dis. 2017. Jul 20;8(7):e2949. PubMed PMID: 28726776; PubMed Central PMCID: PMCPMC5550874. doi:10.1038/cddis.2017.330. PubMed DOI PMC

Rabouille C, Strous GJ, Crapo JD, et al. The differential degradation of two cytosolic proteins as a tool to monitor autophagy in hepatocytes by immunocytochemistry. J Cell Biol. 1993. Feb;120(4):897–908. PubMed PMID: 8432730; PubMed Central PMCID: PMC2200086. eng. PubMed PMC

Kovács AL, Pálfia Z, Réz G, et al. Sequestration revisited: integrating traditional electron microscopy, de novo assembly and new results. Autophagy. 2007;3:655–662. PubMed

Gao W, Kang JH, Liao Y, et al. Biochemical isolation and characterization of the tubulovesicular LC3-positive autophagosomal compartment. J Biol Chem. 2010. Jan 8;285(2):1371–83. PubMed PMID: 19910472; PubMed Central PMCID: PMC2801263. eng. doi:10.1074/jbc.M109.054197. PubMed DOI PMC

Lajoie P, Guay G, Dennis JW, et al. The lipid composition of autophagic vacuoles regulates expression of multilamellar bodies. J Cell Sci. 2005. May 1;118(Pt 9):1991–2003. PubMed PMID: 15840653. doi:10.1242/jcs.02324. PubMed DOI

Pentchev PG, Comly ME, Kruth HS, et al. Group C Niemann-Pick disease: faulty regulation of low-density lipoprotein uptake and cholesterol storage in cultured fibroblasts. FASEB J. 1987. Jul;1(1):40–5. PubMed PMID: 3609608. doi:10.1096/fasebj.1.1.3609608. PubMed DOI

Garcia-Sanz P, Orgaz L, Bueno-Gil G, et al. N370S-GBA1 mutation causes lysosomal cholesterol accumulation in Parkinson’s disease. Mov Disord. 2017. Oct;32(10):1409–1422. PubMed PMID:28779532. doi:10.1002/mds.27119. PubMed DOI

Garcia-Sanz P, Orgaz L, Fuentes JM, et al. Cholesterol and multilamellar bodies: lysosomal dysfunction in GBA-Parkinson disease. Autophagy. 2018;14(4):717–718. PubMed PMID: 29368986; PubMed Central PMCID: PMCPMC5959320. doi:10.1080/15548627.2018.1427396. PubMed DOI PMC

Shahmoradian SH, Lewis AJ, Genoud C, et al. Lewy pathology in Parkinson’s disease consists of crowded organelles and lipid membranes. Nat Neurosci. 2019. Jul;22(7):1099–1109. PubMed PMID: 31235907. doi:10.1038/s41593-019-0423-2. PubMed DOI

Cenedella RJ. Cholesterol synthesis inhibitor U18666A and the role of sterol metabolism and trafficking in numerous pathophysiological processes. Lipids. 2009. Jun;44(6):477–87. PubMed PMID: 19440746. doi:10.1007/s11745-009-3305-7. PubMed DOI

Elgner F, Ren H, Medvedev R, et al. The intracellular cholesterol transport inhibitor U18666A inhibits the exosome-dependent release of mature hepatitis C virus. J Virol. 2016. Dec 15;90(24):11181–11196. PubMed PMID: 27707921; PubMed Central PMCID: PMCPMC5126375. doi:10.1128/JVI.01053-16. PubMed DOI PMC

King MA, Ganley IG, Flemington V.. Inhibition of cholesterol metabolism underlies synergy between mTOR pathway inhibition and chloroquine in bladder cancer cells. Oncogene. 2016. Aug 25;35(34):4518–28. PubMed PMID: 26853465; PubMed Central PMCID: PMCPMC5000518 interest. doi:10.1038/onc.2015.511. PubMed DOI PMC

Mayhew TM. Quantitative immunoelectron microscopy: alternative ways of assessing subcellular patterns of gold labeling. Methods Mol Biol. 2007;369:309–29. PubMed PMID: 17656757; eng. PubMed

Mayhew TM, Lucocq JM, Griffiths G.. Relative labelling index: a novel stereological approach to test for non-random immunogold labelling of organelles and membranes on transmission electron microscopy thin sections. J Microsc. 2002. Feb;205(Pt 2):153–64. PubMed PMID: 11879430; eng. PubMed

Isidoro C, Biagioni F, Giorgi FS, et al. The role of autophagy on the survival of dopamine neurons. Curr Top Med Chem. 2009;9(10):869–79. PubMed PMID: 19754403. PubMed

Avin-Wittenberg T, Baluska F, Bozhkov PV, et al. Autophagy-related approaches for improving nutrient use efficiency and crop yield protection. J Exp Bot. 2018. Mar 14;69(6):1335–1353. PubMed PMID: 29474677. doi:10.1093/jxb/ery069. PubMed DOI

Kuzuoglu-Ozturk D, Cebeci Yalcinkaya O, Akpinar BA, et al. Autophagy-related gene, TdAtg8, in wild emmer wheat plays a role in drought and osmotic stress response. Planta. 2012. Oct;236(4):1081–92. PubMed PMID: 22569921. doi:10.1007/s00425-012-1657-3. PubMed DOI

Schmid D, Pypaert M, Münz C.. Antigen-loading compartments for major histocompatibility complex class II molecules continuously receive input from autophagosomes. Immunity. 2007. Jan;26(1):79–92. PubMed PMID: 17182262; eng. PubMed PMC

Runwal G, Stamatakou E, Siddiqi FH, et al. LC3-positive structures are prominent in autophagy-deficient cells. Sci Rep. 2019. Jul 12;9(1):10147. PubMed PMID: 31300716; PubMed Central PMCID: PMCPMC6625982. doi:10.1038/s41598-019-46657-z. PubMed DOI PMC

Ponpuak M, Mandell MA, Kimura T, et al. Secretory autophagy. Curr Opin Cell Biol. 2015. Aug;35:106–16. PubMed PMID: 25988755; PubMed Central PMCID: PMC4529791. doi: 10.1016/j.ceb.2015.04.016. PubMed DOI PMC

Subramani S, Malhotra V.. Non-autophagic roles of autophagy-related proteins. EMBO Rep. 2013. Feb;14(2):143–51. PubMed PMID: 23337627; PubMed Central PMCID: PMC3566844. doi: 10.1038/embor.2012.220. PubMed DOI PMC

Addis R, Campesi I, Fois M, et al. Human umbilical endothelial cells (HUVECs) have a sex: characterisation of the phenotype of male and female cells. Biol Sex Differ. 2014;5(1):18. PubMed PMID: 25535548; PubMed Central PMCID: PMCPMC4273493. doi: 10.1186/s13293-014-0018-2. PubMed DOI PMC

Campesi I, Occhioni S, Capobianco G, et al. Sex-specific pharmacological modulation of autophagic process in human umbilical artery smooth muscle cells. Pharmacol Res. 2016. Nov;113(Pt A):166–174. PubMed PMID: 27521838. doi: 10.1016/j.phrs.2016.08.014. PubMed DOI

Campesi I, Straface E, Occhioni S, et al. Protein oxidation seems to be linked to constitutive autophagy: a sex study. Life Sci. 2013. Aug 6;93(4):145–52. doi: 10.1016/j.lfs.2013.06.001. PubMed PMID: 23770210. PubMed DOI

Cosper PF, Leinwand LA.. Cancer causes cardiac atrophy and autophagy in a sexually dimorphic manner. Cancer Res. 2011. Mar 1;71(5):1710–20. doi: 10.1158/0008-5472.CAN-10-3145. PubMed PMID: 21163868; PubMed Central PMCID: PMCPMC3049989. PubMed DOI PMC

Du L, Hickey RW, Bayir H, et al. Starving neurons show sex difference in autophagy. J Biol Chem. 2009. Jan 23;284(4):2383–96. doi: 10.1074/jbc.M804396200. PubMed PMID: 19036730; PubMed Central PMCID: PMCPMC2629091. PubMed DOI PMC

Saito T, Asai K, Sato S, et al. Proof of myocardial autophagy by combining antigen retrieval and the avidin-biotin peroxidase complex method. Int J Cardiol. 2013. Oct 12;168(5):4843–4. doi: 10.1016/j.ijcard.2013.07.032. PubMed PMID: 23871334. PubMed DOI

Kovács J. Regression of autophagic vacuoles in seminal vesicle cells following cycloheximide treatment. Exp Cell Res. 1983. Mar;144(1):231–4. PubMed PMID: 6840208; eng. PubMed

Réz G, Csak J, Fellinger E, et al. Time course of vinblastine-induced autophagocytosis and changes in the endoplasmic reticulum in murine pancreatic acinar cells: a morphometric and biochemical study. Eur J Cell Biol. 1996. Dec;71(4):341–50. PubMed PMID: 8980904; eng. PubMed

Kovács AL, Grinde B, Seglen PO.. Inhibition of autophagic vacuole formation and protein degradation by amino acids in isolated hepatocytes. Exp Cell Res. 1981. Jun;133(2):431–6. PubMed PMID: 7238609; eng. PubMed

Mortimore GE, Hutson NJ, Surmacz CA.. Quantitative correlation between proteolysis and macro- and microautophagy in mouse hepatocytes during starvation and refeeding. Proc Natl Acad Sci U S A. 1983. Apr;80(8):2179–83. PubMed PMID: 6340116; eng. PubMed PMC

Mortimore GE, Lardeux BR, Adams CE.. Regulation of microautophagy and basal protein turnover in rat liver. Effects of short-term starvation. J Biol Chem. 1988. Feb 15;263(5):2506–12. PubMed PMID: 3257493; eng. PubMed

Zhu JH, Horbinski C, Guo F, et al. Regulation of autophagy by extracellular signal-regulated protein kinases during 1-methyl-4-phenylpyridinium-induced cell death. Am J Pathol. 2007. Jan;170(1):75–86. PubMed PMID: 17200184; eng. PubMed PMC

Bjørkøy G, Lamark T, Brech A, et al. p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death. J Cell Biol. 2005. Nov 21;171(4):603–14. PubMed PMID: 16286508; eng. PubMed PMC

Goginashvili A, Zhang Z, Erbs E, et al. Insulin granules. Insulin secretory granules control autophagy in pancreatic beta cells. Science. 2015. Feb 20;347(6224):878–82. doi: 10.1126/science.aaa2628. PubMed PMID: 25700520. PubMed DOI

Orvedahl A, Sumpter R, Jr., Xiao G, et al. Image-based genome-wide siRNA screen identifies selective autophagy factors. Nature. 2011. Dec 1;480(7375):113–7. doi: 10.1038/nature10546. PubMed PMID: 22020285; PubMed Central PMCID: PMC3229641. PubMed DOI PMC

Razi M, Tooze SA.. Correlative light and electron microscopy. Methods Enzymol. 2009;452:261–75. doi: 10.1016/S0076-6879(08)03617-3. PubMed PMID: 19200888; eng. PubMed DOI

Shu X, Lev-Ram V, Deerinck TJ, et al. A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms. PLoS Biol. 2011. Apr;9(4):e1001041. doi:10.1371/journal.pbio.1001041. PubMed PMID: 21483721; PubMed Central PMCID: PMC3071375. eng. PubMed DOI PMC

Giulivi C, Sarcansky M, Rosenfeld E, et al. The photodynamic effect of rose bengal on proteins of the mitochondrial inner membrane. Photochem Photobiol. 1990. Oct;52(4):745–51. doi:10.1111/j.1751-1097.1990.tb08676.x. PubMed PMID: 2089421. PubMed DOI

Castillo K, Rojas-Rivera D, Lisbona F, et al. BAX inhibitor-1 regulates autophagy by controlling the IRE1α/JNK branch of the unfolded protein response. EMBO J. 2011;30:4465–78. PubMed PMC

Hayashi-Nishino M, Fujita N, Noda T, et al. Electron tomography reveals the endoplasmic reticulum as a membrane source for autophagosome formation. Autophagy. 2010. Feb;6(2):301–3. PubMed PMID: 20104025; eng. PubMed

Yla-Anttila P, Vihinen H, Jokitalo E, et al. 3D tomography reveals connections between the phagophore and endoplasmic reticulum. Autophagy. 2009. Nov;5(8):1180–5. PubMed PMID: 19855179; eng. PubMed

Zhuang X, Chung KP, Cui Y, et al. ATG9 regulates autophagosome progression from the endoplasmic reticulum in Arabidopsis. Proc Natl Acad Sci U S A. 2017. Jan 17;114(3):E426–E435. doi: 10.1073/pnas.1616299114. PubMed PMID: 28053229; PubMed Central PMCID: PMCPMC5255614. PubMed DOI PMC

Lai LTF, Yu C, Wong JSK, et al. Subnanometer resolution cryo-EM structure of Arabidopsis thaliana ATG9. Autophagy. 2019. Jul 16:in press. doi: 10.1080/15548627.2019.1639300. PubMed PMID: 31276439. PubMed DOI PMC

Duke EM, Razi M, Weston A, et al. Imaging endosomes and autophagosomes in whole mammalian cells using correlative cryo-fluorescence and cryo-soft X-ray microscopy (cryo-CLXM). Ultramicroscopy. 2014. Aug;143:77–87. doi: 10.1016/j.ultramic.2013.10.006. PubMed PMID: 24238600; PubMed Central PMCID: PMC4045213. PubMed DOI PMC

Ciuffa R, Lamark T, Tarafder AK, et al. The selective autophagy receptor p62 forms a flexible filamentous helical scaffold. Cell Rep. 2015. May 5;11(5):748–58. doi: 10.1016/j.celrep.2015.03.062. PubMed PMID: 25921531. PubMed DOI

Hurley JH, Nogales E.. Next-generation electron microscopy in autophagy research. Curr Opin Struct Biol. 2016. Dec;41:211–216. doi: 10.1016/j.sbi.2016.08.006. PubMed PMID: 27614295; PubMed Central PMCID: PMCPMC5154772. PubMed DOI PMC

Massey AC, Kaushik S, Sovak G, et al. Consequences of the selective blockage of chaperone-mediated autophagy. Proc Natl Acad Sci U S A. 2006. Apr 11;103(15):5805–10. PubMed PMID: 16585521; eng. PubMed PMC

Felszeghy S, Viiri J, Paterno JJ, et al. Loss of NRF-2 and PGC-1alpha genes leads to retinal pigment epithelium damage resembling dry age-related macular degeneration. Redox Biol. 2019. Jan;20:1–12. PubMed PMID: 30253279; PubMed Central PMCID: PMCPMC6156745. PubMed PMC

Baba M, Osumi M, Ohsumi Y.. Analysis of the membrane structures involved in autophagy in yeast by freeze-replica method. Cell Struct Funct. 1995. Dec;20(6):465–71. PubMed PMID: 8825067; eng. PubMed

Rez G, Meldolesi J.. Freeze-fracture of drug-induced autophagocytosis in the mouse exocrine pancreas. Lab Invest. 1980. Sep;43(3):269–77. PubMed PMID: 7401637; eng. PubMed

Fengsrud M, Erichsen ES, Berg TO, et al. Ultrastructural characterization of the delimiting membranes of isolated autophagosomes and amphisomes by freeze-fracture electron microscopy. Eur J Cell Biol. 2000. Dec;79(12):871–82. PubMed PMID: 11152279; eng. PubMed

Punnonen E-L, Pihakaski K, Mattila K, et al. Intramembrane particles and filipin labelling on the membranes of autophagic vacuoles and lysosomes in mouse liver. Cell Tissue Res. 1989. Nov;258(2):269–76. PubMed PMID: 2582478; eng. PubMed

Dickey JS, Gonzalez Y, Aryal B, et al. Mito-tempol and dexrazoxane exhibit cardioprotective and chemotherapeutic effects through specific protein oxidation and autophagy in a syngeneic breast tumor preclinical model. PLoS One. 2013;8(8):e70575. doi:10.1371/journal.pone.0070575. PubMed PMID: 23940596; PubMed Central PMCID: PMC3734284. PubMed DOI PMC

Rao VA, Klein SR, Bonar SJ, et al. The antioxidant transcription factor Nrf2 negatively regulates autophagy and growth arrest induced by the anticancer redox agent mitoquinone. J Biol Chem. 2010. Nov 5;285(45):34447–59. doi: 10.1074/jbc.M110.133579. PubMed PMID: 20805228; PubMed Central PMCID: PMC2966059. eng. PubMed DOI PMC

Klionsky DJ. Autophagy: from phenomenology to molecular understanding in less than a decade. Nat Rev Mol Cell Biol. 2007;8:931–937. PubMed

Krick R, Muhe Y, Prick T, et al. Piecemeal microautophagy of the nucleus: genetic and morphological traits. Autophagy. 2009. Feb;5(2):270–2. PubMed PMID: 19182523; eng. PubMed

Meschini S, Condello M, Calcabrini A, et al. The plant alkaloid voacamine induces apoptosis-independent autophagic cell death on both sensitive and multidrug resistant human osteosarcoma cells. Autophagy. 2008. Nov;4(8):1020–33. PubMed PMID: 18838862; eng. PubMed

Proikas-Cezanne T, Robenek H.. Freeze-fracture replica immunolabelling reveals human WIPI-1 and WIPI-2 as membrane proteins of autophagosomes. J Cell Mol Med. 2011. Sep;15(9):2007–10. doi: 10.1111/j.1582-4934.2011.01339.x. PubMed PMID: 21564513; eng. PubMed DOI PMC

Hirsimaki Y, Hirsimaki P, Lounatmaa K.. Vinblastine-induced autophagic vacuoles in mouse liver and Ehrlich ascites tumor cells as assessed by freeze-fracture electron microscopy. Eur J Cell Biol. 1982. Jun;27(2):298–301. PubMed PMID: 7117273; eng. PubMed

Kovacs J, Rez G, Kovacs AL, et al. Autophagocytosis: freeze-fracture morphology, effects of vinblastine and influence of transcriptional and translational inhibitors. Acta Biol Med Ger. 1982;41(1):131–5. PubMed PMID: 7113544; eng. PubMed

Backues SK, Chen D, Ruan J, et al. Estimating the size and number of autophagic bodies by electron microscopy. Autophagy. 2014. Jan;10(1):155–64. doi: 10.4161/auto.26856. PubMed PMID: 24270884. PubMed DOI PMC

Cheong H, Yorimitsu T, Reggiori F, et al. Atg17 regulates the magnitude of the autophagic response. Mol Biol Cell. 2005. Jul;16(7):3438–53. doi:10.1091/mbc.E04-10-0894. PubMed PMID: 15901835; PubMed Central PMCID: PMC1165424. eng. PubMed DOI PMC

Xie Z, Nair U, Klionsky DJ.. Atg8 controls phagophore expansion during autophagosome formation. Mol Biol Cell. 2008. Aug;19(8):3290–8. doi: 10.1091/mbc.E07-12-1292. PubMed PMID: 18508918; PubMed Central PMCID: PMC2488302. eng. PubMed DOI PMC

Colasuonno F, Borghi R, Niceforo A, et al. Senescence-associated ultrastructural features of long-term cultures of induced pluripotent stem cells (iPSCs). Aging (Albany NY). 2017. Oct 23;9(10):2209–2222. doi: 10.18632/aging.101309. PubMed PMID: 29064821; PubMed Central PMCID: PMCPMC5680563. PubMed DOI PMC

McDonald KL, Webb RI.. Freeze substitution in 3 hours or less. J Microsc. 2011. Sep;243(3):227–33. doi: 10.1111/j.1365-2818.2011.03526.x. PubMed PMID: 21827481. PubMed DOI

Reipert S, Goldammer H, Richardson C, et al. Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution. J Histochem Cytochem. 2018. Dec;66(12):903–921. doi: 10.1369/0022155418786698. PubMed PMID: 29969056; PubMed Central PMCID: PMCPMC6262506. PubMed DOI PMC

Kovács AL, Vellai T, Müller F.. Autophagy in Caenorhabditis elegans. In: Klionsky DJ, editor. Autophagy. Georgetown, Texas: Landes Bioscience; 2004. p. 217–23.

Sigmond T, Feher J, Baksa A, et al. Qualitative and quantitative characterization of autophagy in Caenorhabditis elegans by electron microscopy. Methods Enzymol. 2008;451:467–91. doi:10.1016/S0076-6879(08)03228-X. PubMed PMID: 19185736; eng. PubMed DOI

Electron microscopy of model systems. In: Müller-Reichert T, editor. Methods cell biol. Vol. 96. 2010. 2010 09 28.

Nowikovsky K, Reipert S, Devenish RJ, et al. Mdm38 protein depletion causes loss of mitochondrial K+/H+ exchange activity, osmotic swelling and mitophagy. Cell Death Differ. 2007. Sep;14(9):1647–56. doi: 10.1038/sj.cdd.4402167. PubMed PMID: 17541427. PubMed DOI

Roberts P, Moshitch-Moshkovitz S, Kvam E, et al. Piecemeal microautophagy of nucleus in Saccharomyces cerevisiae. Mol Biol Cell. 2003. Jan;14(1):129–41. PubMed PMID: 12529432. PubMed PMC

Howard V, Reed MG.. Unbiased stereology; three dimensional measurement in microscopy. U Bios Scientific Publishers; 1998.

Weibel ER. Practical Methods for Biological Morphometry. In: Stereological Methods. Vol. 1. Academic Press, New York; 1979.

Williams MA. Quantitative methods in biology: Practical methods in electron microscopy. Vol. 6. Amsterdam, New York, Oxford: North-Holland Publishing Company; 1977.

Eskelinen EL. Fine structure of the autophagosome. Methods Mol Biol. 2008;445:11–28. doi:10.1007/978-1-59745-157-4_2. PubMed PMID: 18425441. PubMed DOI

Kovacs AL. A simple method to estimate the number of autophagic elements by electron microscopic morphometry in real cellular dimensions. Biomed Res Int. 2014;2014:578698. doi: 10.1155/2014/578698. PubMed PMID: 25105130; PubMed Central PMCID: PMC4106081. PubMed DOI PMC

Xie Z, Nair U, Geng J, et al. Indirect estimation of the area density of Atg8 on the phagophore. Autophagy. 2009. Feb;5(2):217–20. PubMed PMID: 19088501; PubMed Central PMCID: PMC2941343. PubMed PMC

Kovacs AL, Laszlo L, Fellinger E, et al. Combined effects of fasting and vinblastine treatment on serum insulin level, the size of autophagic-lysosomal compartment, protein content and lysosomal enzyme activities of liver and exocrine pancreatic cells of the mouse. Comp biochem physiol B Comp biochem. 1989;94(3):505–10. PubMed PMID: 2695284; eng. PubMed

Punnonen EL, Reunanen H.. Effects of vinblastine, leucine, and histidine, and 3-methyladenine on autophagy in Ehrlich ascites cells. Exp Mol Pathol. 1990. Feb;52(1):87–97. PubMed PMID: 2307216; eng. PubMed

Griffiths G. Fine structure immunocytochemistry Heidelberg, Germany: Springer-Verlag; 1993.

Reyes FC, Chung T, Holding D, et al. Delivery of prolamins to the protein storage vacuole in maize aleurone cells. Plant Cell. 2011. Feb;23(2):769–84. doi: 10.1105/tpc.110.082156. PubMed PMID: 21343414; PubMed Central PMCID: PMC3077793. eng. PubMed DOI PMC

Dunn WA, Jr., Cregg JM, Kiel JAKW, et al. Pexophagy: the selective autophagy of peroxisomes. Autophagy. 2005. Jul;1(2):75–83. PubMed PMID: 16874024. PubMed

Wang K, Klionsky DJ.. Mitochondria removal by autophagy. Autophagy. 2011. Mar;7(3):297–300. PubMed PMID: 21252623; eng. PubMed PMC

Belanger M, Rodrigues PH, Dunn WA, Jr., et al. Autophagy: a highway for Porphyromonas gingivalis in endothelial cells. Autophagy. 2006. Jul-Sep;2(3):165–70. PubMed PMID: 16874051; eng. PubMed

Birmingham CL, Brumell JH.. Autophagy recognizes intracellular Salmonella enterica serovar Typhimurium in damaged vacuoles. Autophagy. 2006. Jul-Sep;2(3):156–8. PubMed PMID: 16874057; eng. PubMed

Colombo MI, Gutierrez MG, Romano PS.. The two faces of autophagy: Coxiella and Mycobacterium. Autophagy. 2006. Jul-Sep;2(3):162–4. PubMed PMID: 16874070; eng. PubMed

Ogawa M, Sasakawa C.. Shigella and autophagy. Autophagy. 2006. Jul-Sep;2(3):171–4. PubMed PMID: 16874102; eng. PubMed

Vergne I, Singh S, Roberts E, et al. Autophagy in immune defense against Mycobacterium tuberculosis. Autophagy. 2006. Jul-Sep;2(3):175–8. PubMed PMID: 16874111; eng. PubMed

Yoshimori T. Autophagy vs. Group A Streptococcus. Autophagy. 2006. Jul-Sep;2(3):154–5. PubMed PMID: 16874113; eng. PubMed

Gorbunov NV, McDaniel DP, Zhai M, et al. Autophagy and mitochondrial remodelling in mouse mesenchymal stromal cells challenged with Staphylococcus epidermidis. J Cell Mol Med. 2015. May;19(5):1133–50. doi: 10.1111/jcmm.12518. PubMed PMID: 25721260; PubMed Central PMCID: PMC4420615. PubMed DOI PMC

Lynch-Day MA, Klionsky DJ.. The Cvt pathway as a model for selective autophagy [Review]. FEBS Lett. 2010. Apr 2;584(7):1359–66. doi: 10.1016/j.febslet.2010.02.013. PubMed PMID: 20146925; PubMed Central PMCID: PMC2843786. eng. PubMed DOI PMC

Birmingham CL, Canadien V, Gouin E, et al. Listeria monocytogenes evades killing by autophagy during colonization of host cells. Autophagy. 2007. Sep-Oct;3(5):442–51. PubMed PMID: 17568179; eng. PubMed

Klionsky DJ. Protein transport from the cytoplasm into the vacuole. J Membr Biol. 1997. May 15;157(2):105–15. PubMed PMID: 9151652. PubMed

Baba M, Osumi M, Scott SV, et al. Two distinct pathways for targeting proteins from the cytoplasm to the vacuole/lysosome. J Cell Biol. 1997. Dec 29;139(7):1687–95. PubMed PMID: 9412464; PubMed Central PMCID: PMC2132654. PubMed PMC

Dini L, Pagliara P, Carla EC.. Phagocytosis of apoptotic cells by liver: a morphological study [Review]. Microsc Res Tech. 2002. Jun 15;57(6):530–40. doi: 10.1002/jemt.10107. PubMed PMID: 12112436; eng. PubMed DOI

Kroemer G, El-Deiry WS, Golstein P, et al. Classification of cell death: recommendations of the Nomenclature Committee on Cell Death [Guideline]. Cell Death Differ. 2005. Nov;12:1463–7. doi: 10.1038/sj.cdd.4401724. PubMed PMID: 16247491; eng. PubMed DOI

Nagy P, Varga A, Kovács AL, et al. How and why to study autophagy in Drosophila: It’s more than just a garbage chute. Methods. 2015;75:151–61. PubMed PMC

Rez G, Palfia Z, Fellinger E.. Occurrence and inhibition by cycloheximide of apoptosis in vinblastine-treated murine pancreas. A role for autophagy? Acta Biol Hung. 1991; 42 (1–3): 133–40. PubMed PMID: 1844306; eng. PubMed

Giammarioli AM, Gambardella L, Barbati C, et al. Differential effects of the glycolysis inhibitor 2-deoxy-D-glucose on the activity of pro-apoptotic agents in metastatic melanoma cells, and induction of a cytoprotective autophagic response. int J cancer J Inter du cancer. 2012. Sep 12;131:E337–47. doi: 10.1002/ijc.26420. PubMed PMID: 21913183; Eng. PubMed DOI

Cheng XT, Xie YX, Zhou B, et al. Characterization of LAMP1-labeled nondegradative lysosomal and endocytic compartments in neurons. J Cell Biol. 2018. Sep 3;217(9):3127–3139. doi: 10.1083/jcb.201711083. PubMed PMID: 29695488; PubMed Central PMCID: PMCPMC6123004. PubMed DOI PMC

Cheng XT, Xie YX, Zhou B, et al. Revisiting LAMP1 as a marker for degradative autophagy-lysosomal organelles in the nervous system. Autophagy. 2018;14(8):1472–1474. doi:10.1080/15548627.2018.1482147. PubMed PMID: 29940787; PubMed Central PMCID: PMCPMC6103665. PubMed DOI PMC

Xie Y, Zhou B, Lin MY, et al. Progressive endolysosomal deficits impair autophagic clearance beginning at early asymptomatic stages in fALS mice. Autophagy. 2015;11(10):1934–6. doi: 10.1080/15548627.2015.1084460. PubMed PMID: 26290961; PubMed Central PMCID: PMCPMC4824580. PubMed DOI PMC

Xie Y, Zhou B, Lin MY, et al. Endolysosomal Deficits Augment Mitochondria Pathology in Spinal Motor Neurons of Asymptomatic fALS Mice. Neuron. 2015. Jul 15;87(2):355–70. doi: 10.1016/j.neuron.2015.06.026. PubMed PMID: 26182418; PubMed Central PMCID: PMCPMC4511489. PubMed DOI PMC

Karanasios E. Correlative Live-Cell Imaging and Super-Resolution Microscopy of Autophagy. Methods Mol Biol. 2019;1880:231–242. doi: 10.1007/978-1-4939-8873-0_15. PubMed PMID: 30610701. PubMed DOI

Kenny SJ, Chen X, Ge L, et al. Super-resolution microscopy unveils FIP200-scaffolded, cup-shaped organization of mammalian autophagic initiation machinery. bioRxiv. 2019. 10.1101/712828. DOI

Sou YS, Tanida I, Komatsu M, et al. Phosphatidylserine in addition to phosphatidylethanolamine is an in vitro target of the mammalian Atg8 modifiers, LC3, GABARAP, and GATE-16. J Biol Chem. 2006. Feb 10;281(6):3017–24. doi: 10.1074/jbc.M505888200. PubMed PMID: 16303767; eng. PubMed DOI

Le Grand JN, Chakrama FZ, Seguin-Py S, et al. GABARAPL1 (GEC1): Original or copycat? Autophagy. 2011. Oct 1;7(10):1098–107. PubMed PMID: 21597319; Eng. PubMed

Hemelaar J, Lelyveld VS, Kessler BM, et al. A single protease, Apg4B, is specific for the autophagy-related ubiquitin-like proteins GATE-16, MAP1-LC3, GABARAP, and Apg8L. J Biol Chem. 2003. Dec 19;278(51):51841–50. doi: 10.1074/jbc.M308762200. PubMed PMID: 14530254. PubMed DOI

Tanida I, Sou YS, Ezaki J, et al. HsAtg4B/HsApg4B/autophagin-1 cleaves the carboxyl termini of three human Atg8 homologues and delipidates microtubule-associated protein light chain 3- and GABAA receptor-associated protein-phospholipid conjugates. J Biol Chem. 2004. Aug 27;279(35):36268–76. doi: 10.1074/jbc.M401461200. PubMed PMID: 15187094. PubMed DOI

Bhujabal Z, Birgisdottir AB, Sjottem E, et al. FKBP8 recruits LC3A to mediate Parkin-independent mitophagy. EMBO Rep. 2017. Jun;18(6):947–961. doi: 10.15252/embr.201643147. PubMed PMID: 28381481; PubMed Central PMCID: PMCPMC5452039. PubMed DOI PMC

Koukourakis MI, Kalamida D, Giatromanolaki A, et al. Autophagosome proteins LC3A, LC3B and LC3C have distinct subcellular distribution kinetics and expression in cancer cell lines. PLoS One. 2015;10(9):e0137675. doi: 10.1371/journal.pone.0137675. PubMed PMID: 26378792; PubMed Central PMCID: PMCPMC4574774. PubMed DOI PMC

Kabeya Y, Mizushima N, Yamamoto A, et al. LC3, GABARAP and GATE16 localize to autophagosomal membrane depending on form-II formation. J Cell Sci. 2004. Jun 1;117(Pt 13):2805–12. doi: 10.1242/jcs.01131. PubMed PMID: 15169837; eng. PubMed DOI

Weidberg H, Shvets E, Shpilka T, et al. LC3 and GATE-16/GABARAP subfamilies are both essential yet act differently in autophagosome biogenesis. EMBO J. 2010. Jun 2;29(11):1792–802. doi: 10.1038/emboj.2010.74. PubMed PMID: 20418806; PubMed Central PMCID: PMC2885923. eng. PubMed DOI PMC

Sugawara K, Suzuki NN, Fujioka Y, et al. The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8. Genes Cells. 2004. Jul;9(7):611–8. doi: 10.1111/j.1356-9597.2004.00750.x. PubMed PMID: 15265004. PubMed DOI

Chu CT, Ji J, Dagda RK, et al. Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells. Nat Cell Biol. 2013. Oct;15(10):1197–205. doi: 10.1038/ncb2837. PubMed PMID: 24036476; PubMed Central PMCID: PMC3806088. PubMed DOI PMC

Lystad AH, Ichimura Y, Takagi K, et al. Structural determinants in GABARAP required for the selective binding and recruitment of ALFY to LC3B-positive structures. EMBO Rep. 2014. Mar 25;15:557–565. doi: 10.1002/embr.201338003. PubMed PMID: 24668264. PubMed DOI PMC

von Muhlinen N, Akutsu M, Ravenhill BJ, et al. LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy. Mol Cell. 2012. Nov 9;48(3):329–42. doi: 10.1016/j.molcel.2012.08.024. PubMed PMID: 23022382; PubMed Central PMCID: PMC3510444. PubMed DOI PMC

Huang W-P, Scott SV, Kim J, et al. The itinerary of a vesicle component, Aut7p/Cvt5p, terminates in the yeast vacuole via the autophagy/Cvt pathways. J Biol Chem. 2000. Feb 25;275(8):5845–51. PubMed PMID: 10681575; eng. PubMed

Nash Y, Schmukler E, Trudler D, et al. DJ-1 deficiency impairs autophagy and reduces alpha-synuclein phagocytosis by microglia. J Neurochem. 2017. Dec;143(5):584–594. doi: 10.1111/jnc.14222. PubMed PMID: 28921554. PubMed DOI

Cai Q, Lu L, Tian J-H, et al. Snapin-regulated late endosomal transport is critical for efficient autophagy-lysosomal function in neurons. Neuron. 2010. Oct 6;68(1):73–86. doi:10.1016/j.neuron.2010.09.022. PubMed PMID: 20920792; PubMed Central PMCID: PMC2953270. eng. PubMed DOI PMC

Castino R, Fiorentino I, Cagnin M, et al. Chelation of lysosomal iron protects dopaminergic SH-SY5Y neuroblastoma cells from hydrogen peroxide toxicity by precluding autophagy and Akt dephosphorylation. Toxicol Sci. 2011. Jul 8:523–41. doi: 10.1093/toxsci/kfr179. PubMed PMID: 21742779; Eng. PubMed DOI PMC

Michiorri S, Gelmetti V, Giarda E, et al. The Parkinson-associated protein PINK1 interacts with Beclin1 and promotes autophagy. Cell Death Differ. 2010. Jun;17(6):962–74. doi: 10.1038/cdd.2009.200. PubMed PMID: 20057503; eng. PubMed DOI

Abdul Rahim SA, Dirkse A, Oudin A, et al. Regulation of hypoxia-induced autophagy in glioblastoma involves ATG9A. Br J Cancer. 2017. Sep 5;117(6):813–825. doi: 10.1038/bjc.2017.263. PubMed PMID: 28797031; PubMed Central PMCID: PMCPMC5590001. PubMed DOI PMC

Altmann C, Hardt S, Fischer C, et al. Progranulin overexpression in sensory neurons attenuates neuropathic pain in mice: Role of autophagy. Neurobiol Dis. 2016. Dec;96:294–311. doi: 10.1016/j.nbd.2016.09.010. PubMed PMID: 27629805. PubMed DOI

Rehorova M, Vargova I, Forostyak S, et al. A Combination of Intrathecal and Intramuscular Application of Human Mesenchymal Stem Cells Partly Reduces the Activation of Necroptosis in the Spinal Cord of SOD1(G93A) Rats. Stem Cells Transl Med. 2019. Jun;8(6):535–547. doi: 10.1002/sctm.18-0223. PubMed PMID: 30802001; PubMed Central PMCID: PMCPMC6525562. PubMed DOI PMC

Yang DS, Stavrides P, Mohan PS, et al. Reversal of autophagy dysfunction in the TgCRND8 mouse model of Alzheimer’s disease ameliorates amyloid pathologies and memory deficits. Brain. 2011. Jan;134(Pt 1):258–77. doi: 10.1093/brain/awq341. PubMed PMID: 21186265; PubMed Central PMCID: PMC3009842. PubMed DOI PMC

Liu S, Li Y, Choi HMC, et al. Lysosomal damage after spinal cord injury causes accumulation of RIPK1 and RIPK3 proteins and potentiation of necroptosis. Cell Death Dis. 2018. May 1;9(5):476. doi:10.1038/s41419-018-0469-1. PubMed PMID: 29686269; PubMed Central PMCID: PMCPMC5913300. PubMed DOI PMC

Sarkar C, Zhao Z, Aungst S, et al. Impaired autophagy flux is associated with neuronal cell death after traumatic brain injury. Autophagy. 2014. Nov 11;10:2208–22. doi: 10.4161/15548627.2014.981787. PubMed PMID: 25484084. PubMed DOI PMC

Padman BS, Bach M, Lucarelli G, et al. The protonophore CCCP interferes with lysosomal degradation of autophagic cargo in yeast and mammalian cells. Autophagy. 2013. Nov 1;9(11):1862–75. doi: 10.4161/auto.26557. PubMed PMID: 24150213. PubMed DOI

Engedal N, Torgersen ML, Guldvik IJ, et al. Modulation of intracellular calcium homeostasis blocks autophagosome formation. Autophagy. 2013. Oct;9(10):1475–90. doi: 10.4161/auto.25900. PubMed PMID: 23970164. PubMed DOI

Jahreiss L, Menzies FM, Rubinsztein DC.. The itinerary of auto-phagosomes: from peripheral formation to kiss-and-run fusion with lysosomes. Traffic. 2008. Apr;9(4):574–87. doi: 10.1111/j.1600-0854.2008.00701.x. PubMed PMID: 18182013; PubMed Central PMCID: PMC2329914. PubMed DOI PMC

Klionsky DJ, Elazar Z, Seglen PO, et al. Does bafilomycin A1 block the fusion of auto-phagosomes with lysosomes? [Editorial]. Autophagy. 2008. Oct;4(7):849–950. PubMed PMID: 18758232; eng. PubMed

Yamamoto A, Tagawa Y, Yoshimori T, et al. Bafilomycin A1 prevents maturation of autophagic vacuoles by inhibiting fusion between auto-phagosomes and lysosomes in rat hepatoma cell line, H-4-II-E cells. Cell Struct Funct. 1998. Feb;23(1):33–42. PubMed PMID: 9639028; eng. PubMed

Ahlberg J, Berkenstam A, Henell F, et al. Degradation of short and long lived proteins in isolated rat liver lysosomes. Effects of pH, temperature, and proteolytic inhibitors. J Biol Chem. 1985. May 10;260(9):5847–54. PubMed PMID: 3988775; eng. PubMed

Yoon YH, Cho KS, Hwang JJ, et al. Induction of lysosomal dilatation, arrested autophagy, and cell death by chloroquine in cultured ARPE-19 cells. Invest Ophthalmol Vis Sci. 2010. Nov;51(11):6030–7. doi: 10.1167/iovs.10-5278. PubMed PMID: 20574031. PubMed DOI

Juhasz G. Interpretation of bafilomycin, pH neutralizing or protease inhibitor treatments in autophagic flux experiments: novel considerations. Autophagy. 2012. Dec;8(12):1875–6. PubMed PMID: 22874642; PubMed Central PMCID: PMC3541311. PubMed PMC

Li M, Khambu B, Zhang H, et al. Suppression of lysosome function induces autophagy via a feedback down-regulation of MTOR complex 1 (MTORC1) activity. J Biol Chem. 2013. Dec 13;288(50):35769–80. doi: 10.1074/jbc.M113.511212. PubMed PMID: 24174532; PubMed Central PMCID: PMC3861628. PubMed DOI PMC

Thomas G, Hall MN.. TOR signalling and control of cell growth. Curr Opin Cell Biol. 1997. Dec;9(6):782–7. PubMed PMID: 9425342. PubMed

Seglen PO, Grinde B, Solheim AE.. Inhibition of the lysosomal pathway of protein degradation in isolated rat hepatocytes by ammonia, methylamine, chloroquine and leupeptin. Eur J Biochem/FEBS. 1979. Apr 2;95(2):215–25. PubMed PMID: 456353. PubMed

Yoshimori T, Yamamoto A, Moriyama Y, et al. Bafilomycin A1, a specific inhibitor of vacuolar-type H(+)-ATPase, inhibits acidification and protein degradation in lysosomes of cultured cells. J Biol Chem. 1991. Sep 15;266(26):17707–12. PubMed PMID: 1832676. PubMed

Artero-Castro A, Perez-Alea M, Feliciano A, et al. Disruption of the ribosomal P complex leads to stress-induced autophagy. Autophagy. 2015;11(9):1499–519. doi: 10.1080/15548627.2015.1063764. PubMed PMID: 26176264; PubMed Central PMCID: PMCPMC4590587. PubMed DOI PMC

Bahr BA, Wisniewski ML, Butler D.. Positive lysosomal modulation as a unique strategy to treat age-related protein accumulation diseases. Rejuvenation Res. 2012. Apr;15(2):189–97. doi: 10.1089/rej.2011.1282. PubMed PMID: 22533430; PubMed Central PMCID: PMCPMC3332372. PubMed DOI PMC

McLeland CB, Rodriguez J, Stern ST.. Autophagy monitoring assay: qualitative analysis of MAP LC3-I to II conversion by immunoblot. Methods Mol Biol. 2011;697:199–206. doi: 10.1007/978-1-60327-198-1_21. PubMed PMID: 21116969; eng. PubMed DOI

Chakrama FZ, Seguin-Py S, Le Grand JN, et al. GABARAPL1 (GEC1) associates with autophagic vesicles. Autophagy. 2010. May 22;6(4):495–505. PubMed PMID: 20404487; Eng. PubMed

Maynard S, Ghosh R, Wu Y, et al. GABARAP is a determinant of apoptosis in growth-arrested chicken embryo fibroblasts. J Cell Physiol. 2015. Jul;230(7):1475–88. doi: 10.1002/jcp.24889. PubMed PMID: 25514832. PubMed DOI

Kim J, Huang W-P, Klionsky DJ.. Membrane recruitment of Aut7p in the autophagy and cytoplasm to vacuole targeting pathways requires Aut1p, Aut2p, and the autophagy conjugation complex. J Cell Biol. 2001. Jan 8;152(1):51–64. PubMed PMID: 11149920; PubMed Central PMCID: PMC2193654. eng. PubMed PMC

Lopez-Otin C, Marino G.. Tagged ATG8-Coding Constructs for the In Vitro and In Vivo Assessment of ATG4 Activity. Methods Enzymol. 2017;587:189–205. doi: 10.1016/bs.mie.2016.11.001. PubMed PMID: 28253955. PubMed DOI

Shu CW, Drag M, Bekes M, et al. Synthetic substrates for measuring activity of autophagy proteases: autophagins (Atg4). Autophagy. 2010. Oct;6(7):936–47. doi: 10.4161/auto.6.7.13075. PubMed PMID: 20818167; PubMed Central PMCID: PMC3039740. eng. PubMed DOI PMC

Li M, Chen X, Ye Q-Z, et al. A High-throughput FRET-based Assay for Determination of Atg4 Activity. Autophagy. 2012;8:401–412. PubMed PMC

Ketteler R, Seed B.. Quantitation of autophagy by luciferase release assay [Evaluation Studies Research Support, Non-U.S. Gov’t]. Autophagy. 2008. Aug;4(6):801–6. PubMed PMID: 18641457; PubMed Central PMCID: PMC2910585. eng. PubMed PMC

Li M, Hou Y, Wang J, et al. Kinetics comparisons of mammalian Atg4 homologues indicate selective preferences toward diverse Atg8 substrates. J Biol Chem. 2011. Mar 4;286(9):7327–38. doi: 10.1074/jbc.M110.199059. PubMed PMID: 21177865; PubMed Central PMCID: PMC3044989. eng. PubMed DOI PMC

Klionsky DJ. For the last time, it is GFP-Atg8, not Atg8-GFP (and the same goes for LC3). Autophagy. 2011;7:1093–4. PubMed PMC

Mizushima N, Yamamoto A, Matsui M, et al. In vivo analysis of autophagy in response to nutrient starvation using transgenic mice expressing a fluorescent autophagosome marker. Mol Biol Cell. 2004. Mar;15(3):1101–11. PubMed PMID: 14699058; eng. PubMed PMC

Tanida I, Minematsu-Ikeguchi N, Ueno T, et al. Lysosomal turnover, but not a cellular level, of endogenous LC3 is a marker for autophagy. Autophagy 2005. Jul;1(2):84–91. PubMed PMID: 16874052; eng. PubMed

Matsui Y, Takagi H, Qu X, et al. Distinct roles of autophagy in the heart during ischemia and reperfusion: roles of AMP-activated protein kinase and Beclin 1 in mediating autophagy. Circ Res. 2007. Mar 30;100(6):914–22. PubMed PMID: 17332429; eng. PubMed

Suzuki K, Kirisako T, Kamada Y, et al. The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation. EMBO J. 2001. Nov 1;20(21):5971–81. doi: 10.1093/emboj/20.21.5971. PubMed PMID: 11689437; PubMed Central PMCID: PMC125692. eng. PubMed DOI PMC

Hanson HH, Kang S, Fernandez-Monreal M, et al. LC3-dependent intracellular membrane tubules induced by gamma-protocadherins A3 and B2: a role for intraluminal interactions. J Biol Chem. 2010. Jul 2;285(27):20982–92. doi: 10.1074/jbc.M109.092031. PubMed PMID: 20439459; PubMed Central PMCID: PMC2898317. eng. PubMed DOI PMC

Florey O, Kim SE, Sandoval CP, et al. Autophagy machinery mediates macroendocytic processing and entotic cell death by targeting single membranes. Nat Cell Biol. 2011;13(11):1335–43. doi: 10.1038/ncb2363. PubMed PMID: 22002674; eng. PubMed DOI PMC

Martinez J, Almendinger J, Oberst A, et al. Microtubule-associated protein 1 light chain 3 alpha (LC3)-associated phagocytosis is required for the efficient clearance of dead cells. Proc Natl Acad Sci U S A. 2011. Oct 18;108(42):17396–401. doi: 10.1073/pnas.1113421108. PubMed PMID: 21969579; PubMed Central PMCID: PMCPMC3198353. eng. PubMed DOI PMC

Choi J, Park S, Biering SB, et al. The parasitophorous vacuole membrane of Toxoplasma gondii is targeted for disruption by ubiquitin-like conjugation systems of autophagy. Immunity. 2014. Jun 19;40(6):924–35. doi: 10.1016/j.immuni.2014.05.006. PubMed PMID: 24931121; PubMed Central PMCID: PMC4107903. PubMed DOI PMC

Sanjuan MA, Dillon CP, Tait SW, et al. Toll-like receptor signalling in macrophages links the autophagy pathway to phagocytosis. Nature. 2007. Dec 20;450(7173):1253–7. doi: 10.1038/nature06421. PubMed PMID: 18097414; eng. PubMed DOI

Sanjuan MA, Milasta S, Green DR.. Toll-like receptor signaling in the lysosomal pathways [Review]. Immunol Rev. 2009. Jan;227(1):203–20. doi: 10.1111/j.1600-065X.2008.00732.x. PubMed PMID: 19120486; eng. PubMed DOI

Ushio H, Ueno T, Kojima Y, et al. Crucial role for autophagy in degranulation of mast cells. J Allergy Clin Immunol. 2011. May;127(5):1267–76 e6. doi: 10.1016/j.jaci.2010.12.1078. PubMed PMID: 21333342. PubMed DOI

Ishibashi K, Uemura T, Waguri S, et al. Atg16L1, an essential factor for canonical autophagy, participates in hormone secretion from PC12 cells independently of autophagic activity. Mol Biol Cell. 2012. Aug;23(16):3193–202. doi: 10.1091/mbc.E12-01-0010. PubMed PMID: 22740627; PubMed Central PMCID: PMC3418313. PubMed DOI PMC

DeSelm CJ, Miller BC, Zou W, et al. Autophagy proteins regulate the secretory component of osteoclastic bone resorption. Dev Cell. 2011. Nov 15;21(5):966–74. doi: 10.1016/j.devcel.2011.08.016. PubMed PMID: 22055344; PubMed Central PMCID: PMC3244473. PubMed DOI PMC

Patel KK, Miyoshi H, Beatty WL, et al. Autophagy proteins control goblet cell function by potentiating reactive oxygen species production. EMBO J. 2013. Dec 11;32(24):3130–44. doi: 10.1038/emboj.2013.233. PubMed PMID: 24185898; PubMed Central PMCID: PMC3981139. PubMed DOI PMC

Dupont N, Lacas-Gervais S, Bertout J, et al. Shigella phagocytic vacuolar membrane remnants participate in the cellular response to pathogen invasion and are regulated by autophagy. Cell Host Microbe. 2009. Aug 20;6(2):137–49. doi: 10.1016/j.chom.2009.07.005. PubMed PMID: 19683680; eng. PubMed DOI

Cottam EM, Maier HJ, Manifava M, et al. Coronavirus nsp6 proteins generate auto-phagosomes from the endoplasmic reticulum via an omegasome intermediate. Autophagy. 2011. Nov;7(11):1335–47. doi: 10.4161/auto.7.11.16642. PubMed PMID: 21799305; PubMed Central PMCID: PMC3242798. PubMed DOI PMC

Reggiori F, Monastyrska I, Verheije MH, et al. Coronaviruses Hijack the LC3-I-positive EDEMosomes, ER-derived vesicles exporting short-lived ERAD regulators, for replication. Cell Host Microbe. 2010. Jun 25;7(6):500–8. doi: 10.1016/j.chom.2010.05.013. PubMed PMID: 20542253; eng. PubMed DOI PMC

Sharma M, Bhattacharyya S, Nain M, et al. Japanese encephalitis virus replication is negatively regulated by autophagy and occurs on LC3-I- and EDEM1-containing membranes. Autophagy. 2014. Sep;10(9):1637–51. doi: 10.4161/auto.29455. PubMed PMID: 25046112. PubMed DOI PMC

English L, Chemali M, Duron J, et al. Autophagy enhances the presentation of endogenous viral antigens on MHC class I molecules during HSV-1 infection. Nat Immunol. 2009. May;10(5):480–7. doi:10.1038/ni.1720. PubMed PMID: 19305394; eng. PubMed DOI PMC

Beale R, Wise H, Stuart A, et al. A LC3-interacting motif in the influenza A virus M2 protein is required to subvert autophagy and maintain virion stability. Cell Host Microbe. 2014. Feb 12;15(2):239–47. doi: 10.1016/j.chom.2014.01.006. PubMed PMID: 24528869; PubMed Central PMCID: PMC3991421. PubMed DOI PMC

Bello-Morales R, Lopez-Guerrero JA.. Extracellular Vesicles in Herpes Viral Spread and Immune Evasion. Front Microbiol. 2018;9:2572. doi: 10.3389/fmicb.2018.02572. PubMed PMID: 30410480; PubMed Central PMCID: PMCPMC6209645. PubMed DOI PMC

Kemball CC, Alirezaei M, Flynn CT, et al. Coxsackievirus infection induces autophagy-like vesicles and megaphagosomes in pancreatic acinar cells in vivo. J Virol. 2010. Dec;84(23):12110–24. doi: 10.1128/JVI.01417-10. PubMed PMID: 20861268; PubMed Central PMCID: PMC2976412. PubMed DOI PMC

Alirezaei M, Flynn CT, Wood MR, et al. Pancreatic acinar cell-specific autophagy disruption reduces coxsackievirus replication and pathogenesis in vivo. Cell Host Microbe. 2012. Mar 15;11(3):298–305. doi: 10.1016/j.chom.2012.01.014. PubMed PMID: 22423969; PubMed Central PMCID: PMC3308121. PubMed DOI PMC

Agrotis A, von Chamier L, Oliver H, et al. Human ATG4 autophagy proteases counteract attachment of ubiquitin-like LC3/GABARAP proteins to other cellular proteins. J Biol Chem. 2019. Aug 23;294(34):12610–12621. doi: 10.1074/jbc.AC119.009977. PubMed PMID: 31315929; PubMed Central PMCID: PMCPMC6709618. PubMed DOI PMC

Ichimura Y, Imamura Y, Emoto K, et al. In vivo and in vitro reconstitution of Atg8 conjugation essential for autophagy. J Biol Chem. 2004. Sep 24;279(39):40584–92. doi: 10.1074/jbc.M405860200. PubMed PMID: 15277523. PubMed DOI

Plowey ED, Cherra SJ, 3rd, Liu YJ, et al. Role of autophagy in G2019S-LRRK2-associated neurite shortening in differentiated SH-SY5Y cells. J Neurochem. 2008. May;105(3):1048–56. doi: 10.1111/j.1471-4159.2008.05217.x. PubMed PMID: 18182054; PubMed Central PMCID: PMC2361385. eng. PubMed DOI PMC

Nicotra G, Mercalli F, Peracchio C, et al. Autophagy-active beclin-1 correlates with favourable clinical outcome in non-Hodgkin lymphomas. Mod Pathol. 2010. Jul;23(7):937–50. doi: 10.1038/modpathol.2010.80. PubMed PMID: 20473282; eng. PubMed DOI

Tanida I, Ueno T, Kominami E.. LC3 and autophagy. Methods Mol Biol. 2008;445:77–88. PubMed

Gros F, Arnold J, Page N, et al. Macroautophagy is deregulated in murine and human lupus T lymphocytes. Autophagy. 2012. Jul 1;8(7):1113–23. doi: 10.4161/auto.20275. PubMed PMID: 22522825; PubMed Central PMCID: PMC3429547. PubMed DOI PMC

Welinder C, Ekblad L.. Coomassie staining as loading control in Western blot analysis. J Proteome Res. 2011. Mar 4;10(3):1416–9. doi: 10.1021/pr1011476. PubMed PMID: 21186791. PubMed DOI

Rocha-Martins M, Njaine B, Silveira MS.. Avoiding pitfalls of internal controls: validation of reference genes for analysis by qRT-PCR and Western blot throughout rat retinal development. PLoS One. 2012;7(8):e43028. doi: 10.1371/journal.pone.0043028. PubMed PMID: 22916200; PubMed Central PMCID: PMCPMC3423434. PubMed DOI PMC

Colecchia D, Rossi M, Sasdelli F, et al. MAPK15 mediates BCR-ABL1-induced autophagy and regulates oncogene-dependent cell proliferation and tumor formation. Autophagy 2015;11(10):1790–802. doi: 10.1080/15548627.2015.1084454. PubMed PMID: 26291129; PubMed Central PMCID: PMCPMC4824572. PubMed DOI PMC

Colecchia D, Stasi M, Leonardi M, et al. Alterations of autophagy in the peripheral neuropathy Charcot-Marie-Tooth type 2B. Autophagy. 2018;14(6):930–941. doi: 10.1080/15548627.2017.1388475. PubMed PMID: 29130394; PubMed Central PMCID: PMCPMC6103410. PubMed DOI PMC

Colecchia D, Strambi A, Sanzone S, et al. MAPK15/ERK8 stimulates autophagy by interacting with LC3 and GABARAP proteins. Autophagy. 2012. Dec;8(12):1724–40. doi: 10.4161/auto.21857. PubMed PMID: 22948227; PubMed Central PMCID: PMC3541284. PubMed DOI PMC

Colella AD, Chegenii N, Tea MN, et al. Comparison of Stain-Free gels with traditional immunoblot loading control methodology. Anal Biochem. 2012. Nov 15;430(2):108–10. doi: 10.1016/j.ab.2012.08.015. PubMed PMID: 22929699. PubMed DOI

Ghosh R, Gilda JE, Gomes AV.. The necessity of and strategies for improving confidence in the accuracy of western blots. Expert Rev Proteomics. 2014. Oct;11(5):549–60. doi: 10.1586/14789450.2014.939635. PubMed PMID: 25059473. PubMed DOI PMC

Yan L, Vatner DE, Kim SJ, et al. Autophagy in chronically ischemic myocardium. Proc Natl Acad Sci U S A. 2005. Sep 27;102(39):13807–12. doi: 10.1073/pnas.0506843102. PubMed PMID: 16174725; PubMed Central PMCID: PMC1224362. PubMed DOI PMC

Russ DW, Boyd IM, McCoy KM, et al. Muscle-specificity of age-related changes in markers of autophagy and sphingolipid metabolism. Biogerontology. 2015. Aug 22. doi: 10.1007/s10522-015-9598-4. PubMed PMID: 26296420. PubMed

Russ DW, Krause J, Wills A, et al. “SR stress” in mixed hindlimb muscles of aging male rats. Biogerontology. 2012. Oct;13(5):547–55. doi: 10.1007/s10522-012-9399-y. PubMed PMID: 22955580. PubMed DOI

Simonovitch S, Schmukler E, Bespalko A, et al. Impaired Autophagy in APOE4 Astrocytes. J Alzheimers Dis. 2016;51(3):915–27. doi: 10.3233/JAD-151101. PubMed PMID: 26923027. PubMed DOI

He H, Dang Y, Dai F, et al. Post-translational modifications of three members of the human MAP1LC3 family and detection of a novel type of modification for MAP1LC3B. J Biol Chem. 2003. Aug 1;278(31):29278–87. PubMed PMID: 12740394; eng. PubMed

Shpilka T, Weidberg H, Pietrokovski S, et al. Atg8: an autophagy-related ubiquitin-like protein family. Genome Biol. 2011. Jul 27;12(7):226. doi: 10.1186/gb-2011-12-7-226. PubMed PMID: 21867568; Eng. PubMed DOI PMC

Zois CE, Koukourakis MI.. Radiation-induced autophagy in normal and cancer cells: towards novel cytoprotection and radio-sensitization policies?. Autophagy. 2009. May;5(4):442–50. PubMed PMID: 19164950; eng. PubMed

Klionsky DJ. Location, location, location? No. Catalog number. Autophagy. 2009;5:441.

Xin Y, Yu L, Chen Z, et al. Cloning, expression patterns, and chromosome localization of three human and two mouse homologues of GABA(A) receptor-associated protein. Genomics. 2001. Jun 15;74(3):408–13. doi: 10.1006/geno.2001.6555. PubMed PMID: 11414770; eng. PubMed DOI

Novak I, Kirkin V, McEwan DG, et al. Nix is a selective autophagy receptor for mitochondrial clearance. EMBO Rep. 2010. Jan;11(1):45–51. doi:10.1038/embor.2009.256. PubMed PMID: 20010802; PubMed Central PMCID: PMC2816619. eng. PubMed DOI PMC

Schwarten M, Mohrluder J, Ma P, et al. Nix directly binds to GABARAP: a possible crosstalk between apoptosis and autophagy. Autophagy. 2009. Jul;5(5):690–8. PubMed PMID: 19363302. PubMed

Gassmann M, Grenacher B, Rohde B, et al. Quantifying Western blots: pitfalls of densitometry. Electrophoresis. 2009. Jun;30(11):1845–55. doi: 10.1002/elps.200800720. PubMed PMID: 19517440; eng. PubMed DOI

Agrotis A, Pengo N, Burden JJ, et al. Redundancy of human ATG4 protease isoforms in autophagy and LC3/GABARAP processing revealed in cells. Autophagy. 2019. Jun;15(6):976–997. doi: 10.1080/15548627.2019.1569925. PubMed PMID: 30661429; PubMed Central PMCID: PMCPMC6526816. PubMed DOI PMC

Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway. J Cell Biol. 2000. Oct 16;151(2):263–76. PubMed PMID: 11038174; PubMed Central PMCID: PMC2192639. eng. PubMed PMC

Chung T, Phillips AR, Vierstra RD.. ATG8 lipidation and ATG8-mediated autophagy in Arabidopsis require ATG12 expressed from the differentially controlled ATG12A AND ATG12B loci. Plant J. 2010. May;62(3):483–93. doi: 10.1111/j.1365-313X.2010.04166.x. PubMed PMID: 20136727; eng. PubMed DOI

Chung T, Suttangkakul A, Vierstra RD.. The ATG autophagic conjugation system in maize: ATG transcripts and abundance of the ATG8-lipid adduct are regulated by development and nutrient availability. Plant Physiol. 2009. Jan;149(1):220–34. doi:10.1104/pp.108.126714. PubMed PMID: 18790996; PubMed Central PMCID: PMC2613746. eng. PubMed DOI PMC

Wang W, Chen Z, Billiar TR, et al. The carboxyl-terminal amino acids render pro-human LC3B migration similar to lipidated LC3B in SDS-PAGE. PLoS One. 2013;8(9):e74222. doi: 10.1371/journal.pone.0074222. PubMed PMID: 24040206; PubMed Central PMCID: PMCPMC3769297. PubMed DOI PMC

Kovsan J, Bluher M, Tarnovscki T, et al. Altered autophagy in human adipose tissues in obesity. J Clin Endocrinol Metab. 2011. Feb;96(2):E268–77. doi: 10.1210/jc.2010-1681. PubMed PMID: 21047928; eng. PubMed DOI

Cherra SJ, III, Kulich SM, Uechi G, et al. Regulation of the autophagy protein LC3 by phosphorylation. J Cell Biol. 2010. Aug 23;190(4):533–9. doi: 10.1083/jcb.201002108. PubMed PMID: 20713600; PubMed Central PMCID: PMC2928022. eng. PubMed DOI PMC

Gao Z, Gammoh N, Wong PM, et al. Processing of autophagic protein LC3 by the 20S proteasome. Autophagy. 2010. Jan;6(1):126–37. PubMed PMID: 20061800. PubMed

Harris VM. Protein detection by Simple Western analysis. Methods Mol Biol. 2015;1312:465–8. doi: 10.1007/978-1-4939-2694-7_47. PubMed PMID: 26044028. PubMed DOI

Voeten RLC, Ventouri IK, Haselberg R, et al. Capillary Electrophoresis: Trends and Recent Advances. Anal Chem. 2018. Feb 6;90(3):1464–1481. doi: 10.1021/acs.analchem.8b00015. PubMed PMID: 29298038; PubMed Central PMCID: PMCPMC5994730. PubMed DOI PMC

Beekman C, Janson AA, Baghat A, et al. Use of capillary Western immunoassay (Wes) for quantification of dystrophin levels in skeletal muscle of healthy controls and individuals with Becker and Duchenne muscular dystrophy. PLoS One. 2018;13(4):e0195850. doi: 10.1371/journal.pone.0195850. PubMed PMID: 29641567; PubMed Central PMCID: PMCPMC5895072. PubMed DOI PMC

Pierzynowska K, Gaffke L, Cyske Z, et al. Genistein induces degradation of mutant huntingtin in fibroblasts from Huntington’s disease patients. Metab Brain Dis. 2019. Jun;34(3):715–720. doi: 10.1007/s11011-019-00405-4. PubMed PMID: 30850940; PubMed Central PMCID: PMCPMC6520327. PubMed DOI PMC

Saetre F, Hagen LK, Engedal N, et al. Novel steps in the autophagic-lysosomal pathway. FEBS J. 2015. Jun;282(11):2202–14. doi: 10.1111/febs.13268. PubMed PMID: 25779646. PubMed DOI

Degtyarev M, De Maziere A, Orr C, et al. Akt inhibition promotes autophagy and sensitizes PTEN-null tumors to lysosomotropic agents. J Cell Biol. 2008. Oct 6;183(1):101–16. doi: 10.1083/jcb.200801099. PubMed PMID: 18838554; PubMed Central PMCID: PMC2557046. eng. PubMed DOI PMC

Ju JS, Varadhachary AS, Miller SE, et al. Quantitation of “autophagic flux” in mature skeletal muscle. Autophagy. 2010. Oct;6(7):929–35. doi:10.4161/auto.6.7.12785. PubMed PMID: 20657169; PubMed Central PMCID: PMC3039739. eng. PubMed DOI PMC

Mauthe M, Orhon I, Rocchi C, et al. Chloroquine inhibits autophagic flux by decreasing autophagosome-lysosome fusion. Autophagy. 2018;14(8):1435–1455. doi: 10.1080/15548627.2018.1474314. PubMed PMID: 29940786; PubMed Central PMCID: PMCPMC6103682. PubMed DOI PMC

Mauvezin C, Nagy P, Juhasz G, et al. Autophagosome-lysosome fusion is independent of V-ATPase-mediated acidification. Nat Commun. 2015;6:7007. doi: 10.1038/ncomms8007. PubMed PMID: 25959678; PubMed Central PMCID: PMC4428688. PubMed DOI PMC

Xie R, Nguyen S, McKeehan WL, et al. Acetylated microtubules are required for fusion of auto-phagosomes with lysosomes. BMC Cell Biol. 2010;11:89. doi: 10.1186/1471-2121-11-89. PubMed PMID: 21092184; PubMed PMID: 21092184; PubMed Central PMCID: PMC2995476. eng PubMed DOI PMC

Morell C, Bort A, Vara-Ciruelos D, et al. Up-Regulated Expression of LAMP2 and Autophagy Activity during Neuroendocrine Differentiation of Prostate Cancer LNCaP Cells. PLoS One. 2016;11(9):e0162977. doi: 10.1371/journal.pone.0162977. PubMed PMID: 27627761; PubMed Central PMCID: PMCPMC5023108. PubMed DOI PMC

Gonzalez-Polo RA, Boya P, Pauleau AL, et al. The apoptosis/autophagy paradox: autophagic vacuolization before apoptotic death. J Cell Sci. 2005. Jul 15;118:3091–102. PubMed PMID: 15985464; eng. PubMed

Cuervo AM, Stefanis L, Fredenburg R, et al. Impaired degradation of mutant alpha-synuclein by chaperone-mediated autophagy. Science. 2004. Aug 27;305(5688):1292–5. doi:10.1126/science.1101738. PubMed PMID: 15333840; eng. PubMed DOI

Trincheri NF, Follo C, Nicotra G, et al. Resveratrol-induced apoptosis depends on the lipid kinase activity of Vps34 and on the formation of autophagolysosomes. Carcinogenesis. 2008. Feb;29(2):381–9. doi:10.1093/carcin/bgm271. PubMed PMID: 18048384; eng. PubMed DOI

Rubinsztein DC, Cuervo AM, Ravikumar B, et al. In search of an “autophagomometer” [Editorial]. Autophagy. 2009. Jul;5(5):585–9. PubMed PMID: 19411822; eng. PubMed

Sarkar S, Ravikumar B, Rubinsztein DC.. Autophagic clearance of aggregate-prone proteins associated with neurodegeneration. Methods Enzymol. 2009;453:83–110. doi:10.1016/S0076-6879(08)04005-6. PubMed PMID: 19216903; eng. PubMed DOI

Sarkar S, Korolchuk V, Renna M, et al. Methodological considerations for assessing autophagy modulators: a study with calcium phosphate precipitates. Autophagy. 2009. Apr;5(3):307–13. PubMed PMID: 19182529; eng. PubMed

du Toit A, Hofmeyr JS, Gniadek TJ, et al. Measuring autophagosome flux. Autophagy. 2018;14(6):1060–1071. doi:10.1080/15548627.2018.1469590. PubMed PMID: 29909716; PubMed Central PMCID: PMCPMC6103398. PubMed DOI PMC

Martins WK, Severino D, Souza C, et al. Rapid screening of potential autophagic inductor agents using mammalian cell lines. Biotechnol J. 2013. Jun;8(6):730–7. doi:10.1002/biot.201200306. PubMed PMID: 23420785. PubMed DOI

Martins WK, Costa ET, Cruz MC, et al. Parallel damage in mitochondrial and lysosomal compartments promotes efficient cell death with autophagy: The case of the pentacyclic triterpenoids. Sci Rep. 2015;5:12425. doi:10.1038/srep12425. PubMed PMID: 26213355. PubMed DOI PMC

Martins WK, Gomide AB, Costa ET, et al. Membrane damage by betulinic acid provides insights into cellular aging. Biochim Biophys Acta Gen Subj. 2017. Jan;1861(1 Pt A):3129–3143. doi:10.1016/j.bbagen.2016.10.018. PubMed PMID: 27773704. PubMed DOI

Martins WK, Santos NF, Rocha CS, et al. Parallel damage in mitochondria and lysosomes is an efficient way to photoinduce cell death. Autophagy. 2019. Feb;15(2):259–279. doi:10.1080/15548627.2018.1515609. PubMed PMID: 30176156; PubMed Central PMCID: PMCPMC6333451. PubMed DOI PMC

Tsubone TM, Martins WK, Pavani C, et al. Enhanced efficiency of cell death by lysosome-specific photodamage. Sci Rep. 2017. Jul 27;7(1):6734. doi:10.1038/s41598-017-06788-7. PubMed PMID: 28751688; PubMed Central PMCID: PMCPMC5532215. PubMed DOI PMC

Hakonarson H, Grant SF, Bradfield JP, et al. A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene. Nature. 2007. Aug 2;448(7153):591–4. doi:10.1038/nature06010. PubMed PMID: 17632545. PubMed DOI

Pandey R, Bakay M, Hain HS, et al. CLEC16A regulates splenocyte and NK cell function in part through MEK signaling. PLoS One. 2018;13(9):e0203952. doi:10.1371/journal.pone.0203952. PubMed PMID: 30226884; PubMed Central PMCID: PMCPMC6143231. PubMed DOI PMC

Pandey R, Bakay M, Hain HS, et al. The autoimmune disorder susceptibility gene CLEC16A restrains NK Cell function in YTS NK cell line and Clec16a knockout mice. Front Immunol. 2019;10:68. doi:10.3389/fimmu.2019.00068. PubMed PMID: 30774629; PubMed Central PMCID: PMCPMC6367972. PubMed DOI PMC

Martin-Maestro P, Gargini R, AS A, et al. Mitophagy failure in fibroblasts and iPSC-derived neurons of Alzheimer’s disease-associated presenilin 1 mutation. Front Mol Neurosci. 2017;10:291. doi:10.3389/fnmol.2017.00291. PubMed PMID: 28959184; PubMed Central PMCID: PMCPMC5603661. PubMed DOI PMC

Martin-Maestro P, Gargini R, Perry G, et al. PARK2 enhancement is able to compensate mitophagy alterations found in sporadic Alzheimer’s disease. Hum Mol Genet. 2016. Feb 15;25(4):792–806. doi:10.1093/hmg/ddv616. PubMed PMID: 26721933; PubMed Central PMCID: PMCPMC4743695. PubMed DOI PMC

Schmukler E, Wolfson E, Elazar Z, et al. Continuous treatment with FTS confers resistance to apoptosis and affects autophagy. PLoS One. 2017;12(2):e0171351. doi:10.1371/journal.pone.0171351. PubMed PMID: 28151959; PubMed Central PMCID: PMCPMC5289601. PubMed DOI PMC

Shintani T, Klionsky DJ.. Cargo proteins facilitate the formation of transport vesicles in the cytoplasm to vacuole targeting pathway. J Biol Chem. 2004. Jul 16;279(29):29889–94. PubMed PMID: 15138258; eng. PubMed PMC

Barmada SJ, Serio A, Arjun A, et al. Autophagy induction enhances TDP43 turnover and survival in neuronal ALS models. Nat Chem Biol. 2014. Aug;10(8):677–85. doi:10.1038/nchembio.1563. PubMed PMID: 24974230; PubMed Central PMCID: PMCPMC4106236. PubMed DOI PMC

Tsvetkov AS, Arrasate M, Barmada S, et al. Proteostasis of polyglutamine varies among neurons and predicts neurodegeneration. Nat Chem Biol. 2013. Sep;9(9):586–92. doi:10.1038/nchembio.1308. PubMed PMID: 23873212; PubMed Central PMCID: PMC3900497. PubMed DOI PMC

Loos B, du Toit A, Hofmeyr JH. Defining and measuring autophagosome flux-concept and reality. Autophagy. 2014. Oct 30;10:2087–96. doi:10.4161/15548627.2014.973338. PubMed PMID: 25484088. PubMed DOI PMC

Khuansuwan S, Barnhill LM, Cheng S, et al. A novel transgenic zebrafish line allows for in vivo quantification of autophagic activity in neurons. Autophagy. 2019. Aug;15(8):1322–1332. doi:10.1080/15548627.2019.1580511. PubMed PMID: 30755067; PubMed Central PMCID: PMCPMC6613892. PubMed DOI PMC

du Toit A, De Wet S, Hofmeyr JS, et al. The precision control of autophagic flux and vesicle dynamics-a micropattern approach. Cells. 2018. Aug 3;7(8). doi:10.3390/cells7080094. PubMed PMID: 30081508; PubMed Central PMCID: PMCPMC6116198. PubMed DOI PMC

Farkas T, Hoyer-Hansen M, Jaattela M.. Identification of novel autophagy regulators by a luciferase-based assay for the kinetics of autophagic flux. Autophagy. 2009. Oct;5(7):1018–25. PubMed PMID: 19652534; eng. PubMed

Farkas T, Daugaard M, Jaattela M.. Identification of small molecule inhibitors of phosphatidylinositol 3-kinase and autophagy. J Biol Chem. 2011. Sep 19;286:38904–12. doi:10.1074/jbc.M111.269134. PubMed PMID: 21930714; Eng. PubMed DOI PMC

Frankel LB, Di Malta C, Wen J, et al. A non-conserved miRNA regulates lysosomal function and impacts on a human lysosomal storage disorder. Nat Commun. 2014;5:5840. doi:10.1038/ncomms6840. PubMed PMID: 25524633. PubMed DOI

Frankel LB, Lund AH.. MicroRNA regulation of autophagy. Carcinogenesis. 2012. Nov;33(11):2018–25. doi:10.1093/carcin/bgs266. PubMed PMID: 22902544. PubMed DOI

Frankel LB, Wen J, Lees M, et al. microRNA-101 is a potent inhibitor of autophagy. EMBO J. 2011. Sep 13:4628–41. doi:10.1038/emboj.2011.331. PubMed PMID: 21915098; Eng. PubMed DOI PMC

Nguyen HT, Dalmasso G, Muller S, et al. Crohn’s disease-associated adherent invasive Escherichia coli modulate levels of microRNAs in intestinal epithelial cells to reduce autophagy. Gastroenterology. 2014. Feb;146(2):508–19. doi:10.1053/j.gastro.2013.10.021. PubMed PMID: 24148619. PubMed DOI

Szyniarowski P, Corcelle-Termeau E, Farkas T, et al. A comprehensive siRNA screen for kinases that suppress macroautophagy in optimal growth conditions. Autophagy. 2011. Aug 1;7(8):892–903. PubMed PMID: 21508686; eng. PubMed

Yeganeh B, Ghavami S, Kroeker AL, et al. Suppression of influenza A virus replication in human lung epithelial cells by noncytotoxic concentrations bafilomycin A1. Am J Physiol Lung Cell Mol Physiol. 2015. Feb 1;308(3):L270–86. doi:10.1152/ajplung.00011.2014. PubMed PMID: 25361566; PubMed Central PMCID: PMCPMC4338931. PubMed DOI PMC

Iwata J, Ezaki J, Komatsu M, et al. Excess peroxisomes are degraded by autophagic machinery in mammals. J Biol Chem. 2006. Feb17;281(7):4035–41. PubMed PMID: 16332691. PubMed

Narendra D, Tanaka A, Suen DF, et al. Parkin is recruited selectively to impaired mitochondria and promotes their autophagy. J Cell Biol. 2008. Dec 1;183(5):795–803. doi:10.1083/jcb.200809125. PubMed PMID: 19029340; PubMed Central PMCID: PMC2592826. eng. PubMed DOI PMC

Nogalska A, Terracciano C, D’Agostino C, et al. p62/SQSTM1 is overexpressed and prominently accumulated in inclusions of sporadic inclusion-body myositis muscle fibers, and can help differentiating it from polymyositis and dermatomyositis. Acta Neuropathol. 2009. Sep;118(3):407–13. doi:10.1007/s00401-009-0564-6. PubMed PMID: 19557423; eng. PubMed DOI

Ivanova S, Repnik U, Bojic L, et al. Lysosomes in apoptosis. Methods Enzymol. 2008;442:183–99. doi:10.1016/S0076-6879(08)01409-2. PubMed PMID: 18662570. PubMed DOI

Chahory S, Keller N, Martin E, et al. Light induced retinal degeneration activates a caspase-independent pathway involving cathepsin D. Neurochem Int. 2010. Oct;57(3):278–87. doi:10.1016/j.neuint.2010.06.006. PubMed PMID: 20558223. PubMed DOI

Padron-Barthe L, Courta J, Lepretre C, et al. Leukocyte Elastase Inhibitor, the precursor of L-DNase II, inhibits apoptosis by interfering with caspase-8 activation. Biochim Biophys Acta. 2008. Oct;1783(10):1755–66. doi:10.1016/j.bbamcr.2008.06.018. PubMed PMID: 18674571. PubMed DOI

Kimura S, Noda T, Yoshimori T.. Dissection of the autophagosome maturation process by a novel reporter protein, tandem fluorescent-tagged LC3. Autophagy. 2007. Sep 21;3(5):452–460. PubMed PMID: 17534139; Eng. PubMed

Gutierrez MG, Saka HA, Chinen I, et al. Protective role of autophagy against Vibrio cholerae cytolysin, a pore-forming toxin from V. cholerae. Proc Natl Acad Sci USA 2007. Feb 6;104(6):1829–34. PubMed PMID: 17267617; eng PubMed PMC

Hosokawa N, Hara Y, Mizushima N.. Generation of cell lines with tetracycline-regulated autophagy and a role for autophagy in controlling cell size. FEBS Lett. 2006. May 15;580(11):2623–9. PubMed PMID: 16647067; eng. PubMed

Guedes A, Ludovico P, Sampaio-Marques B.. Caloric restriction alleviates alpha-synuclein toxicity in aged yeast cells by controlling the opposite roles of Tor1 and Sir2 on autophagy. Mech Ageing Dev. 2017. Jan;161(Pt B):270–276. doi:10.1016/j.mad.2016.04.006. PubMed PMID: 27109470. PubMed DOI

Pinar M, Pantazopoulou A, Peñalva MA.. Live-cell imaging of Aspergillus nidulans autophagy: RAB1 dependence, Golgi independence and ER involvement. Autophagy. 2013. Jul;9(7):1024–43. doi:10.4161/auto.24483. PubMed PMID: 23722157; PubMed Central PMCID: PMC3722313. PubMed DOI PMC

Sampaio-Marques B, Guedes A, Vasilevskiy I, et al. alpha-Synuclein toxicity in yeast and human cells is caused by cell cycle re-entry and autophagy degradation of ribonucleotide reductase 1. Aging cell. 2019. Aug;18(4):e12922. doi:10.1111/acel.12922. PubMed PMID: 30977294; PubMed Central PMCID: PMCPMC6612645. PubMed DOI PMC

Suttangkakul A, Li F, Chung T, et al. The ATG1/13 protein kinase complex is both a regulator and a substrate of autophagic recycling in Arabidopsis. Plant Cell. 2011;23:3761–3779. PubMed PMC

Ni HM, Bockus A, Wozniak AL, et al. Dissecting the dynamic turnover of GFP-LC3 in the autolysosome. Autophagy. 2011. Feb;7(2):188–204. PubMed PMID: 21107021; PubMed Central PMCID: PMC3039769. eng. PubMed PMC

Balgi AD, Fonseca BD, Donohue E, et al. Screen for chemical modulators of autophagy reveals novel therapeutic inhibitors of mTORC1 signaling. PLoS One. 2009;4(9):e7124. doi:10.1371/journal.pone.0007124. PubMed PMID: 19771169; PubMed Central PMCID: PMC2742736. eng. PubMed DOI PMC

Patterson GH, Lippincott-Schwartz J.. Selective photolabeling of proteins using photoactivatable GFP. Methods. 2004. Apr;32(4):445–50. PubMed PMID: 15003607; eng. PubMed

Hamacher-Brady A, Brady NR, Gottlieb RA.. Enhancing macroautophagy protects against ischemia/reperfusion injury in cardiac myocytes. J Biol Chem. 2006. Oct 6;281(40):29776–87. PubMed PMID: 16882669; eng. PubMed

Klionsky DJ. Monitoring autophagy in yeast: the Pho8∆60 assay. Methods Mol Biol. 2007;390:363–71. PubMed PMID: 17951700; eng. PubMed

Noda T, Klionsky DJ.. The quantitative Pho8∆60 assay of nonspecific autophagy. Methods Enzymol. 2008;451:33–42. doi:10.1016/S0076-6879(08)03203-5. PubMed PMID: 19185711; eng. PubMed DOI

Dauphinee AN, Cardoso C, Dalman K, et al. Chemical screening pipeline for identification of specific plant autophagy modulators. Plant Physiol. 2019. Nov;181(3):855–866. doi:10.1104/pp.19.00647. PubMed PMID: 31488572; PubMed Central PMCID: PMCPMC6836817. PubMed DOI PMC

Shvets E, Elazar Z.. Autophagy-independent incorporation of GFP-LC3 into protein aggregates is dependent on its interaction with p62/SQSTM1. Autophagy. 2008. Nov;4(8):1054–6. doi:10.4161/auto.6823. PubMed PMID: 18776740. PubMed DOI

Viiri J, Amadio M, Marchesi N, et al. Autophagy activation clears ELAVL1/HuR-mediated accumulation of SQSTM1/p62 during proteasomal inhibition in human retinal pigment epithelial cells. PLoS One. 2013;8(7):e69563. doi:10.1371/journal.pone.0069563. PubMed PMID: 23922739; PubMed Central PMCID: PMCPMC3726683. PubMed DOI PMC

Takahashi Y, He H, Tang Z, et al. An autophagy assay reveals the ESCRT-III component CHMP2A as a regulator of phagophore closure. Nat Commun. 2018. Jul 20;9(1):2855. doi:10.1038/s41467-018-05254-w. PubMed PMID: 30030437; PubMed Central PMCID: PMCPMC6054611. PubMed DOI PMC

Los GV, Encell LP, McDougall MG, et al. HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem Biol. 2008. Jun 20;3(6):373–82. doi:10.1021/cb800025k. PubMed PMID: 18533659. PubMed DOI

Takahashi Y, Liang X, Hattori T, et al. VPS37A directs ESCRT recruitment for phagophore closure. J Cell Biol. 2019. Oct 7;218(10):3336–3354. doi:10.1083/jcb.201902170. PubMed PMID: 31519728; PubMed Central PMCID: PMCPMC6781443. PubMed DOI PMC

Divakaruni AS, Wiley SE, Rogers GW, et al. Thiazolidinediones are acute, specific inhibitors of the mitochondrial pyruvate carrier. Proc Natl Acad Sci U S A. 2013. Apr 2;110(14):5422–7. doi: 10.1073/pnas.1303360110. PubMed PMID: 23513224; PubMed Central PMCID: PMCPMC3619368. PubMed DOI PMC

Badr CE, Wurdinger T, Nilsson J, et al. Lanatoside C sensitizes glioblastoma cells to tumor necrosis factor-related apoptosis-inducing ligand and induces an alternative cell death pathway. Neuro Oncol. 2011. Nov;13(11):1213–24. doi: 10.1093/neuonc/nor067. PubMed PMID: 21757445; PubMed Central PMCID: PMC3199161. eng. PubMed DOI PMC

Kabeya Y, Mizushima N, Ueno T, et al. LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. EMBO J. 2000. Nov 1;19(21):5720–8. PubMed PMID: 11060023; eng. PubMed PMC

Sampaio-Marques B, Felgueiras C, Silva A, et al. SNCA (alpha-synuclein)-induced toxicity in yeast cells is dependent on sirtuin 2 (Sir2)-mediated mitophagy. Autophagy. 2012. Oct;8(10):1494–509. doi: 10.4161/auto.21275. PubMed PMID: 22914317. PubMed DOI

Meléndez A, Tallóczy Z, Seaman M, et al. Autophagy genes are essential for dauer development and life-span extension in C. elegans. Science. 2003. Sep 5;301(5638):1387–91. PubMed PMID: 12958363; eng. PubMed

Otto GP, Wu MY, Kazgan N, et al. Macroautophagy is required for multicellular development of the social amoeba Dictyostelium discoideum. J Biol Chem 2003. May 16;278(20):17636–45. PubMed PMID: 12626495; eng. PubMed

Kikuma T, Ohneda M, Arioka M, et al. Functional analysis of the ATG8 homologue Aoatg8 and role of autophagy in differentiation and germination in Aspergillus oryzae. Eukaryot Cell. 2006. Aug;5(8):1328–36. doi:10.1128/EC.00024-06. PubMed PMID: 16896216; PubMed Central PMCID: PMC1539149. eng. PubMed DOI PMC

Liu XH, Liu TB, Lin FC.. Monitoring autophagy in Magnaporthe oryzae. Methods Enzymol. 2008;451:271–94. doi:10.1016/S0076-6879(08)03219-9. PubMed PMID: 19185727; eng. PubMed DOI

Nolting N, Bernhards Y, Poggeler S.. SmATG7 is required for viability in the homothallic ascomycete Sordaria macrospora. Fungal Genet biol FG & B. 2009. Aug;46(8):531–42. doi:10.1016/j.fgb.2009.03.008. PubMed PMID: 19351563; eng. PubMed DOI

Pinan-Lucarre B, Paoletti M, Dementhon K, et al. Autophagy is induced during cell death by incompatibility and is essential for differentiation in the filamentous fungus Podospora anserina. Mol Microbiol. 2003. Jan;47(2):321–33. PubMed PMID: 12519185; eng. PubMed

Veneault-Fourrey C, Barooah M, Egan M, et al. Autophagic fungal cell death is necessary for infection by the rice blast fungus. Science. 2006. Apr 28;312(5773):580–3. doi:10.1126/science.1124550. PubMed PMID: 16645096; eng. PubMed DOI

Baghdiguian S, Martinand-Mari C, Mangeat P.. Using Ciona to study developmental programmed cell death. Semin Cancer Biol. 2007. Apr;17(2):147–53. doi:10.1016/j.semcancer.2006.11.005. PubMed PMID: 17197195; eng. PubMed DOI

Denton D, Shravage B, Simin R, et al. Autophagy, not apoptosis, is essential for midgut cell death in Drosophila. Curr Biol. 2009. Nov 3;19(20):1741–6. doi:10.1016/j.cub.2009.08.042. PubMed PMID: 19818615; PubMed Central PMCID: PMC2783269. eng. PubMed DOI PMC

Rusten TE, Lindmo K, Juhasz G, et al. Programmed autophagy in the Drosophila fat body is induced by ecdysone through regulation of the PI3K pathway. Dev Cell. 2004. Aug;7(2):179–92. PubMed PMID: 15296715; eng. PubMed

Scott RC, Schuldiner O, Neufeld TP.. Role and regulation of starvation-induced autophagy in the Drosophila fat body. Dev Cell. 2004. Aug;7(2):167–78. PubMed PMID: 15296714; eng. PubMed

Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy. Plant Cell. 2004. Nov;16(11):2967–83. PubMed PMID: 15494556; eng. PubMed PMC

Li F, Chung T, Pennington JG, et al. Autophagic recycling plays a central role in maize nitrogen remobilization. Plant Cell. 2015. May;27(5):1389–408. doi:10.1105/tpc.15.00158. PubMed PMID: 25944100; PubMed Central PMCID: PMC4456646. PubMed DOI PMC

Brennand A, Rico E, Rigden DJ, et al. ATG24 represses autophagy and differentiation and is essential for homeostasy of the flagellar pocket in trypanosoma brucei. PLoS One. 2015;10(6):e0130365. doi:10.1371/journal.pone.0130365. PubMed PMID: 26090847; PubMed Central PMCID: PMC4474607. PubMed DOI PMC

Li FJ, Shen Q, Wang C, et al. A role of autophagy in Trypanosoma brucei cell death. Cell Microbiol. 2012. Aug;14(8):1242–56. doi:10.1111/j.1462-5822.2012.01795.x. PubMed PMID: 22463696. PubMed DOI

Schmidt RS, Butikofer P.. Autophagy in Trypanosoma brucei: amino acid requirement and regulation during different growth phases. PLoS One. 2014;9(4):e93875. doi:10.1371/journal.pone.0093875. PubMed PMID: 24699810; PubMed Central PMCID: PMC3974859. PubMed DOI PMC

Besteiro S, Williams RA, Morrison LS, et al. Endosome sorting and autophagy are essential for differentiation and virulence of Leishmania major. J Biol Chem. 2006. Apr 21;281(16):11384–96. doi:10.1074/jbc.M512307200. PubMed PMID: 16497676; eng. PubMed DOI

Williams RA, Tetley L, Mottram JC, et al. Cysteine peptidases CPA and CPB are vital for autophagy and differentiation in Leishmania mexicana. Mol Microbiol. 2006. Aug;61(3):655–74. doi:10.1111/j.1365-2958.2006.05274.x. PubMed PMID: 16803590; eng. PubMed DOI

Williams RA, Woods KL, Juliano L, et al. Characterization of unusual families of ATG8-like proteins and ATG12 in the protozoan parasite Leishmania major. Autophagy. 2009. Feb;5(2):159–72. PubMed PMID: 19066473; PubMed Central PMCID: PMC2642932. eng. PubMed PMC

Alvarez VE, Kosec G, Sant’Anna C, et al. Autophagy is involved in nutritional stress response and differentiation in Trypanosoma cruzi. J Biol Chem. 2008. Feb 8;283(6):3454–64. doi:10.1074/jbc.M708474200. PubMed PMID: 18039653; eng. PubMed DOI

Schoijet AC, Sternlieb T, Alonso GD.. The Phosphatidylinositol 3-kinase Class III Complex Containing TcVps15 and TcVps34 Participates in Autophagy in Trypanosoma cruzi. J Eukaryot Microbiol. 2017. May;64(3):308–321. doi: 10.1111/jeu.12367. PubMed PMID: 27603757. PubMed DOI

He C, Bartholomew CR, Zhou W, et al. Assaying autophagic activity in transgenic GFP-Lc3 and GFP-Gabarap zebrafish embryos. Autophagy. 2009. May;5(4):520–6. PubMed PMID: 19221467; PubMed Central PMCID: PMC2754832. eng. PubMed PMC

Banerjee M, Huang Y, Ouseph MM, et al. Autophagy in platelets. Methods Mol Biol. 2019;1880:511–528. doi:10.1007/978-1-4939-8873-0_32. PubMed PMID: 30610718. PubMed DOI PMC

Ouseph MM, Huang Y, Banerjee M, et al. Autophagy is induced upon platelet activation and is essential for hemostasis and thrombosis. Blood. 2015. Sep 3;126(10):1224–33. doi:10.1182/blood-2014-09-598722. PubMed PMID: 26209658; PubMed Central PMCID: PMCPMC4559933. PubMed DOI PMC

Elsasser A, Vogt AM, Nef H, et al. Human hibernating myocardium is jeopardized by apoptotic and autophagic cell death. J Am Coll Cardiol. 2004. Jun 16;43(12):2191–9. PubMed PMID: 15193679; eng. PubMed

Knaapen MW, Davies MJ, De Bie M, et al. Apoptotic versus autophagic cell death in heart failure. Cardiovasc Res. 2001. Aug 1;51(2):304–12. PubMed PMID: 11470470; eng. PubMed

Koike M, Shibata M, Waguri S, et al. Participation of autophagy in storage of lysosomes in neurons from mouse models of neuronal ceroid-lipofuscinoses (Batten disease). Am J Pathol. 2005. Dec;167(6):1713–28. PubMed PMID: 16314482; eng. PubMed PMC

Kostin S, Pool L, Elsasser A, et al. Myocytes die by multiple mechanisms in failing human hearts. Circ Res. 2003. Apr 18;92(7):715–24. PubMed PMID: 12649263; eng. PubMed

Motori E, Puyal J, Toni N, et al. Inflammation-induced alteration of astrocyte mitochondrial dynamics requires autophagy for mitochondrial network maintenance. Cell Metab. 2013. Dec 3;18(6):844–59. doi: 10.1016/j.cmet.2013.11.005. PubMed PMID: 24315370. PubMed DOI

Ost A, Svensson K, Ruishalme I, et al. Attenuated mTOR signaling and enhanced autophagy in adipocytes from obese patients with type 2 diabetes. Mol Med. 2010. Jul-Aug;16(7–8):235–46. doi:10.2119/molmed.2010.00023. PubMed PMID: 20386866; PubMed Central PMCID: PMC2896460. PubMed DOI PMC

Perez-Perez ME, Florencio FJ, Crespo JL.. Inhibition of target of rapamycin signaling and stress activate autophagy in Chlamydomonas reinhardtii. Plant Physiol. 2010. Apr;152(4):1874–88. doi: 10.1104/pp.109.152520. PubMed PMID: 20107021; PubMed Central PMCID: PMC2850011. eng. PubMed DOI PMC

Tang D, Kang R, Livesey KM, et al. Endogenous HMGB1 regulates autophagy. J Cell Biol. 2010. Sep 6;190(5):881–92. doi:10.1083/jcb.200911078. PubMed PMID: 20819940; PubMed Central PMCID: PMC2935581. eng. PubMed DOI PMC

Decuypere J-P, Welkenhuyzen K, Luyten Y, et al.IP3 receptor-mediated Ca2+ signaling and autophagy induction are interrelated. Autophagy. 2011;7:1472–1489. PubMed PMC

Gniadek TJ, Warren G.. WatershedCounting3D: a new method for segmenting and counting punctate structures from confocal image data. Traffic. 2007. Apr;8(4):339–46. doi:10.1111/j.1600-0854.2007.00538.x. PubMed PMID: 17319897; eng. PubMed DOI

Anwar T, Liu X, Suntio T, et al. ER-targeted beclin 1 supports autophagosome biogenesis in the absence of ULK1 and ULK2 Kinases. Cells. 2019. May 17;8(5). doi:10.3390/cells8050475. PubMed PMID: 31108943; PubMed Central PMCID: PMCPMC6562811. PubMed DOI PMC

Jackson W, Yamada M, Moninger T, et al. Visualization and quantitation of abundant macroautophagy in virus-infected cells by confocal three-dimensional fluorescence imaging. J Virol Methods. 2013. Oct;193(1):244–50. doi:10.1016/j.jviromet.2013.06.018. PubMed PMID: 23792686; PubMed Central PMCID: PMCPMC3735810. PubMed DOI PMC

Lamb CA, Joachim J, Tooze SA.. Quantifying autophagic structures in mammalian cells using confocal microscopy. Methods Enzymol. 2017;587:21–42. doi:10.1016/bs.mie.2016.09.051. PubMed PMID: 28253957. PubMed DOI

Xu Y, Yuan J, Lipinski MM.. Live imaging and single-cell analysis reveal differential dynamics of autophagy and apoptosis. Autophagy. 2013. Sep;9(9):1418–30. doi:10.4161/auto.25080. PubMed PMID: 23748697; PubMed Central PMCID: PMC4026027. PubMed DOI PMC

Wu Z, Zhao J, Qiu M, et al. CRISPR/Cas9 mediated GFP knock-in at the MAP1LC3B locus in 293FT cells is better for bona fide monitoring cellular autophagy. Biotechnol J. 2018. Nov;13(11):e1700674. doi:10.1002/biot.201700674. PubMed PMID: 29673078. PubMed DOI

Kamentsky L, Jones TR, Fraser A, et al. Improved structure, function and compatibility for cellprofiler: modular high-throughput image analysis software. Bioinformatics. 2011. Apr 15;27(8):1179–80. doi:10.1093/bioinformatics/btr095. PubMed PMID: 21349861; PubMed Central PMCID: PMC3072555. eng. PubMed DOI PMC

Wu JQ, Pollard TD.. Counting cytokinesis proteins globally and locally in fission yeast. Science. 2005. Oct 14;310(5746):310–4. PubMed PMID: 16224022; eng. PubMed

Geng J, Baba M, Nair U, et al. Quantitative analysis of autophagy-related protein stoichiometry by fluorescence microscopy. J Cell Biol. 2008. Jul 14;182(1):129–40. doi:10.1083/jcb.200711112. PubMed PMID: 18625846; PubMed Central PMCID: PMC2447896. eng. PubMed DOI PMC

Brady NR, Hamacher-Brady A, Yuan H, et al. The autophagic response to nutrient deprivation in the HL-1 cardiac myocyte is modulated by Bcl-2 and sarco/endoplasmic reticulum calcium stores. FEBS J. 2007. Jun;274(12):3184–97. PubMed PMID: 17540004; eng. PubMed

Qadir MA, Kwok B, Dragowska WH, et al. Macroautophagy inhibition sensitizes tamoxifen-resistant breast cancer cells and enhances mitochondrial depolarization. Breast Cancer Res Treat. 2008. Dec;112(3):389–403. doi:10.1007/s10549-007-9873-4. PubMed PMID: 18172760; eng. PubMed DOI

Furuya T, Kim M, Lipinski M, et al. Negative regulation of Vps34 by Cdk mediated phosphorylation. Mol Cell. 2010. May 28;38(4):500–11. doi:10.1016/j.molcel.2010.05.009. PubMed PMID: 20513426; PubMed Central PMCID: PMC2888511. PubMed DOI PMC

Dolloff NG, Ma X, Dicker DT, et al. Spectral imaging-based methods for quantifying autophagy and apoptosis. Cancer Biol Ther. 2011. Aug 15;12(4):349–56. PubMed PMID: 21757995; eng. PubMed PMC

Mastorci K, Montico B, Fae DA, et al. Phospholipid scramblase 1 as a critical node at the crossroad between autophagy and apoptosis in mantle cell lymphoma. Oncotarget. 2016. Jul 5;7(27):41913–41928. doi:10.18632/oncotarget.9630. PubMed PMID: 27248824; PubMed Central PMCID: PMCPMC5173105. PubMed DOI PMC

Lee HK, Lund JM, Ramanathan B, et al. Autophagy-dependent viral recognition by plasmacytoid dendritic cells. Science. 2007. Mar 9;315(5817):1398–401. PubMed PMID: 17272685; eng. PubMed

Phadwal K, Alegre-Abarrategui J, Watson AS, et al. A novel method for autophagy detection in primary cells: Impaired levels of macroautophagy in immunosenescent T cells. Autophagy. 2012;8:677–89. PubMed PMC

Davey HM, Hexley P.. Red but not dead? Membranes of stressed Saccharomyces cerevisiae are permeable to propidium iodide. Environ Microbiol. 2011. Jan;13(1):163–71. doi:10.1111/j.1462-2920.2010.02317.x. PubMed PMID: 21199254. PubMed DOI

Kuma A, Matsui M, Mizushima N.. LC3, an autophagosome marker, can be incorporated into protein aggregates independent of autophagy: caution in the interpretation of LC3 localization. Autophagy. 2007. Jul;3(4):323–328. PubMed PMID: 17387262; Eng. PubMed

Szeto J, Kaniuk NA, Canadien V, et al. ALIS are stress-induced protein storage compartments for substrates of the proteasome and autophagy. Autophagy. 2006. Jul-Sep;2(3):189–99. PubMed PMID: 16874109; eng. PubMed

Fujita K, Maeda D, Xiao Q, et al. Nrf2-mediated induction of p62 controls Toll-like receptor-4-driven aggresome-like induced structure formation and autophagic degradation. Proc Natl Acad Sci U S A. 2011. Jan 25;108(4):1427–32. doi:10.1073/pnas.1014156108. PubMed PMID: 21220332; PubMed Central PMCID: PMC3029726. eng. PubMed DOI PMC

Kaniuk NA, Kiraly M, Bates H, et al. Ubiquitinated-protein aggregates form in pancreatic [beta]-cells during diabetes-induced oxidative stress and are regulated by autophagy. Diabetes. 2007. Apr;56(4):930–9. PubMed PMID: 17395740; eng. PubMed

Pierre P. Dendritic cells, DRiPs, and DALIS in the control of antigen processing. Immunol Rev. 2005. Oct;207:184–90. PubMed PMID: 16181336; eng. PubMed

Calvo-Garrido J, Escalante R.. Autophagy dysfunction and ubiquitin-positive protein aggregates in Dictyostelium cells lacking Vmp1. Autophagy. 2010. Jan;6(1):100–9. PubMed PMID: 20009561; eng. PubMed

Pankiv S, Høyvarde Clausen T, Lamark T, et al. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J Biol Chem. 2007. Jun 19;282:24131–24145. PubMed PMID: 17580304; Eng. PubMed

Hara T, Nakamura K, Matsui M, et al. Suppression of basal autophagy in neural cells causes neurodegenerative disease in mice. Nature. 2006. Jun15;441(7095):885–9. PubMed PMID: 16625204. PubMed

Komatsu M, Waguri S, Chiba T, et al.Loss of autophagy in the central nervous system causes neurodegeneration in mice. Nature. 2006. Jun15;441(7095):880–4. PubMed PMID: 16625205. PubMed

Bjorkoy G, Lamark T, Johansen T.. p62/SQSTM1: a missing link between protein aggregates and the autophagy machinery. Autophagy. 2006. Apr-Jun;2(2):138–9. PubMed PMID: 16874037; eng. PubMed

Matsumoto G, Wada K, Okuno M, et al. Serine 403 phosphorylation of p62/SQSTM1 regulates selective autophagic clearance of ubiquitinated proteins. Mol Cell. 2011. Oct 21;44(2):279–89. doi:10.1016/j.molcel.2011.07.039. PubMed PMID: 22017874; eng. PubMed DOI

Lerner C, Bitto A, Pulliam D, et al. Reduced mammalian target of rapamycin activity facilitates mitochondrial retrograde signaling and increases life span in normal human fibroblasts. Aging cell. 2013. Dec;12(6):966–77. doi:10.1111/acel.12122. PubMed PMID: 23795962. PubMed DOI PMC

Napoli E, Liu S, Marsilio I, et al. Lipid-based DNA/siRNA transfection agents disrupt neuronal bioenergetics and mitophagy. Biochem J. 2017. Nov 10;474(23):3887–3902. doi:10.1042/BCJ20170632. PubMed PMID: 29025974. PubMed DOI

Zahedi-Amiri A, Sequiera GL, Dhingra S, et al. Influenza a virus-triggered autophagy decreases the pluripotency of human-induced pluripotent stem cells. Cell Death Dis. 2019. Apr 18;10(5):337. doi:10.1038/s41419-019-1567-4. PubMed PMID: 31000695; PubMed Central PMCID: PMCPMC6472374. PubMed DOI PMC

Sher AA, Glover KKM, Coombs KM.. Zika Virus Infection Disrupts Astrocytic Proteins Involved in Synapse Control and Axon Guidance. Front Microbiol. 2019;10:596. doi:10.3389/fmicb.2019.00596. PubMed PMID: 30984137; PubMed Central PMCID: PMCPMC6448030. PubMed DOI PMC

Köchl R, Hu XW, Chan EYW, et al. Microtubules facilitate autophagosome formation and fusion of auto-phagosomes with endosomes. Traffic. 2006. Feb;7(2):129–45. PubMed PMID: 16420522; eng. PubMed

Eng KE, Panas MD, Karlsson Hedestam GB, et al. A novel quantitative flow cytometry-based assay for autophagy. Autophagy. 2010. Jul 19;6(5):634–41. PubMed PMID: 20458170; Eng. PubMed

Ciechomska IA, Tolkovsky AM.. Non-autophagic GFP-LC3 puncta induced by saponin and other detergents. Autophagy. 2007;3:586–590. PubMed

Seglen PO, Gordon PB.. 3-Methyladenine: specific inhibitor of autophagic/lysosomal protein degradation in isolated rat hepatocytes. Proc Natl Acad Sci U S A. 1982. Mar;79(6):1889–92. PubMed PMID: 6952238. PubMed PMC

Dembitz V, Lalic H, Visnjic D.. 5-Aminoimidazole-4-carboxamide ribonucleoside-induced autophagy flux during differentiation of monocytic leukemia cells. Cell Death Discov. 2017;3:17066. doi:10.1038/cddiscovery.2017.66. PubMed PMID: 28975042; PubMed Central PMCID:PMCPMC5624282. PubMed DOI PMC

Wu YT, Tan HL, Shui G, et al. Dual role of 3-methyladenine in modulation of autophagy via different temporal patterns of inhibition on class I and III phosphoinositide 3-kinase. J Biol Chem. 2010. Apr 2;285(14):10850–61. doi:10.1074/jbc.M109.080796. PubMed PMID: 20123989; PubMed Central PMCID: PMC2856291. eng. PubMed DOI PMC

Guimar[a]es CA, Benchimol M, Amarante-Mendes GP, et al. Alternative programs of cell death in developing retinal tissue. J Biol Chem. 2003. Oct 24;278(43):41938–46. doi:10.1074/jbc.M306547200. PubMed PMID: 12917395; eng. PubMed DOI

Bampton ET, Goemans CG, Niranjan D, et al. The dynamics of autophagy visualized in live cells: from autophagosome formation to fusion with endo/lysosomes. Autophagy. 2005. Apr;1(1):23–36. PubMed PMID: 16874023; eng. PubMed

Lee HK, Mattei LM, Steinberg BE, et al. In vivo requirement for Atg5 in antigen presentation by dendritic cells. Immunity. 2010. Feb 26;32(2):227–39. doi:10.1016/j.immuni.2009.12.006. PubMed PMID: 20171125; PubMed Central PMCID: PMC2996467. eng. PubMed DOI PMC

Tormo D, Checinska A, Alonso-Curbelo D, et al. Targeted activation of innate immunity for therapeutic induction of autophagy and apoptosis in melanoma cells. Cancer cell. 2009. Aug 4;16(2):103–14. doi:10.1016/j.ccr.2009.07.004. PubMed PMID: 19647221; PubMed Central PMCID: PMC2851205. eng. PubMed DOI PMC

Tamura N, Oku M, Sakai Y.. Atg8 regulates vacuolar membrane dynamics in a lipidation-independent manner in Pichia pastoris. J Cell Sci. 2010. Dec 1;123(Pt 23):4107–16. doi:10.1242/jcs.070045. PubMed PMID: 21045113; eng. PubMed DOI

Stromhaug PE, Reggiori F, Guan J, et al. Atg21 is a phosphoinositide binding protein required for efficient lipidation and localization of Atg8 during uptake of aminopeptidase I by selective autophagy. Mol Biol Cell. 2004. Aug;15(8):3553–66. PubMed PMID: 15155809; eng. PubMed PMC

Zhang J, Nadtochiy SM, Urciuoli WR, et al. The cardioprotective compound cloxyquin uncouples mitochondria and induces autophagy. Am J Physiol Heart Circ Physiol. 2016. Jan 1;310(1):H29–38. doi:10.1152/ajpheart.00926.2014. PubMed PMID: 26519034; PubMed Central PMCID: PMCPMC4796459. PubMed DOI PMC

Mareninova OA, Jia W, Gretler SR, et al. Transgenic expression of GFP-LC3 perturbs autophagy in exocrine pancreas and acute pancreatitis responses in mice. Autophagy. 2020. Jan 16:1–14. doi:10.1080/15548627.2020.1715047. PubMed PMID: 31942816. PubMed DOI PMC

Baens M, Noels H, Broeckx V, et al. The dark side of EGFP: defective polyubiquitination. PLoS One. 2006;1:e54. doi:10.1371/journal.pone.0000054. PubMed PMID: 17183684; PubMed Central PMCID: PMC1762387. eng. PubMed DOI PMC

Al-Younes HM, Al-Zeer MA, Khalil H, et al. Autophagy-independent function of MAP-LC3 during intracellular propagation of Chlamydia trachomatis. Autophagy. 2011. Aug 1;7(8):814–28. PubMed PMID: 21464618; eng. PubMed

Cali T, Galli C, Olivari S, et al. Segregation and rapid turnover of EDEM1 by an autophagy-like mechanism modulates standard ERAD and folding activities. Biochem Biophys Res Commun. 2008. Jul 4;371(3):405–10. doi:10.1016/j.bbrc.2008.04.098. PubMed PMID: 18452703; eng. PubMed DOI

Shroff H, Galbraith CG, Galbraith JA, et al. Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes. Proc Natl Acad Sci U S A. 2007. Dec 18;104(51):20308–13. doi:10.1073/pnas.0710517105. PubMed PMID: 18077327; PubMed Central PMCID: PMC2154427. eng. PubMed DOI PMC

Tanida I, Ueno T, Uchiyama Y.. A super-ecliptic, pHluorin-mKate2, tandem fluorescent protein-tagged human LC3 for the monitoring of mammalian autophagy. PLoS One. 2014;9(10):e110600. doi: doi:s10.1371/journal.pone.0110600. PubMed PMID: 25340751; PubMed Central PMCID: PMCPMC4207750. PubMed DOI PMC

Lee JH, Rao MV, Yang DS, et al. Transgenic expression of a ratiometric autophagy probe specifically in neurons enables the interrogation of brain autophagy in vivo. Autophagy. 2019. Mar;15(3):543–557. doi:10.1080/15548627.2018.1528812. PubMed PMID: 30269645; PubMed Central PMCID: PMCPMC6351128. PubMed DOI PMC

Nicklin P, Bergman P, Zhang B, et al. Bidirectional transport of amino acids regulates mTOR and autophagy. Cell. 2009. Feb 6;136(3):521–34. doi:10.1016/j.cell.2008.11.044. PubMed PMID: 19203585; eng. PubMed DOI PMC

Nyfeler B, Bergman P, Triantafellow E, et al. Relieving autophagy and 4EBP1 from rapamycin resistance. Mol Cell Biol. 2011. Jul;31(14):2867–76. doi:10.1128/MCB.05430-11. PubMed PMID: 21576371; PubMed Central PMCID: PMC3133392. eng. PubMed DOI PMC

Singh K, Sharma A, Mir MC, et al. Autophagic flux determines cell death and survival in response to Apo2L/ TRAIL (dulanermin). Mol Cancer. 2014;13:70. doi:10.1186/1476-4598-13-70. PubMed PMID: 24655592; PubMed Central PMCID: PMC3998041. PubMed DOI PMC

Sarkar S, Korolchuk VI, Renna M, et al. Complex inhibitory effects of nitric oxide on autophagy. Mol Cell. 2011. Jul 8;43(1):19–32. doi:10.1016/j.molcel.2011.04.029. PubMed PMID: 21726807; PubMed Central PMCID: PMC3149661. eng. PubMed DOI PMC

Khmelinskii A, Keller PJ, Bartosik A, et al. Tandem fluorescent protein timers for in vivo analysis of protein dynamics. Nat Biotechnol. 2012. Jun 24;30(7):708–14. doi:10.1038/nbt.2281. PubMed PMID: 22729030. PubMed DOI

Wen RH, Stanar P, Tam B, et al. Autophagy in Xenopus laevis rod photoreceptors is independently regulated by phototransduction and misfolded RHO(P23H). Autophagy. 2019. Nov;15(11):1970–1989. doi:10.1080/15548627.2019.1596487. PubMed PMID: 30975014; PubMed Central PMCID: PMCPMC6844500. PubMed DOI PMC

Nazarko TY, Ozeki K, Till A, et al. Peroxisomal Atg37 binds Atg30 or palmitoyl-CoA to regulate phagophore formation during pexophagy. J Cell Biol. 2014. Feb 17;204(4):541–57. doi:10.1083/jcb.201307050. PubMed PMID: 24535825; PubMed Central PMCID: PMC3926955. PubMed DOI PMC

Deosaran E, Larsen KB, Hua R, et al. NBR1 acts as an autophagy receptor for peroxisomes. J Cell Sci. 2013. Feb 15;126(Pt 4):939–52. doi:10.1242/jcs.114819. PubMed PMID: 23239026. PubMed DOI

Allen GF, Toth R, James J, et al. Loss of iron triggers PINK1/Parkin-independent mitophagy. EMBO Rep. 2013. Dec;14(12):1127–35. doi: 10.1038/embor.2013.168. PubMed PMID: 24176932. PubMed DOI PMC

Kim SJ, Syed GH, Khan M, et al. Hepatitis C virus triggers mitochondrial fission and attenuates apoptosis to promote viral persistence. Proc Natl Acad Sci U S A. 2014. Apr 29;111(17):6413–8. doi:10.1073/pnas.1321114111. PubMed PMID: 24733894; PubMed Central PMCID: PMC4035934. PubMed DOI PMC

Wang Y, Nartiss Y, Steipe B, et al. ROS-induced mitochondrial depolarization initiates PARK2/PARKIN-dependent mitochondrial degradation by autophagy. Autophagy. 2012. Oct;8(10):1462–76. doi:10.4161/auto.21211. PubMed PMID: 22889933. PubMed DOI

Zhang Y, Mun SR, Linares JF, et al. ZZ-dependent regulation of p62/SQSTM1 in autophagy. Nat Commun. 2018. Oct 22;9(1):4373. doi:10.1038/s41467-018-06878-8. PubMed PMID: 30349045; PubMed Central PMCID: PMCPMC6197226. PubMed DOI PMC

Chino H, Hatta T, Natsume T, et al. Intrinsically Disordered Protein TEX264 Mediates ER-phagy. Mol Cell. 2019. Jun 6;74(5):909–921 e6. doi:10.1016/j.molcel.2019.03.033. PubMed PMID: 31006538. PubMed DOI

Liang JR, Lingeman E, Ahmed S, et al. Atlastins remodel the endoplasmic reticulum for selective autophagy. J Cell Biol. 2018. Oct 1;217(10):3354–3367. doi:10.1083/jcb.201804185. PubMed PMID: 30143524; PubMed Central PMCID: PMCPMC6168278. PubMed DOI PMC

Lee JJ, Sanchez-Martinez A, Zarate AM, et al. Basal mitophagy is widespread in Drosophila but minimally affected by loss of Pink1 or parkin. J Cell Biol. 2018. May 7;217(5):1613–1622. doi:10.1083/jcb.201801044. PubMed PMID: 29500189; PubMed Central PMCID: PMCPMC5940313. PubMed DOI PMC

Mijaljica D, Rosado CJ, Devenish RJ, et al. Biosensors for monitoring autophagy. In: Serra PA, editor. Biosensors-emerging materials and applications croatia: intech; 2011. p. 383–400.

Rosado CJ, Mijaljica D, Hatzinisiriou I, et al. Rosella: a fluorescent pH-biosensor for reporting vacuolar turnover of cytosol and organelles in yeast [Evaluation Studies Research Support, Non-U.S. Gov’t]. Autophagy. 2008. Feb;4(2):205–13. PubMed PMID: 18094608; eng. PubMed

Mukherjee R, Chakrabarti O.. Ubiquitin-mediated regulation of the E3 ligase GP78 by MGRN1 in trans affects mitochondrial homeostasis. J Cell Sci. 2016. Feb 15;129(4):757–73. doi:10.1242/jcs.176537. PubMed PMID: 26743086. PubMed DOI

Kobayashi S, Patel J, Zhao F, et al. Novel Dual-Fluorescent Mitophagy Reporter Reveals a Reduced Mitophagy Flux in Type 1 Diabetic Mouse Heart. J Am Osteopath Assoc. 2020. Jul 1;120(7):446–455. doi:10.7556/jaoa.2020.072. PubMed PMID: 32598458. PubMed DOI

Hill SE, Kauffman KJ, Krout M, et al. Maturation and clearance of auto-phagosomes in neurons depends on a specific cysteine protease isoform, ATG-4.2. Dev Cell. 2019. Apr 22;49(2):251–266 e8. doi:10.1016/j.devcel.2019.02.013. PubMed PMID: 30880001; PubMed Central PMCID: PMCPMC6482087. PubMed DOI PMC

Chudakov DM, Matz MV, Lukyanov S, et al. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol Rev. 2010. Jul;90(3):1103–63. doi:10.1152/physrev.00038.2009. PubMed PMID: 20664080; eng. PubMed DOI

Luhr M, Torgersen ML, Szalai P, et al. The kinase PERK and the transcription factor ATF4 play distinct and essential roles in autophagy resulting from tunicamycin-induced ER stress. J Biol Chem. 2019. May 17;294(20):8197–8217. doi:10.1074/jbc.RA118.002829. PubMed PMID: 30926605; PubMed Central PMCID: PMCPMC6527152. PubMed DOI PMC

Zhou C, Zhong W, Zhou J, et al. Monitoring autophagic flux by an improved tandem fluorescent-tagged LC3 (mTagRFP-mWasabi-LC3) reveals that high-dose rapamycin impairs autophagic flux in cancer cells. Autophagy. 2012. Aug;8(8):1215–26. doi:10.4161/auto.20284. PubMed PMID: 22647982. PubMed DOI

Tanida I, Ueno T, Uchiyama Y.. Use of pHlurorin-mKate2-human LC3 to Monitor Autophagic Responses. Methods Enzymol. 2017;587:87–96. doi:10.1016/bs.mie.2016.09.054. PubMed PMID: 28253978. PubMed DOI

Lie PPY, Nixon RA.. Lysosome trafficking and signaling in health and neurodegenerative diseases. Neurobiol Dis. 2019. Feb;122:94–105. doi:10.1016/j.nbd.2018.05.015. PubMed PMID: 29859318; PubMed Central PMCID: PMCPMC6381838. PubMed DOI PMC

Cossarizza A, Chang HD, Radbruch A, et al. Guidelines for the use of flow cytometry and cell sorting in immunological studies. Eur J Immunol. 2017. Oct;47(10):1584–1797. doi:10.1002/eji.201646632. PubMed PMID: 29023707. PubMed DOI PMC

Patterson GH, Knobel SM, Sharif WD, et al. Use of the green fluorescent protein and its mutants in quantitative fluorescence microscopy. Biophys J. 1997. Nov;73(5):2782–90. PubMed PMID: 9370472; eng. PubMed PMC

Oliva Trejo JA, Tanida I, Suzuki C, et al. Characterization of starvation-induced autophagy in cerebellar Purkinje cells of pHluorin-mKate2-human LC3B transgenic mice. Sci Rep. 2020. Jun 15;10(1):9643. doi:10.1038/s41598-020-66370-6. PubMed PMID: 32541814; PubMed Central PMCID: PMCPMC7295967. PubMed DOI PMC

Yazawa R, Nishida Y, Aoyama S, et al. Establishment of a system for screening autophagic flux regulators using a modified fluorescent reporter and CRISPR/Cas9. Biochem Biophys Res Commun. 2019. Aug 27;516(3):686–692. doi:10.1016/j.bbrc.2019.06.129. PubMed PMID: 31253397. PubMed DOI

Magidson V, Khodjakov A.. Circumventing photodamage in live-cell microscopy. Methods Cell Biol. 2013;114:545–60. doi:10.1016/B978-0-12-407761-4.00023-3. PubMed PMID: 23931522; PubMed Central PMCID: PMCPMC3843244. PubMed DOI PMC

Bogdanov AM, Kudryavtseva EI, Lukyanov KA.. Anti-fading media for live cell GFP imaging. PLoS One. 2012;7(12):e53004. doi:10.1371/journal.pone.0053004. PubMed PMID: 23285248; PubMed Central PMCID: PMCPMC3528736. PubMed DOI PMC

Coffey EE, Beckel JM, Laties AM, et al. Lysosomal alkalization and dysfunction in human fibroblasts with the Alzheimer’s disease-linked presenilin 1 A246E mutation can be reversed with cAMP. Neuroscience. 2014. Mar 28;263:111–24. doi:10.1016/j.neuroscience.2014.01.001. PubMed PMID: 24418614; PubMed Central PMCID: PMCPMC4028113. PubMed DOI PMC

Guha S, Coffey EE, Lu W, et al. Approaches for detecting lysosomal alkalinization and impaired degradation in fresh and cultured RPE cells: evidence for a role in retinal degenerations. Exp Eye Res. 2014. Sep;126:68–76. doi:10.1016/j.exer.2014.05.013. PubMed PMID: 25152362; PubMed Central PMCID: PMCPMC4143779. PubMed DOI PMC

Ramachandra Rao S, Pfeffer BA, Mas Gomez N, et al. Compromised phagosome maturation underlies RPE pathology in cell culture and whole animal models of Smith-Lemli-Opitz Syndrome. Autophagy. 2018;14(10):1796–1817. doi:10.1080/15548627.2018.1490851. PubMed PMID: 29979914; PubMed Central PMCID: PMCPMC6135634. PubMed DOI PMC

Zhou J, Lin J, Zhou C, et al. Cytotoxicity of red fluorescent protein DsRed is associated with the suppression of Bcl-xL translation. FEBS Lett. 2011. Mar 9;585(5):821–7. doi:10.1016/j.febslet.2011.02.013. PubMed PMID: 21320495; eng. PubMed DOI

Wen Y, Zand B, Ozpolat B, et al. Antagonism of tumoral prolactin receptor promotes autophagy-related cell death. Cell Rep. 2014. Apr 24;7(2):488–500. doi:10.1016/j.celrep.2014.03.009. PubMed PMID: 24703838; PubMed Central PMCID: PMC4038960. PubMed DOI PMC

Loos B, Genade S, Ellis B, et al. At the core of survival: autophagy delays the onset of both apoptotic and necrotic cell death in a model of ischemic cell injury. Exp Cell Res. 2011. Jun 10;317(10):1437–53. doi:10.1016/j.yexcr.2011.03.011. PubMed PMID: 21420401; eng. PubMed DOI

de la Calle C, Joubert PE, Law HK, et al. Simultaneous assessment of autophagy and apoptosis using multispectral imaging cytometry. Autophagy. 2011. Sep 1;7(9):1045–51. PubMed PMID: 21606680; eng. PubMed

Degtyarev M, Reichelt M, Lin K.. Novel quantitative autophagy analysis by organelle flow cytometry after cell sonication. PLoS One. 2014;9(1):e87707. doi:10.1371/journal.pone.0087707. PubMed PMID: 24489953; PubMed Central PMCID: PMC3906200. PubMed DOI PMC

Hundeshagen P, Hamacher-Brady A, Eils R, et al. Concurrent detection of autolysosome formation and lysosomal degradation by flow cytometry in a high-content screen for inducers of autophagy. BMC Biol. 2011;9:38. doi:10.1186/1741-7007-9-38. PubMed PMID: 21635740; PubMed Central PMCID: PMC3121655. eng. PubMed DOI PMC

Shvets E, Fass E, Elazar Z.. Utilizing flow cytometry to monitor autophagy in living mammalian cells. Autophagy. 2008. Jul;4(5):621–8. PubMed PMID: 18376137; eng. PubMed

Gannage M, Dormann D, Albrecht R, et al. Matrix protein 2 of influenza A virus blocks autophagosome fusion with lysosomes. Cell Host Microbe. 2009. Oct 22;6(4):367–80. doi: 10.1016/j.chom.2009.09.005. PubMed PMID: 19837376; PubMed Central PMCID: PMC2774833. eng. PubMed DOI PMC

Kaizuka T, Morishita H, Hama Y, et al. An Autophagic Flux Probe that Releases an Internal Control. Mol Cell. 2016. Nov 17;64(4):835–849. doi:10.1016/j.molcel.2016.09.037. PubMed PMID: 27818143. PubMed DOI

Kaminskyy V, Abdi A, Zhivotovsky B.. A quantitative assay for the monitoring of autophagosome accumulation in different phases of the cell cycle. Autophagy. 2011. Jan;7(1):83–90. PubMed PMID: 20980814; eng. PubMed

Kirkin V, Lamark T, Sou YS, et al. A role for NBR1 in autophagosomal degradation of ubiquitinated substrates. Mol Cell. 2009. Feb 27;33(4):505–16. doi: 10.1016/j.molcel.2009.01.020. PubMed PMID: 19250911; eng. PubMed DOI

Larsen KB, Lamark T, Overvatn A, et al. A reporter cell system to monitor autophagy based on p62/SQSTM1. Autophagy. 2010. Aug;6(6):784–93. PubMed PMID: 20574168; eng. PubMed

Wilson RB, Murphy RF.. Flow-cytometric analysis of endocytic compartments. Methods Cell Biol. 1989;31:293–317. doi:10.1016/s0091-679x(08)61616-7. PubMed PMID: 2674626. PubMed DOI

Cossarizza A, Ceccarelli D, Masini A.. Functional heterogeneity of an isolated mitochondrial population revealed by cytofluorometric analysis at the single organelle level. Exp Cell Res. 1996. Jan 10;222(1):84–94. doi:10.1006/excr.1996.0011. PubMed PMID: 8549677. PubMed DOI

Dhandayuthapani S, Via LE, Thomas CA, et al. Green fluorescent protein as a marker for gene expression and cell biology of mycobacterial interactions with macrophages. Mol Microbiol. 1995. Sep;17(5):901–12. doi:10.1111/j.1365-2958.1995.mmi_17050901.x. PubMed PMID: 8596439. PubMed DOI

Koga H, Kaushik S, Cuervo AM.. Altered lipid content inhibits autophagic vesicular fusion. FASEB J. 2010. Aug;24(8):3052–65. doi:10.1096/fj.09-144519. PubMed PMID: 20375270; PubMed Central PMCID: PMCPMC2909278. PubMed DOI PMC

Picot S, Morga B, Faury N, et al. A study of autophagy in hemocytes of the Pacific oyster, Crassostrea gigas. Autophagy. 2019. Oct;15(10):1801–1809. doi:10.1080/15548627.2019.1596490. PubMed PMID: 30939979; PubMed Central PMCID: PMCPMC6735588. PubMed DOI PMC

Rong Y, Liu W, Wang J, et al. Neural stem cell-derived small extracellular vesicles attenuate apoptosis and neuroinflammation after traumatic spinal cord injury by activating autophagy. Cell Death Dis. 2019. Apr 18;10(5):340. doi:10.1038/s41419-019-1571-8. PubMed PMID: 31000697; PubMed Central PMCID: PMCPMC6472377. PubMed DOI PMC

Guo S, Liang Y, Murphy SF, et al. A rapid and high content assay that measures cyto-ID-stained autophagic compartments and estimates autophagy flux with potential clinical applications. Autophagy. 2015;11(3):560–72. doi:10.1080/15548627.2015.1017181. PubMed PMID: 25714620; PubMed Central PMCID: PMCPMC4502761. PubMed DOI PMC

Skah S, Richartz N, Duthil E, et al. cAMP-mediated autophagy inhibits DNA damage-induced death of leukemia cells independent of p53. Oncotarget. 2018. Jul 13;9(54):30434–30449. doi:10.18632/oncotarget.25758. PubMed PMID: 30100998; PubMed Central PMCID: PMCPMC6084393. PubMed DOI PMC

Bas L, Papinski D, Licheva M, et al. Reconstitution reveals Ykt6 as the autophagosomal SNARE in autophagosome-vacuole fusion. J Cell Biol. 2018. Oct 1;217(10):3656–3669. doi:10.1083/jcb.201804028. PubMed PMID: 30097514; PubMed Central PMCID: PMCPMC6168255. PubMed DOI PMC

Gao J, Reggiori F, Ungermann C.. A novel in vitro assay reveals SNARE topology and the role of Ykt6 in autophagosome fusion with vacuoles. J Cell Biol. 2018. Oct 1;217(10):3670–3682. doi:10.1083/jcb.201804039. PubMed PMID: 30097515; PubMed Central PMCID: PMCPMC6168247. PubMed DOI PMC

Matsui T, Jiang P, Nakano S, et al. Autophagosomal YKT6 is required for fusion with lysosomes independently of syntaxin 17. J Cell Biol. 2018. Aug 6;217(8):2633–2645. doi:10.1083/jcb.201712058. PubMed PMID: 29789439; PubMed Central PMCID: PMCPMC6080929. PubMed DOI PMC

Huang JJ, Li HR, Huang Y, et al. Beclin 1 expression: a predictor of prognosis in patients with extranodal natural killer T-cell lymphoma, nasal type. Autophagy. 2010. Aug;6(6):777–83. PubMed PMID: 20639699; eng. PubMed

Lefort S, Joffre C, Kieffer Y, et al. Inhibition of autophagy as a new means of improving chemotherapy efficiency in high-LC3B triple-negative breast cancers. Autophagy. 2014;10(12):2122–42. doi:10.4161/15548627.2014.981788. PubMed PMID: 25427136; PubMed Central PMCID: PMCPMC4502743. PubMed DOI PMC

Sivridis E, Giatromanolaki A, Zois C, et al. The “stone-like” pattern of autophagy in human epithelial tumors and tumor-like lesions: an approach to the clinical outcome. Autophagy. 2010. Aug;6(6):830–3. PubMed PMID: 20622525; eng. PubMed

Giatromanolaki A, Koukourakis MI, Koutsopoulos A, et al. High Beclin 1 expression defines a poor prognosis in endometrial adenocarcinomas. Gynecol Oncol. 2011. Oct;123(1):147–51. doi:10.1016/j.ygyno.2011.06.023. PubMed PMID: 21741077; eng. PubMed DOI

Sivridis E, Giatromanolaki A, Liberis V, et al. Autophagy in endometrial carcinomas and prognostic relevance of ‘stone-like’ structures (SLS): what is destined for the atypical endometrial hyperplasia? Autophagy. 2011. Jan;7(1):74–82. PubMed PMID: 21099253; eng. PubMed

Chen Y, Lu Y, Lu C, et al. Beclin-1 expression is a predictor of clinical outcome in patients with esophageal squamous cell carcinoma and correlated to hypoxia-inducible factor (HIF)-1alpha expression. Pathol Oncol Res. 2009. Sep;15(3):487–93. doi:10.1007/s12253-008-9143-8. PubMed PMID: 19130303; PubMed Central PMCID: PMC2791489. eng. PubMed DOI PMC

Sakakura K, Takahashi H, Kaira K, et al. Immunological significance of the accumulation of autophagy components in oral squamous cell carcinoma. Cancer Sci. 2015. Jan;106(1):1–8. doi:10.1111/cas.12559. PubMed PMID: 25338734. PubMed DOI PMC

Wan XB, Fan XJ, Chen MY, et al. Elevated Beclin 1 expression is correlated with HIF-1[a] in predicting poor prognosis of nasopharyngeal carcinoma. Autophagy. 2010. Apr;6(3):395–404. PubMed PMID: 20150769; eng. PubMed

Ding ZB, Shi YH, Zhou J, et al. Association of autophagy defect with a malignant phenotype and poor prognosis of hepatocellular carcinoma. Cancer Res. 2008. Nov 15;68(22):9167–75. doi:10.1158/0008-5472.CAN-08-1573. PubMed PMID: 19010888; eng. PubMed DOI

Shi YH, Ding ZB, Zhou J, et al. Prognostic significance of Beclin 1-dependent apoptotic activity in hepatocellular carcinoma. Autophagy. 2009. Apr;5(3):380–2. PubMed PMID: 19145109; eng. PubMed

Pirtoli L, Cevenini G, Tini P, et al. The prognostic role of Beclin 1 protein expression in high-grade gliomas. Autophagy. 2009. Oct;5(7):930–6. PubMed PMID: 19556884; eng. PubMed

Karpathiou G, Sivridis E, Koukourakis MI, et al. Light-chain 3A autophagic activity and prognostic significance in non-small cell lung carcinomas. Chest. 2011. Jul;140(1):127–34. doi:10.1378/chest.10-1831. PubMed PMID: 21148243; eng. PubMed DOI

Fujii S, Mitsunaga S, Yamazaki M, et al. Autophagy is activated in pancreatic cancer cells and correlates with poor patient outcome. Cancer Sci. 2008. Sep;99(9):1813–9. doi:10.1111/j.1349-7006.2008.00893.x. PubMed PMID: 18616529; eng. PubMed DOI PMC

Giatromanolaki A, Koukourakis MI, Harris AL, et al. Prognostic relevance of light chain 3 (LC3A) autophagy patterns in colorectal adenocarcinomas. J Clin Pathol. 2010. Oct;63(10):867–72. doi:10.1136/jcp.2010.079525. PubMed PMID: 20876316; eng. PubMed DOI

Koukourakis MI, Giatromanolaki A, Sivridis E, et al. Beclin 1 over- and underexpression in colorectal cancer: distinct patterns relate to prognosis and tumour hypoxia. Br J Cancer. 2010. Oct 12;103(8):1209–14. doi:10.1038/sj.bjc.6605904. PubMed PMID: 20842118; PubMed Central PMCID: PMC2967071. eng. PubMed DOI PMC

Li BX, Li CY, Peng RQ, et al. The expression of beclin 1 is associated with favorable prognosis in stage IIIB colon cancers. Autophagy. 2009. Apr;5(3):303–6. PubMed PMID: 19066461; eng. PubMed

Giatromanolaki AN, St Charitoudis G, Bechrakis NE, et al. Autophagy patterns and prognosis in uveal melanomas. Mod Pathol. 2011. Aug;24(8):1036–45. doi:10.1038/modpathol.2011.63. PubMed PMID: 21499230; eng. PubMed DOI

Sivridis E, Koukourakis MI, Mendrinos SE, et al. Beclin-1 and LC3A expression in cutaneous malignant melanomas: a biphasic survival pattern for beclin-1. Melanoma Res. 2011. Jun;21(3):188–95. doi:10.1097/CMR.0b013e328346612c. PubMed PMID: 21537144; eng. PubMed DOI

Long M, McWilliams TG.. Monitoring autophagy in cancer: from bench to bedside. Semin Cancer Biol. 2019. Jul 15. doi:10.1016/j.semcancer.2019.05.016. PubMed PMID: 31319163. PubMed DOI

Langer R, Neppl C, Keller MD, et al. Expression analysis of autophagy related markers LC3B, p62 and HMGB1 indicate an autophagy-independent negative prognostic impact of high p62 expression in pulmonary squamous cell carcinomas. Cancers (Basel). 2018. Aug 21;10(9). doi:10.3390/cancers10090281. PubMed PMID: 30134604; PubMed Central PMCID: PMCPMC6162479. PubMed DOI PMC

Schlafli AM, Adams O, Galvan JA, et al. Prognostic value of the autophagy markers LC3 and p62/SQSTM1 in early-stage non-small cell lung cancer. Oncotarget. 2016. Jun 28;7(26):39544–39555. doi:10.18632/oncotarget.9647. PubMed PMID: 27250032; PubMed Central PMCID: PMCPMC5129952. PubMed DOI PMC

McShane LM, Altman DG, Sauerbrei W, et al. Reporting recommendations for tumor marker prognostic studies (REMARK). J Natl Cancer Inst. 2005. Aug 17;97(16):1180–4. doi:10.1093/jnci/dji237. PubMed PMID: 16106022; eng. PubMed DOI

Hou YJ, Dong LW, Tan YX, et al. Inhibition of active autophagy induces apoptosis and increases chemosensitivity in cholangiocarcinoma. Lab Invest. 2011. Aug;91(8):1146–57. doi:10.1038/labinvest.2011.97. PubMed PMID: 21647092; eng. PubMed DOI

Kuwahara Y, Oikawa T, Ochiai Y, et al. Enhancement of autophagy is a potential modality for tumors refractory to radiotherapy. Cell Death Dis. 2011;2:e177. doi:10.1038/cddis.2011.56. PubMed PMID: 21716292; eng. PubMed DOI PMC

O’Donovan TR, O’Sullivan GC, McKenna SL.. Induction of autophagy by drug-resistant esophageal cancer cells promotes their survival and recovery following treatment with chemotherapeutics. Autophagy. 2011. May;7(5):509–24. PubMed PMID: 21325880; PubMed Central PMCID: PMC3127212. eng. PubMed PMC

Ginet V, Pittet MP, Rummel C, et al. Dying neurons in thalamus of asphyxiated term newborns and rats are autophagic. Ann Neurol. 2014. Nov;76(5):695–711. doi:10.1002/ana.24257. PubMed PMID: 25146903. PubMed DOI

Xie C, Ginet V, Sun Y, et al. Neuroprotection by selective neuronal deletion of Atg7 in neonatal brain injury. Autophagy. 2016;12(2):410–23. doi:10.1080/15548627.2015.1132134. PubMed PMID: 26727396; PubMed Central PMCID: PMCPMC4835980. PubMed DOI PMC

Cui J, Bai XY, Shi S, et al. Age-related changes in the function of autophagy in rat kidneys. Age (Omaha). 2011. Apr 1;10.1007/s11357-011-9237-1. doi:10.1007/s11357-011-9237-1. PubMed PMID: 21455601; Eng. PubMed DOI PMC

Tamura H, Shibata M, Koike M, et al. Atg9A protein, an autophagy-related membrane protein, is localized in the neurons of mouse brains. J Histochem Cytochem. 2010. May;58(5):443–53. doi:10.1369/jhc.2010.955690. PubMed PMID: 20124090; PubMed Central PMCID: PMC2857816. eng. PubMed DOI PMC

Yoshimura K, Shibata M, Koike M, et al. Effects of RNA interference of Atg4B on the limited proteolysis of LC3 in PC12 cells and expression of Atg4B in various rat tissues. Autophagy. 2006. Jul-Sep;2(3):200–8. PubMed PMID: 16874114; eng. PubMed

Zhan L, Liu L, Li K, et al. Neuroprotection of hypoxic postconditioning against global cerebral ischemia through influencing posttranslational regulations of heat shock protein 27 in adult rats. Brain Pathol. 2017. Nov;27(6):822–838. doi:10.1111/bpa.12472. PubMed PMID: 27936516. PubMed DOI PMC

Marinelli S, Nazio F, Tinari A, et al. Schwann cell autophagy counteracts the onset and chronification of neuropathic pain. Pain. 2014. Jan;155(1):93–107. doi:10.1016/j.pain.2013.09.013. PubMed PMID: 24041962. PubMed DOI

Adolph TE, Tomczak MF, Niederreiter L, et al. Paneth cells as a site of origin for intestinal inflammation. Nature. 2013. Nov 14;503(7475):272–6. doi:10.1038/nature12599. PubMed PMID: 24089213; PubMed Central PMCID: PMC3862182. PubMed DOI PMC

Gorbunov NV, Kiang JG.. Autophagy-Mediated Innate Defense Mechanism in Crypt Paneth Cells Responding to Impairment of Small Intestine Barrier after Total-Body Gamma-Photon Irradiation. In: Gorbunov NV, editor. Autophagy: Principles, Regulation and Roles in Disease. Hauppauge, NY: NOVA SCIENCE PUBLISHERS, INC; 2011. p. 61–84.

Thachil E, Hugot JP, Arbeille B, et al. Abnormal activation of autophagy-induced crinophagy in Paneth cells from patients with Crohn’s disease. Gastroenterology. 2012. May;142(5):1097–1099 e4. doi:10.1053/j.gastro.2012.01.031. PubMed PMID: 22285936. PubMed DOI

Sepe S, Nardacci R, Fanelli F, et al. Expression of Ambra1 in mouse brain during physiological and Alzheimer type aging. Neurobiol Aging. 2014. Jan;35(1):96–108. doi:10.1016/j.neurobiolaging.2013.07.001. PubMed PMID: 23910655. PubMed DOI

Rosso P, Moreno S, Fracassi A, et al. Nerve growth factor and autophagy: effect of nasal anti-NGF-antibodies administration on Ambra1 and Beclin-1 expression in rat brain. Growth Factors. 2015;33(5–6):401–9. doi:10.3109/08977194.2015.1122002. PubMed PMID: 26728403. PubMed DOI

Morais RD, Thome RG, Lemos FS, et al. Autophagy and apoptosis interplay during follicular atresia in fish ovary: a morphological and immunocytochemical study. Cell Tissue Res. 2012. Feb;347(2):467–78. doi:10.1007/s00441-012-1327-6. PubMed PMID: 22314847. PubMed DOI

Shibata M, Yoshimura K, Furuya N, et al. The MAP1-LC3 conjugation system is involved in lipid droplet formation. Biochem Biophys Res Commun. 2009. May 1;382(2):419–23. doi:10.1016/j.bbrc.2009.03.039. PubMed PMID: 19285958; eng. PubMed DOI

Komatsu M, Waguri S, Koike M, et al. Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice. Cell. 2007;131:1149–63. PubMed

Lazzeri G, Biagioni F, Fulceri F, et al. mTOR modulates methamphetamine-induced toxicity through cell clearing systems. Oxid Med Cell Longev. 2018;2018:6124745. doi:10.1155/2018/6124745. PubMed PMID: 30647813; PubMed Central PMCID: PMCPMC6311854. PubMed DOI PMC

Saito T, Asai K, Sato S, et al. Autophagic vacuoles in cardiomyocytes of dilated cardiomyopathy with initially decompensated heart failure predict improved prognosis. Autophagy. 2016;12(3):579–87. doi:10.1080/15548627.2016.1145326. PubMed PMID: 26890610; PubMed Central PMCID: PMCPMC4836017. PubMed DOI PMC

Vega-Rubin-de-Celis S, Wiemann S.. Autophagy LC3 HiBiT reporter assay system demonstrates mTORC1 regulation of autophagic flux. Promega Rep. 2018.

Landajuela A, Hervas JH, Anton Z, et al. Lipid Geometry and Bilayer Curvature Modulate LC3/GABARAP-Mediated Model Autophagosomal Elongation. Biophys J. 2016. Jan 19;110(2):411–422. doi:10.1016/j.bpj.2015.11.3524. PubMed PMID: 26789764; PubMed Central PMCID: PMCPMC4724631. PubMed DOI PMC

Germain M, Nguyen AP, Le Grand JN, et al. MCL-1 is a stress sensor that regulates autophagy in a developmentally regulated manner. EMBO J. 2011. Jan 19;30(2):395–407. doi:10.1038/emboj.2010.327. PubMed PMID: 21139567; PubMed Central PMCID: PMC3025469. eng. PubMed DOI PMC

Ladoire S, Chaba K, Martins I, et al. Immunohistochemical detection of cytoplasmic LC3 puncta in human cancer specimens. Autophagy. 2012. Aug;8(8):1175–84. doi:10.4161/auto.20353. PubMed PMID: 22647537; PubMed Central PMCID: PMCPMC3973657. PubMed DOI PMC

Rosenfeldt MT, Nixon C, Liu E, et al. Analysis of macroautophagy by immunohistochemistry. Autophagy. 2012. Jun;8(6):963–9. doi:10.4161/auto.20186. PubMed PMID: 22562096; PubMed Central PMCID: PMCPMC3427261. PubMed DOI PMC

Zhu L, Zhu Y, Han S, et al. Impaired autophagic degradation of lncRNA ARHGAP5-AS1 promotes chemoresistance in gastric cancer. Cell Death Dis. 2019. May 16;10(6):383. doi:10.1038/s41419-019-1585-2. PubMed PMID: 31097692; PubMed Central PMCID: PMCPMC6522595. PubMed DOI PMC

Bartlett BJ, Isakson P, Lewerenz J, et al. p62, Ref(2)P and ubiquitinated proteins are conserved markers of neuronal aging, aggregate formation and progressive autophagic defects. Autophagy. 2011. Jun;7(6):572–83. PubMed PMID: 21325881; PubMed Central PMCID: PMC3127048. eng. PubMed PMC

Komatsu M, Wang QJ, Holstein GR, et al. Essential role for autophagy protein Atg7 in the maintenance of axonal homeostasis and the prevention of axonal degeneration. Proc Natl Acad Sci U S A. 2007. Sep 4;104(36):14489–94. PubMed PMID: 17726112; eng. PubMed PMC

Masiero E, Agatea L, Mammucari C, et al. Autophagy is required to maintain muscle mass [Research Support, Non-U.S. Gov’t]. Cell Metab. 2009. Dec;10(6):507–15. doi:10.1016/j.cmet.2009.10.008. PubMed PMID: 19945408; eng. PubMed DOI

Nezis IP, Simonsen A, Sagona AP, et al. Ref(2)P, the Drosophila melanogaster homologue of mammalian p62, is required for the formation of protein aggregates in adult brain. J Cell Biol. 2008. Mar 24;180(6):1065–71. doi:10.1083/jcb.200711108. PubMed PMID: 18347073; PubMed Central PMCID: PMC2290837. eng. PubMed DOI PMC

Wang QJ, Ding Y, Kohtz DS, et al. Induction of autophagy in axonal dystrophy and degeneration. J Neurosci. 2006. Aug 2;26(31):8057–68. PubMed PMID: 16885219; eng. PubMed PMC

Zhang H, Chang JT, Guo B, et al. Guidelines for monitoring autophagy in Caenorhabditis elegans. Autophagy. 2015;11(1):9–27. doi:10.1080/15548627.2014.1003478. PubMed PMID: 25569839; PubMed Central PMCID: PMC4502811. PubMed DOI PMC

Ullrich M, Assmus B, Augustin AM, et al. SPRED2 deficiency elicits cardiac arrhythmias and premature death via impaired autophagy. J Mol Cell Cardiol. 2019. Apr;129:13–26. doi: 10.1016/j.yjmcc.2019.01.023. PubMed PMID: 30771306. PubMed DOI

Navarro-Yepes J, Anandhan A, Bradley E, et al. Inhibition of protein ubiquitination by paraquat and 1-methyl-4-phenylpyridinium impairs ubiquitin-dependent protein degradation pathways. Mol Neurobiol. 2016. Oct;53(8):5229–51. doi:10.1007/s12035-015-9414-9. PubMed PMID: 26409479; PubMed Central PMCID: PMCPMC4842169. PubMed DOI PMC

El-Khoury V, Pierson S, Szwarcbart E, et al. Disruption of autophagy by the histone deacetylase inhibitor MGCD0103 and its therapeutic implication in B-cell chronic lymphocytic leukemia. Leukemia. 2014. Aug;28(8):1636–46. doi:10.1038/leu.2014.19. PubMed PMID: 24418989; PubMed Central PMCID: PMC4131250. PubMed DOI PMC

Guo B, Huang X, Zhang P, et al. Genome-wide screen identifies signaling pathways that regulate autophagy during Caenorhabditis elegans development. EMBO Rep. 2014. Jun;15(6):705–13. doi:10.1002/embr.201338310. PubMed PMID: 24764321; PubMed Central PMCID: PMCPMC4197881. PubMed DOI PMC

Aqbi HF, Tyutyunyk-Massey L, Keim RC, et al. Autophagy-deficient breast cancer shows early tumor recurrence and escape from dormancy. Oncotarget. 2018. Apr 24;9(31):22113–22122. doi:10.18632/oncotarget.25197. PubMed PMID: 29774126; PubMed Central PMCID: PMCPMC5955162. PubMed DOI PMC

Nakaso K, Yoshimoto Y, Nakano T, et al. Transcriptional activation of p62/A170/ZIP during the formation of the aggregates: possible mechanisms and the role in Lewy body formation in Parkinson’s disease. Brain Res. 2004. Jun 25;1012(1–2):42–51. PubMed PMID: 15158159; eng. PubMed

Trocoli A, Bensadoun P, Richard E, et al. p62/SQSTM1 upregulation constitutes a survival mechanism that occurs during granulocytic differentiation of acute myeloid leukemia cells. Cell Death Differ. 2014. Jul 18. doi:10.1038/cdd.2014.102. PubMed PMID: 25034783. PubMed DOI PMC

B’Chir W, Maurin AC, Carraro V, et al. The eIF2alpha/ATF4 pathway is essential for stress-induced autophagy gene expression. Nucleic Acids Res. 2013. Sep;41(16):7683–99. doi:10.1093/nar/gkt563. PubMed PMID: 23804767; PubMed Central PMCID: PMC3763548. PubMed DOI PMC

Cnop M, Abdulkarim B, Bottu G, et al. RNA sequencing identifies dysregulation of the human pancreatic islet transcriptome by the saturated fatty acid palmitate. Diabetes. 2014. Jun;63(6):1978–93. doi: 10.2337/db13-1383. PubMed PMID: 24379348. PubMed DOI

Kumsta C, Chang JT, Schmalz J, et al. Hormetic heat stress and HSF-1 induce autophagy to improve survival and proteostasis in C. elegans. Nat Commun. 2017. Feb 15;8:14337. doi:10.1038/ncomms14337. PubMed PMID: 28198373; PubMed Central PMCID: PMCPMC5316864. PubMed DOI PMC

Lapierre LR, De Magalhaes Filho CD, McQuary PR, et al. The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans. Nat Commun. 2013;4:2267. doi:10.1038/ncomms3267. PubMed PMID: 23925298; PubMed Central PMCID: PMC3866206. PubMed DOI PMC

Colosetti P, Puissant A, Robert G, et al. Autophagy is an important event for megakaryocytic differentiation of the chronic myelogenous leukemia K562 cell line. Autophagy. 2009. Nov;5(8):1092–8. PubMed PMID: 19786835; eng. PubMed

Toepfer N, Childress C, Parikh A, et al. Atorvastatin induces autophagy in prostate cancer PC3 cells through activation of LC3 transcription. Cancer Biol Ther. 2011. Oct 15;12(8):691–9. doi:10.4161/cbt.12.8.15978. PubMed PMID: 21768780; eng. PubMed DOI

Zheng Q, Su H, Ranek MJ, et al. Autophagy and p62 in cardiac proteinopathy. Circ Res. 2011. Jul 22;109(3):296–308. doi:10.1161/CIRCRESAHA.111.244707. PubMed PMID: 21659648; PubMed Central PMCID: PMC3142307. eng. PubMed DOI PMC

Trocoli A, Mathieu J, Priault M, et al. ATRA-induced upregulation of Beclin 1 prolongs the life span of differentiated acute promyelocytic leukemia cells. Autophagy. 2011. Oct;7(10):1108–14. doi:10.4161/auto.7.10.16623. PubMed PMID: 21691148; PubMed Central PMCID: PMC3242613. PubMed DOI PMC

Kato M, Ospelt C, Gay RE, et al. Dual role of autophagy in stress-induced cell death in rheumatoid arthritis synovial fibroblasts. Arthritis Rheumatol. 2014. Jan;66(1):40–8. doi:10.1002/art.38190. PubMed PMID: 24449574. PubMed DOI

Kim JH, Hong SK, Wu PK, et al. Raf/MEK/ERK can regulate cellular levels of LC3B and SQSTM1/p62 at expression levels. Exp Cell Res. 2014. Oct 1;327(2):340–52. doi:10.1016/j.yexcr.2014.08.001. PubMed PMID: 25128814; PubMed Central PMCID: PMC4164593. PubMed DOI PMC

B’Chir W, Chaveroux C, Carraro V, et al. Dual role for CHOP in the crosstalk between autophagy and apoptosis to determine cell fate in response to amino acid deprivation. Cell Signal. 2014. Jul;26(7):1385–91. doi:10.1016/j.cellsig.2014.03.009. PubMed PMID: 24657471. PubMed DOI

Sahani MH, Itakura E, Mizushima N.. Expression of the autophagy substrate SQSTM1/p62 is restored during prolonged starvation depending on transcriptional upregulation and autophagy-derived amino acids. Autophagy. 2014. Mar 1;10(3):431–41. doi:10.4161/auto.27344. PubMed PMID: 24394643. PubMed DOI PMC

Jamart C, Naslain D, Gilson H, et al. Higher activation of autophagy in skeletal muscle of mice during endurance exercise in the fasted state. Am J Physiol Endocrinol Metab. 2013. Oct 15;305(8):E964–74. doi:10.1152/ajpendo.00270.2013. PubMed PMID: 23964069. PubMed DOI

Sanchez AM, Bernardi H, Py G, et al. Autophagy is essential to support skeletal muscle plasticity in response to endurance exercise. Am J Physiol Regul Integr Comp Physiol. 2014. Oct 15;307(8):R956–69. doi:10.1152/ajpregu.00187.2014. PubMed PMID: 25121614. PubMed DOI

Stingele S, Stoehr G, Peplowska K, et al. Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells. Mol Syst Biol. 2012;8:608. doi:10.1038/msb.2012.40. PubMed PMID: 22968442; PubMed Central PMCID: PMC3472693. PubMed DOI PMC

Tang YC, Williams BR, Siegel JJ, et al. Identification of aneuploidy-selective antiproliferation compounds. Cell. 2011. Feb 18;144(4):499–512. doi:10.1016/j.cell.2011.01.017. PubMed PMID: 21315436; PubMed Central PMCID: PMC3532042. PubMed DOI PMC

Marchesi N, Thongon N, Pascale A, et al. Autophagy Stimulus Promotes Early HuR Protein Activation and p62/SQSTM1 Protein Synthesis in ARPE-19 Cells by Triggering Erk1/2, p38(MAPK), and JNK Kinase Pathways. Oxid Med Cell Longev. 2018;2018:4956080. doi:10.1155/2018/4956080. PubMed PMID: 29576851; PubMed Central PMCID: PMCPMC5822911. PubMed DOI PMC

Penna F, Costamagna D, Pin F, et al. Autophagic degradation contributes to muscle wasting in cancer cachexia. Am J Pathol. 2013. Apr;182(4):1367–78. doi:10.1016/j.ajpath.2012.12.023. PubMed PMID: 23395093. PubMed DOI

BenYounes A, Tajeddine N, Tailler M, et al. A fluorescence-microscopic and cytofluorometric system for monitoring the turnover of the autophagic substrate p62/SQSTM1 [Research Support, Non-U.S. Gov’t]. Autophagy. 2011. Aug 1;7(8):883–91. PubMed PMID: 21460612; eng. PubMed

Chang Y-Y, Neufeld TP.. An Atg1/Atg13 complex with multiple roles in TOR-mediated autophagy regulation. Mol Biol Cell. 2009. Apr;20(7):2004–14. doi:10.1091/mbc.E08-12-1250. PubMed PMID: 19225150; PubMed Central PMCID: PMC2663935. eng. PubMed DOI PMC

Jiang Y, Zhu J, Wu L, et al. Tetracycline inhibits local inflammation induced by cerebral ischemia via modulating autophagy. PLoS One. 2012;7(11):e48672. doi: 10.1371/journal.pone.0048672. PubMed PMID: 23144925; PubMed Central PMCID: PMC3492486. PubMed DOI PMC

Moullan N, Mouchiroud L, Wang X, et al. Tetracyclines Disturb Mitochondrial Function across Eukaryotic Models: A Call for Caution in Biomedical Research. Cell Rep. 2015. Mar 17;10(10):1681–1691. doi:10.1016/j.celrep.2015.02.034. PubMed PMID: 25772356; PubMed Central PMCID: PMCPMC4565776. PubMed DOI PMC

Bjorkoy G, Lamark T, Pankiv S, et al. Monitoring autophagic degradation of p62/SQSTM1. Methods Enzymol. 2009;452:181–97. doi:10.1016/S0076-6879(08)03612-4. PubMed PMID: 19200883; eng. PubMed DOI

Moscat J, Diaz-Meco MT.. p62 at the crossroads of autophagy, apoptosis, and cancer. Cell. 2009. Jun 12;137(6):1001–4. doi:10.1016/j.cell.2009.05.023. PubMed PMID: 19524504; eng. PubMed DOI PMC

Duran A, Amanchy R, Linares JF, et al. p62 is a key regulator of nutrient sensing in the mTORC1 pathway. Mol Cell. 2011. Oct 7;44(1):134–46. doi:10.1016/j.molcel.2011.06.038. PubMed PMID: 21981924; PubMed Central PMCID: PMC3190169. eng. PubMed DOI PMC

Gonzalez Y, Aryal B, Chehab L, et al. Atg7- and Keap1-dependent autophagy protects breast cancer cell lines against mitoquinone-induced oxidative stress. Oncotarget. 2014. Mar 30;5(6):1526–37. PubMed PMID: 24681637; PubMed Central PMCID: PMC4039229. PubMed PMC

Komatsu M, Kurokawa H, Waguri S, et al. The selective autophagy substrate p62 activates the stress responsive transcription factor Nrf2 through inactivation of Keap1. Nat Cell Biol. 2010. Mar;12(3):213–23. doi:10.1038/ncb2021. PubMed PMID: 20173742; eng. PubMed DOI

Jain A, Lamark T, Sjottem E, et al. p62/SQSTM1 is a target gene for transcription factor NRF2 and creates a positive feedback loop by inducing antioxidant response element-driven gene transcription. J Biol Chem. 2010. Jul 16;285(29):22576–91. doi: 10.1074/jbc.M110.118976. PubMed PMID: 20452972; PubMed Central PMCID: PMC2903417. eng. PubMed DOI PMC

Korolchuk VI, Menzies FM, Rubinsztein DC.. Mechanisms of cross-talk between the ubiquitin-proteasome and autophagy-lysosome systems. FEBS Lett. 2010. Apr 2;584(7):1393–8. doi:10.1016/j.febslet.2009.12.047. PubMed PMID: 20040365. PubMed DOI

Cecarini V, Bonfili L, Cuccioloni M, et al. The fine-tuning of proteolytic pathways in Alzheimer’s disease. Cell Mol Life Sci.: CMLS. 2016. Sep;73(18):3433–51. doi:10.1007/s00018-016-2238-6. PubMed PMID: 27120560. PubMed DOI PMC

Bardag-Gorce F, Francis T, Nan L, et al. Modifications in p62 occur due to proteasome inhibition in alcoholic liver disease. Life Sci 2005. Sep 30;77(20):2594–602. PubMed PMID: 15964033; eng. PubMed

Myeku N, Figueiredo-Pereira ME.. Dynamics of the degradation of ubiquitinated proteins by proteasomes and autophagy: association with sequestosome 1/p62. J Biol Chem. 2011. Jun 24;286(25):22426–40. doi:10.1074/jbc.M110.149252. PubMed PMID: 21536669; PubMed Central PMCID: PMC3121389. eng. PubMed DOI PMC

Korolchuk VI, Mansilla A, Menzies FM, et al. Autophagy inhibition compromises degradation of ubiquitin-proteasome pathway substrates. Mol Cell. 2009. Feb 27;33(4):517–27. doi: 10.1016/j.molcel.2009.01.021. PubMed PMID: 19250912; PubMed Central PMCID: PMC2669153. PubMed DOI PMC

Yoshiyama Y, Higuchi M, Zhang B, et al. Synapse loss and microglial activation precede tangles in a P301S tauopathy mouse model. Neuron. 2007. Feb 1;53(3):337–51. doi:10.1016/j.neuron.2007.01.010. PubMed PMID: 17270732. PubMed DOI

Akwa Y, Gondard E, Mann A, et al. Synaptic activity protects against AD and FTD-like pathology via autophagic-lysosomal degradation. Mol Psychiatry. 2018. Jun;23(6):1530–1540. doi:10.1038/mp.2017.142. PubMed PMID: 28696431; PubMed Central PMCID: PMCPMC5641448. PubMed DOI PMC

Sharma A, Alswillah T, Kapoor I, et al. USP14 is a deubiquitinase for Ku70 and critical determinant of non-homologous end joining repair in autophagy and PTEN-deficient cells. Nucleic Acids Res. 2020. Jan 24;48(2):736–747. doi:10.1093/nar/gkz1103. PubMed PMID: 31740976; PubMed Central PMCID: PMC7145659. PubMed DOI PMC

Sharma A, Alswillah T, Singh K, et al. USP14 regulates DNA damage repair by targeting RNF168-dependent ubiquitination. Autophagy. 2018;14(11):1976–1990. doi:10.1080/15548627.2018.1496877. PubMed PMID: 29995557; PubMed Central PMCID: PMCPMC6152509; PubMed Central PMCID: PMC6152509. PubMed DOI PMC

Dantuma NP, Lindsten K, Glas R, et al. Short-lived green fluorescent proteins for quantifying ubiquitin/proteasome-dependent proteolysis in living cells. Nat Biotechnol. 2000. May;18(5):538–43. doi:10.1038/75406. PubMed PMID: 10802622. PubMed DOI

Monick MM, Powers LS, Walters K, et al. Identification of an autophagy defect in smokers’ alveolar macrophages. J Iimmunol. 2010. Nov 1;185(9):5425–35. doi:10.4049/jimmunol.1001603. PubMed PMID: 20921532; PubMed Central PMCID: PMC3057181. PubMed DOI PMC

Vallelian F, Deuel JW, Opitz L, et al. Proteasome inhibition and oxidative reactions disrupt cellular homeostasis during heme stress. Cell Death Differ. 2015. Apr;22(4):597–611. doi:10.1038/cdd.2014.154. PubMed PMID: 25301065; PubMed Central PMCID: PMC4356336. PubMed DOI PMC

Long J, Garner TP, Pandya MJ, et al. Dimerisation of the UBA domain of p62 inhibits ubiquitin binding and regulates NF-kappaB signalling. J Mol Biol. 2010. Feb 12;396(1):178–94. doi:10.1016/j.jmb.2009.11.032. PubMed PMID: 19931284. PubMed DOI

Norman JM, Cohen GM, Bampton ET.. The in vitro cleavage of the hAtg proteins by cell death proteases. Autophagy. 2010. Nov;6(8):1042–56. PubMed PMID: 21121091; eng. PubMed

Lelouard H, Schmidt EK, Camosseto V, et al. Regulation of translation is required for dendritic cell function and survival during activation. J Cell Biol. 2007. Dec 31;179(7):1427–39. doi:10.1083/jcb.200707166. PubMed PMID: 18166652; PubMed Central PMCID: PMC2373495. eng. PubMed DOI PMC

Cecarini V, Bonfili L, Cuccioloni M, et al. Wild type and mutant amyloid precursor proteins influence downstream effects of proteasome and autophagy inhibition. Biochim Biophys Acta. 2014. Feb;1842(2):127–34. doi:10.1016/j.bbadis.2013.11.002. PubMed PMID: 24215712. PubMed DOI

Schmidt EK, Clavarino G, Ceppi M, et al. SUnSET, a nonradioactive method to monitor protein synthesis [Research Support, Non-U.S. Gov’t]. Nat Methods. 2009. Apr;6(4):275–7. doi:10.1038/nmeth.1314. PubMed PMID: 19305406; eng. PubMed DOI

Lim J, Kim HW, Youdim MB, et al. Binding preference of p62 towards LC3-ll during dopaminergic neurotoxin-induced impairment of autophagic flux. Autophagy. 2011. Jan;7(1):51–60. PubMed PMID: 21045561; eng. PubMed

Fouillet A, Levet C, Virgone A, et al. ER stress inhibits neuronal death by promoting autophagy. Autophagy. 2012. Jun;8(6):915–26. doi:10.4161/auto.19716. PubMed PMID: 22660271; PubMed Central PMCID: PMC3427257. PubMed DOI PMC

Waguri S, Komatsu M.. Biochemical and morphological detection of inclusion bodies in autophagy-deficient mice. Methods Enzymol. 2009;453:181–96. doi:10.1016/S0076-6879(08)04009-3. PubMed PMID: 19216907; eng. PubMed DOI

Hocking LJ, Lucas GJ, Daroszewska A, et al. Domain-specific mutations in sequestosome 1 (SQSTM1) cause familial and sporadic Paget’s disease. Hum Mol Genet. 2002. Oct 15;11(22):2735–9. PubMed PMID: 12374763; eng. PubMed

Kara NZ, Toker L, Agam G, et al. Trehalose induced antidepressant-like effects and autophagy enhancement in mice. Psychopharmacology (Berl). 2013. Sep;229(2):367–75. doi:10.1007/s00213-013-3119-4. PubMed PMID: 23644913. PubMed DOI

Nimmerjahn F, Milosevic S, Behrends U, et al. Major histocompatibility complex class II-restricted presentation of a cytosolic antigen by autophagy. Eur J Immunol. 2003. May;33(5):1250–9. PubMed PMID: 12731050; eng. PubMed

Guha P, Tyagi R, Chowdhury S, et al. IPMK Mediates Activation of ULK Signaling and Transcriptional Regulation of Autophagy Linked to Liver Inflammation and Regeneration. Cell Rep. 2019. Mar 5;26(10):2692–2703 e7. doi:10.1016/j.celrep.2019.02.013. PubMed PMID: 30840891; PubMed Central PMCID: PMCPMC6494083. PubMed DOI PMC

Beasley CL, Pennington K, Behan A, et al. Proteomic analysis of the anterior cingulate cortex in the major psychiatric disorders: Evidence for disease-associated changes. Proteomics. 2006. Jun;6(11):3414–25. doi:10.1002/pmic.200500069. PubMed PMID: 16637010. PubMed DOI

Behan AT, Byrne C, Dunn MJ, et al. Proteomic analysis of membrane microdomain-associated proteins in the dorsolateral prefrontal cortex in schizophrenia and bipolar disorder reveals alterations in LAMP, STXBP1 and BASP1 protein expression. Mol Psychiatry. 2009. Jun;14(6):601–13. doi:10.1038/mp.2008.7, PubMed PMID: 18268500. PubMed DOI

Chetcuti A, Adams LJ, Mitchell PB, et al. Microarray gene expression profiling of mouse brain mRNA in a model of lithium treatment. Psychiatr Genet. 2008. Apr;18(2):64–72. doi:10.1097/YPG.0b013e3282fb0051. PubMed PMID: 18349697. PubMed DOI

Focking M, Dicker P, English JA, et al. Common proteomic changes in the hippocampus in schizophrenia and bipolar disorder and particular evidence for involvement of cornu ammonis regions 2 and 3. Arch gen psychiatry. 2011. May;68(5):477–88. doi:10.1001/archgenpsychiatry.2011.43. PubMed PMID: 21536977. PubMed DOI

Nielsen J, Hoffert JD, Knepper MA, et al. Proteomic analysis of lithium-induced nephrogenic diabetes insipidus: mechanisms for aquaporin 2 down-regulation and cellular proliferation. Proc Natl Acad Sci U S A. 2008. Mar 4;105(9):3634–9. doi:10.1073/pnas.0800001105. PubMed PMID: 18296634; PubMed Central PMCID: PMC2265122. PubMed DOI PMC

Lu K, Psakhye I, Jentsch S.. Autophagic Clearance of PolyQ Proteins Mediated by Ubiquitin-Atg8 Adaptors of the Conserved CUET Protein Family. Cell. 2014. Jul 31;158(3):549–63. doi:10.1016/j.cell.2014.05.048. PubMed PMID: 25042851. PubMed DOI

Mesquita A, Cardenal-Munoz E, Dominguez E, et al. Autophagy in Dictyostelium: Mechanisms, regulation and disease in a simple biomedical model. Autophagy. 2017. Jan 2;13(1):24–40. doi:10.1080/15548627.2016.1226737. PubMed PMID: 27715405; PubMed Central PMCID: PMCPMC5240833. PubMed DOI PMC

Sampaio-Marques B, Pereira H, Santos AR, et al. Caloric restriction rescues yeast cells from alpha-synuclein toxicity through autophagic control of proteostasis. Aging (Albany NY). 2018. Dec 7;10(12):3821–3833. doi:10.18632/aging.101675. PubMed PMID: 30530923; PubMed Central PMCID: PMCPMC6326672. PubMed DOI PMC

Baker B, Geng S, Chen K, et al. Alteration of Lysosome Fusion and Low-grade Inflammation Mediated by Super-low-dose Endotoxin. J Biol Chem. 2015. Mar 6;290(10):6670–8. doi:10.1074/jbc.M114.611442. PubMed PMID: 25586187; PubMed Central PMCID: PMC4358298. PubMed DOI PMC

Li T, Hu J, Li L.. Characterization of Tollip protein upon Lipopolysaccharide challenge. Mol Immunol. 2004. May;41(1):85–92. doi:10.1016/j.molimm.2004.03.009. PubMed PMID: 15140579. PubMed DOI

Mitra S, Traughber CA, Brannon MK, et al. Ubiquitin interacts with the Tollip C2 and CUE domains and inhibits binding of Tollip to phosphoinositides. J Biol Chem. 2013. Sep 6;288(36):25780–91. doi:10.1074/jbc.M113.484170. PubMed PMID: 23880770; PubMed Central PMCID: PMCPMC3764785. PubMed DOI PMC

Chen K, Yuan R, Zhang Y, et al. Tollip Deficiency Alters Atherosclerosis and Steatosis by Disrupting Lipophagy. J Am Heart Assoc. 2017. Apr 10;6(4). doi:10.1161/JAHA.116.004078. PubMed PMID: 28396568; PubMed Central PMCID: PMCPMC5532987. PubMed DOI PMC

Chen K, Yuan R, Geng S, et al. Toll-interacting protein deficiency promotes neurodegeneration via impeding autophagy completion in high-fat diet-fed ApoE(-/-) mouse model. Brain Behav Immun. 2017. Jan;59:200–210. doi:10.1016/j.bbi.2016.10.002. PubMed PMID: 27720815; PubMed Central PMCID: PMCPMC5154796. PubMed DOI PMC

Tian Z, Wang C, Hu C, et al. Autophagic-lysosomal inhibition compromises ubiquitin-proteasome system performance in a p62 dependent manner in cardiomyocytes. PLoS One. 2014;9(6):e100715. doi:10.1371/journal.pone.0100715. PubMed PMID: 24959866; PubMed Central PMCID: PMCPMC4069113. PubMed DOI PMC

Mizushima N, Levine B.. Autophagy in mammalian development and differentiation. Nat Cell Biol. 2010. Sep;12(9):823–30. doi:10.1038/ncb0910-823. PubMed PMID: 20811354; PubMed Central PMCID: PMC3127249. eng. PubMed DOI PMC

Maloverjan A, Piirsoo M, Michelson P, et al. Identification of a novel serine/threonine kinase ULK3 as a positive regulator of Hedgehog pathway [Research Support, Non-U.S. Gov’t]. Exp Cell Res. 2010. Feb 15;316(4):627–37. doi:10.1016/j.yexcr.2009.10.018. PubMed PMID: 19878745; eng. PubMed DOI

Young ARJ, Narita M, Ferreira M, et al. Autophagy mediates the mitotic senescence transition. Genes Dev. 2009. Apr 1;23(7):798–803. doi:10.1101/gad.519709. PubMed PMID: 19279323; PubMed Central PMCID: PMC2666340. eng. PubMed DOI PMC

Chan EY, Tooze SA.. Evolution of Atg1 function and regulation [Review]. Autophagy. 2009. Aug;5(6):758–65. PubMed PMID: 19411825; eng. PubMed

Chan EYW, Kir S, Tooze SA.. siRNA screening of the kinome identifies ULK1 as a multidomain modulator of autophagy. J Biol Chem. 2007. Aug 31;282(35):25464–74. doi:M703663200[pii] doi:10.1074/jbc.M703663200. PubMed PMID: 17595159; eng. PubMed DOI

Fuqua JD, Mere CP, Kronemberger A, et al. ULK2 is essential for degradation of ubiquitinated protein aggregates and homeostasis in skeletal muscle. FASEB J. 2019. Nov;33(11):11735–11745. doi:10.1096/fj.201900766R. PubMed PMID: 31361156; PubMed Central PMCID: PMCPMC6902739. PubMed DOI PMC

Lee EJ, Tournier C.. The requirement of uncoordinated 51-like kinase 1 (ULK1) and ULK2 in the regulation of autophagy. Autophagy. 2011. Jul;7(7):689–95. doi:10.4161/auto.7.7.15450. PubMed PMID: 21460635; PubMed Central PMCID: PMCPMC3149696. PubMed DOI PMC

Ro SH, Jung CH, Hahn WS, et al. Distinct functions of Ulk1 and Ulk2 in the regulation of lipid metabolism in adipocytes. Autophagy. 2013. Dec;9(12):2103–14. doi:10.4161/auto.26563. PubMed PMID: 24135897; PubMed Central PMCID: PMCPMC4028344. PubMed DOI PMC

Shukla S, Patric IR, Patil V, et al. Methylation silencing of ULK2, an autophagy gene, is essential for astrocyte transformation and tumor growth. J Biol Chem. 2014. Aug 8;289(32):22306–18. doi:10.1074/jbc.M114.567032. PubMed PMID: 24923441; PubMed Central PMCID: PMCPMC4139240. PubMed DOI PMC

Balke D, Tatenhorst L, Dambeck V, et al. AAV-Mediated Expression of Dominant-Negative ULK1 Increases Neuronal Survival and Enhances Motor Performance in the MPTP Mouse Model of Parkinson’s Disease. Mol Neurobiol. 2019. Aug 24. doi:10.1007/s12035-019-01744-0. PubMed PMID: 31446549. PubMed DOI

Chan EYW, Longatti A, McKnight NC, et al. Kinase-inactivated ULK proteins inhibit autophagy via their conserved C-terminal domains using an Atg13-independent mechanism [Research Support, Non-U.S. Gov’t]. Mol Cell Biol. 2009. Jan;29(1):157–71. doi:10.1128/MCB.01082-08. PubMed PMID: 18936157; PubMed Central PMCID: PMC2612494. eng. PubMed DOI PMC

Joo JH, Dorsey FC, Joshi A, et al. Hsp90-Cdc37 chaperone complex regulates Ulk1- and Atg13-mediated mitophagy [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Mol Cell. 2011. Aug 19;43(4):572–85. doi:10.1016/j.molcel.2011.06.018. PubMed PMID: 21855797; eng. PubMed DOI PMC

Liu CC, Lin YC, Chen YH, et al. Cul3-KLHL20 Ubiquitin Ligase Governs the Turnover of ULK1 and VPS34 Complexes to Control Autophagy Termination. Mol Cell. 2016. Jan 7;61(1):84–97. doi:10.1016/j.molcel.2015.11.001. PubMed PMID: 26687681. PubMed DOI

Han SH, Korm S, Han YG, et al. GCA links TRAF6-ULK1-dependent autophagy activation in resistant chronic myeloid leukemia. Autophagy. 2019. Dec;15(12):2076–2090. doi:10.1080/15548627.2019.1596492. PubMed PMID: 30929559; PubMed Central PMCID: PMCPMC6844495. PubMed DOI PMC

Samari HR, Moller MT, Holden L, et al. Stimulation of hepatocytic AMP-activated protein kinase by okadaic acid and other autophagy-suppressive toxins. Biochem J. 2005. Mar 1;386(Pt 2):237–44. doi:10.1042/BJ20040609. PubMed PMID: 15461583; PubMed Central PMCID: PMC1134787. eng. PubMed DOI PMC

Carling D, Mayer FV, Sanders MJ, et al. AMP-activated protein kinase: nature’s energy sensor. Nat Chem Biol. 2011. Aug;7(8):512–8. doi:10.1038/nchembio.610. PubMed PMID: 21769098; eng. PubMed DOI

Puustinen P, Keldsbo A, Corcelle-Termeau E, et al. DNA-dependent protein kinase regulates lysosomal AMP-dependent protein kinase activation and autophagy. Autophagy. 2020. Jan 26:1–18. doi:10.1080/15548627.2019.1710430. PubMed PMID: 31983282. PubMed DOI PMC

Dando I, Donadelli M, Costanzo C, et al. Cannabinoids inhibit energetic metabolism and induce AMPK-dependent autophagy in pancreatic cancer cells. Cell Death Dis. 2013;4:e664. doi:10.1038/cddis.2013.151. PubMed PMID: 23764845; PubMed Central PMCID: PMC3698539. PubMed DOI PMC

Hawley SA, Ross FA, Chevtzoff C, et al. Use of cells expressing gamma subunit variants to identify diverse mechanisms of AMPK activation. Cell Metab. 2010. Jun 9;11(6):554–65. doi:10.1016/j.cmet.2010.04.001. PubMed PMID: 20519126; PubMed Central PMCID: PMC2935965. PubMed DOI PMC

Gross AS, Zimmermann A, Pendl T, et al. Acetyl-CoA carboxylase 1-dependent lipogenesis promotes autophagy downstream of AMPK. J Biol Chem. 2019. Aug 9;294(32):12020–12039. doi:10.1074/jbc.RA118.007020. PubMed PMID: 31209110; PubMed Central PMCID: PMCPMC6690696. PubMed DOI PMC

Nwadike C, Williamson LE, Gallagher LE, et al. AMPK Inhibits ULK1-Dependent Autophagosome Formation and Lysosomal Acidification via Distinct Mechanisms. Mol Cell Biol. 2018. May 15;38(10). doi: 10.1128/MCB.00023-18. PubMed PMID: 29507183; PubMed Central PMCID: PMCPMC5954193. PubMed DOI PMC

Ha S, Jeong SH, Yi K, et al. Phosphorylation of p62 by AMP-activated protein kinase mediates autophagic cell death in adult hippocampal neural stem cells. J Biol Chem. 2017. Aug 18;292(33):13795–13808. doi:10.1074/jbc.M117.780874. PubMed PMID: 28655770; PubMed Central PMCID: PMCPMC5566532. PubMed DOI PMC

Behrends C, Sowa ME, Gygi SP, et al. Network organization of the human autophagy system. Nature. 2010. Jul 1;466(7302):68–76. doi:10.1038/nature09204. PubMed PMID: 20562859; PubMed Central PMCID: PMC2901998. eng. PubMed DOI PMC

Chiacchiera F, Matrone A, Ferrari E, et al. p38alpha blockade inhibits colorectal cancer growth in vivo by inducing a switch from HIF1alpha- to FoxO-dependent transcription. Cell Death Differ. 2009. Sep;16(9):1203–14. doi:10.1038/cdd.2009.36. PubMed PMID: 19343039; eng. PubMed DOI

Kovács AL, Seglen PO.. Inhibition of hepatocytic protein degradation by methylaminopurines and inhibitors of protein synthesis. Biochim Biophys Acta. 1981. Aug 17;676(2):213–20. PubMed PMID: 7260116; eng. PubMed

Liu HY, Han J, Cao SY, et al. Hepatic autophagy is suppressed in the presence of insulin resistance and hyperinsulinemia: inhibition of FoxO1-dependent expression of key autophagy genes by insulin. J Biol Chem. 2009. Nov 6;284(45):31484–92. doi:10.1074/jbc.M109.033936. PubMed PMID: 19758991; PubMed Central PMCID: PMC2781544. eng. PubMed DOI PMC

Mammucari C, Milan G, Romanello V, et al. FoxO3 controls autophagy in skeletal muscle in vivo. Cell Metab. 2007. Dec;6(6):458–71. doi:10.1016/j.cmet.2007.11.001. PubMed PMID: 18054315; eng. PubMed DOI

Mihaylova MM, Vasquez DS, Ravnskjaer K, et al. Class IIa histone deacetylases are hormone-activated regulators of FOXO and mammalian glucose homeostasis. Cell. 2011. May 13;145(4):607–21. doi:10.1016/j.cell.2011.03.043. PubMed PMID: 21565617; PubMed Central PMCID: PMC3117637. eng. PubMed DOI PMC

Pfisterer SG, Mauthe M, Codogno P, et al. Ca2+/calmodulin-dependent kinase (CaMK) signaling via CaMKI and AMP-activated protein kinase contributes to the regulation of WIPI-1 at the onset of autophagy. Mol Pharmacol. 2011. Sep 6;80:1066–75. doi:10.1124/mol.111.071761. PubMed PMID: 21896713; Eng. PubMed DOI

Rodgers JT, Lerin C, Gerhart-Hines Z, et al. Metabolic adaptations through the PGC-1 alpha and SIRT1 pathways. FEBS Lett. 2008. Jan 9;582(1):46–53. doi:10.1016/j.febslet.2007.11.034. PubMed PMID: 18036349; PubMed Central PMCID: PMC2275806. eng. PubMed DOI PMC

Samari HR, Seglen PO.. Inhibition of hepatocytic autophagy by adenosine, aminoimidazole-4-carboxamide riboside, and N6-mercaptopurine riboside. Evidence for involvement of amp-activated protein kinase. J Biol Chem. 1998. Sep 11;273(37):23758–63. PubMed PMID: 9726984; eng. PubMed

Sanchez AM, Csibi A, Raibon A, et al. AMPK promotes skeletal muscle autophagy through activation of Forkhead FoxO3a and interaction with Ulk1. J Cell Biochem. 2011. Oct 17. doi:10.1002/jcb.23399. PubMed PMID: 22006269; Eng. PubMed DOI

Cardenas C, Miller RA, Smith I, et al. Essential regulation of cell bioenergetics by constitutive InsP3 receptor Ca2+ transfer to mitochondria [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Cell. 2010. Jul 23;142(2):270–83. doi:10.1016/j.cell.2010.06.007. PubMed PMID: 20655468; PubMed Central PMCID: PMC2911450. eng. PubMed DOI PMC

Dalle Pezze P, Ruf S, Sonntag AG, et al. A systems study reveals concurrent activation of AMPK and mTOR by amino acids. Nat Commun. 2016. Nov 21;7:13254. doi:10.1038/ncomms13254. PubMed PMID: 27869123; PubMed Central PMCID: PMCPMC5121333. PubMed DOI PMC

Inoki K, Zhu T, Guan KL.. TSC2 mediates cellular energy response to control cell growth and survival. Cell. 2003. Nov 26;115(5):577–90. PubMed PMID: 14651849; eng. PubMed

Egan D, Kim J, Shaw RJ, et al. The autophagy initiating kinase ULK1 is regulated via opposing phosphorylation by AMPK and mTOR. Autophagy. 2011. Jun;7(6):643–4. PubMed PMID: 21460621; eng. PubMed PMC

Egan DF, Shackelford DB, Mihaylova MM, et al. Phosphorylation of ULK1 (hATG1) by AMP-activated protein kinase connects energy sensing to mitophagy [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Science. 2011. Jan 28;331(6016):456–61. doi:10.1126/science.1196371. PubMed PMID: 21205641; PubMed Central PMCID: PMC3030664. eng. PubMed DOI PMC

Kim J, Kundu M, Viollet B, et al. AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1 [Research Support, N.I.H., Extramural]. Nat Cell Biol. 2011. Feb;13(2):132–41. doi:10.1038/ncb2152. PubMed PMID: 21258367; eng. PubMed DOI PMC

Sharma A, Singh K, Mazumder S, et al. BECN1 and BIM interactions with MCL-1 determine fludarabine resistance in leukemic B cells. Cell Death Dis. 2013;4:e628. doi:10.1038/cddis.2013.155. PubMed PMID: 23681223; PubMed Central PMCID: PMC3674362. PubMed DOI PMC

Zhou G, Myers R, Li Y, et al. Role of AMP-activated protein kinase in mechanism of metformin action. J Clin Invest. 2001. Oct;108(8):1167–74. doi:10.1172/JCI13505. PubMed PMID: 11602624; PubMed Central PMCID: PMC209533. eng. PubMed DOI PMC

Emerling BM, Viollet B, Tormos KV, et al. Compound C inhibits hypoxic activation of HIF-1 independent of AMPK. FEBS Lett. 2007. Dec 11;581(29):5727–31. doi:10.1016/j.febslet.2007.11.038. PubMed PMID: 18036344; PubMed Central PMCID: PMC2169511. eng. PubMed DOI PMC

Vucicevic L, Misirkic M, Janjetovic K, et al. Compound C induces protective autophagy in cancer cells through AMPK inhibition-independent blockade of Akt/mTOR pathway. Autophagy. 2011. Jan;7(1):40–50. PubMed PMID: 20980833; eng. PubMed

Ezquerro S, Mocha F, Fruhbeck G, et al. Ghrelin Reduces TNF-alpha-Induced Human Hepatocyte Apoptosis, Autophagy, and Pyroptosis: Role in Obesity-Associated NAFLD. J Clin Endocrinol Metab. 2019. Jan 1;104(1):21–37. doi:10.1210/jc.2018-01171. PubMed PMID: 30137403. PubMed DOI

Meley D, Bauvy C, Houben-Weerts JH, et al. AMP-activated protein kinase and the regulation of autophagic proteolysis. J Biol Chem. 2006. Nov 17;281(46):34870–9. doi:10.1074/jbc.M605488200. PubMed PMID: 16990266; eng. PubMed DOI

Grotemeier A, Alers S, Pfisterer SG, et al. AMPK-independent induction of autophagy by cytosolic Ca2+ increase. Cell Signal. 2010. Jun;22(6):914–25. doi:10.1016/j.cellsig.2010.01.015. PubMed PMID: 20114074; eng. PubMed DOI

Williams T, Forsberg LJ, Viollet B, et al. Basal autophagy induction without AMP-activated protein kinase under low glucose conditions. Autophagy. 2009. Nov;5(8):1155–65. PubMed PMID: 19844161; eng. PubMed PMC

Beck-Wodl S, Harzer K, Sturm M, et al. Homozygous TBC1 domain-containing kinase (TBCK) mutation causes a novel lysosomal storage disease - a new type of neuronal ceroid lipofuscinosis (CLN15)? Acta Neuropathol Commun. 2018. Dec 27;6(1):145. doi:10.1186/s40478-018-0646-6. PubMed PMID: 30591081; PubMed Central PMCID: PMCPMC6307319. PubMed DOI PMC

Liu Y, Yan X, Zhou T.. TBCK influences cell proliferation, cell size and mTOR signaling pathway. PLoS One. 2013;8(8):e71349. doi:10.1371/journal.pone.0071349. PubMed PMID: 23977024; PubMed Central PMCID: PMCPMC3747267. PubMed DOI PMC

Li W, Han M, Guan KL.. The leucine-rich repeat protein SUR-8 enhances MAP kinase activation and forms a complex with Ras and Raf. Genes Dev. 2000. Apr 15;14(8):895–900. PubMed PMID: 10783161; PubMed Central PMCID: PMCPMC316541. PubMed PMC

Sieburth DS, Sun Q, Han M.. SUR-8, a conserved Ras-binding protein with leucine-rich repeats, positively regulates Ras-mediated signaling in C. elegans. Cell. 1998. Jul 10;94(1):119–30. PubMed PMID: 9674433. PubMed

Xie CM, The Sun Y.. MTORC1-mediated autophagy is regulated by the FBXW7-SHOC2-RPTOR axis. Autophagy. 2019. Aug;15(8):1470–1472. doi:10.1080/15548627.2019.1609864. PubMed PMID: 31010381; PubMed Central PMCID: PMCPMC6613887. PubMed DOI PMC

Xie CM, Tan M, Lin XT, et al. The FBXW7-SHOC2-Raptor Axis Controls the Cross-Talks between the RAS-ERK and mTORC1 Signaling Pathways. Cell Rep. 2019. Mar 12;26(11):3037–3050 e4. doi:10.1016/j.celrep.2019.02.052. PubMed PMID: 30865892; PubMed Central PMCID: PMCPMC6503676. PubMed DOI PMC

Shang L, Chen S, Du F, et al. Nutrient starvation elicits an acute autophagic response mediated by Ulk1 dephosphorylation and its subsequent dissociation from AMPK. Proc Natl Acad Sci U S A. 2011. Mar 22;108(12):4788–93. doi:10.1073/pnas.1100844108. PubMed PMID: 21383122; PubMed Central PMCID: PMC3064373. eng. PubMed DOI PMC

Gwinn DM, Shackelford DB, Egan DF, et al. AMPK phosphorylation of raptor mediates a metabolic checkpoint [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Mol Cell. 2008. Apr 25;30(2):214–26. doi:10.1016/j.molcel.2008.03.003. PubMed PMID: 18439900; PubMed Central PMCID: PMC2674027. eng. PubMed DOI PMC

Guha P, Snyder SH.. Noncatalytic functions of IPMK are essential for activation of autophagy and liver regeneration. Autophagy. 2019. Aug;15(8):1473–1474. doi:10.1080/15548627.2019.1615305. PubMed PMID: 31066329; PubMed Central PMCID: PMCPMC6613895. PubMed DOI PMC

Li Z, Tian X, Ji X, et al. ULK1-ATG13 and their mitotic phospho-regulation by CDK1 connect autophagy to cell cycle. PLoS Biol. 2020. Jun;18(6):e3000288. doi:10.1371/journal.pbio.3000288. PubMed PMID: 32516310; PubMed Central PMCID: PMCPMC7282624. PubMed DOI PMC

Liu Z, Sin KWT, Ding H, et al. p38beta MAPK mediates ULK1-dependent induction of autophagy in skeletal muscle of tumor-bearing mice. Cell Stress. 2018. Oct 10;2(11):311–324. doi:10.15698/cst2018.11.163. PubMed PMID: 31225455; PubMed Central PMCID: PMCPMC6551802. PubMed DOI PMC

Alers S, Löffler AS, Paasch F, et al. Atg13 and FIP200 act independently of Ulk1 and Ulk2 in autophagy induction. Autophagy. 2011. Dec 1;7(12):1424–1433. PubMed PMID: 22024743; Eng. PubMed PMC

Bach M, Larance M, James DE, et al. The serine/threonine kinase ULK1 is a target of multiple phosphorylation events. Biochem J. 2011. Dec 1;440(2):283–91. doi:10.1042/BJ20101894. PubMed PMID: 21819378. PubMed DOI

Egan DF, Chun MG, Vamos M, et al. Small Molecule Inhibition of the Autophagy Kinase ULK1 and Identification of ULK1 Substrates. Mol Cell. 2015. Jul 16;59(2):285–97. doi:10.1016/j.molcel.2015.05.031. PubMed PMID: 26118643; PubMed Central PMCID: PMCPMC4530630. PubMed DOI PMC

Lazarus MB, Novotny CJ, Shokat KM.. Structure of the human autophagy initiating kinase ULK1 in complex with potent inhibitors. ACS Chem Biol. 2015. Jan 16;10(1):257–61. doi:10.1021/cb500835z. PubMed PMID: 25551253; PubMed Central PMCID: PMCPMC4301081. PubMed DOI PMC

Dorsey FC, Rose KL, Coenen S, et al. Mapping the phosphorylation sites of Ulk1. J Proteome Res. 2009. Nov;8(11):5253–63. doi:10.1021/pr900583m. PubMed PMID: 19807128. PubMed DOI

Ganley IG, Lam du H, Wang J, et al. ULK1.ATG13.FIP200 complex mediates mTOR signaling and is essential for autophagy. J Biol Chem. 2009. May 1;284(18):12297–305. doi:10.1074/jbc.M900573200. PubMed PMID: 19258318; PubMed Central PMCID: PMC2673298. PubMed DOI PMC

Hara T, Takamura A, Kishi C, et al. FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells. J Cell Biol. 2008. May 5;181(3):497–510. doi:jcb.200712064 [pii] doi:10.1083/jcb.200712064. PubMed PMID: 18443221; PubMed Central PMCID: PMC2364687. eng. PubMed DOI PMC

Hosokawa N, Hara T, Kaizuka T, et al. Nutrient-dependent mTORC1 association with the ULK1-Atg13-FIP200 complex required for autophagy. Mol Biol Cell. 2009. Apr;20(7):1981–91. doi:10.1091/mbc.E08-12-1248. PubMed PMID: 19211835; PubMed Central PMCID: PMC2663915. eng. PubMed DOI PMC

Jung CH, Jun CB, Ro S-H, et al. ULK-Atg13-FIP200 complexes mediate mTOR signaling to the autophagy machinery. Mol Biol Cell. 2009. Apr;20(7):1992–2003. doi:10.1091/mbc.E08-12-1249. PubMed PMID: 19225151; PubMed Central PMCID: PMC2663920. eng. PubMed DOI PMC

Park JM, Jung CH, Seo M, et al. The ULK1 complex mediates MTORC1 signaling to the autophagy initiation machinery via binding and phosphorylating ATG14. Autophagy. 2016;12(3):547–64. doi:10.1080/15548627.2016.1140293. PubMed PMID: 27046250; PubMed Central PMCID: PMCPMC4835982. PubMed DOI PMC

Di Bartolomeo S, Corazzari M, Nazio F, et al. The dynamic interaction of AMBRA1 with the dynein motor complex regulates mammalian autophagy. J Cell Biol. 2010. Oct 4;191(1):155–68. doi:10.1083/jcb.201002100. PubMed PMID: 20921139; PubMed Central PMCID: PMC2953445. eng. PubMed DOI PMC

Ma X, Zhang S, He L, et al. MTORC1-mediated NRBF2 phosphorylation functions as a switch for the class III PtdIns3K and autophagy. Autophagy. 2017. Mar 4;13(3):592–607. doi:10.1080/15548627.2016.1269988. PubMed PMID: 28059666; PubMed Central PMCID: PMCPMC5361594. PubMed DOI PMC

Russell RC, Tian Y, Yuan H, et al. ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase. Nat Cell Biol. 2013. Jul;15(7):741–50. doi:10.1038/ncb2757. PubMed PMID: 23685627; PubMed Central PMCID: PMC3885611. PubMed DOI PMC

Park JM, Seo M, Jung CH, et al. ULK1 phosphorylates Ser30 of BECN1 in association with ATG14 to stimulate autophagy induction. Autophagy. 2018;14(4):584–597. doi:10.1080/15548627.2017.1422851. PubMed PMID: 29313410; PubMed Central PMCID: PMCPMC5959323. PubMed DOI PMC

Zhou C, Ma K, Gao R, et al. Regulation of mATG9 trafficking by Src- and ULK1-mediated phosphorylation in basal and starvation-induced autophagy. Cell Res. 2017. Feb;27(2):184–201. doi:10.1038/cr.2016.146. PubMed PMID: 27934868; PubMed Central PMCID: PMCPMC5339848. PubMed DOI PMC

Pengo N, Agrotis A, Prak K, et al. A reversible phospho-switch mediated by ULK1 regulates the activity of autophagy protease ATG4B. Nat Commun. 2017. Aug 18;8(1):294. doi:10.1038/s41467-017-00303-2. PubMed PMID: 28821708; PubMed Central PMCID: PMCPMC5562857. PubMed DOI PMC

Alsaadi RM, Losier TT, Tian W, et al. ULK1-mediated phosphorylation of ATG16L1 promotes xenophagy, but destabilizes the ATG16L1 Crohn’s mutant. EMBO Rep. 2019. Jul;20(7):e46885. doi:10.15252/embr.201846885. PubMed PMID: 31267703; PubMed Central PMCID: PMCPMC6607016. PubMed DOI PMC

Löffler AS, Alers S, Dieterle AM, et al. Ulk1-mediated phosphorylation of AMPK constitutes a negative regulatory feedback loop. Autophagy. 2011. Jul;7(7):696–706. PubMed PMID: 21460634; eng. PubMed

Dunlop EA, Hunt DK, Acosta-Jaquez HA, et al. ULK1 inhibits mTORC1 signaling, promotes multisite Raptor phosphorylation and hinders substrate binding. Autophagy. 2011. Jul;7(7):737–47. PubMed PMID: 21460630; PubMed Central PMCID: PMC3149699. PubMed PMC

Dunlop EA, Seifan S, Claessens T, et al. FLCN, a novel autophagy component, interacts with GABARAP and is regulated by ULK1 phosphorylation. Autophagy. 2014. Oct 1;10(10):1749–60. doi:10.4161/auto.29640. PubMed PMID: 25126726; PubMed Central PMCID: PMC4198360. PubMed DOI PMC

Li TY, Sun Y, Liang Y, et al. ULK1/2 Constitute a Bifurcate Node Controlling Glucose Metabolic Fluxes in Addition to Autophagy. Mol Cell. 2016. May 5;62(3):359–370. doi:10.1016/j.molcel.2016.04.009. PubMed PMID: 27153534. PubMed DOI

Lim J, Lachenmayer ML, Wu S, et al. Proteotoxic stress induces phosphorylation of p62/SQSTM1 by ULK1 to regulate selective autophagic clearance of protein aggregates. PLoS Genet. 2015;11(2):e1004987. doi:10.1371/journal.pgen.1004987. PubMed PMID: 25723488; PubMed Central PMCID: PMCPMC4344198. PubMed DOI PMC

Sellier C, Campanari ML, Julie Corbier C, et al. Loss of C9ORF72 impairs autophagy and synergizes with polyQ Ataxin-2 to induce motor neuron dysfunction and cell death. EMBO J. 2016. Jun 15;35(12):1276–97. doi:10.15252/embj.201593350. PubMed PMID: 27103069; PubMed Central PMCID: PMCPMC4910533. PubMed DOI PMC

Tang HW, Wang YB, Wang SL, et al. Atg1-mediated myosin II activation regulates autophagosome formation during starvation-induced autophagy. EMBO J. 2011. Feb 16;30(4):636–51. doi:10.1038/emboj.2010.338. PubMed PMID: 21169990; PubMed Central PMCID: PMC3041946. eng. PubMed DOI PMC

Xu J, Fotouhi M, McPherson PS.. Phosphorylation of the exchange factor DENND3 by ULK in response to starvation activates Rab12 and induces autophagy. EMBO Rep. 2015. Jun;16(6):709–18. doi:10.15252/embr.201440006. PubMed PMID: 25925668; PubMed Central PMCID: PMCPMC4467855. PubMed DOI PMC

Jung CH, Seo M, Otto NM, et al. ULK1 inhibits the kinase activity of mTORC1 and cell proliferation. Autophagy. 2011. Oct 1;7(10):1212–21. PubMed PMID: 21795849; Eng. PubMed PMC

Gan W, Zhang C, Siu KY, et al. ULK1 phosphorylates Sec23A and mediates autophagy-induced inhibition of ER-to-Golgi traffic. BMC Cell Biol. 2017. May 10;18(1):22. doi:10.1186/s12860-017-0138-8. PubMed PMID: 28486929; PubMed Central PMCID: PMCPMC5424413. PubMed DOI PMC

Joo JH, Wang B, Frankel E, et al. The noncanonical role of ULK/ATG1 in ER-to-Golgi trafficking is essential for cellular homeostasis. Mol Cell. 2016. May 19;62(4):491–506. doi:10.1016/j.molcel.2016.04.020. PubMed PMID: 27203176; PubMed Central PMCID: PMCPMC4993601. PubMed DOI PMC

Konno H, Konno K, Barber GN.. Cyclic dinucleotides trigger ULK1 (ATG1) phosphorylation of STING to prevent sustained innate immune signaling. Cell. 2013. Oct 24;155(3):688–98. doi:10.1016/j.cell.2013.09.049. PubMed PMID: 24119841; PubMed Central PMCID: PMCPMC3881181. PubMed DOI PMC

Hwang SH, Bang S, Kang KS, et al. ULK1 negatively regulates Wnt signaling by phosphorylating Dishevelled. Biochem Biophys Res Commun. 2019. Jan 1;508(1):308–313. doi:10.1016/j.bbrc.2018.11.139. PubMed PMID: 30497781. PubMed DOI

Jeong YT, Simoneschi D, Keegan S, et al. The ULK1-FBXW5-SEC23B nexus controls autophagy. eLife. 2018. Dec 31;7. doi:10.7554/eLife.42253. PubMed PMID: 30596474; PubMed Central PMCID: PMCPMC6351106. PubMed DOI PMC

Li R, Yuan F, Fu W, et al. Serine/threonine kinase Unc-51-like kinase-1 (Ulk1) phosphorylates the co-chaperone cell division cycle protein 37 (Cdc37) and thereby disrupts the stability of Cdc37 client proteins. J Biol Chem. 2017. Feb 17;292(7):2830–2841. doi:10.1074/jbc.M116.762443. PubMed PMID: 28073914; PubMed Central PMCID: PMCPMC5314178. PubMed DOI PMC

Rajesh S, Bago R, Odintsova E, et al. Binding to syntenin-1 protein defines a new mode of ubiquitin-based interactions regulated by phosphorylation. J Biol Chem. 2011. Nov 11;286(45):39606–14. doi:10.1074/jbc.M111.262402. PubMed PMID: 21949238; PubMed Central PMCID: PMCPMC3234783. PubMed DOI PMC

Kim K, Park SG, Park BC, et al. Serine 389 phosphorylation of 3-phosphoinositide-dependent kinase 1 by UNC-51-like kinase 1 affects its ability to regulate Akt and p70 S6kinase. BMB Rep. 2020. Apr 22. PubMed PMID: 32317083. PubMed PMC

Saleiro D, Mehrotra S, Kroczynska B, et al. Central role of ULK1 in type I interferon signaling. Cell Rep. 2015. Apr 28;11(4):605–17. doi:10.1016/j.celrep.2015.03.056. PubMed PMID: 25892232; PubMed Central PMCID: PMCPMC4477687. PubMed DOI PMC

Shibata S, Ishizawa K, Wang Q, et al. ULK1 Phosphorylates and Regulates Mineralocorticoid Receptor. Cell Rep. 2018. Jul 17;24(3):569–576. doi:10.1016/j.celrep.2018.06.072. PubMed PMID: 30021155. PubMed DOI

Wang B, Maxwell BA, Joo JH, et al. ULK1 and ULK2 regulate stress granule disassembly through phosphorylation and activation of VCP/p97. Mol Cell. 2019. May 16;74(4):742–757 e8. doi:10.1016/j.molcel.2019.03.027. PubMed PMID: 30979586; PubMed Central PMCID: PMCPMC6859904. PubMed DOI PMC

Yuan F, Jin X, Li D, et al. ULK1 phosphorylates Mad1 to regulate spindle assembly checkpoint. Nucleic Acids Res. 2019. Sep 5;47(15):8096–8110. doi:10.1093/nar/gkz602. PubMed PMID: 31291454; PubMed Central PMCID: PMCPMC6736072. PubMed DOI PMC

Zhao P, Wong KI, Sun X, et al. TBK1 at the Crossroads of Inflammation and Energy Homeostasis in Adipose Tissue. Cell. 2018. Feb 8;172(4):731–743 e12. doi:10.1016/j.cell.2018.01.007. PubMed PMID: 29425491; PubMed Central PMCID: PMCPMC5808582. PubMed DOI PMC

Tyra LK, Nandi N, Tracy C, et al. Yorkie growth-promoting activity is limited by Atg1-mediated phosphorylation. Dev Cell. 2020. Mar 9;52(5):605–616 e7. doi:10.1016/j.devcel.2020.01.011. PubMed PMID: 32032548; PubMed Central PMCID: PMCPMC7105283. PubMed DOI PMC

Mao L, Zhan YY, Wu B, et al. ULK1 phosphorylates Exo70 to suppress breast cancer metastasis. Nat Commun. 2020. Jan 8;11(1):117. doi:10.1038/s41467-019-13923-7. PubMed PMID: 31913283; PubMed Central PMCID: PMCPMC6949295. PubMed DOI PMC

Wu W, Wang X, Berleth N, et al. The autophagy-initiating kinase ULK1 controls RIPK1-mediated cell death. Cell Rep. 2020. Apr 21;31(3):107547. doi:10.1016/j.celrep.2020.107547. PubMed PMID: 32320653. PubMed DOI

Wu W, Tian W, Hu Z, et al. ULK1 translocates to mitochondria and phosphorylates FUNDC1 to regulate mitophagy. EMBO Rep. 2014. May;15(5):566–75. doi:10.1002/embr.201438501. PubMed PMID: 24671035; PubMed Central PMCID: PMCPMC4210082. PubMed DOI PMC

Brunn GJ, Hudson CC, Sekulic A, et al. Phosphorylation of the translational repressor PHAS-I by the mammalian target of rapamycin. Science. 1997. Jul 4;277(5322):99–101. PubMed PMID: 9204908; eng. PubMed

Erlich S, Alexandrovich A, Shohami E, et al. Rapamycin is a neuroprotective treatment for traumatic brain injury. Neurobiol Dis. 2007. Apr;26(1):86–93. PubMed PMID: 17270455; eng. PubMed

Lavieu G, Scarlatti F, Sala G, et al. Regulation of autophagy by sphingosine kinase 1 and its role in cell survival during nutrient starvation. J Biol Chem. 2006. Mar 31;281(13):8518–27. PubMed PMID: 16415355; eng. PubMed

Yip CK, Murata K, Walz T, et al. Structure of the human mTOR complex I and its implications for rapamycin inhibition. Mol Cell. 2010. Jun 11;38(5):768–74. doi:10.1016/j.molcel.2010.05.017. PubMed PMID: 20542007; PubMed Central PMCID: PMC2887672. eng. PubMed DOI PMC

Roux PP, Shahbazian D, Vu H, et al. RAS/ERK signaling promotes site-specific ribosomal protein S6 phosphorylation via RSK and stimulates cap-dependent translation. J Biol Chem. 2007. May 11;282(19):14056–64. doi:10.1074/jbc.M700906200. PubMed PMID: 17360704; PubMed Central PMCID: PMCPMC3618456. PubMed DOI PMC

Nazio F, Strappazzon F, Antonioli M, et al. mTOR inhibits autophagy by controlling ULK1 ubiquitylation, self-association and function through AMBRA1 and TRAF6. Nat Cell Biol. 2013. Apr;15(4):406–16. doi:10.1038/ncb2708. PubMed PMID: 23524951. PubMed DOI

Cheong H, Nair U, Geng J, et al. The Atg1 kinase complex is involved in the regulation of protein recruitment to initiate sequestering vesicle formation for nonspecific autophagy in Saccharomyces cerevisiae. Mol Biol Cell. 2008. Feb;19(2):668–81. doi:10.1091/mbc.E07-08-0826. PubMed PMID: 18077553; PubMed Central PMCID: PMC2230592. eng. PubMed DOI PMC

Kabeya Y, Kamada Y, Baba M, et al. Atg17 functions in cooperation with Atg1 and Atg13 in yeast autophagy. Mol Biol Cell. 2005. May;16(5):2544–53. doi:10.1091/mbc.E04-08-0669. PubMed PMID: 15743910; PubMed Central PMCID: PMC1087256. eng. PubMed DOI PMC

Kamada Y, Funakoshi T, Shintani T, et al. Tor-mediated induction of autophagy via an Apg1 protein kinase complex. J Cell Biol. 2000. Sep 18;150(6):1507–13. PubMed PMID: 10995454; eng. PubMed PMC

Scott SV, Nice DC, III, Nau JJ, et al. Apg13p and Vac8p are part of a complex of phosphoproteins that are required for cytoplasm to vacuole targeting. J Biol Chem. 2000. Aug 18;275(33):25840–9. doi:10.1074/jbc.M002813200. PubMed PMID: 10837477; eng. PubMed DOI

Miller-Fleming L, Cheong H, Antas P, et al. Detection of Saccharomyces cerevisiae Atg13 by western blot. Autophagy. 2014. Mar;10(3):514–7. doi:10.4161/auto.27707. PubMed PMID: 24430166; PubMed Central PMCID: PMC4077888. PubMed DOI PMC

Mao K, Wang K, Zhao M, et al. Two MAPK-signaling pathways are required for mitophagy in Saccharomyces cerevisiae. J Cell Biol. 2011. May 16;193(4):755–67. doi:10.1083/jcb.201102092. PubMed PMID: 21576396; eng. PubMed DOI PMC

Yeh YY, Wrasman K, Herman PK.. Autophosphorylation within the Atg1 activation loop is required for both kinase activity and the induction of autophagy in Saccharomyces cerevisiae. Genetics. 2010. Jul;185(3):871–82. doi:10.1534/genetics.110.116566. PubMed PMID: 20439775; PubMed Central PMCID: PMC2907206. eng. PubMed DOI PMC

Kim M, Park HL, Park HW, et al. Drosophila Fip200 is an essential regulator of autophagy that attenuates both growth and aging. Autophagy. 2013. Aug;9(8):1201–13. doi:10.4161/auto.24811. PubMed PMID: 23819996; PubMed Central PMCID: PMC3748192. PubMed DOI PMC

Nagy P, Karpati M, Varga A, et al. Atg17/FIP200 localizes to perilysosomal Ref(2)P aggregates and promotes autophagy by activation of Atg1 in Drosophila. Autophagy. 2014. Mar;10(3):453–67. doi:10.4161/auto.27442. PubMed PMID: 24419107; PubMed Central PMCID: PMC4077884. PubMed DOI PMC

Shang L, AMP Wang X.. K and mTOR coordinate the regulation of Ulk1 and mammalian autophagy initiation. Autophagy. 2011. Aug;7(8):924–6. PubMed PMID: 21521945. PubMed

Singh K, Matsuyama S, Drazba JA, et al. Autophagy-dependent senescence in response to DNA damage and chronic apoptotic stress. Autophagy. 2012;8(2):236-51. doi:10.4161/auto.8.2.18600. PMID: 22240589; PMCID: PMC3336077 PubMed DOI PMC

Karanasios E, Stapleton E, Manifava M, et al. Dynamic association of the ULK1 complex with omegasomes during autophagy induction. J Cell Sci. 2013. Nov 15;126(Pt 22):5224–38. doi:10.1242/jcs.132415. PubMed PMID: 24013547. PubMed DOI

Karanasios E, Walker SA, Okkenhaug H, et al. Autophagy initiation by ULK complex assembly on ER tubulovesicular regions marked by ATG9 vesicles. Nat Commun. 2016. Aug 11;7:12420. doi:10.1038/ncomms12420. PubMed PMID: 27510922; PubMed Central PMCID: PMCPMC4987534. PubMed DOI PMC

Follo C, Barbone D, Richards WG, et al. Autophagy initiation correlates with the autophagic flux in 3D models of mesothelioma and with patient outcome. Autophagy. 2016. Jul 2;12(7):1180–94. . PubMed PMID: 27097020; PubMed Central PMCID: PMCPMC4990992. PubMed PMC

Follo C, Cheng Y, Richards WG, et al. Inhibition of autophagy initiation potentiates chemosensitivity in mesothelioma. Mol Carcinog. 2018. Mar;57(3):319–332. doi:10.1002/mc.22757. PubMed PMID: 29073722. PubMed DOI

Li W, Zou W, Yang Y, et al. Autophagy genes function sequentially to promote apoptotic cell corpse degradation in the engulfing cell. J Cell Biol. 2012. Apr 2;197(1):27–35. doi:10.1083/jcb.201111053. PubMed PMID: 22451698; PubMed Central PMCID: PMC3317810. PubMed DOI PMC

Fazeli G, Trinkwalder M, Irmisch L, et al. C. elegans midbodies are released, phagocytosed and undergo LC3-dependent degradation independent of macroautophagy. J Cell Sci. 2016. Oct 15;129(20):3721–3731. doi:10.1242/jcs.190223. PubMed PMID: 27562069; PubMed Central PMCID: PMCPMC5087666. PubMed DOI PMC

Ruck A, Attonito J, Garces KT, et al. The Atg6/Vps30/Beclin 1 ortholog BEC-1 mediates endocytic retrograde transport in addition to autophagy in C. elegans. Autophagy. 2011. Apr;7(4):386–400. PubMed PMID: 21183797; PubMed Central PMCID: PMC3108013. PubMed PMC

De Faveri F, Chvanov M, Voronina S, et al. LAP-like non-canonical autophagy and evolution of endocytic vacuoles in pancreatic acinar cells. Autophagy. 2020. Jul;16(7):1314–1331. doi:10.1080/15548627.2019.1679514. PubMed PMID: 31651224. PubMed DOI PMC

Cunha LD, Yang M, Carter R, et al. LC3-Associated Phagocytosis in Myeloid Cells Promotes Tumor Immune Tolerance. Cell. 2018. Oct 4;175(2):429–441 e16. doi:10.1016/j.cell.2018.08.061. PubMed PMID: 30245008; PubMed Central PMCID: PMCPMC6201245. PubMed DOI PMC

Dohmen M, Krieg S, Agalaridis G, et al. AMPK-dependent activation of the Cyclin Y/CDK16 complex controls autophagy. Nat Commun. 2020. Feb 25;11(1):1032. doi:10.1038/s41467-020-14812-0. PubMed PMID: 32098961; PubMed Central PMCID: PMCPMC7042329. PubMed DOI PMC

Cap M, Stepanek L, Harant K, et al. Cell differentiation within a yeast colony: metabolic and regulatory parallels with a tumor-affected organism. Mol Cell. 2012. May 25;46(4):436–48. doi:10.1016/j.molcel.2012.04.001. PubMed PMID: 22560924. PubMed DOI

Djavaheri-Mergny M, Amelotti M, Mathieu J, et al. NF-[kappa]B activation represses tumor necrosis factor-alpha-induced autophagy. J Biol Chem. 2006. Oct 13;281(41):30373–82. PubMed PMID: 16857678; eng. PubMed

Liu Z, Lenardo MJ.. Reactive oxygen species regulate autophagy through redox-sensitive proteases. Dev Cell. 2007. Apr;12(4):484–5. PubMed PMID: 17419989; eng. PubMed

Scarlatti F, Bauvy C, Ventruti A, et al. Ceramide-mediated macroautophagy involves inhibition of protein kinase B and up-regulation of beclin 1. J Biol Chem. 2004. Apr 30;279(18):18384–91. PubMed PMID: 14970205; eng. PubMed

Scherz-Shouval R, Shvets E, Fass E, et al. Reactive oxygen species are essential for autophagy and specifically regulate the activity of Atg4. EMBO J. 2007. Apr 4;26(7):1749–60. PubMed PMID: 17347651; eng. PubMed PMC

Pereira O, Teixeira A, Sampaio-Marques B, et al. Signalling mechanisms that regulate metabolic profile and autophagy of acute myeloid leukaemia cells. J Cell Mol Med. 2018. Oct;22(10):4807–4817. doi:10.1111/jcmm.13737. PubMed PMID: 30117681; PubMed Central PMCID: PMCPMC6156238. PubMed DOI PMC

Sujobert P, Poulain L, Paubelle E, et al. Co-activation of AMPK and mTORC1 induces cytotoxicity in acute myeloid leukemia. Cell Rep. 2015. Jun 9;11(9):1446–57. doi:10.1016/j.celrep.2015.04.063. PubMed PMID: 26004183. PubMed DOI

Datan E, Shirazian A, Benjamin S, et al. mTOR/p70S6K signaling distinguishes routine, maintenance-level autophagy from autophagic cell death during influenza A infection. Virology. 2014. Mar;452-453:175–190. doi:10.1016/j.virol.2014.01.008. PubMed PMID: 24606695; PubMed Central PMCID: PMCPMC4005847. PubMed DOI PMC

Zeng X, Kinsella TJ.. Mammalian target of rapamycin and S6 kinase 1 positively regulate 6-thioguanine-induced autophagy. Cancer Res. 2008. Apr 1;68(7):2384–90. doi:10.1158/0008-5472.CAN-07-6163. PubMed PMID: 18381446; eng. PubMed DOI

Lee JW, Nam H, Kim LE, et al. TLR4 (toll-like receptor 4) activation suppresses autophagy through inhibition of FOXO3 and impairs phagocytic capacity of microglia. Autophagy. 2019. May;15(5):753–770. doi:10.1080/15548627.2018.1556946. PubMed PMID: 30523761; PubMed Central PMCID: PMCPMC6526818. PubMed DOI PMC

Losier TT, Russell RC.. Bacterial outer membrane vesicles trigger pre-activation of a xenophagic response via AMPK. Autophagy. 2019. Aug;15(8):1489–1491. doi:10.1080/15548627.2019.1618640. PubMed PMID: 31107135; PubMed Central PMCID: PMCPMC6613880. PubMed DOI PMC

Wang RC, Wei Y, An Z, et al. Akt-mediated regulation of autophagy and tumorigenesis through Beclin 1 phosphorylation. Science. 2012. Nov 16;338(6109):956–9. doi:10.1126/science.1225967. PubMed PMID: 23112296; PubMed Central PMCID: PMC3507442. PubMed DOI PMC

Wei Y, Zou Z, Becker N, et al. EGFR-mediated Beclin 1 phosphorylation in autophagy suppression, tumor progression, and tumor chemoresistance. Cell. 2013. Sep 12;154(6):1269–84. doi:10.1016/j.cell.2013.08.015. PubMed PMID: 24034250; PubMed Central PMCID: PMC3917713. PubMed DOI PMC

Yasugi M, Takigawa N, Ochi N, et al. Everolimus prolonged survival in transgenic mice with EGFR-driven lung tumors. Exp Cell Res. 2014. Aug 15;326(2):201–9. doi:10.1016/j.yexcr.2014.04.012. PubMed PMID: 24768699. PubMed DOI

Castets P, Lin S, Rion N, et al. Sustained activation of mTORC1 in skeletal muscle inhibits constitutive and starvation-induced autophagy and causes a severe, late-onset myopathy. Cell Metab. 2013. May 7;17(5):731–44. doi:10.1016/j.cmet.2013.03.015. PubMed PMID: 23602450. PubMed DOI

Castets P, Ruegg MA.. MTORC1 determines autophagy through ULK1 regulation in skeletal muscle. Autophagy. 2013. Sep;9(9):1435–7. doi:10.4161/auto.25722. PubMed PMID: 23896646. PubMed DOI

Wang Z, Zhou L, Zheng X, et al. Autophagy protects against PI3K/Akt/mTOR-mediated apoptosis of spinal cord neurons after mechanical injury. Neurosci Lett. 2017. Aug 24;656:158–164. doi:10.1016/j.neulet.2017.07.036. PubMed PMID: 28739349. PubMed DOI

Bernard M, Dieude M, Yang B, et al. Autophagy fosters myofibroblast differentiation through MTORC2 activation and downstream upregulation of CTGF. Autophagy. 2014. Dec 12:0. doi:10.4161/15548627.2014.981786. PubMed PMID: 25495560. PubMed DOI PMC

Yu L, McPhee CK, Zheng L, et al. Termination of autophagy and reformation of lysosomes regulated by mTOR. Nature. 2010. Jun 17;465(7300):942–6. doi:10.1038/nature09076. PubMed PMID: 20526321; PubMed Central PMCID: PMC2920749. eng. PubMed DOI PMC

Narita M, Young AR, Arakawa S, et al. Spatial coupling of mTOR and autophagy augments secretory phenotypes. Science. 2011. May 20;332(6032):966–70. doi:10.1126/science.1205407. PubMed PMID: 21512002; eng. PubMed DOI PMC

Holla S, Kurowska-Stolarska M, Bayry J, et al. Selective inhibition of IFNG-induced autophagy by Mir155- and Mir31-responsive WNT5A and SHH signaling. Autophagy. 2014. Feb;10(2):311–30. doi:10.4161/auto.27225. PubMed PMID: 24343269. PubMed DOI PMC

Joshi A, Iyengar R, Joo JH, et al. Nuclear ULK1 promotes cell death in response to oxidative stress through PARP1. Cell Death Differ. 2016. Feb;23(2):216–30. doi:10.1038/cdd.2015.88. PubMed PMID: 26138443; PubMed Central PMCID: PMCPMC4716304. PubMed DOI PMC

Hamamichi S, Rivas RN, Knight AL, et al. Hypothesis-based RNAi screening identifies neuroprotective genes in a Parkinson’s disease model. Proc Natl Acad Sci U S A. 2008. Jan 15;105(2):728–33. doi:10.1073/pnas.0711018105. PMCID:PubMed PMIDPMCPMC2206604. PubMed DOI PMC

Okazaki N, Yan J, Yuasa S, et al. Interaction of the Unc-51-like kinase and microtubule-associated protein light chain 3 related proteins in the brain: possible role of vesicular transport in axonal elongation. Brain Res Mol Brain Res. 2000. Dec 28;85(1–2):1–12. PubMed PMID: 11146101; eng. PubMed

Tomoda T, Kim JH, Zhan C, et al. Role of Unc51.1 and its binding partners in CNS axon outgrowth. Genes Dev. 2004. Mar 1;18(5):541–58. doi: 10.1101/gad.1151204:15014045; PubMed Central PMCID: PMC374236. eng. PubMed DOI PMC

Loh SH, Francescut L, Lingor P, et al. Identification of new kinase clusters required for neurite outgrowth and retraction by a loss-of-function RNA interference screen. Cell Death Differ. 2008. Feb;15(2):283–98. doi:10.1038/sj.cdd.4402258. PubMed PMID: 18007665; eng. PubMed DOI

Mochizuki H, Toda H, Ando M, et al. Unc-51/ATG1 controls axonal and dendritic development via kinesin-mediated vesicle transport in the Drosophila brain. PLoS One. 2011;6(5):e19632. doi:10.1371/journal.pone.0019632. PubMed PMID: 21589871; PubMed Central PMCID: PMC3093397. eng. PubMed DOI PMC

Wairkar YP, Toda H, Mochizuki H, et al. Unc-51 controls active zone density and protein composition by downregulating ERK signaling. J Neurosci. 2009. Jan 14;29(2):517–28. doi:10.1523/JNEUROSCI.3848-08.2009. PubMed PMID: 19144852; PubMed Central PMCID: PMC2741695. eng. PubMed DOI PMC

Zhou X, Babu JR, da Silva S, et al. Unc-51-like kinase 1/2-mediated endocytic processes regulate filopodia extension and branching of sensory axons. Proc Natl Acad Sci U S A. 2007. Apr 3;104(14):5842–7. doi: 10.1073/pnas.0701402104. PubMed PMID: 17389358; PubMed Central PMCID: PMC1851579. eng. PubMed DOI PMC

Ribas VT, Schnepf B, Challagundla M, et al. Early and sustained activation of autophagy in degenerating axons after spinal cord injury. Brain Pathol. 2015. Mar;25(2):157–70. doi:10.1111/bpa.12170. PubMed PMID: 25040536. PubMed DOI PMC

Schu PV, Takegawa K, Fry MJ, et al. Phosphatidylinositol 3-kinase encoded by yeast VPS34 gene essential for protein sorting. Science. 1993. Apr 2;260(5104):88–91. doi:10.1126/science.8385367. PubMed PMID: 8385367. PubMed DOI

Volinia S, Dhand R, Vanhaesebroeck B, et al. A human phosphatidylinositol 3-kinase complex related to the yeast Vps34p-Vps15p protein sorting system. EMBO J. 1995. Jul 17;14(14):3339–48. PubMed PMID: 7628435; PubMed Central PMCID: PMCPMC394401. PubMed PMC

Itakura E, Kishi C, Inoue K, et al. Beclin 1 forms two distinct phosphatidylinositol 3-kinase complexes with mammalian Atg14 and UVRAG. Mol Biol Cell. 2008. Dec;19(12):5360–72. doi:10.1091/mbc.E08-01-0080. PubMed PMID: 18843052; PubMed Central PMCID: PMC2592660. eng. PubMed DOI PMC

Kihara A, Noda T, Ishihara N, et al. Two distinct Vps34 phosphatidylinositol 3-kinase complexes function in autophagy and carboxypeptidase Y sorting in Saccharomyces cerevisiae. J Cell Biol. 2001. Feb 5;152(3):519–30. PubMed PMID: 11157979; PubMed Central PMCID: PMC2196002. eng. PubMed PMC

Liang C, Feng P, Ku B, et al. Autophagic and tumour suppressor activity of a novel Beclin1-binding protein UVRAG. Nat Cell Biol. 2006. Jul;8(7):688–99. doi: ncb1426 [pii] doi:10.1038/ncb1426. PubMed PMID: 16799551; eng. PubMed DOI

Matsunaga K, Saitoh T, Tabata K, et al. Two Beclin 1-binding proteins, Atg14L and Rubicon, reciprocally regulate autophagy at different stages. Nat Cell Biol. 2009. Apr;11(4):385–96. doi:10.1038/ncb1846. PubMed PMID: 19270696; eng. PubMed DOI

Sun Q, Fan W, Chen K, et al. Identification of Barkor as a mammalian autophagy-specific factor for Beclin 1 and class III phosphatidylinositol 3-kinase [Research Support, Non-U.S. Gov’t]. Proc Natl Acad Sci U S A. 2008. Dec 9;105(49):19211–6. doi:10.1073/pnas.0810452105. PubMed PMID: 19050071; PubMed Central PMCID: PMC2592986. eng. PubMed DOI PMC

Rostislavleva K, Soler N, Ohashi Y, et al. Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes. Science. 2015. Oct 9;350(6257):aac7365. doi:10.1126/science.aac7365. PubMed PMID: 26450213; PubMed Central PMCID: PMCPMC4601532. PubMed DOI PMC

Martinez J, Malireddi RK, Lu Q, et al. Molecular characterization of LC3-associated phagocytosis reveals distinct roles for Rubicon, NOX2 and autophagy proteins. Nat Cell Biol. 2015. Jul;17(7):893–906. doi:10.1038/ncb3192. PubMed PMID: 26098576; PubMed Central PMCID: PMCPMC4612372. PubMed DOI PMC

Thoreen CC, Kang SA, Chang JW, et al. An ATP-competitive mammalian target of rapamycin inhibitor reveals rapamycin-resistant functions of mTORC1. J Biol Chem. 2009. Mar 20;284(12):8023–32. doi:10.1074/jbc.M900301200. PubMed PMID: 19150980; PubMed Central PMCID: PMC2658096. eng. PubMed DOI PMC

Yan Y, Flinn RJ, Wu H, et al. hVps15, but not Ca2+/CaM, is required for the activity and regulation of hVps34 in mammalian cells. Biochem J. 2009. Feb 1;417(3):747–55. doi:10.1042/BJ20081865. PubMed PMID: 18957027; PubMed Central PMCID: PMC2652830. eng. PubMed DOI PMC

Ohashi Y, Tremel S, Williams RL.. VPS34 complexes from a structural perspective. J Lipid Res. 2019. Feb;60(2):229–241. doi:10.1194/jlr.R089490. PubMed PMID: 30397185; PubMed Central PMCID: PMCPMC6358306. PubMed DOI PMC

Young ARJ, Chan EYW, Hu XW, et al. Starvation and ULK1-dependent cycling of mammalian Atg9 between the TGN and endosomes. J Cell Sci. 2006. Sep 15;119(Pt 18):3888–900. PubMed PMID: 16940348; eng. PubMed

Yamaguchi J, Suzuki C, Nanao T, et al. Atg9a deficiency causes axon-specific lesions including neuronal circuit dysgenesis. Autophagy. 2018;14(5):764–777. doi:10.1080/15548627.2017.1314897. PubMed PMID: 28513333; PubMed Central PMCID: PMCPMC6070006. PubMed DOI PMC

Reggiori F, Shintani T, Nair U, et al. Atg9 cycles between mitochondria and the pre-autophagosomal structure in yeasts. Autophagy. 2005. Jul;1(2):101–9. PubMed PMID: 16874040. PubMed PMC

Mari M, Griffith J, Rieter E, et al. An Atg9-containing compartment that functions in the early steps of autophagosome biogenesis. J Cell Biol. 2010. Sep 20;190(6):1005–22. doi:10.1083/jcb.200912089. PubMed PMID: 20855505; PubMed Central PMCID: PMC3101592. eng. PubMed DOI PMC

Reggiori F, Tucker KA, Stromhaug PE, et al. The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure. Dev cell 2004. Jan;6(1):79–90. PubMed PMID: 14723849. PubMed

Barve G, Sridhar S, Aher A, et al. Septins are involved at the early stages of macroautophagy in S. cerevisiae. J Cell Sci. 2018. Feb 22;131(4). doi:10.1242/jcs.209098. PubMed PMID: 29361537; PubMed Central PMCID: PMCPMC5868950. PubMed DOI PMC

Imai K, Hao F, Fujita N, et al. Atg9A trafficking through the recycling endosomes is required for autophagosome formation. J Cell Sci. 2016. Oct 15;129(20):3781–3791. doi:10.1242/jcs.196196. PubMed PMID: 27587839. PubMed DOI

Corcelle-Termeau E, Vindelov SD, Hamalisto S, et al. Excess sphingomyelin disturbs ATG9A trafficking and autophagosome closure. Autophagy. 2016. May 3;12(5):833–49. doi:10.1080/15548627.2016.1159378. PubMed PMID: 27070082; PubMed Central PMCID: PMCPMC4854555. PubMed DOI PMC

Mizushima N, Kuma A, Kobayashi Y, et al. Mouse Apg16L, a novel WD-repeat protein, targets to the autophagic isolation membrane with the Apg12-Apg5 conjugate. J Cell Sci. 2003. May 1;116(Pt 9):1679–88. PubMed PMID: 12665549; eng. PubMed

Mizushima N, Yamamoto A, Hatano M, et al. Dissection of autophagosome formation using Apg5-deficient mouse embryonic stem cells. J Cell Biol. 2001. Feb 19;152(4):657–68. PubMed PMID: 11266458; eng. PubMed PMC

Mikhaylova O, Stratton Y, Hall D, et al. VHL-regulated MiR-204 suppresses tumor growth through inhibition of LC3B-mediated autophagy in renal clear cell carcinoma. Cancer cell. 2012. Apr 17;21(4):532–46. doi:10.1016/j.ccr.2012.02.019. PubMed PMID: 22516261; PubMed Central PMCID: PMC3331999. PubMed DOI PMC

Thompson AR, Doelling JH, Suttangkakul A, et al. Autophagic nutrient recycling in Arabidopsis directed by the ATG8 and ATG12 conjugation pathways. Plant Physiol. 2005. Aug;138(4):2097–110. doi:10.1104/pp.105.060673. PubMed PMID: 16040659; PubMed Central PMCID: PMC1183398. eng. PubMed DOI PMC

Yousefi S, Perozzo R, Schmid I, et al. Calpain-mediated cleavage of Atg5 switches autophagy to apoptosis. Nat Cell Biol. 2006. Oct;8(10):1124–32. PubMed PMID: 16998475; eng. PubMed

Maskey D, Yousefi S, Schmid I, et al. ATG5 is induced by DNA-damaging agents and promotes mitotic catastrophe independent of autophagy. Nat Commun. 2013;4:2130. doi:10.1038/ncomms3130. PubMed PMID: 23945651; PubMed Central PMCID: PMC3753548. PubMed DOI PMC

Haller M, Hock AK, Giampazolias E, et al. Ubiquitination and proteasomal degradation of ATG12 regulates its proapoptotic activity. Autophagy. 2014;10(12):2269–78. doi:10.4161/15548627.2014.981914. PubMed PMID: 25629932; PubMed Central PMCID: PMCPMC4502749. PubMed DOI PMC

Li SP, He JD, Wang Z, et al. miR-30b inhibits autophagy to alleviate hepatic ischemia-reperfusion injury via decreasing the Atg12-Atg5 conjugate. World J Gastroenterol. 2016. May 14;22(18):4501–14. doi:10.3748/wjg.v22.i18.4501. PubMed PMID: 27182160; PubMed Central PMCID: PMCPMC4858632. PubMed DOI PMC

Lin TY, Chan HH, Chen SH, et al. BIRC5/Survivin is a novel ATG12-ATG5 conjugate interactor and an autophagy-induced DNA damage suppressor in human cancer and mouse embryonic fibroblast cells. Autophagy. 2019. Oct 15:1–18. doi:10.1080/15548627.2019.1671643. PubMed PMID: 31612776. PubMed DOI PMC

Bec N, Bonhoure A, Henry L, et al. Proteasome 19S RP and translation preinitiation complexes are secreted within exosomes upon serum starvation. Traffic. 2019. Jul;20(7):516–536. doi:10.1111/tra.12653 PubMed PMID: 31042005. PubMed DOI

Zhong Y, Wang QJ, Li X, et al. Distinct regulation of autophagic activity by Atg14L and Rubicon associated with Beclin 1-phosphatidylinositol-3-kinase complex. Nat Cell Biol. 2009. Apr;11(4):468–76. doi:10.1038/ncb1854. PubMed PMID: 19270693; PubMed Central PMCID: PMC2664389. eng. PubMed DOI PMC

Fan W, Nassiri A, Zhong Q.. Autophagosome targeting and membrane curvature sensing by Barkor/Atg14(L). Proc Natl Acad Sci U S A. 2011. May 10;108(19):7769–74. doi:10.1073/pnas.1016472108. PubMed PMID: 21518905; PubMed Central PMCID: PMC3093500. eng. PubMed DOI PMC

Matsunaga K, Morita E, Saitoh T, et al. Autophagy requires endoplasmic reticulum targeting of the PI3-kinase complex via Atg14L. J Cell Biol. 2010. Aug 23;190(4):511–21. doi:10.1083/jcb.200911141. PubMed PMID: 20713597; PubMed Central PMCID: PMC2928018. eng. PubMed DOI PMC

Ravikumar B, Moreau K, Jahreiss L, et al. Plasma membrane contributes to the formation of pre-autophagosomal structures. Nat Cell Biol. 2010. Aug;12(8):747–57. doi:10.1038/ncb2078. PubMed PMID: 20639872; PubMed Central PMCID: PMC2923063. eng. PubMed DOI PMC

Tian W, Alsaadi R, Guo Z, et al. An antibody for analysis of autophagy induction. Nat Methods. 2020. Feb;17(2):232–239. doi:10.1038/s41592-019-0661-y. PubMed PMID: 31768061. PubMed DOI

Scrivo A, Codogno P, Bomont P.. Gigaxonin E3 ligase governs ATG16L1 turnover to control autophagosome production. Nat Commun. 2019. Feb 15;10(1):780. doi:10.1038/s41467-019-08331-w. PubMed PMID: 30770803; PubMed Central PMCID: PMCPMC6377711. PubMed DOI PMC

Lassen KG, Kuballa P, Conway KL, et al. Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense. Proc Natl Acad Sci U S A. 2014. May 27;111(21):7741–6. doi:10.1073/pnas.1407001111. PubMed PMID: 24821797; PubMed Central PMCID: PMCPMC4040621. PubMed DOI PMC

Murthy A, Li Y, Peng I, et al. A Crohn’s disease variant in Atg16l1 enhances its degradation by caspase 3. Nature. 2014. Feb 27;506(7489):456–62. doi:10.1038/nature13044. PubMed PMID: 24553140. PubMed DOI

Guan J, Stromhaug PE, George MD, et al. Cvt18/Gsa12 is required for cytoplasm-to-vacuole transport, pexophagy, and autophagy in Saccharomyces cerevisiae and Pichia pastoris. Mol Biol Cell. 2001. Dec;12(12):3821–38. PubMed PMID: 11739783; eng. PubMed PMC

Barth H, Meiling-Wesse K, Epple UD, et al. Autophagy and the cytoplasm to vacuole targeting pathway both require Aut10p. FEBS Lett. 2001. Nov 9;508(1):23–8. PubMed PMID: 11707261; eng. PubMed

Proikas-Cezanne T, Waddell S, Gaugel A, et al. WIPI-1alpha (WIPI49), a member of the novel 7-bladed WIPI protein family, is aberrantly expressed in human cancer and is linked to starvation-induced autophagy. Oncogene. 2004. Dec 16;23(58):9314–25. doi:10.1038/sj.onc.1208331. PubMed PMID: 15602573; eng. PubMed DOI

Monastyrska I, Klionsky DJ.. Autophagy in organelle homeostasis: peroxisome turnover. Mol Aspects Med. 2006. Oct-Dec;27(5–6):483–94. PubMed PMID: 16973210; eng. PubMed PMC

Nair U, Klionsky DJ.. Molecular mechanisms and regulation of specific and nonspecific autophagy pathways in yeast. J Biol Chem. 2005. Dec 23;280(51):41785–8. PubMed PMID: 16230342; eng. PubMed

Tallóczy Z, Virgin HW, IV, Levine B.. PKR-dependent autophagic degradation of herpes simplex virus type 1. Autophagy. 2006. Jan-Mar;2(1):24–9. PubMed PMID: 16874088. PubMed

Polson HE, de Lartigue J, Rigden DJ, et al. Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation. Autophagy. 2010. May 16;6(4):506–522. PubMed PMID: 20505359; Eng. PubMed

Proikas-Cezanne T, Ruckerbauer S, Stierhof YD, et al. Human WIPI-1 puncta-formation: A novel assay to assess mammalian autophagy. FEBS Lett. 2007. Jun 27;581:3396–404. PubMed PMID: 17618624; Eng. PubMed

Scacioc A, Schmidt C, Hofmann T, et al. Structure based biophysical characterization of the PROPPIN Atg18 shows Atg18 oligomerization upon membrane binding. Sci Rep. 2017. Oct 25;7(1):14008. doi:10.1038/s41598-017-14337-5. PubMed PMID: 29070817; PubMed Central PMCID: PMCPMC5656675. PubMed DOI PMC

Gopaldass N, Fauvet B, Lashuel H, et al. Membrane scission driven by the PROPPIN Atg18. EMBO J. 2017. Nov 15;36(22):3274–3291. doi:10.15252/embj.201796859. PubMed PMID: 29030482; PubMed Central PMCID: PMCPMC5686546. PubMed DOI PMC

Itakura E, Mizushima N.. Characterization of autophagosome formation site by a hierarchical analysis of mammalian Atg proteins. Autophagy. 2010. Aug;6(6):764–76. PubMed PMID: 20639694; eng. PubMed PMC

Mauthe M, Jacob A, Freiberger S, et al. Resveratrol-mediated autophagy requires WIPI-1 regulated LC3 lipidation in the absence of induced phagophore formation. Autophagy. 2011. Dec 1;7(12):1448–1461. PubMed PMID: 22082875; Eng. PubMed PMC

Bakula D, Mueller AJ, Proikas-Cezanne T.. WIPI beta-propellers function as scaffolds for STK11/LKB1-AMPK and AMPK-related kinase signaling in autophagy. Autophagy. 2018;14(6):1082–1083. doi:10.1080/15548627.2017.1382784. PubMed PMID: 28976799; PubMed Central PMCID: PMCPMC6103416. PubMed DOI PMC

Bakula D, Muller AJ, Zuleger T, et al. WIPI3 and WIPI4 beta-propellers are scaffolds for LKB1-AMPK-TSC signalling circuits in the control of autophagy. Nat Commun. 2017. May 31;8:15637. doi:10.1038/ncomms15637. PubMed PMID: 28561066; PubMed Central PMCID: PMCPMC5460038. PubMed DOI PMC

Lu Q, Yang P, Huang X, et al. The WD40 repeat PtdIns(3)P-binding protein EPG-6 regulates progression of omegasomes to auto-phagosomes. Dev Cell. 2011. Aug 16;21(2):343–57. doi:10.1016/j.devcel.2011.06.024. PubMed PMID: 21802374; eng. PubMed DOI

Cao Y, Klionsky DJ.. Physiological functions of Atg6/Beclin 1: a unique autophagy-related protein. Cell Res. 2007. Oct;17(10):839–49. doi:10.1038/cr.2007.78. PubMed PMID: 17893711; eng. PubMed DOI

Yang Z, Klionsky DJ.. Mammalian autophagy: core molecular machinery and signaling regulation [Review]. Curr Opin Cell Biol. 2010. Apr;22(2):124–31. doi:10.1016/j.ceb.2009.11.014. PubMed PMID: 20034776; PubMed Central PMCID: PMC2854249. eng. PubMed DOI PMC

Pattingre S, Tassa A, Qu X, et al. Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy. Cell. 2005. Sep 23;122(6):927–39. PubMed PMID: 16179260; eng. PubMed

Erlich S, Mizrachy L, Segev O, et al. Differential interactions between Beclin 1 and Bcl-2 family members. Autophagy. 2007. Nov-Dec;3(6):561–8. doi:10.4161/auto.4713. PubMed PMID: 17643073. PubMed DOI

Oberstein A, Jeffrey PD, Shi Y.. Crystal structure of the Bcl-XL-Beclin 1 peptide complex: Beclin 1 is a novel BH3-only protein. J Biol Chem. 2007. Apr 27;282(17):13123–32. doi:10.1074/jbc.M700492200. PubMed PMID: 17337444. PubMed DOI

Shiloh R, Gilad Y, Ber Y, et al. Non-canonical activation of DAPK2 by AMPK constitutes a new pathway linking metabolic stress to autophagy. Nat Commun. 2018. May 1;9(1):1759. doi:10.1038/s41467-018-03907-4. PubMed PMID: 29717115; PubMed Central PMCID: PMCPMC5931534. PubMed DOI PMC

Zalckvar E, Berissi H, Mizrachy L, et al. DAP-kinase-mediated phosphorylation on the BH3 domain of beclin 1 promotes dissociation of beclin 1 from Bcl-XL and induction of autophagy. EMBO Rep. 2009. Mar;10(3):285–92. doi:10.1038/embor.2008.246. PubMed PMID: 19180116; PubMed Central PMCID: PMC2658558. eng. PubMed DOI PMC

Wei Y, Pattingre S, Sinha S, et al. JNK1-mediated phosphorylation of Bcl-2 regulates starvation-induced autophagy. Mol Cell. 2008. Jun 20;30(6):678–88. doi:10.1016/j.molcel.2008.06.001. PubMed PMID: 18570871; PubMed Central PMCID: PMC2478643. eng. PubMed DOI PMC

Wei Y, Sinha S, Levine B.. Dual role of JNK1-mediated phosphorylation of Bcl-2 in autophagy and apoptosis regulation. Autophagy. 2008. Oct;4(7):949–51. PubMed PMID: 18769111; PubMed Central PMCID: PMC2677707. eng. PubMed PMC

Fernandez AF, Sebti S, Wei Y, et al. Disruption of the beclin 1-BCL2 autophagy regulatory complex promotes longevity in mice. Nature. 2018. Jun;558(7708):136–140. doi:10.1038/s41586-018-0162-7. PubMed PMID: 29849149; PubMed Central PMCID: PMCPMC5992097. PubMed DOI PMC

Lossi L, Gambino G, Ferrini F, et al. Posttranslational regulation of BCL2 levels in cerebellar granule cells: A mechanism of neuronal survival. Dev Neurobiol. 2009. Nov;69(13):855–70. doi:10.1002/dneu.20744. PubMed PMID: 19672954; eng. PubMed DOI

Lossi L, Gambino G, Salio C, et al. Autophagy regulates the post-translational cleavage of BCL-2 and promotes neuronal survival. ScientificWorldJournal. 2010;10:924–9. doi:10.1100/tsw.2010.82. PubMed PMID: 20495771; eng. PubMed DOI PMC

Scarlatti F, Maffei R, Beau I, et al. Role of non-canonical Beclin 1-independent autophagy in cell death induced by resveratrol in human breast cancer cells. Cell Death Differ. 2008. Aug;15(8):1318–29. doi:10.1038/cdd.2008.51. PubMed PMID: 18421301; eng. PubMed DOI

Sok SP, Arshad NM, Azmi MN, et al. The apoptotic effect of 1’S-1ʹ-Acetoxychavicol Acetate (ACA) enhanced by inhibition of non-canonical autophagy in human non-small cell lung cancer cells. PLoS One. 2017;12(2):e0171329. doi:10.1371/journal.pone.0171329. PubMed PMID: 28158287; PubMed Central PMCID: PMCPMC5291426. PubMed DOI PMC

Kang R, Zeh HJ, Lotze MT, et al. The Beclin 1 network regulates autophagy and apoptosis. Cell Death Differ. 2011. Apr;18(4):571–80. doi:10.1038/cdd.2010.191. PubMed PMID: 21311563; eng. PubMed DOI PMC

Kihara A, Kabeya Y, Ohsumi Y, et al. Beclin-phosphatidylinositol 3-kinase complex functions at the trans-Golgi network. EMBO Rep. 2001. Apr;2(4):330–5. doi:10.1093/embo-reports/kve061. PubMed PMID: 11306555; PubMed Central PMCID: PMC1083858. eng. PubMed DOI PMC

Amritraj A, Peake K, Kodam A, et al. Increased activity and altered subcellular distribution of lysosomal enzymes determine neuronal vulnerability in Niemann-Pick type C1-deficient mice. Am J Pathol. 2009. Dec;175(6):2540–56. doi:10.2353/ajpath.2009.081096. PubMed PMID: 19893049; PubMed Central PMCID: PMC2789601. eng. PubMed DOI PMC

McKnight NC, Zhenyu Y.. Beclin 1, an essential component and master regulator of PI3K-III in health and disease. Curr Pathobiol Rep. 2013. Dec 1;1(4):231–238. doi:10.1007/s40139-013-0028-5. PubMed PMID: 24729948; PubMed Central PMCID: PMCPMC3979578. PubMed DOI PMC

Castino R, Bellio N, Follo C, et al. Inhibition of PI3k class III-dependent autophagy prevents apoptosis and necrosis by oxidative stress in dopaminergic neuroblastoma cells. Toxicol Sci. 2010. Sep;117(1):152–62. doi:10.1093/toxsci/kfq170. PubMed PMID: 20525898; eng. PubMed DOI

Yue Z, Horton A, Bravin M, et al. A novel protein complex linking the delta 2 glutamate receptor and autophagy: implications for neurodegeneration in lurcher mice. Neuron. 2002. Aug 29;35(5):921–33. PubMed PMID: 12372286; eng. PubMed

Luo S, Rubinsztein DC.. Apoptosis blocks Beclin 1-dependent autophagosome synthesis: an effect rescued by Bcl-xL. Cell Death Differ. 2010. Feb;17(2):268–77. doi:10.1038/cdd.2009.121. PubMed PMID: 19713971; PubMed Central PMCID: PMC2894406. PubMed DOI PMC

Furuya N, Yu J, Byfield M, et al. The evolutionarily conserved domain of Beclin 1 is required for Vps34 binding, autophagy and tumor suppressor function. Autophagy. 2005. Apr;1(1):46–52. PubMed PMID: 16874027. PubMed

Kim J, Kim YC, Fang C, et al. Differential regulation of distinct Vps34 complexes by AMPK in nutrient stress and autophagy. Cell. 2013. Jan 17;152(1–2):290–303. doi:10.1016/j.cell.2012.12.016. PubMed PMID: 23332761; PubMed Central PMCID: PMC3587159. PubMed DOI PMC

Nemazanyy I, Montagnac G, Russell RC, et al. Class III PI3K regulates organismal glucose homeostasis by providing negative feedback on hepatic insulin signalling. Nat Commun. 2015. Sep 21;6:8283. doi:10.1038/ncomms9283. PubMed PMID: 26387534; PubMed Central PMCID: PMCPMC4579570. PubMed DOI PMC

Takats S, Nagy P, Varga A, et al. Autophagosomal Syntaxin17-dependent lysosomal degradation maintains neuronal function in Drosophila. J Cell Biol. 2013. May 13;201(4):531–9. doi:10.1083/jcb.201211160. PubMed PMID: 23671310; PubMed Central PMCID: PMC3653357. PubMed DOI PMC

Itakura E, Kishi-Itakura C, Mizushima N.. The hairpin-type tail-anchored SNARE syntaxin 17 targets to auto-phagosomes for fusion with endosomes/lysosomes. Cell. 2012. Dec 7;151(6):1256–69. doi:10.1016/j.cell.2012.11.001. PubMed PMID: 23217709. PubMed DOI

Hamasaki M, Furuta N, Matsuda A, et al. Autophagosomes form at ER-mitochondria contact sites. Nature. 2013. Mar 21;495(7441):389–93. doi:10.1038/nature11910. PubMed PMID: 23455425. PubMed DOI

Arasaki K, Shimizu H, Mogari H, et al. A role for the ancient SNARE syntaxin 17 in regulating mitochondrial division. Dev Cell. 2015. Feb 9;32(3):304–17. doi:10.1016/j.devcel.2014.12.011. PubMed PMID: 25619926. PubMed DOI

Morelli E, Ginefra P, Mastrodonato V, et al. Multiple functions of the SNARE protein Snap29 in autophagy, endocytic, and exocytic trafficking during epithelial formation in Drosophila. Autophagy. 2014;10(12):2251–68. doi:10.4161/15548627.2014.981913. PubMed PMID: 25551675; PubMed Central PMCID: PMC4502674. PubMed DOI PMC

Tsuboyama K, Koyama-Honda I, Sakamaki Y, et al. The ATG conjugation systems are important for degradation of the inner autophagosomal membrane. Science. 2016. Nov 25;354(6315):1036–1041. doi:10.1126/science.aaf6136. PubMed PMID: 27885029. PubMed DOI

Arasaki K, Mikami Y, Shames SR, et al. Legionella effector Lpg1137 shuts down ER-mitochondria communication through cleavage of syntaxin 17. Nat Commun. 2017. May 15;8:15406. doi:10.1038/ncomms15406. PubMed PMID: 28504273; PubMed Central PMCID: PMCPMC5440676. PubMed DOI PMC

Kumar S, Gu Y, Abudu YP, et al. Phosphorylation of syntaxin 17 by TBK1 controls autophagy initiation. Dev Cell. 2019. Apr 8;49(1):130–144 e6. doi:10.1016/j.devcel.2019.01.027. PubMed PMID: 30827897; PubMed Central PMCID: PMCPMC6907693. PubMed DOI PMC

Sugo M, Kimura H, Arasaki K, et al. Syntaxin 17 regulates the localization and function of PGAM5 in mitochondrial division and mitophagy. EMBO J. 2018. Nov 2;37(21). doi:10.15252/embj.201798899. PubMed PMID: 30237312; PubMed Central PMCID: PMCPMC6213275. PubMed DOI PMC

Xian H, Yang Q, Xiao L, et al. STX17 dynamically regulated by Fis1 induces mitophagy via hierarchical macroautophagic mechanism. Nat Commun. 2019. May 3;10(1):2059. doi:10.1038/s41467-019-10096-1. PubMed PMID: 31053718; PubMed Central PMCID: PMCPMC6499814. PubMed DOI PMC

Cheng XT, Zhou B, Lin MY, et al. Axonal auto-phagosomes recruit dynein for retrograde transport through fusion with late endosomes. J Cell Biol. 2015. May 11;209(3):377–86. doi:10.1083/jcb.201412046. PubMed PMID: 25940348; PubMed Central PMCID: PMCPMC4427784. PubMed DOI PMC

Cheng XT, Zhou B, Lin MY, et al. Axonal auto-phagosomes use the ride-on service for retrograde transport toward the soma. Autophagy. 2015;11(8):1434–6. doi: 10.1080/15548627.2015.1062203. PubMed PMID: 26102591; PubMed Central PMCID: PMCPMC4590659. PubMed DOI PMC

Kim JH, Hong SB, Lee JK, et al. Insights into autophagosome maturation revealed by the structures of ATG5 with its interacting partners. Autophagy. 2015;11(1):75–87. doi:10.4161/15548627.2014.984276. PubMed PMID: 25484072; PubMed Central PMCID: PMCPMC4502675. PubMed DOI PMC

Chen D, Zhong Q.. A tethering coherent protein in autophagosome maturation. Autophagy. 2012. Jun;8(6):985–6. doi:10.4161/auto.20255. PubMed PMID: 22617511; PubMed Central PMCID: PMC3427267. PubMed DOI PMC

Axe EL, Walker SA, Manifava M, et al. Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J Cell Biol. 2008. Aug 25;182(4):685–701. doi:10.1083/jcb.200803137. PubMed PMID: 18725538; PubMed Central PMCID: PMC2518708. eng. PubMed DOI PMC

Karunakaran I, van Echten-Deckert G.. Sphingosine 1-phosphate - A double edged sword in the brain. Biochim Biophys Acta Biomembr. 2017. Sep;1859(9 Pt B):1573–1582. doi:10.1016/j.bbamem.2017.03.008. PubMed PMID: 28315304. PubMed DOI

Ogretmen B. Sphingolipid metabolism in cancer signalling and therapy. Nat Rev Cancer. 2018. Jan;18(1):33–50. doi:10.1038/nrc.2017.96. PubMed PMID: 29147025; PubMed Central PMCID: PMCPMC5818153. PubMed DOI PMC

van Echten-Deckert G, Alam S.. Sphingolipid metabolism - an ambiguous regulator of autophagy in the brain. Biol Chem. 2018. Jul 26;399(8):837–850. doi:10.1515/hsz-2018-0237. PubMed PMID: 29908127. PubMed DOI

Mitroi DN, Karunakaran I, Graler M, et al. SGPL1 (sphingosine phosphate lyase 1) modulates neuronal autophagy via phosphatidylethanolamine production. Autophagy. 2017. May 4;13(5):885–899. doi:10.1080/15548627.2017.1291471. PubMed PMID: 28521611; PubMed Central PMCID: PMCPMC5446076. PubMed DOI PMC

Moruno Manchon JF, Uzor NE, Dabaghian Y, et al. Cytoplasmic sphingosine-1-phosphate pathway modulates neuronal autophagy. Sci Rep. 2015. Oct 19;5:15213. doi:10.1038/srep15213. PubMed PMID: 26477494; PubMed Central PMCID: PMCPMC4609990. PubMed DOI PMC

Bamborschke D, Pergande M, Becker K, et al. A novel mutation in sphingosine-1-phosphate lyase causing congenital brain malformation. Brain Dev. 2018. Jun;40(6):480–483. doi:10.1016/j.braindev.2018.02.008. PubMed PMID: 29501407. PubMed DOI

Taniguchi M, Kitatani K, Kondo T, et al. Regulation of autophagy and its associated cell death by “sphingolipid rheostat”: reciprocal role of ceramide and sphingosine 1-phosphate in the mammalian target of rapamycin pathway. J Biol Chem. 2012. Nov 16;287(47):39898–910. doi:10.1074/jbc.M112.416552. PubMed PMID: 23035115; PubMed Central PMCID: PMC3501064. PubMed DOI PMC

Justice MJ, Petrusca DN, Rogozea AL, et al. Effects of lipid interactions on model vesicle engulfment by alveolar macrophages. Biophys J. 2014. Feb 4;106(3):598–609. doi:10.1016/j.bpj.2013.12.036. PubMed PMID: 24507600; PubMed Central PMCID: PMC3944992. PubMed DOI PMC

Tagaya M, Arasaki K.. Regulation of mitochondrial dynamics and autophagy by the mitochondria-associated membrane. Adv Exp Med Biol. 2017;997:33–47. doi:10.1007/978-981-10-4567-7_3. PubMed PMID: 28815520. PubMed DOI

Guenther GG, Peralta ER, Rosales KR, et al. Ceramide starves cells to death by downregulating nutrient transporter proteins. Proc Natl Acad Sci U S A. 2008. Nov 11;105(45):17402–7. doi:10.1073/pnas.0802781105. PubMed PMID: 18981422; PubMed Central PMCID: PMC2582319. PubMed DOI PMC

Pattingre S, Bauvy C, Levade T, et al. Ceramide-induced autophagy: to junk or to protect cells? Autophagy. 2009. May;5(4):558–60. PubMed PMID: 19337026; PubMed Central PMCID: PMC3501009. PubMed PMC

Sentelle RD, Senkal CE, Jiang W, et al. Ceramide targets auto-phagosomes to mitochondria and induces lethal mitophagy. Nat Chem Biol. 2012. Oct;8(10):831–8. doi:10.1038/nchembio.1059. PubMed PMID: 22922758; PubMed Central PMCID: PMC3689583. PubMed DOI PMC

Dany M, Gencer S, Nganga R, et al. Targeting FLT3-ITD signaling mediates ceramide-dependent mitophagy and attenuates drug resistance in AML. Blood. 2016. Oct 13;128(15):1944–1958. doi:10.1182/blood-2016-04-708750. PubMed PMID: 27540013; PubMed Central PMCID: PMCPMC5064718. PubMed DOI PMC

Jiang W, Ogretmen B.. Ceramide stress in survival versus lethal autophagy paradox: ceramide targets auto-phagosomes to mitochondria and induces lethal mitophagy. Autophagy. 2013. Feb 1;9(2):258–9. doi:10.4161/auto.22739. PubMed PMID: 23182807; PubMed Central PMCID: PMC3552895. PubMed DOI PMC

Jiang W, Ogretmen B.. Autophagy paradox and ceramide. Biochim Biophys Acta. 2014. May;1841(5):783–92. doi:10.1016/j.bbalip.2013.09.005. PubMed PMID: 24055889; PubMed Central PMCID: PMC3960371. PubMed DOI PMC

Thomas RJ, Oleinik N, Panneer Selvam S, et al. HPV/E7 induces chemotherapy-mediated tumor suppression by ceramide-dependent mitophagy. EMBO Mol Med. 2017. Aug;9(8):1030–1051. doi:10.15252/emmm.201607088. PubMed PMID: 28606997; PubMed Central PMCID: PMCPMC5538428. PubMed DOI PMC

Oleinik N, Kim J, Roth BM, et al. Mitochondrial protein import is regulated by p17/PERMIT to mediate lipid metabolism and cellular stress. Sci Adv. 2019. Sep;5(9):eaax1978. doi:10.1126/sciadv.aax1978. PubMed PMID: 31535025; PubMed Central PMCID: PMCPMC6739097. PubMed DOI PMC

Lepine S, Allegood JC, Park M, et al. Sphingosine-1-phosphate phosphohydrolase-1 regulates ER stress-induced autophagy. Cell Death Differ. 2011. Feb;18(2):350–61. doi:10.1038/cdd.2010.104. PubMed PMID: 20798685; eng. PubMed DOI PMC

Cervia D, Assi E, De Palma C, et al. Essential role for acid sphingomyelinase-inhibited autophagy in melanoma response to cisplatin. Oncotarget. 2016. May 3;7(18):24995–5009. doi:10.18632/oncotarget.8735. PubMed PMID: 27107419; PubMed Central PMCID: PMCPMC5041885. PubMed DOI PMC

Gluschko A, Herb M, Wiegmann K, et al. The beta2 Integrin Mac-1 Induces Protective LC3-Associated Phagocytosis of Listeria monocytogenes. Cell Host Microbe. 2018. Mar 14;23(3):324–337 e5. doi:10.1016/j.chom.2018.01.018. PubMed PMID: 29544096. PubMed DOI

Signorelli P, Munoz-Olaya JM, Gagliostro V, et al. Dihydroceramide intracellular increase in response to resveratrol treatment mediates autophagy in gastric cancer cells. Cancer Lett. 2009. Sep 18;282(2):238–43. doi:10.1016/j.canlet.2009.03.020 PubMed PMID: 19394759. PubMed DOI

Hernandez-Tiedra S, Fabrias G, Davila D, et al. Dihydroceramide accumulation mediates cytotoxic autophagy of cancer cells via autolysosome destabilization. Autophagy. 2016. Nov;12(11):2213–2229. doi:10.1080/15548627.2016.1213927. PubMed PMID: 27635674; PubMed Central PMCID: PMCPMC5103338. PubMed DOI PMC

Matarrese P, Garofalo T, Manganelli V, et al. Evidence for the involvement of GD3 ganglioside in autophagosome formation and maturation. Autophagy. 2014. May 1;10(5):750–65. doi:10.4161/auto.27959. PubMed PMID: 24589479. PubMed DOI PMC

Garofalo T, Matarrese P, Manganelli V, et al. Evidence for the involvement of lipid rafts localized at the ER-mitochondria associated membranes in autophagosome formation. Autophagy. 2016. Jun 2;12(6):917–35. doi:10.1080/15548627.2016.1160971. PubMed PMID: 27123544; PubMed Central PMCID: PMCPMC4922444. PubMed DOI PMC

Russ DW, Wills AM, Boyd IM, et al. Weakness, SR function and stress in gastrocnemius muscles of aged male rats. Exp Gerontol. 2014. Feb;50:40–4. doi:10.1016/j.exger.2013.11.018. PubMed PMID: 24316040. PubMed DOI

Bernard A, Jin M, Xu Z, et al. A large-scale analysis of autophagy-related gene expression identifies new regulators of autophagy.Autophagy. 2015. Nov 2;11(11):2114–2122. doi:10.1080/15548627.2015.1099796. PubMed PMID: 26649943; PubMed Central PMCID: PMCPMC4824583. PubMed DOI PMC

Barany I, Berenguer E, Solis MT, et al. Autophagy is activated and involved in cell death with participation of cathepsins during stress-induced microspore embryogenesis in barley. J Exp Bot. 2018. Mar 14;69(6):1387–1402. doi:10.1093/jxb/erx455. PubMed PMID: 29309624; PubMed Central PMCID: PMCPMC6019037. PubMed DOI PMC

Bernard A, Jin M, Gonzalez-Rodriguez P, et al. Rph1/KDM4 mediates nutrient-limitation signaling that leads to the transcriptional induction of autophagy. Curr Biol. 2015. Mar 2;25(5):546–55. doi:10.1016/j.cub.2014.12.049. PubMed PMID: 25660547; PubMed Central PMCID: PMC4348152. PubMed DOI PMC

Bernard A, Klionsky DJ.. Rph1 mediates the nutrient-limitation signaling pathway leading to transcriptional activation of autophagy. Autophagy. 2015. Apr 3;11(4):718–9. doi:10.1080/15548627.2015.1018503. PubMed PMID: 25751780; PubMed Central PMCID: PMC4502745. PubMed DOI PMC

Kirisako T, Baba M, Ishihara N, et al. Formation process of autophagosome is traced with Apg8/Aut7p in yeast. J Cell Biol. 1999. Oct 18;147(2):435–46. PubMed PMID: 10525546; PubMed Central PMCID: PMC2174223. eng. PubMed PMC

Nara A, Mizushima N, Yamamoto A, et al. SKD1 AAA ATPase-dependent endosomal transport is involved in autolysosome formation. Cell Struct Funct. 2002. Feb;27(1):29–37. PubMed PMID: 11937716; eng. PubMed

Tsuyuki S, Takabayashi M, Kawazu M, et al. Detection of WIPI1 mRNA as an indicator of autophagosome formation. Autophagy. 2014. Mar;10(3):497–513. doi:10.4161/auto.27419. PubMed PMID: 24384561; PubMed Central PMCID: PMCPMC4077887. PubMed DOI PMC

Jin M, He D, Backues SK, et al. Transcriptional regulation by Pho23 modulates the frequency of autophagosome formation. Curr Biol. 2014. Jun 16;24(12):1314–22. doi:10.1016/j.cub.2014.04.048. PubMed PMID: 24881874; PubMed Central PMCID: PMC4169046. PubMed DOI PMC

Kouroku Y, Fujita E, Tanida I, et al. ER stress (PERK/eIF2[alpha] phosphorylation) mediates the polyglutamine-induced LC3 conversion, an essential step for autophagy formation. Cell Death Differ. 2007. Feb;14(2):230–9. PubMed PMID: 16794605; eng. PubMed

Xiong X, Tao R, DePinho RA, et al. The autophagy-related gene 14 (Atg14) is regulated by forkhead box O transcription factors and circadian rhythms and plays a critical role in hepatic autophagy and lipid metabolism. J Biol Chem. 2012. Nov 9;287(46):39107–14. doi:10.1074/jbc.M112.412569. PubMed PMID: 22992773; PubMed Central PMCID: PMC3493951. PubMed DOI PMC

Moussay E, Kaoma T, Baginska J, et al. The acquisition of resistance to TNFalpha in breast cancer cells is associated with constitutive activation of autophagy as revealed by a transcriptome analysis using a custom microarray. Autophagy. 2011. Jul;7(7):760–70. PubMed PMID: 21490427; eng. PubMed

Lee JM, Wagner M, Xiao R, et al. Nutrient-sensing nuclear receptors coordinate autophagy. Nature. 2014. Dec 4;516(7529):112–5. doi:10.1038/nature13961. PubMed PMID: 25383539; PubMed Central PMCID: PMC4267857. PubMed DOI PMC

Conte A, Paladino S, Bianco G, et al. High mobility group A1 protein modulates autophagy in cancer cells. Cell Death Differ. 2017. Nov;24(11):1948–1962. doi:10.1038/cdd.2017.117. PubMed PMID: 28777374; PubMed Central PMCID: PMCPMC5635219. PubMed DOI PMC

Mitroulis I, Kourtzelis I, Kambas K, et al. Regulation of the autophagic machinery in human neutrophils [Research Support, Non-U.S. Gov’t]. Eur J Immunol. 2010. May;40(5):1461–72. doi:10.1002/eji.200940025. PubMed PMID: 20162553; eng. PubMed DOI

Rodriguez-Muela N, Germain F, Marino G, et al. Autophagy promotes survival of retinal ganglion cells after optic nerve axotomy in mice. Cell Death Differ. 2012. Jan;19(1):162–9. doi:10.1038/cdd.2011.88. PubMed PMID: 21701497; eng. PubMed DOI PMC

Vázquez P, Arroba AI, Cecconi F, et al. Atg5 and Ambra1 differentially modulate neurogenesis in neural stem cells. 2012;8:187–99. PubMed

Rouschop KM, van den Beucken T, Dubois L, et al. The unfolded protein response protects human tumor cells during hypoxia through regulation of the autophagy genes MAP1LC3B and ATG5. J Clin Invest. 2010. Jan 4;120(1):127–41. doi:10.1172/JCI40027. PubMed PMID: 20038797; PubMed Central PMCID: PMC2798689. eng. PubMed DOI PMC

Haim Y, Blüher M, Slutsky N, et al. Elevated autophagy gene expression in adipose tissue of obese humans: A potential noncell- cycle-dependent function of E2F1. Autophagy. 2015;11:2074–88. PubMed PMC

Zhang J, Wang J, Lee YM, et al. Proteomic profiling of de novo protein synthesis in starvation-induced autophagy using Bioorthogonal noncanonical amino acid tagging. Methods Enzymol. 2017;588:41–59. doi:10.1016/bs.mie.2016.09.075. PubMed PMID: 28237112. PubMed DOI

Pourpirali S, Valacca C, Merlo P, et al. Prolonged pseudohypoxia targets Ambra1 mRNA to P-bodies for translational repression. PLoS One. 2015;10(6):e0129750. doi:10.1371/journal.pone.0129750. PubMed PMID: 26086269; PubMed Central PMCID: PMCPMC4473010. PubMed DOI PMC

Las G, Serada SB, Wikstrom JD, et al. Fatty acids suppress autophagic turnover in beta-cells. J Biol Chem. 2011. Dec 9;286(49):42534–44. doi:10.1074/jbc.M111.242412. PubMed PMID: 21859708; PubMed Central PMCID: PMC3234912. PubMed DOI PMC

Woldt E, Sebti Y, Solt LA, et al. Rev-erb-alpha modulates skeletal muscle oxidative capacity by regulating mitochondrial biogenesis and autophagy. Nat Med. 2013. Aug;19(8):1039–46. doi:10.1038/nm.3213. PubMed PMID: 23852339; PubMed Central PMCID: PMC3737409. PubMed DOI PMC

Huang G, Zhang F, Ye Q, et al. The circadian clock regulates autophagy directly through the nuclear hormone receptor Nr1d1/Rev-erbalpha and indirectly via Cebpb/(C/ebpbeta) in zebrafish. Autophagy. 2016. Aug 2;12(8):1292–309. doi:10.1080/15548627.2016.1183843. PubMed PMID: 27171500; PubMed Central PMCID: PMCPMC4968235. PubMed DOI PMC

Ferder IC, Fung L, Ohguchi Y, et al. Meiotic gatekeeper STRA8 suppresses autophagy by repressing Nr1d1 expression during spermatogenesis in mice. PLoS Genet. 2019. May;15(5):e1008084. doi:10.1371/journal.pgen.1008084. PubMed PMID: 31059511; PubMed Central PMCID: PMCPMC6502318. PubMed DOI PMC

Chandra V, Bhagyaraj E, Nanduri R, et al. NR1D1 ameliorates Mycobacterium tuberculosis clearance through regulation of autophagy. Autophagy. 2015. Nov 2;11(11):1987–1997. doi:10.1080/15548627.2015.1091140. PubMed PMID: 26390081; PubMed Central PMCID: PMCPMC4824569. PubMed DOI PMC

Luo R, Su LY, Li G, et al. Activation of PPARA-mediated autophagy reduces Alzheimer disease-like pathology and cognitive decline in a murine model. Autophagy. 2020. Jan;16(1):52–69. doi:10.1080/15548627.2019.1596488, PubMed PMID: 30898012. PubMed DOI PMC

Seok S, Fu T, Choi SE, et al. Transcriptional regulation of autophagy by an FXR-CREB axis. Nature. 2014. Dec 4;516(7529):108–11. doi:10.1038/nature13949. PubMed PMID: 25383523; PubMed Central PMCID: PMC4257899. PubMed DOI PMC

Jiang H, Martin V, Gomez-Manzano C, et al. The RB-E2F1 pathway regulates autophagy. Cancer Res. 2010. Oct 15;70(20):7882–93. doi: 0008-5472.CAN-10-1604 [pii] doi:10.1158/0008-5472.CAN-10-1604. PubMed PMID: 20807803; eng. PubMed DOI PMC

Polager S, Ofir M, Ginsberg D.. E2F1 regulates autophagy and the transcription of autophagy genes. Oncogene. 2008. Aug 14;27(35):4860–4. doi: onc2008117 [pii] doi:10.1038/onc.2008.117. PubMed PMID: 18408756; eng. PubMed DOI

Gorski SM, Chittaranjan S, Pleasance ED, et al. A SAGE approach to discovery of genes involved in autophagic cell death. Curr Biol CB. 2003. Feb 18;13(4):358–63. PubMed PMID: 12593804; eng. PubMed

Lee C-Y, Clough EA, Yellon P, et al. Genome-wide analyses of steroid- and radiation-triggered programmed cell death in Drosophila. Curr Biol. 2003. Feb 18;13(4):350–7. PubMed PMID: 12593803; eng. PubMed

Denton D, Shravage B, Simin R, et al. Larval midgut destruction in Drosophila: not dependent on caspases but suppressed by the loss of autophagy. Autophagy. 2010. Jan;6(1):163–5. PubMed PMID: 20009534; PubMed Central PMCID: PMC2819273. eng. PubMed PMC

Franzetti E, Huang ZJ, Shi YX, et al. Autophagy precedes apoptosis during the remodeling of silkworm larval midgut. Apoptosis. 2012;17:305–24. PubMed

Tian L, Ma L, Guo E, et al. 20-Hydroxyecdysone upregulates Atg genes to induce autophagy in the Bombyx fat body. Autophagy. 2013. Aug;9(8):1172–87. doi:10.4161/auto.24731. PubMed PMID: 23674061; PubMed Central PMCID: PMC3748190. PubMed DOI PMC

Montali A, Romanelli D, Cappellozza S, et al. Timing of autophagy and apoptosis during posterior silk gland degeneration in Bombyx mori. Arthropod Struct Dev. 2017. Jul;46(4):518–528. doi:10.1016/j.asd.2017.05.003. PubMed PMID: 28549564. PubMed DOI

Juhasz G, Puskas LG, Komonyi O, et al. Gene expression profiling identifies FKBP39 as an inhibitor of autophagy in larval Drosophila fat body. Cell Death Differ. 2007. Jun;14(6):1181–90. PubMed PMID: 17363962; eng. PubMed PMC

Erdi B, Nagy P, Zvara A, et al. Loss of the starvation-induced gene Rack1 leads to glycogen deficiency and impaired autophagic responses in Drosophila. Autophagy. 2012. Jul 1;8(7):1124–35. doi:10.4161/auto.20069. PubMed PMID: 22562043; PubMed Central PMCID: PMC3429548. PubMed DOI PMC

Barth JM, Szabad J, Hafen E, et al. Autophagy in Drosophila ovaries is induced by starvation and is required for oogenesis. Cell Death Differ. 2011. Jun;18(6):915–24. doi:10.1038/cdd.2010.157. PubMed PMID: 21151027; eng. PubMed DOI PMC

O’Rourke EJ, Ruvkun G.. MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability. Nat Cell Biol. 2013. Jun;15(6):668–76. doi:10.1038/ncb2741. PubMed PMID: 23604316; PubMed Central PMCID: PMC3723461. PubMed DOI PMC

Settembre C, Di Malta C, Polito VA, et al. TFEB links autophagy to lysosomal biogenesis. Science. 2011. Jun 17;332(6036):1429–33. doi:10.1126/science.1204592. PubMed PMID: 21617040; eng. PubMed DOI PMC

Lecker SH, Jagoe RT, Gilbert A, et al. Multiple types of skeletal muscle atrophy involve a common program of changes in gene expression. FASEB J. 2004. Jan;18(1):39–51. doi:10.1096/fj.03-0610com. PubMed PMID: 14718385; eng. PubMed DOI

Phillips AR, Suttangkakul A, Vierstra RD.. The ATG12-conjugating enzyme ATG10 Is essential for autophagic vesicle formation in Arabidopsis thaliana. Genetics. 2008. Mar;178(3):1339–53. doi:10.1534/genetics.107.086199. PubMed PMID: 18245858; PubMed Central PMCID: PMC2278079. eng. PubMed DOI PMC

Seiliez I, Gutierrez J, Salmeron C, et al. An in vivo and in vitro assessment of autophagy-related gene expression in muscle of rainbow trout (Oncorhynchus mykiss). Comp Biochem Physiol Part B Biochem Mol Bio. 2010. Nov;157(3):258–66. doi:10.1016/j.cbpb.2010.06.011. PubMed PMID: 20601058; eng. PubMed DOI

Alshudukhi AA, Zhu J, Huang D, et al. Lipin-1 regulates Bnip3-mediated mitophagy in glycolytic muscle. FASEB J. 2018. Dec;32(12):6796–6807. doi:10.1096/fj.201800374. PubMed PMID: 29939786; PubMed Central PMCID: PMCPMC6219840. PubMed DOI PMC

Sandri M. Autophagy in health and disease. 3. Involvement of autophagy in muscle atrophy. Am J Physiol Cell Physiol. 2010. Jun;298(6):C1291–7. doi:10.1152/ajpcell.00531.2009. PubMed PMID: 20089936; eng. PubMed DOI

Eisenberg T, Knauer H, Schauer A, et al. Induction of autophagy by spermidine promotes longevity [Research Support, Non-U.S. Gov’t]. Nat Cell Biol. 2009. Nov;11(11):1305–14. doi:10.1038/ncb1975. PubMed PMID: 19801973; eng. PubMed DOI

Yue F, Li W, Zou J, et al. Spermidine Prolongs Lifespan and Prevents Liver Fibrosis and Hepatocellular Carcinoma by Activating MAP1S-Mediated Autophagy. Cancer Res. 2017. Jun 1;77(11):2938–2951. . PubMed PMID: 28386016; PubMed Central PMCID: PMCPMC5489339. PubMed PMC

Allaire M, Rautou P-E, Codogno P, et al. Autophagy in liver diseases: Time for translation?. J Hepatol. 2019. May;70(5):985–998. doi:10.1016/j.jhep.2019.01.026. PubMed PMID: 30711404.. PubMed DOI

Zhang H, Alsaleh G, Feltham J, et al. Polyamines control eIF5A hypusination, TFEB translation, and autophagy to reverse B cell senescence. Mol Cell. 2019. Oct 3;76(1):110–125 e9. doi:10.1016/j.molcel.2019.08.005. PubMed PMID: 31474573; PubMed Central PMCID: PMCPMC6863385. PubMed DOI PMC

Eisenberg T, Abdellatif M, Schroeder S, et al. Cardioprotection and lifespan extension by the natural polyamine spermidine. Nat Med. 2016. Dec;22(12):1428–1438. doi:10.1038/nm.4222. PubMed PMID: 27841876; PubMed Central PMCID: PMCPMC5806691. PubMed DOI PMC

Xu W, Cai SY, Zhang Y, et al. Melatonin enhances thermotolerance by promoting cellular protein protection in tomato plants. J Pineal Res. 2016. Nov;61(4):457–469. doi:10.1111/jpi.12359. PubMed PMID: 27484733. PubMed DOI

Cai SY, Zhang Y, Xu YP, et al. HsfA1a upregulates melatonin biosynthesis to confer cadmium tolerance in tomato plants. J Pineal Res. 2017. Mar;62(2):e12387. doi:10.1111/jpi.12387. PubMed PMID: 28095626. PubMed DOI

Wang Y, Cai S, Yin L, et al. Tomato HsfA1a plays a critical role in plant drought tolerance by activating ATG genes and inducing autophagy. Autophagy. 2015. Nov 2;11(11):2033–2047. doi:10.1080/15548627.2015.1098798. PubMed PMID: 26649940; PubMed Central PMCID: PMCPMC4824577. PubMed DOI PMC

Wang Y, Cao JJ, Wang KX, et al. BZR1 mediates brassinosteroid-induced autophagy and nitrogen starvation in tomato. Plant Physiol. 2019. Feb;179(2):671–685. doi:10.1104/pp.18.01028. PubMed PMID: 30482787; PubMed Central PMCID: PMCPMC6426427. PubMed DOI PMC

Ropolo A, Grasso D, Pardo R, et al. The pancreatitis-induced vacuole membrane protein 1 triggers autophagy in mammalian cells. J Biol Chem. 2007. Dec 21;282(51):37124–33. doi:10.1074/jbc.M706956200. PubMed PMID: 17940279; eng. PubMed DOI

Tian Y, Li Z, Hu W, et al. C. elegans screen identifies autophagy genes specific to multicellular organisms. Cell. 2010. Jun 11;141(6):1042–55. doi:10.1016/j.cell.2010.04.034. PubMed PMID: 20550938; eng. PubMed DOI

Tabara LC, Escalante R.. VMP1 Establishes ER-Microdomains that Regulate Membrane Contact Sites and Autophagy. PLoS One. 2016;11(11):e0166499. doi:10.1371/journal.pone.0166499. PubMed PMID: 27861594; PubMed Central PMCID: PMCPMC5115753. PubMed DOI PMC

Re AE Lo, Fernandez-Barrena MG, Almada LL, et al. Novel AKT1-GLI3-VMP1 pathway mediates KRAS oncogene-induced autophagy in cancer cells. J Biol Chem. 2012. Jul 20;287(30):25325–34. doi:10.1074/jbc.M112.370809. PubMed PMID: 22535956; PubMed Central PMCID: PMC3408195. PubMed DOI PMC

Sardiello M, Palmieri M, di Ronza A, et al. A gene network regulating lysosomal biogenesis and function. Science. 2009. Jul 24;325(5939):473–7. doi:10.1126/science.1174447. PubMed PMID: 19556463; eng. PubMed DOI

Palmieri M, Impey S, Kang H, et al. Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways. Hum Mol Genet. 2011. Oct 1;20(19):3852–66. doi:10.1093/hmg/ddr306. PubMed PMID: 21752829; eng. PubMed DOI

Martina JA, Chen Y, Gucek M, et al. MTORC1 functions as a transcriptional regulator of autophagy by preventing nuclear transport of TFEB. Autophagy. 2012. Jun;8(6):903–14. doi:10.4161/auto.19653. PubMed PMID: 22576015; PubMed Central PMCID: PMC3427256. PubMed DOI PMC

Settembre C, Zoncu R, Medina DL, et al. A lysosome-to-nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB. EMBO J. 2012. Mar 7;31(5):1095–108. doi:10.1038/emboj.2012.32. PubMed PMID: 22343943; PubMed Central PMCID: PMC3298007. PubMed DOI PMC

Vega-Rubin-de-Celis S, Pena-Llopis S, Konda M, et al. Multistep regulation of TFEB by MTORC1. Autophagy. 2017. Mar 4;13(3):464–472. doi:10.1080/15548627.2016.1271514. PubMed PMID: 28055300; PubMed Central PMCID: PMCPMC5361595. PubMed DOI PMC

Palmieri M, Pal R, Nelvagal HR, et al. mTORC1-independent TFEB activation via Akt inhibition promotes cellular clearance in neurodegenerative storage diseases. Nat Commun. 2017. Feb 6;8:14338. doi:10.1038/ncomms14338. PubMed PMID: 28165011; PubMed Central PMCID: PMCPMC5303831. PubMed DOI PMC

Napolitano G, Esposito A, Choi H, et al. mTOR-dependent phosphorylation controls TFEB nuclear export. Nat Commun. 2018. Aug 17;9(1):3312. doi:10.1038/s41467-018-05862-6. PubMed PMID: 30120233; PubMed Central PMCID: PMCPMC6098152. PubMed DOI PMC

Silvestrini MJ, Johnson JR, Kumar AV, et al. Nuclear export inhibition enhances HLH-30/TFEB activity, autophagy, and lifespan. Cell Rep. 2018. May 15;23(7):1915–1921. doi:10.1016/j.celrep.2018.04.063. PubMed PMID: 29768192; PubMed Central PMCID: PMCPMC5991088. PubMed DOI PMC

Li L, Friedrichsen HJ, Andrews S, et al. A TFEB nuclear export signal integrates amino acid supply and glucose availability. Nat Commun. 2018. Jul 11;9(1):2685. doi: 10.1038/s41467-018-04849-7. PubMed PMID: 29992949; PubMed Central PMCID: PMCPMC6041281. PubMed DOI PMC

Nezich CL, Wang C, Fogel AI, et al. MiT/TFE transcription factors are activated during mitophagy downstream of Parkin and Atg5. J Cell Biol. 2015. Aug 3;210(3):435–50. doi:10.1083/jcb.201501002. PubMed PMID: 26240184; PubMed Central PMCID: PMC4523611. PubMed DOI PMC

Perera RM, Stoykova S, Nicolay BN, et al. Transcriptional control of autophagy-lysosome function drives pancreatic cancer metabolism. Nature. 2015. Aug 20;524(7565):361–5. doi:10.1038/nature14587. PubMed PMID: 26168401. PubMed DOI PMC

Zhang J, Wang J, Zhou Z, et al. Importance of TFEB acetylation in control of its transcriptional activity and lysosomal function in response to histone deacetylase inhibitors. Autophagy. 2018;14(6):1043–1059. doi:10.1080/15548627.2018.1447290. PubMed PMID: 30059277; PubMed Central PMCID: PMCPMC6103407. PubMed DOI PMC

Shin HJ, Kim H, Oh S, et al. AMPK-SKP2-CARM1 signalling cascade in transcriptional regulation of autophagy. Nature. 2016. Jun 23;534(7608):553–7. doi:10.1038/nature18014. PubMed PMID: 27309807; PubMed Central PMCID: PMCPMC5568428. PubMed DOI PMC

Kang YA, Sanalkumar R, O’Geen H, et al. Autophagy driven by a master regulator of hematopoiesis. Mol Cell Biol. 2012. Jan;32(1):226–39. doi:10.1128/MCB.06166-11. PubMed PMID: 22025678; eng. PubMed DOI PMC

Brigger D, Proikas-Cezanne T, Tschan MP.. WIPI-dependent autophagy during neutrophil differentiation of NB4 acute promyelocytic leukemia cells. Cell Death Dis. 2014. Jul 3;5:e1315. doi:10.1038/cddis.2014.261. PubMed PMID: 24991767; PubMed Central PMCID: PMCPMC4123064. PubMed DOI PMC

Jin J, Britschgi A, Schlafli AM, et al. Low autophagy (ATG) gene expression is associated with an immature AML blast cell phenotype and can be restored during AML differentiation therapy. Oxid Med Cell Longev. 2018;2018:1482795. doi:10.1155/2018/1482795. PubMed PMID: 29743969; PubMed Central PMCID: PMCPMC5878891. PubMed DOI PMC

Zhao J, Brault JJ, Schild A, et al. FoxO3 coordinately activates protein degradation by the autophagic/lysosomal and proteasomal pathways in atrophying muscle cells. Cell Metab. 2007. Dec;6(6):472–83. doi:S1550-4131(07)00339-7 [pii] doi:10.1016/j.cmet.2007.11.004. PubMed PMID: 18054316; eng. PubMed DOI

Chauhan S, Goodwin JG, Chauhan S, et al. ZKSCAN3 is a master transcriptional repressor of autophagy. Mol Cell. 2013. Apr 11;50(1):16–28. doi:10.1016/j.molcel.2013.01.024. PubMed PMID: 23434374; PubMed Central PMCID: PMC3628091. PubMed DOI PMC

Peeters JGC, Picavet LW, Coenen S, et al. Transcriptional and epigenetic profiling of nutrient-deprived cells to identify novel regulators of autophagy. Autophagy. 2019. Jan;15(1):98–112. doi:10.1080/15548627.2018.1509608. PubMed PMID: 30153076; PubMed Central PMCID: PMCPMC6287694. PubMed DOI PMC

Pajares M, Jimenez-Moreno N, Garcia-Yague AJ, et al. Transcription factor NFE2L2/NRF2 is a regulator of macroautophagy genes. Autophagy. 2016. Oct 2;12(10):1902–1916. doi:10.1080/15548627.2016.1208889. PubMed PMID: 27427974; PubMed Central PMCID: PMCPMC5079676. PubMed DOI PMC

Pajares M, Rojo AI, Arias E, et al. Transcription factor NFE2L2/NRF2 modulates chaperone-mediated autophagy through the regulation of LAMP2A. Autophagy. 2018;14(8):1310–1322. doi:10.1080/15548627.2018.1474992. PubMed PMID: 29950142; PubMed Central PMCID: PMCPMC6103698. PubMed DOI PMC

Ma D, Panda S, Lin JD.. Temporal orchestration of circadian autophagy rhythm by C/EBPbeta. EMBO J. 2011. Nov 16;30(22):4642–51. doi:10.1038/emboj.2011.322. PubMed PMID: 21897364; PubMed Central PMCID: PMC3243590. PubMed DOI PMC

Brest P, Lapaquette P, Souidi M, et al. A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn’s disease [Research Support, Non-U.S. Gov’t]. Nat Genet. 2011. Mar;43(3):242–5. doi:10.1038/ng.762. PubMed PMID: 21278745; eng. PubMed DOI

Meenhuis A, van Veelen PA, de Looper H, et al. MiR-17/20/93/106 promote hematopoietic cell expansion by targeting sequestosome 1-regulated pathways in mice. Blood. 2011. Jul 28;118(4):916–25. doi:10.1182/blood-2011-02-336487. PubMed PMID: 21628417; eng. PubMed DOI PMC

Roccaro AM, Sacco A, Jia X, et al. microRNA-dependent modulation of histone acetylation in Waldenstrom macroglobulinemia. Blood. 2010. Sep 2;116(9):1506–14. doi:10.1182/blood-2010-01-265686. PubMed PMID: 20519629; PubMed Central PMCID: PMC2938840. eng. PubMed DOI PMC

Engedal N, Zerovnik E, Rudov A, et al. From Oxidative Stress Damage to Pathways, Networks, and Autophagy via MicroRNAs. Oxid Med Cell Longev. 2018;2018:4968321. doi:10.1155/2018/4968321. PubMed PMID: 29849898; PubMed Central PMCID: PMCPMC5932428. PubMed DOI PMC

Colangelo T, Polcaro G, Ziccardi P, et al. The miR-27a-calreticulin axis affects drug-induced immunogenic cell death in human colorectal cancer cells. Cell Death Dis. 2016. Feb 25;7:e2108. doi:10.1038/cddis.2016.29. PubMed PMID: 26913599; PubMed Central PMCID: PMCPMC4849155. PubMed DOI PMC

Martinet W, De Meyer GR, Andries L, et al. In situ detection of starvation-induced autophagy. J Histochem Cytochem. 2006. Jan;54(1):85–96. PubMed PMID: 16148314; eng. PubMed

Banreti A, Sass M, Graba Y.. The emerging role of acetylation in the regulation of autophagy. Autophagy. 2013. Jun 1;9(6):819–29. doi:10.4161/auto.23908. PubMed PMID: 23466676; PubMed Central PMCID: PMC3672293. PubMed DOI PMC

Jin M, Klionsky DJ.. Regulation of autophagy: Modulation of the size and number of auto-phagosomes. FEBS Lett. 2014. Aug 1;588(15):2457–2463. doi:10.1016/j.febslet.2014.06.015. PubMed PMID: 24928445; PubMed Central PMCID: PMC4118767. PubMed DOI PMC

Feng Y, Yao Z, Klionsky DJ.. How to control self-digestion: transcriptional, post-transcriptional, and post-translational regulation of autophagy. Trends Cell Biol. 2015. Jun;25(6):354–363. doi:10.1016/j.tcb.2015.02.002. PubMed PMID: 25759175; PubMed Central PMCID: PMC4441840. PubMed DOI PMC

Xie Y, Kang R, Sun X, et al. Posttranslational modification of autophagy-related proteins in macroautophagy. Autophagy. 2015;11(1):28–45. doi:10.4161/15548627.2014.984267. PubMed PMID: 25484070; PubMed Central PMCID: PMC4502723. PubMed DOI PMC

Jin S, Zhang X, Miao Y, et al. m(6)A RNA modification controls autophagy through upregulating ULK1 protein abundance. Cell Res. 2018. Sep;28(9):955–957. doi:10.1038/s41422-018-0069-8. PubMed PMID: 30046135; PubMed Central PMCID: PMCPMC6123428. PubMed DOI PMC

Pietrocola F, Marino G, Lissa D, et al. Pro-autophagic polyphenols reduce the acetylation of cytoplasmic proteins. Cell cycle. 2012. Oct 15;11(20):3851–60. doi:10.4161/cc.22027. PubMed PMID: 23070521; PubMed Central PMCID: PMC3495827. PubMed DOI PMC

Marino G, Pietrocola F, Madeo F, et al. Caloric restriction mimetics: natural/physiological pharmacological autophagy inducers. Autophagy. 2014. Nov 2;10(11):1879–82. doi:10.4161/auto.36413. PubMed PMID: 25484097. PubMed DOI PMC

Madeo F, Pietrocola F, Eisenberg T, et al. Caloric restriction mimetics: towards a molecular definition. Nat Rev Drug Discov. 2014. Oct;13(10):727–40. doi:10.1038/nrd4391. PubMed PMID: 25212602. PubMed DOI

Huang R, Xu Y, Wan W, et al. Deacetylation of Nuclear LC3 Drives Autophagy Initiation under Starvation. Mol Cell. 2015. Jan 13. doi:10.1016/j.molcel.2014.12.013. PubMed PMID: 25601754. PubMed DOI

Lee IH, Finkel T.. Regulation of autophagy by the p300 acetyltransferase. J Biol Chem. 2009. Mar 6;284(10):6322–8. doi:10.1074/jbc.M807135200. PubMed PMID: 19124466. PubMed DOI PMC

Yakhine-Diop SMS, Niso-Santano M, Rodriguez-Arribas M, et al. Impaired mitophagy and protein acetylation levels in fibroblasts from parkinson’s disease patients. Mol Neurobiol. 2019. Apr;56(4):2466–2481. doi:10.1007/s12035-018-1206-6. PubMed PMID: 30032424. PubMed DOI

Ruan HB, Ma Y, Torres S, et al. Calcium-dependent O-GlcNAc signaling drives liver autophagy in adaptation to starvation. Genes Dev. 2017. Aug 15;31(16):1655–1665. doi:10.1101/gad.305441.117. PubMed PMID: 28903979; PubMed Central PMCID: PMCPMC5647936. PubMed DOI PMC

Pyo KE, Kim CR, Lee M, et al. ULK1 O-GlcNAcylation is crucial for activating VPS34 via ATG14L during autophagy initiation. Cell Rep. 2018. Dec 4;25(10):2878–2890 e4. doi:10.1016/j.celrep.2018.11.042. PubMed PMID: 30517873. PubMed DOI

Montagna C, Rizza S, Maiani E, et al. To eat, or NOt to eat: S-nitrosylation signaling in autophagy. FEBS J. 2016. Nov;283(21):3857–3869. doi:10.1111/febs.13736. PubMed PMID: 27083138. PubMed DOI

Sadhu A, Moriyasu Y, Acharya K, et al. Nitric oxide and ROS mediate autophagy and regulate Alternaria alternata toxin-induced cell death in tobacco BY-2 cells. Sci Rep. 2019. Jun 20;9(1):8973. doi:10.1038/s41598-019-45470-y. PubMed PMID: 31222105; PubMed Central PMCID: PMCPMC6586778. PubMed DOI PMC

Rizza S, Cardaci S, Montagna C, et al. S-nitrosylation drives cell senescence and aging in mammals by controlling mitochondrial dynamics and mitophagy. Proc Natl Acad Sci U S A. 2018. Apr 10;115(15):E3388–E3397. doi:10.1073/pnas.1722452115. PubMed PMID: 29581312; PubMed Central PMCID: PMCPMC5899480. PubMed DOI PMC

Rizza S, Filomeni G.. Denitrosylate and live longer: how ADH5/GSNOR links mitophagy to aging. Autophagy. 2018;14(7):1285–1287. doi:10.1080/15548627.2018.1475818. PubMed PMID: 30029585; PubMed Central PMCID: PMCPMC6103690. PubMed DOI PMC

Vandiver MS, Paul BD, Xu R, et al. Sulfhydration mediates neuroprotective actions of parkin. Nat Commun. 2013;4:1626. doi:10.1038/ncomms2623. PubMed PMID: 23535647; PubMed Central PMCID: PMCPMC3622945. PubMed DOI PMC

Sun Y, Lu F, Yu X, et al. Exogenous H2S promoted USP8 sulfhydration to regulate mitophagy in the hearts of db/db mice. Aging Dis. 2020;11:in press. PubMed PMC

Aroca A, Benito JM, Gotor C, et al. Persulfidation proteome reveals the regulation of protein function by hydrogen sulfide in diverse biological processes in Arabidopsis. J Exp Bot. 2017. Oct 13;68(17):4915–4927. doi:10.1093/jxb/erx294. PubMed PMID: 28992305; PubMed Central PMCID: PMCPMC5853657. PubMed DOI PMC

Wang X, Wu R, Liu Y, et al. m(6)A mRNA methylation controls autophagy and adipogenesis by targeting Atg5 and Atg7. Autophagy. 2019. Aug 26:1–15. doi:10.1080/15548627.2019.1659617. PubMed PMID: 31451060. PubMed DOI PMC

Pattingre S, Petiot A, Codogno P.. Analyses of Gα-interacting protein and activator of G-protein-signaling-3 functions in macroautophagy. Methods Enzymol. 2004;390:17–31. PubMed PMID: 15488168; eng. PubMed

Zhang J, Wang J, Ng S, et al. Development of a novel method for quantification of autophagic protein degradation by AHA labeling. Autophagy. 2014. May 1;10(5):901–12. doi:10.4161/auto.28267. PubMed PMID: 24675368. PubMed DOI PMC

Wang J, Zhang J, Lee YM, et al. Nonradioactive quantification of autophagic protein degradation with L-azidohomoalanine labeling. Nat Protoc. 2017. Dec;12(2):279–288. doi:10.1038/nprot.2016.160. PubMed PMID: 28079880. PubMed DOI

Ichimura Y, Kumanomidou T, Sou YS, et al. Structural basis for sorting mechanism of p62 in selective autophagy. J Biol Chem. 2008. Aug 15;283(33):22847–57. doi:10.1074/jbc.M802182200. PubMed PMID: 18524774; eng. PubMed DOI

Kabuta T, Furuta A, Aoki S, et al. Aberrant interaction between Parkinson disease-associated mutant UCH-L1 and the lysosomal receptor for chaperone-mediated autophagy. J Biol Chem. 2008. Aug 29;283(35):23731–8. doi:10.1074/jbc.M801918200. PubMed PMID: 18550537; eng. PubMed DOI PMC

Saitoh Y, Fujikake N, Okamoto Y, et al. p62 plays a protective role in the autophagic degradation of polyglutamine protein oligomers in polyglutamine disease model flies. J Biol Chem. 2015. Jan 16;290(3):1442–53. doi:10.1074/jbc.M114.590281. PubMed PMID: 25480790; PubMed Central PMCID: PMC4340391. PubMed DOI PMC

Ding WX, Ni HM, Gao W, et al. Linking of autophagy to ubiquitin-proteasome system is important for the regulation of endoplasmic reticulum stress and cell viability. Am J Pathol. 2007. Aug;171(2):513–24. PubMed PMID: 17620365; eng. PubMed PMC

Iwata A, Riley BE, Johnston JA, et al. HDAC6 and microtubules are required for autophagic degradation of aggregated huntingtin. J Biol Chem. 2005. Dec 2;280(48):40282–92. PubMed PMID: 16192271; eng. PubMed

Pandey UB, Nie Z, Batlevi Y, et al. HDAC6 rescues neurodegeneration and provides an essential link between autophagy and the UPS. Nature. 2007. Jun 14;447(7146):859–63. PubMed PMID: 17568747; eng. PubMed

Tomek K, Wagner R, Varga F, et al. Blockade of fatty acid synthase induces ubiquitination and degradation of phosphoinositide-3-kinase signaling proteins in ovarian cancer. Mol Cancer Res. 2011. Nov 28:1767–79. doi:10.1158/1541-7786.MCR-10-0467. PubMed PMID: 21970855; Eng. PubMed DOI

Fuertes G, Martin De Llano JJ, Villarroya A, et al. Changes in the proteolytic activities of proteasomes and lysosomes in human fibroblasts produced by serum withdrawal, amino-acid deprivation and confluent conditions. Biochem J. 2003. Oct 1;375(Pt 1):75–86. doi:10.1042/BJ20030282. PubMed PMID: 12841850; PubMed Central PMCID: PMCPMC1223664. PubMed DOI PMC

Zimmermann AC, Zarei M, Eiselein S, et al. Quantitative proteomics for the analysis of spatio-temporal protein dynamics during autophagy. Autophagy. 2010. Nov;6(8):1009–16. PubMed PMID: 20603599; eng. PubMed

Kristensen AR, Schandorff S, Hoyer-Hansen M, et al. Ordered organelle degradation during starvation-induced autophagy. Mol Cell Proteomics. 2008. Dec;7(12):2419–28. doi:10.1074/mcp.M800184-MCP200. PubMed PMID: 18687634; eng. PubMed DOI

Furuya N, Kanazawa T, Fujimura S, et al. Leupeptin-induced appearance of partial fragment of betaine homocysteine methyltransferase during autophagic maturation in rat hepatocytes. J Biochem (Tokyo). 2001. Feb;129(2):313–20. PubMed PMID: 11173534; eng. PubMed

Ueno T, Ishidoh K, Mineki R, et al. Autolysosomal membrane-associated betaine homocysteine methyltransferase. Limited degradation fragment of a sequestered cytosolic enzyme monitoring autophagy. J Biol Chem. 1999. May 21;274(21):15222–9. PubMed PMID: 10329731; eng. PubMed

Overbye A, Saetre F, Hagen LK, et al. Autophagic activity measured in whole rat hepatocytes as the accumulation of a novel BHMT fragment (p10), generated in amphisomes by the asparaginyl proteinase, legumain. Autophagy. 2011. Sep;7(9):1011–27. PubMed PMID: 21610319; PubMed Central PMCID: PMC3210315. eng. PubMed PMC

Seglen PO, Overbye A, Saetre F.. Sequestration assays for mammalian autophagy. Methods Enzymol. 2009;452:63–83. doi:10.1016/S0076-6879(08)03605-7. PubMed PMID: 19200876; eng. PubMed DOI

Mercer CA, Kaliappan A, Dennis PB.. Macroautophagy-dependent, intralysosomal cleavage of a betaine homocysteine methyltransferase fusion protein requires stable multimerization. Autophagy. 2008. Feb;4(2):185–94. PubMed PMID: 18059170; eng. PubMed

Taylor GS, Long HM, Haigh TA, et al. A role for intercellular antigen transfer in the recognition of EBV-transformed B cell lines by EBV nuclear antigen-specific CD4+ T cells. J Iimmunol. 2006. Sep 15;177(6):3746–56. PubMed PMID: 16951335; eng. PubMed

Katayama H, Kogure T, Mizushima N, et al. A sensitive and quantitative technique for detecting autophagic events based on lysosomal delivery. Chem biol. 2011. Aug 26;18(8):1042–52. doi:10.1016/j.chembiol.2011.05.013. PubMed PMID: 21867919; eng. PubMed DOI

An H, Harper JW.. Systematic analysis of ribophagy in human cells reveals bystander flux during selective autophagy. Nat Cell Biol. 2018. Feb;20(2):135–143. doi:10.1038/s41556-017-0007-x. PubMed PMID: 29230017; PubMed Central PMCID: PMCPMC5786475. PubMed DOI PMC

Klionsky DJ, Emr SD.. Membrane protein sorting: biosynthesis, transport and processing of yeast vacuolar alkaline phosphatase. EMBO J. 1989. Aug;8(8):2241–50. PubMed PMID: 2676517; PubMed Central PMCID: PMC401154. eng. PubMed PMC

Venerando R, Miotto G, Kadowaki M, et al. Multiphasic control of proteolysis by leucine and alanine in the isolated rat hepatocyte. Am J Physiol. 1994. Feb;266(2):C455–61. PubMed PMID: 8141260; eng. PubMed

Häussinger D, Hallbrucker C, vom Dahl S, et al. Cell swelling inhibits proteolysis in perfused rat liver. Biochem J. 1990. Nov 15;272(1):239–42. PubMed PMID: 2264828; eng. PubMed PMC

vom Dahl S, Häussinger D.. Cell hydration and proteolysis control in liver. Biochem J. 1995. Dec 15;312:988–9. PubMed PMID: 8554549; eng. PubMed PMC

Vincow ES, Merrihew G, Thomas RE, et al. The PINK1-Parkin pathway promotes both mitophagy and selective respiratory chain turnover in vivo. Proc Natl Acad Sci U S A. 2013. Apr 16;110(16):6400–5. doi:10.1073/pnas.1221132110. PubMed PMID: 23509287; PubMed Central PMCID: PMC3631677. PubMed DOI PMC

Jaeger K, Sukseree S, Zhong S, et al. Cornification of nail keratinocytes requires autophagy for bulk degradation of intracellular proteins while sparing components of the cytoskeleton. Apoptosis. 2019. Feb;24(1–2):62–73. doi:10.1007/s10495-018-1505-4. PubMed PMID: 30552537; PubMed Central PMCID: PMCPMC6373260. PubMed DOI PMC

Reggiori F, Monastyrska I, Shintani T, et al. The actin cytoskeleton is required for selective types of autophagy, but not nonspecific autophagy, in the yeast Saccharomyces cerevisiae [Research Support, N.I.H., Extramural]. Mol Biol Cell. 2005. Dec;16(12):5843–56. doi: 10.1091/mbc.E05-07-0629, PubMed PMID: 16221887; PubMed Central PMCID: PMC1289426. eng. PubMed DOI PMC

Manjithaya R, Jain S, Farre JC, et al. A yeast MAPK cascade regulates pexophagy but not other autophagy pathways. J Cell Biol. 2010. Apr 19;189(2):303–10. doi:10.1083/jcb.200909154. PubMed PMID: 20385774; PubMed Central PMCID: PMC2856896. eng. PubMed DOI PMC

Journo D, Mor A, Abeliovich H.. Aup1-mediated regulation of Rtg3 during mitophagy. J Biol Chem. 2009. Dec 18;284(51):35885–95. doi:10.1074/jbc.M109.048140. PubMed PMID: 19840933; PubMed Central PMCID: PMC2791017. eng. PubMed DOI PMC

Kanki T, Klionsky DJ.. Mitophagy in yeast occurs through a selective mechanism. J Biol Chem. 2008. Nov 21;283(47):32386–93. doi:10.1074/jbc.M802403200. PubMed PMID: 18818209; PubMed Central PMCID: PMC2583303. eng. PubMed DOI PMC

Kanki T, Wang K, Baba M, et al. A genomic screen for yeast mutants defective in selective mitochondria autophagy. Mol Biol Cell. 2009. Nov;20(22):4730–8. doi:10.1091/mbc.E09-03-0225. PubMed PMID: 19793921; PubMed Central PMCID: PMC2777103. eng. PubMed DOI PMC

Kanki T, Wang K, Cao Y, et al. Atg32 is a mitochondrial protein that confers selectivity during mitophagy. Dev Cell. 2009. Jul;17(1):98–109. doi:10.1016/j.devcel.2009.06.014. PubMed PMID: 19619495; PubMed Central PMCID: PMC2746076. eng. PubMed DOI PMC

Okamoto K, Kondo-Okamoto N, Ohsumi Y.. Mitochondria-anchored receptor Atg32 mediates degradation of mitochondria via selective autophagy. Dev Cell. 2009. Jul;17(1):87–97. doi:10.1016/j.devcel.2009.06.013. PubMed PMID: 19619494; eng. PubMed DOI

Kolitsida P, Abeliovich H.. Methods for studying mitophagy in yeast. Methods Mol Biol. 2019;1880:669–678. doi:10.1007/978-1-4939-8873-0_44. PubMed PMID: 30610730. PubMed DOI

Werner A, Herzog B, Voigt O, et al. NBR1 is involved in selective pexophagy in filamentous ascomycetes and can be functionally replaced by a tagged version of its human homolog. Autophagy. 2019. Jan;15(1):78–97. doi:10.1080/15548627.2018.1507440. PubMed PMID: 30081713; PubMed Central PMCID: PMCPMC6287692. PubMed DOI PMC

Sakai Y, Koller A, Rangell LK, et al. Peroxisome degradation by microautophagy in Pichia pastoris: identification of specific steps and morphological intermediates. J Cell Biol. 1998. May 4;141(3):625–36. PubMed PMID: 9566964; PubMed Central PMCID: PMC2132739. eng. PubMed PMC

Nazarko TY, Nicaud JM, Sibirny AA.. Observation of the Yarrowia lipolytica peroxisome-vacuole dynamics by fluorescence microscopy with a single filter set. Cell Biol Int. 2005;29:65–70. PubMed

Roetzer A, Gratz N, Kovarik P, et al. Autophagy supports Candida glabrata survival during phagocytosis. Cell Microbiol. 2010. Feb;12(2):199–216. doi:10.1111/j.1462-5822.2009.01391.x. PubMed PMID: 19811500; PubMed Central PMCID: PMC2816358. eng. PubMed DOI PMC

Bormann C, Sahm H.. Degradation of microbodies in relation to activities of alcohol oxidase and catalase in Candida boidinii. Arch Microbiol. 1978. Apr 27;117(1):67–72. PubMed PMID: 678013; eng. PubMed

Clare DA, Duong MN, Darr D, et al. Effects of molecular oxygen on detection of superoxide radical with nitroblue tetrazolium and on activity stains for catalase. Anal Biochem 1984. Aug1;140(2):532–7. PubMed PMID: 6091498. PubMed

Vachova L, Kucerova H, Devaux F, et al. Metabolic diversification of cells during the development of yeast colonies. Environ Microbiol. 2009. Feb;11(2):494–504. doi:10.1111/j.1462-2920.2008.01789.x. PubMed PMID: 19196279. PubMed DOI

Hutchins MU, Veenhuis M, Klionsky DJ.. Peroxisome degradation in Saccharomyces cerevisiae is dependent on machinery of macroautophagy and the Cvt pathway. J Cell Sci. 1999. Nov;112:4079–87. PubMed PMID: 10547367. PubMed

Mukaiyama H, Oku M, Baba M, et al. Paz2 and 13 other PAZ gene products regulate vacuolar engulfment of peroxisomes during micropexophagy. Genes Cells. 2002. Jan;7(1):75–90. PubMed PMID: 11856375; eng. PubMed

Tuttle DL, Dunn WA, Jr.. Divergent modes of autophagy in the methylotrophic yeast Pichia pastoris. J Cell Sci. 1995. Jan;108(Pt 1):25–35. PubMed PMID: 7738102; eng. PubMed

Nazarko TY, Huang J, Nicaud JM, et al. Trs85 is required for macroautophagy, pexophagy and cytoplasm to vacuole targeting in Yarrowia lipolytica and Saccharomyces cerevisiae. Autophagy. 2005. Apr;1(1):37–45. PubMed PMID: 16874038; PubMed Central PMCID: PMC1828867. eng. PubMed PMC

Veenhuis M, Douma A, Harder W, et al. Degradation and turnover of peroxisomes in the yeast Hansenula polymorpha induced by selective inactivation of peroxisomal enzymes. Arch Microbiol. 1983. Jun;134(3):193–203. PubMed PMID: 6351780; eng. PubMed

Monosov EZ, Wenzel TJ, Luers GH, et al. Labeling of peroxisomes with green fluorescent protein in living P. pastoris cells. J Histochem Cytochem. 1996. Jun;44(6):581–9. PubMed PMID: 8666743; eng. PubMed

Wiemer EA, Wenzel T, Deerinck TJ, et al. Visualization of the peroxisomal compartment in living mammalian cells: dynamic behavior and association with microtubules. J Cell Biol 1997. Jan 13;136(1):71–80. PubMed PMID: 9008704; PubMed Central PMCID: PMC2132450. eng. PubMed PMC

Monastyrska I, van der Heide M, Krikken AM, et al. Atg8 is essential for macropexophagy in Hansenula polymorpha. Traffic. 2005. Jan;6(1):66–74. doi:10.1111/j.1600-0854.2004.00252.x. PubMed PMID: 15569246; eng. PubMed DOI

Devenish RJ, Prescott M, Turcic K, et al. Monitoring organelle turnover in yeast using fluorescent protein tags. Methods Enzymol. 2008;451:109–31. doi:10.1016/S0076-6879(08)03209-6. PubMed PMID: 19185717; eng. PubMed DOI

Farre JC, Manjithaya R, Mathewson RD, et al. PpAtg30 tags peroxisomes for turnover by selective autophagy [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Dev Cell. 2008. Mar;14(3):365–76. doi:10.1016/j.devcel.2007.12.011. PubMed PMID: 18331717; eng. PubMed DOI PMC

He Y, Deng YZ, Naqvi NI.. Atg24-assisted mitophagy in the foot cells is necessary for proper asexual differentiation in Magnaporthe oryzae. Autophagy. 2013. Nov 1;9(11):1818–27. doi:10.4161/auto.26057. PubMed PMID: 23958498. PubMed DOI

Kiššová I, Deffieu M, Manon S, et al. Uth1p is involved in the autophagic degradation of mitochondria. J Biol Chem. 2004. Sep 10;279(37):39068–74. PubMed PMID: 15247238. PubMed

Kiššová I, Salin B, Schaeffer J, et al. Selective and non-selective autophagic degradation of mitochondria in yeast. Autophagy. 2007;3:329–336. PubMed

Kanki T, Klionsky DJ.. The molecular mechanism of mitochondria autophagy in yeast. Mol Microbiol. 2010. Feb;75(4):795–800. doi:10.1111/j.1365-2958.2009.07035.x. PubMed PMID: 20487284; eng. PubMed DOI PMC

Tal R, Winter G, Ecker N, et al. Aup1p, a yeast mitochondrial protein phosphatase homolog, is required for efficient stationary phase mitophagy and cell survival. J Biol Chem. 2007. Feb 23;282(8):5617–24. doi:10.1074/jbc.M605940200. PubMed PMID: 17166847; eng. PubMed DOI

Abeliovich H. Stationary-phase mitophagy in respiring Saccharomyces cerevisiae. Antioxid Redox Signal. 2011. May 15;14(10):2003–11. doi:10.1089/ars.2010.3807. PubMed PMID: 21194383; eng. PubMed DOI

Eiyama A, Kondo-Okamoto N, Okamoto K.. Mitochondrial degradation during starvation is selective and temporally distinct from bulk autophagy in yeast. FEBS Lett. 2013. Jun 19;587(12):1787–92. doi:10.1016/j.febslet.2013.04.030. PubMed PMID: 23660403. PubMed DOI

Aksam EB, Koek A, Kiel JAKW, et al. A peroxisomal lon protease and peroxisome degradation by autophagy play key roles in vitality of Hansenula polymorpha cells. Autophagy. 2007. Mar-Apr;3(2):96–105. PubMed PMID: 17172804; eng. PubMed

Krick R, Muehe Y, Prick T, et al. Piecemeal microautophagy of the nucleus requires the core macroautophagy genes. Mol Biol Cell. 2008. Oct;19(10):4492–505. doi:10.1091/mbc.E08-04-0363. PubMed PMID: 18701704; PubMed Central PMCID: PMC2555948. eng. PubMed DOI PMC

Farre JC, Krick R, Subramani S, et al. Turnover of organelles by autophagy in yeast. Curr Opin Cell Biol. 2009. Aug;21(4):522–30. doi:10.1016/j.ceb.2009.04.015. PubMed PMID: 19515549; PubMed Central PMCID: PMC2725217. eng. PubMed DOI PMC

Kvam E, Goldfarb DS.. Structure and function of nucleus-vacuole junctions: outer-nuclear-membrane targeting of Nvj1p and a role in tryptophan uptake. J Cell Sci. 2006. Sep 1;119(Pt 17):3622–33. doi:10.1242/jcs.03093. PubMed PMID: 16912077; eng. PubMed DOI

Millen JI, Krick R, Prick T, et al. Measuring piecemeal microautophagy of the nucleus in Saccharomyces cerevisiae [Research Support, U.S. Gov’t, Non-P.H.S.]. Autophagy. 2009. Jan;5(1):75–81. PubMed PMID: 18989095; eng. PubMed

Mijaljica D, Prescott M, Devenish RJ.. A late form of nucleophagy in Saccharomyces cerevisiae. PLoS One. 2012;7(6):e40013. doi:10.1371/journal.pone.0040013. PubMed PMID: 22768199; PubMed Central PMCID: PMC3386919. PubMed DOI PMC

Shoji JY, Kikuma T, Arioka M, et al. Macroautophagy-mediated degradation of whole nuclei in the filamentous fungus Aspergillus oryzae. PLoS One. 2010;5(12):e15650. doi:10.1371/journal.pone.0015650. PubMed PMID: 21187926; PubMed Central PMCID: PMC3004950. PubMed DOI PMC

He M, Kershaw MJ, Soanes DM, et al. Infection-associated nuclear degeneration in the rice blast fungus Magnaporthe oryzae requires non-selective macro-autophagy. PLoS One. 2012;7(3):e33270. doi:10.1371/journal.pone.0033270. PubMed PMID: 22448240; PubMed Central PMCID: PMC3308974. PubMed DOI PMC

Maheshwari R. Nuclear behavior in fungal hyphae. FEMS Microbiol Lett. 2005. Aug 1;249(1):7–14. doi:10.1016/j.femsle.2005.06.031. PubMed PMID: 16002240. PubMed DOI

Shoji J-y, Craven KD.. Autophagy in basal hyphal compartments: A green strategy of great recyclers. Fungal Biol Rev. 2011;25:79–83.

Voigt O, Poggeler S.. Autophagy genes Smatg8 and Smatg4 are required for fruiting-body development, vegetative growth and ascospore germination in the filamentous ascomycete Sordaria macrospora. Autophagy. 2013. Jan;9(1):33–49. doi:10.4161/auto.22398. PubMed PMID: 23064313; PubMed Central PMCID: PMC3542216. PubMed DOI PMC

Yorimitsu T, Klionsky DJ.. Atg11 links cargo to the vesicle-forming machinery in the cytoplasm to vacuole targeting pathway. Mol Biol Cell. 2005. Apr;16(4):1593–605. doi:10.1091/mbc.E04-11-1035. PubMed PMID: 15659643; PubMed Central PMCID: PMC1073644. eng. PubMed DOI PMC

Shintani T, Huang W-P, Stromhaug PE, et al. Mechanism of cargo selection in the cytoplasm to vacuole targeting pathway. Dev Cell. 2002. Dec;3(6):825–37. PubMed PMID: 12479808; PubMed Central PMCID: PMC2737732. eng. PubMed PMC

Abeliovich H, Darsow T, Emr SD.. Cytoplasm to vacuole trafficking of aminopeptidase I requires a t-SNARE-Sec1p complex composed of Tlg2p and Vps45p. EMBO J. 1999. Nov 1;18(21):6005–16. doi:10.1093/emboj/18.21.6005. PubMed PMID: 10545112; PubMed Central PMCID: PMC1171666. eng. PubMed DOI PMC

Muller M, Schmidt O, Angelova M, et al. The coordinated action of the MVB pathway and autophagy ensures cell survival during starvation. eLife. 2015. Apr 22;4:e07736. doi:10.7554/eLife.07736. PubMed PMID: 25902403; PubMed Central PMCID: PMCPMC4424281. PubMed DOI PMC

Abeliovich H, Zarei M, Rigbolt KT, et al. Involvement of mitochondrial dynamics in the segregation of mitochondrial matrix proteins during stationary phase mitophagy. Nat Commun. 2013;4:2789. doi:10.1038/ncomms3789. PubMed PMID: 24240771; PubMed Central PMCID: PMC3909740. PubMed DOI PMC

Overbye A, Fengsrud M, Seglen PO.. Proteomic analysis of membrane-associated proteins from rat liver auto-phagosomes. Autophagy. 2007;3:300–322. PubMed

Eapen VV, Waterman DP, Bernard A, et al. A pathway of targeted autophagy is induced by DNA damage in budding yeast. Proc Natl Acad Sci U S A. 2017. Feb 14;114(7):E1158–E1167. doi:10.1073/pnas.1614364114. PubMed PMID: 28154131; PubMed Central PMCID: PMCPMC5320992. PubMed DOI PMC

Petroi D, Popova B, Taheri-Talesh N, et al. Aggregate clearance of alpha-synuclein in Saccharomyces cerevisiae depends more on autophagosome and vacuole function than on the proteasome. J Biol Chem. 2012. Aug 10;287(33):27567–79. doi:10.1074/jbc.M112.361865. PubMed PMID: 22722939; PubMed Central PMCID: PMC3431624. PubMed DOI PMC

Shahpasandzadeh H, Popova B, Kleinknecht A, et al. Interplay between sumoylation and phosphorylation for protection against alpha-synuclein inclusions. J Biol Chem. 2014. Nov 7;289(45):31224–40. doi:10.1074/jbc.M114.559237. PubMed PMID: 25231978; PubMed Central PMCID: PMC4223324. PubMed DOI PMC

Kleinknecht A, Popova B, Lazaro DF, et al. C-terminal tyrosine residue modifications modulate the protective phosphorylation of serine 129 of alpha-synuclein in a yeast model of Parkinson’s disease. PLoS Genet. 2016. Jun;12(6):e1006098. doi:10.1371/journal.pgen.1006098. PubMed PMID: 27341336; PubMed Central PMCID: PMCPMC4920419. PubMed DOI PMC

Wafa K, MacLean J, Zhang F, et al. Characterization of growth suppressive functions of a splice variant of cyclin D2. PLoS One. 2013;8(1):e53503. doi:10.1371/journal.pone.0053503. PubMed PMID: 23326442; PubMed Central PMCID: PMC3542336. PubMed DOI PMC

Ju JS, Miller SE, Jackson E, et al. Quantitation of selective autophagic protein aggregate degradation in vitro and in vivo using luciferase reporters. Autophagy. 2009. May;5(4):511–9. PubMed PMID: 19305149; PubMed Central PMCID: PMC2992796. eng. PubMed PMC

Chuang KH, Liang F, Higgins R, et al. Ubiquilin/Dsk2 promotes inclusion body formation and vacuole (lysosome)-mediated disposal of mutated huntingtin. Mol Biol Cell. 2016. Jul 1;27(13):2025–36. doi:10.1091/mbc.E16-01-0026. PubMed PMID: 27170182; PubMed Central PMCID: PMCPMC4927277. PubMed DOI PMC

Higgins R, Kabbaj MH, Hatcher A, et al. The absence of specific yeast heat-shock proteins leads to abnormal aggregation and compromised autophagic clearance of mutant Huntingtin proteins. PLoS One. 2018;13(1):e0191490. doi:10.1371/journal.pone.0191490. PubMed PMID: 29346421; PubMed Central PMCID: PMCPMC5773196. PubMed DOI PMC

Hohn A, Sittig A, Jung T, et al. Lipofuscin is formed independently of macroautophagy and lysosomal activity in stress-induced prematurely senescent human fibroblasts. Free Radic Biol Med. 2012. Nov 1;53(9):1760–9. doi:10.1016/j.freeradbiomed.2012.08.591. PubMed PMID: 22982048. PubMed DOI

Jung T, Hohn A, Catalgol B, et al. Age-related differences in oxidative protein-damage in young and senescent fibroblasts. Arch Biochem Biophys. 2009. Mar 1;483(1):127–35. doi:10.1016/j.abb.2008.12.007. PubMed PMID: 19135972. PubMed DOI

Li L, Wang ZV, Hill JA, et al. New autophagy reporter mice reveal dynamics of proximal tubular autophagy. J Am Soc Nephrol. 2014. Feb;25(2):305–15. doi:10.1681/ASN.2013040374. PubMed PMID: 24179166; PubMed Central PMCID: PMCPMC3904563. PubMed DOI PMC

Arotcarena ML, Bourdenx M, Dutheil N, et al. Transcription factor EB overexpression prevents neurodegeneration in experimental synucleinopathies. JCI Insight. 2019. Aug 22;4(16). doi:10.1172/jci.insight.129719. PubMed PMID: 31434803; PubMed Central PMCID: PMCPMC6777809. PubMed DOI PMC

Decressac M, Mattsson B, Weikop P, et al. TFEB-mediated autophagy rescues midbrain dopamine neurons from alpha-synuclein toxicity. Proc Natl Acad Sci U S A. 2013. May 7;110(19):E1817–26. doi:10.1073/pnas.1305623110. PubMed PMID: 23610405; PubMed Central PMCID: PMCPMC3651458. PubMed DOI PMC

Torra A, Parent A, Cuadros T, et al. Overexpression of TFEB drives a pleiotropic neurotrophic effect and prevents Parkinson’s disease-related neurodegeneration. Mol Ther. 2018. Jun 6;26(6):1552–1567. doi:10.1016/j.ymthe.2018.02.022. PubMed PMID: 29628303; PubMed Central PMCID: PMCPMC5986717. PubMed DOI PMC

Nivon M, Fort L, Muller P, et al. NFkappaB is a central regulator of protein quality control in response to protein aggregation stresses via autophagy modulation. Mol Biol Cell. 2016. Jun 1;27(11):1712–27. doi:10.1091/mbc.E15-12-0835. PubMed PMID: 27075172; PubMed Central PMCID: PMCPMC4884063. PubMed DOI PMC

Fuentealba RA, Marasa J, Diamond MI, et al. An aggregation sensing reporter identifies leflunomide and teriflunomide as polyglutamine aggregate inhibitors. Hum Mol Genet 2012;21:664–80. PubMed PMC

Al Rawi S, Louvet-Vallee S, Djeddi A, et al. Allophagy: a macroautophagic process degrading spermatozoid-inherited organelles. Autophagy. 2012. Mar;8(3):421–3. doi:10.4161/auto.19242. PubMed PMID: 22361582; PubMed Central PMCID: PMCPMC3337843. PubMed DOI PMC

Sato M, Sato K.. Maternal inheritance of mitochondrial DNA: degradation of paternal mitochondria by allogeneic organelle autophagy, allophagy. Autophagy. 2012. Mar;8(3):424–5. doi:10.4161/auto.19243. PubMed PMID: 22302002. PubMed DOI

Al Rawi S, Louvet-Vallee S, Djeddi A, et al. Postfertilization autophagy of sperm organelles prevents paternal mitochondrial DNA transmission. Science. 2011. Oct 27;334:1144–7. doi:10.1126/science.1211878. PubMed PMID: 22033522; Eng. PubMed DOI

Sato M, Sato K.. Degradation of paternal mitochondria by fertilization-triggered autophagy in C. elegans embryos. Science. 2011. Nov 25;334(6059):1141–4. doi:10.1126/science.1210333. PubMed PMID: 21998252; eng. PubMed DOI

Kim I, Rodriguez-Enriquez S, Lemasters JJ.. Selective degradation of mitochondria by mitophagy. Arch Biochem Biophys. 2007. Jun 15;462(2):245–53. doi:10.1016/j.abb.2007.03.034. PubMed PMID: 17475204; PubMed Central PMCID: PMC2756107. PubMed DOI PMC

Djeddi A, Al Rawi S, Deuve JL, et al. Sperm-inherited organelle clearance in C. elegans relies on LC3-dependent autophagosome targeting to the pericentrosomal area. Development. 2015. May 1;142(9):1705–16. doi:10.1242/dev.117879. PubMed PMID: 25922527. PubMed DOI

Manil-Segalen M, Lefebvre C, Jenzer C, et al. The C. elegans LC3 acts downstream of GABARAP to degrade auto-phagosomes by interacting with the HOPS subunit VPS39. Dev Cell. 2014. Jan 13;28(1):43–55. doi:10.1016/j.devcel.2013.11.022. PubMed PMID: 24374177. PubMed DOI

Sato M, Sato K, Tomura K, et al. The autophagy receptor ALLO-1 and the IKKE-1 kinase control clearance of paternal mitochondria in Caenorhabditis elegans. Nat Cell Biol. 2018. Jan;20(1):81–91. doi:10.1038/s41556-017-0008-9. PubMed PMID: 29255173. PubMed DOI

Molina P, Lim Y, Boyd L.. Ubiquitination is required for the initial removal of paternal organelles in C. elegans. Dev Biol. 2019. Sep 15;453(2):168–179. doi:10.1016/j.ydbio.2019.05.015. PubMed PMID: 31153831; PubMed Central PMCID: PMCPMC6685074. PubMed DOI PMC

Zhou Q, Li H, Li H, et al. Mitochondrial endonuclease G mediates breakdown of paternal mitochondria upon fertilization. Science. 2016. Jul 22;353(6297):394–9. doi:10.1126/science.aaf4777. PubMed PMID: 27338704; PubMed Central PMCID: PMCPMC5469823. PubMed DOI PMC

Wang Y, Zhang Y, Chen L, et al. Kinetics and specificity of paternal mitochondrial elimination in Caenorhabditis elegans. Nat Commun. 2016. Sep 1;7:12569. doi:10.1038/ncomms12569. PubMed PMID: 27581092; PubMed Central PMCID: PMCPMC5025750. PubMed DOI PMC

Ding WX, Yin XM.. Mitophagy: mechanisms, pathophysiological roles, and analysis. Biol Chem. 2012. Jul;393(7):547–64. doi:10.1515/hsz-2012-0119. PubMed PMID: 22944659; PubMed Central PMCID: PMC3630798. PubMed DOI PMC

Ding WX, Li M, Chen X, et al. Autophagy reduces acute ethanol-induced hepatotoxicity and steatosis in mice. Gastroenterology. 2010. Nov;139(5):1740–52. doi:10.1053/j.gastro.2010.07.041. PubMed PMID: 20659474; eng. PubMed DOI PMC

Dong H, Cheung SH, Liang Y, et al. “Stainomics”: identification of mitotracker labeled proteins in mammalian cells. Electrophoresis. 2013. Jul;34(13):1957–64. doi:10.1002/elps.201200557. PubMed PMID: 23595693. PubMed DOI

Mauro-Lizcano M, Esteban-Martinez L, Seco E, et al. New method to assess mitophagy flux by flow cytometry. Autophagy. 2015;11(5):833–43. doi:10.1080/15548627.2015.1034403. PubMed PMID: 25945953; PubMed Central PMCID: PMC4509449. PubMed DOI PMC

Presley AD, Fuller KM, Arriaga EA.. MitoTracker Green labeling of mitochondrial proteins and their subsequent analysis by capillary electrophoresis with laser-induced fluorescence detection. J chromatograp B Anal Technol Biomed Life Sci 2003. Aug5;793(1):141–50. PubMed PMID: 12880861. PubMed

Keij JF, Bell-Prince C, Steinkamp JA.. Staining of mitochondrial membranes with 10-nonyl acridine orange, MitoFluor Green, and MitoTracker Green is affected by mitochondrial membrane potential altering drugs. Cytometry. 2000. Mar1;39(3):203–10. PubMed PMID: 10685077. PubMed

Poot M, Zhang YZ, Kramer JA, et al. Analysis of mitochondrial morphology and function with novel fixable fluorescent stains. J Histochem Cytochem Off J Histochem Soc 1996. Dec;44(12):1363–72. PubMed PMID: 8985128; PubMed

Canonico B, Cesarini E, Salucci S, et al. Defective autophagy, mitochondrial clearance and lipophagy in niemann-pick type B lymphocytes. PLoS One. 2016;11(10):e0165780. doi:10.1371/journal.pone.0165780. PubMed PMID: 27798705; PubMed Central PMCID: PMCPMC5087958. PubMed DOI PMC

Geisler S, Holmstrom KM, Skujat D, et al. PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1. Nat Cell Biol. 2010. Feb;12(2):119–31. doi:10.1038/ncb2012. PubMed PMID: 20098416; eng. PubMed DOI

Geisler S, Holmstrom KM, Treis A, et al. The PINK1/Parkin-mediated mitophagy is compromised by PD-associated mutations. Autophagy. 2010. Oct;6(7):871–8. PubMed PMID: 20798600; eng. PubMed

Zhou Y, Long Q, Wu H, et al. Topology-dependent, bifurcated mitochondrial quality control under starvation. Autophagy. 2019. Jul 4:1–13. doi:10.1080/15548627.2019.1634944. PubMed PMID: 31234709. PubMed DOI PMC

Demers-Lamarche J, Guillebaud G, Tlili M, et al. Loss of Mitochondrial Function Impairs Lysosomes. J Biol Chem. 2016. May 6;291(19):10263–76. doi:10.1074/jbc.M115.695825. PubMed PMID: 26987902; PubMed Central PMCID: PMCPMC4858975. PubMed DOI PMC

Ouellet M, Guillebaud G, Gervais V, et al. A novel algorithm identifies stress-induced alterations in mitochondrial connectivity and inner membrane structure from confocal images. PLoS Comput Biol. 2017. Jun;13(6):e1005612. doi:10.1371/journal.pcbi.1005612. PubMed PMID: 28640814; PubMed Central PMCID: PMCPMC5501662. PubMed DOI PMC

Zhu JH, Guo F, Shelburne J, et al. Localization of phosphorylated ERK/MAP kinases to mitochondria and auto-phagosomes in Lewy body diseases. Brain Pathol. 2003. Oct;13(4):473–81. doi:10.1111/j.1750-3639.2003.tb00478.x. PubMed PMID: 14655753; PubMed Central PMCID: PMCPMC1911206. PubMed DOI PMC

Diot A, Hinks-Roberts A, Lodge T, et al. A novel quantitative assay of mitophagy: Combining high content fluorescence microscopy and mitochondrial DNA load to quantify mitophagy and identify novel pharmacological tools against pathogenic heteroplasmic mtDNA. Pharmacol Res. 2015. Jul 18;100:24–35. doi:10.1016/j.phrs.2015.07.014. PubMed PMID: 26196248. PubMed DOI

Ding WX, Guo F, Ni HM, et al. Parkin and mitofusins reciprocally regulate mitophagy and mitochondrial spheroid formation. J Biol Chem. 2012. Dec 7;287(50):42379–88. doi:10.1074/jbc.M112.413682. PubMed PMID: 23095748; PubMed Central PMCID: PMC3516781. PubMed DOI PMC

Ding WX, Li M, Biazik JM, et al. Electron microscopic analysis of a spherical mitochondrial structure. J Biol Chem. 2012. Dec 7;287(50):42373–8. doi:10.1074/jbc.M112.413674. PubMed PMID: 23093403; PubMed Central PMCID: PMC3516780. PubMed DOI PMC

Dagda RK, Cherra SJ, III, Kulich SM, et al. Loss of PINK1 function promotes mitophagy through effects on oxidative stress and mitochondrial fission. J Biol Chem. 2009. May 15;284(20):13843–55. doi:M808515200[pii] doi:10.1074/jbc.M808515200. PubMed PMID: 19279012; PubMed Central PMCID: PMC2679485. eng. PubMed DOI PMC

Dagda RK, Zhu J, Kulich SM, et al. Mitochondrially localized ERK2 regulates mitophagy and autophagic cell stress: implications for Parkinson’s disease. Autophagy. 2008. Aug;4(6):770–82. PubMed PMID: 18594198; PubMed Central PMCID: PMC2574804. eng. PubMed PMC

Boya P, Gonzalez-Polo RA, Casares N, et al. Inhibition of macroautophagy triggers apoptosis. Mol Cell Biol 2005. Feb;25(3):1025–40. PubMed PMID: 15657430. PubMed PMC

Lazarou M, Sliter DA, Kane LA, et al. The ubiquitin kinase PINK1 recruits autophagy receptors to induce mitophagy. Nature. 2015. Aug 20;524(7565):309–314. doi:10.1038/nature14893. PubMed PMID: 26266977; PubMed Central PMCID: PMCPMC5018156. PubMed DOI PMC

Um JH, Kim YY, Finkel T, et al. Sensitive measurement of mitophagy by flow cytometry using the pH-dependent fluorescent reporter mt-keima. J vis exp. 2018. Aug 12(138). doi:10.3791/58099. PubMed PMID: 30148491; PubMed Central PMCID: PMCPMC6126785. PubMed DOI PMC

Wong YC, Ysselstein D, Krainc D.. Mitochondria-lysosome contacts regulate mitochondrial fission via RAB7 GTP hydrolysis. Nature. 2018. Feb 15;554(7692):382–386. doi:10.1038/nature25486. PubMed PMID: 29364868; PubMed Central PMCID: PMCPMC6209448. PubMed DOI PMC

Wong YC, Kim S, Peng W, et al. Regulation and function of mitochondria-lysosome membrane contact sites in cellular homeostasis. Trends Cell Biol. 2019. Jun;29(6):500–513. doi:10.1016/j.tcb.2019.02.004. PubMed PMID: 30898429. PubMed DOI PMC

Wong YC, Peng W, Krainc D.. Lysosomal regulation of inter-mitochondrial contact fate and motility in Charcot-Marie-Tooth type 2. Dev Cell. 2019. Aug 5;50(3):339–354 e4. doi:10.1016/j.devcel.2019.05.033. PubMed PMID: 31231042; PubMed Central PMCID: PMCPMC6726396. PubMed DOI PMC

Sun N, Yun J, Liu J, et al. Measuring in vivo mitophagy. Mol Cell. 2015. Nov 19;60(4):685–96. doi:10.1016/j.molcel.2015.10.009. PubMed PMID: 26549682; PubMed Central PMCID: PMCPMC4656081. PubMed DOI PMC

McWilliams TG, Prescott AR, Villarejo-Zori B, et al. A comparative map of macroautophagy and mitophagy in the vertebrate eye. Autophagy. 2019. Jul;15(7):1296–1308. doi:10.1080/15548627.2019.1580509. PubMed PMID: 30786807; PubMed Central PMCID: PMCPMC6613837. PubMed DOI PMC

Cornelissen T, Vilain S, Vints K, et al. Deficiency of parkin and PINK1 impairs age-dependent mitophagy in Drosophila. eLife. 2018. May 29;7. doi:10.7554/eLife.35878. PubMed PMID: 29809156; PubMed Central PMCID: PMCPMC6008047. PubMed DOI PMC

Kim YY, Um JH, Yoon JH, et al. Assessment of mitophagy in mt-Keima Drosophila revealed an essential role of the PINK1-Parkin pathway in mitophagy induction in vivo. FASEB J. 2019. Sep;33(9):9742–9751. doi:10.1096/fj.201900073R. PubMed PMID: 31120803. PubMed DOI

Reipert S, Berry J, Hughes MF, et al. Changes of mitochondrial mass in the hemopoietic stem cell line FDCP-mix after treatment with etoposide: a correlative study by multiparameter flow cytometry and confocal and electron microscopy. Exp Cell Res. 1995. Dec;221(2):281–8. doi:10.1006/excr.1995.1376. PubMed PMID: 7493625. PubMed DOI

Wilfinger N, Austin S, Scheiber-Mojdehkar B, et al. Novel p53-dependent anticancer strategy by targeting iron signaling and BNIP3L-induced mitophagy. Oncotarget. 2016. Jan 12;7(2):1242–61. doi:10.18632/oncotarget.6233. PubMed PMID: 26517689; PubMed Central PMCID: PMCPMC4811457. PubMed DOI PMC

Esteban-Martinez L, Sierra-Filardi E, McGreal RS, et al. Programmed mitophagy is essential for the glycolytic switch during cell differentiation. EMBO J. 2017. Jun 14;36(12):1688–1706. doi:10.15252/embj.201695916. PubMed PMID: 28465321; PubMed Central PMCID: PMCPMC5470043. PubMed DOI PMC

Valente AJ, Maddalena LA, Robb EL, et al. A simple ImageJ macro tool for analyzing mitochondrial network morphology in mammalian cell culture. Acta Histochem. 2017. Apr;119(3):315–326. doi: 10.1016/j.acthis.2017.03.001. PubMed PMID: 28314612. PubMed DOI

Tanaka A, Cleland MM, Xu S, et al. Proteasome and p97 mediate mitophagy and degradation of mitofusins induced by Parkin. J Cell Biol. 2010. Dec 27;191(7):1367–80. doi:10.1083/jcb.201007013. PubMed PMID: 21173115; PubMed Central PMCID: PMC3010068. eng. PubMed DOI PMC

Yoshii SR, Kishi C, Ishihara N, et al. Parkin mediates proteasome-dependent protein degradation and rupture of the outer mitochondrial membrane. J Biol Chem. 2011. Jun 3;286(22):19630–40. doi:10.1074/jbc.M110.209338. PubMed PMID: 21454557; PubMed Central PMCID: PMC3103342. eng. PubMed DOI PMC

Shiba-Fukushima K, Imai Y, Yoshida S, et al. PINK1-mediated phosphorylation of the Parkin ubiquitin-like domain primes mitochondrial translocation of Parkin and regulates mitophagy. Sci Rep. 2012;2:1002. doi:10.1038/srep01002. PubMed PMID: 23256036; PubMed Central PMCID: PMC3525937. PubMed DOI PMC

Giulivi C, Zhang YF, Omanska-Klusek A, et al. Mitochondrial dysfunction in autism. JAMA. 2010. Dec 1;304(21):2389–96. doi:10.1001/jama.2010.1706. PubMed PMID: 21119085; PubMed Central PMCID: PMCPMC3915058. PubMed DOI PMC

Amadoro G, Corsetti V, Florenzano F, et al. AD-linked, toxic NH2 human tau affects the quality control of mitochondria in neurons. Neurobiol Dis. 2014. Feb;62:489–507. doi:10.1016/j.nbd.2013.10.018. PubMed PMID: 24411077. PubMed DOI

Napoli E, Song G, Wong S, et al. Altered bioenergetics in primary dermal fibroblasts from adult carriers of the FMR1 premutation before the onset of the neurodegenerative disease fragile X-associated tremor/ataxia syndrome. Cerebellum. 2016. Oct;15(5):552–64. doi:10.1007/s12311-016-0779-8. PubMed PMID: 27089882; PubMed Central PMCID: PMCPMC5014718. PubMed DOI PMC

Fujisawa Y, Napoli E, Wong S, et al. Impact of a novel homozygous mutation in nicotinamide nucleotide transhydrogenase on mitochondrial DNA integrity in a case of familial glucocorticoid deficiency. BBA Clin. 2015. Jun 1;3:70–78. doi:10.1016/j.bbacli.2014.12.003. PubMed PMID: 26309815; PubMed Central PMCID: PMCPMC4545511. PubMed DOI PMC

Park YS, Choi SE, Koh HC.. PGAM5 regulates PINK1/Parkin-mediated mitophagy via DRP1 in CCCP-induced mitochondrial dysfunction. Toxicol Lett. 2018. Mar 1;284:120–128. doi:10.1016/j.toxlet.2017.12.004. PubMed PMID: 29241732. PubMed DOI

Lu X, Altshuler-Keylin S, Wang Q, et al. Mitophagy controls beige adipocyte maintenance through a Parkin-dependent and UCP1-independent mechanism. Sci Signal. 2018. Apr 24;11(527). doi:10.1126/scisignal.aap8526. PubMed PMID: 29692364; PubMed Central PMCID: PMCPMC6410368. PubMed DOI PMC

Chang TK, Shravage BV, Hayes SD, et al. Uba1 functions in Atg7- and Atg3-independent autophagy. Nat Cell Biol. 2013. Sep;15(9):1067–78. doi:10.1038/ncb2804. PubMed PMID: 23873149; PubMed Central PMCID: PMC3762904. PubMed DOI PMC

Hsieh CH, Shaltouki A, Gonzalez AE, et al. Functional impairment in miro degradation and mitophagy is a shared feature in familial and sporadic parkinson’s disease. Cell Stem Cell. 2016. Dec 1;19(6):709–724. doi:10.1016/j.stem.2016.08.002. PubMed PMID: 27618216; PubMed Central PMCID: PMCPMC5135570. PubMed DOI PMC

Monzio Compagnoni G, Kleiner G, Bordoni A, et al. Mitochondrial dysfunction in fibroblasts of Multiple System Atrophy. Biochim Biophys Acta Mol Basis Dis. 2018. Dec;1864(12):3588–3597. doi:10.1016/j.bbadis.2018.09.018. PubMed PMID: 30254015. PubMed DOI

Pickrell AM, Youle RJ.. The roles of PINK1, parkin, and mitochondrial fidelity in Parkinson’s disease. Neuron. 2015. Jan 21;85(2):257–73. doi:10.1016/j.neuron.2014.12.007. PubMed PMID: 25611507. PubMed DOI PMC

East DA, Fagiani F, Crosby J, et al. PMI: a DeltaPsim independent pharmacological regulator of mitophagy. Chem Biol. 2014. Nov 20;21(11):1585–96. doi:10.1016/j.chembiol.2014.09.019. PubMed PMID: 25455860; PubMed Central PMCID: PMC4245710. PubMed DOI PMC

Vannini N, Campos V, Girotra M, et al. The NAD-booster nicotinamide riboside potently stimulates hematopoiesis through increased mitochondrial clearance. Cell Stem Cell. 2019. Mar 7;24(3):405–418 e7. doi:10.1016/j.stem.2019.02.012. PubMed PMID: 30849366. PubMed DOI

Fang EF, Kassahun H, Croteau DL, et al. NAD(+) replenishment improves lifespan and healthspan in ataxia telangiectasia models via mitophagy and DNA repair. Cell Metab. 2016. Oct 11;24(4):566–581. doi:10.1016/j.cmet.2016.09.004. PubMed PMID: 27732836; PubMed Central PMCID: PMCPMC5777858. PubMed DOI PMC

Liu L, Feng D, Chen G, et al. Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells. Nat Cell Biol. 2012. Feb;14(2):177–85. doi:10.1038/ncb2422. PubMed PMID: 22267086. PubMed DOI

Bellot G, Garcia-Medina R, Gounon P, et al. Hypoxia-induced autophagy is mediated through hypoxia-inducible factor induction of BNIP3 and BNIP3L via their BH3 domains. Mol Cell Biol. 2009. May;29(10):2570–81. doi:10.1128/MCB.00166-09. PubMed PMID: 19273585; PubMed Central PMCID: PMC2682037. eng. PubMed DOI PMC

Zhang J, Ney PA.. Role of BNIP3 and NIX in cell death, autophagy, and mitophagy. Cell Death Differ. 2009. Jul;16(7):939–46. doi:10.1038/cdd.2009.16. PubMed PMID: 19229244; PubMed Central PMCID: PMCPMC2768230. PubMed DOI PMC

Schiavi A, Maglioni S, Palikaras K, et al. Iron-starvation-induced mitophagy mediates lifespan extension upon mitochondrial stress in C. elegans. Curr Biol. 2015. Jul 20;25(14):1810–22. doi:10.1016/j.cub.2015.05.059. PubMed PMID: 26144971. PubMed DOI

Yang JY, Yang WY.. Spatiotemporally controlled initiation of Parkin-mediated mitophagy within single cells. Autophagy. 2011. Oct;7(10):1230–8. doi:10.4161/auto.7.10.16626. PubMed PMID: 22011618; eng. PubMed DOI

Strappazzon F, Nazio F, Corrado M, et al. AMBRA1 is able to induce mitophagy via LC3 binding, regardless of PARKIN and p62/SQSTM1. Cell Death Differ. 2014. Sep 12;22:419–32. doi:10.1038/cdd.2014.139. PubMed PMID: 25215947. PubMed DOI PMC

Chakraborty J, von Stockum S, Marchesan E, et al. USP14 inhibition corrects an in vivo model of impaired mitophagy. EMBO Mol Med. 2018. Nov;10(11). doi:10.15252/emmm.201809014. PubMed PMID: 30249595; PubMed Central PMCID: PMCPMC6220287. PubMed DOI PMC

Wei Y, Chiang WC, Sumpter R, Jr., et al. Prohibitin 2 Is an Inner Mitochondrial Membrane Mitophagy Receptor. Cell. 2017. Jan 12;168(1–2):224–238 e10. doi:10.1016/j.cell.2016.11.042. PubMed PMID: 28017329; PubMed Central PMCID: PMCPMC5235968. PubMed DOI PMC

Ferree AW, Trudeau K, Zik E, et al. MitoTimer probe reveals the impact of autophagy, fusion, and motility on subcellular distribution of young and old mitochondrial protein and on relative mitochondrial protein age. Autophagy. 2013. Nov 1;9(11):1887–96. doi:10.4161/auto.26503. PubMed PMID: 24149000; PubMed Central PMCID: PMCPMC4028338. PubMed DOI PMC

Hernandez G, Thornton C, Stotland A, et al. MitoTimer: a novel tool for monitoring mitochondrial turnover. Autophagy. 2013. Nov 1;9(11):1852–61. doi:10.4161/auto.26501. PubMed PMID: 24128932; PubMed Central PMCID: PMCPMC4028337. PubMed DOI PMC

Laker RC, Xu P, Ryall KA, et al. A novel MitoTimer reporter gene for mitochondrial content, structure, stress, and damage in vivo. J Biol Chem. 2014. Apr 25;289(17):12005–15. doi:10.1074/jbc.M113.530527. PubMed PMID: 24644293; PubMed Central PMCID: PMCPMC4002107. PubMed DOI PMC

Martin-Maestro P, Gargini R, Garcia E, et al. Slower dynamics and aged mitochondria in sporadic Alzheimer’s disease. Oxid Med Cell Longev. 2017;2017:9302761. doi:10.1155/2017/9302761. PubMed PMID: 29201274; PubMed Central PMCID: PMCPMC5672147. PubMed DOI PMC

Laker RC, Drake JC, Wilson RJ, et al. Ampk phosphorylation of Ulk1 is required for targeting of mitochondria to lysosomes in exercise-induced mitophagy. Nat Commun. 2017. Sep 15;8(1):548. doi:10.1038/s41467-017-00520-9. PubMed PMID: 28916822; PubMed Central PMCID: PMCPMC5601463. PubMed DOI PMC

Call JA, Wilson RJ, Laker RC, et al. Ulk1-mediated autophagy plays an essential role in mitochondrial remodeling and functional regeneration of skeletal muscle. Am J Physiol Cell Physiol. 2017. Jun 1;312(6):C724–C732. doi:10.1152/ajpcell.00348.2016. PubMed PMID: 28356270; PubMed Central PMCID: PMCPMC5494591. PubMed DOI PMC

Perry HM, Huang L, Wilson RJ, et al. Dynamin-related protein 1 deficiency promotes recovery from AKI. J Am Soc Nephrol. 2018. Jan;29(1):194–206. doi:10.1681/ASN.2017060659. PubMed PMID: 29084809; PubMed Central PMCID: PMCPMC5748924. PubMed DOI PMC

Wilson RJ, Drake JC, Cui D, et al. Mitochondrial protein S-nitrosation protects against ischemia reperfusion-induced denervation at neuromuscular junction in skeletal muscle. Free Radic Biol Med. 2018. Mar;117:180–190. doi:10.1016/j.freeradbiomed.2018.02.006. PubMed PMID: 29432799; PubMed Central PMCID: PMCPMC5896769. PubMed DOI PMC

Wilson RJ, Drake JC, Cui D, et al. Voluntary running protects against neuromuscular dysfunction following hindlimb ischemia-reperfusion in mice. J Appl Physiol (1985). 2019 Jan 1;126(1):193–201. doi:10.1152/japplphysiol.00358.2018. PubMed PMID: 30433863; PubMed Central PMCID: PMCPMC6383643. PubMed DOI PMC

Wilson RJ, Drake JC, Cui D, et al. Conditional MitoTimer reporter mice for assessment of mitochondrial structure, oxidative stress, and mitophagy. Mitochondrion. 2019. Jan;44:20–26. doi:10.1016/j.mito.2017.12.008. PubMed PMID: 29274400; PubMed Central PMCID: PMCPMC6387589. PubMed DOI PMC

Xu P, Damschroder D, Zhang M, et al. Atg2, Atg9 and Atg18 in mitochondrial integrity, cardiac function and healthspan in Drosophila. J Mol Cell Cardiol. 2019. Feb;127:116–124. doi:10.1016/j.yjmcc.2018.12.006. PubMed PMID: 30571977; PubMed Central PMCID: PMCPMC6533900. PubMed DOI PMC

Chu CT. Mechanisms of selective autophagy and mitophagy: Implications for neurodegenerative diseases. Neurobiol Dis. 2019. Feb;122:23–34. doi:10.1016/j.nbd.2018.07.015. PubMed PMID: 30030024; PubMed Central PMCID: PMCPMC6396690. PubMed DOI PMC

Kagan VE, Jiang J, Huang Z, et al. NDPK-D (NM23-H4)-mediated externalization of cardiolipin enables elimination of depolarized mitochondria by mitophagy. Cell Death Differ. 2016. Jul;23(7):1140–51. doi:10.1038/cdd.2015.160. PubMed PMID: 26742431; PubMed Central PMCID: PMCPMC4946882. PubMed DOI PMC

Anton Z, Landajuela A, Hervas JH, et al. Human Atg8-cardiolipin interactions in mitophagy: Specific properties of LC3B, GABARAPL2 and GABARAP. Autophagy. 2016. Dec;12(12):2386–2403. doi:10.1080/15548627.2016.1240856. PubMed PMID: 27764541; PubMed Central PMCID: PMCPMC5172498. PubMed DOI PMC

Fiesel FC, Ando M, Hudec R, et al. (Patho-)physiological relevance of PINK1-dependent ubiquitin phosphorylation. EMBO Rep. 2015. Jul 10;16:1114–30. doi:10.15252/embr.201540514. PubMed PMID: 26162776. PubMed DOI PMC

Wang L, Cho YL, Tang Y, et al. PTEN-L is a novel protein phosphatase for ubiquitin dephosphorylation to inhibit PINK1-Parkin-mediated mitophagy. Cell Res. 2018. Aug;28(8):787–802. doi:10.1038/s41422-018-0056-0. PubMed PMID: 29934616; PubMed Central PMCID: PMCPMC6082900. PubMed DOI PMC

Shiba-Fukushima K, Ishikawa KI, Inoshita T, et al. Evidence that phosphorylated ubiquitin signaling is involved in the etiology of Parkinson’s disease. Hum Mol Genet. 2017. Aug 15;26(16):3172–3185. doi:10.1093/hmg/ddx201. PubMed PMID: 28541509. PubMed DOI

Herhaus L, Dikic I.. Expanding the ubiquitin code through post-translational modification. EMBO Rep. 2015. Aug 12. doi:10.15252/embr.201540891. PubMed PMID: 26268526. PubMed DOI PMC

Koyano F, Okatsu K, Kosako H, et al. Ubiquitin is phosphorylated by PINK1 to activate parkin. Nature. 2014. Jun 5;510(7503):162–6. doi:10.1038/nature13392. PubMed PMID: 24784582. PubMed DOI

Chen G, Han Z, Feng D, et al. A regulatory signaling loop comprising the PGAM5 phosphatase and CK2 controls receptor-mediated mitophagy. Mol Cell. 2014. May 8;54(3):362–77. doi:10.1016/j.molcel.2014.02.034. PubMed PMID: 24746696. PubMed DOI

Wu H, Xue D, Chen G, et al. The BCL2L1 and PGAM5 axis defines hypoxia-induced receptor-mediated mitophagy. Autophagy. 2014. Oct 1;10(10):1712–25. doi:10.4161/auto.29568. PubMed PMID: 25126723; PubMed Central PMCID: PMCPMC4198357. PubMed DOI PMC

Banerjee K, Munshi S, Xu H, et al. Mild mitochondrial metabolic deficits by alpha-ketoglutarate dehydrogenase inhibition cause prominent changes in intracellular autophagic signaling: Potential role in the pathobiology of Alzheimer’s disease. Neurochem Int. 2016. Jun;96:32–45. . PubMed PMID: 26923918; PubMed Central PMCID: PMCPMC4860123. PubMed PMC

Lemasters JJ. Variants of mitochondrial autophagy: Types 1 and 2 mitophagy and micromitophagy (Type 3). Redox Biol. 2014;2:749–54. doi:10.1016/j.redox.2014.06.004. PubMed PMID: 25009776; PubMed Central PMCID: PMC4085350. PubMed DOI PMC

Manjithaya R, Nazarko TY, Farre JC, et al. Molecular mechanism and physiological role of pexophagy. FEBS Lett. 2010. Apr 2;584(7):1367–73. doi:10.1016/j.febslet.2010.01.019. PubMed PMID: 20083110; PubMed Central PMCID: PMC2843806. PubMed DOI PMC

Till A, Lakhani R, Burnett SF, et al. Pexophagy: the selective degradation of peroxisomes. Int J Cell Biol. 2012;2012:512721. doi:10.1155/2012/512721. PubMed PMID: 22536249; PubMed Central PMCID: PMC3320016. PubMed DOI PMC

Michalik L, Auwerx J, Berger JP, et al. International Union of Pharmacology. LXI. Peroxisome proliferator-activated receptors. Pharmacol Rev. 2006. Dec;58(4):726–41. doi:10.1124/pr.58.4.5. PubMed PMID: 17132851. PubMed DOI

D’Orio B, Fracassi A, Ceru MP, et al. Targeting PPARalpha in Alzheimer’s Disease. Curr Alzheimer Res. 2018. Feb 22;15(4):345–354. doi:10.2174/1567205014666170505094549. PubMed PMID: 28474570. PubMed DOI

Sargent G, van Zutphen T, Shatseva T, et al. PEX2 is the E3 ubiquitin ligase required for pexophagy during starvation. J Cell Biol. 2016. Sep 12;214(6):677–90. doi:10.1083/jcb.201511034. PubMed PMID: 27597759; PubMed Central PMCID: PMCPMC5021090. PubMed DOI PMC

Riccio V, Demers N, Hua R, et al. Deubiquitinating enzyme USP30 maintains basal peroxisome abundance by regulating pexophagy. J Cell Biol. 2019. Mar 4;218(3):798–807. doi:10.1083/jcb.201804172. PubMed PMID: 30700497; PubMed Central PMCID: PMCPMC6400567. PubMed DOI PMC

Marcassa E, Kallinos A, Jardine J, et al. Dual role of USP30 in controlling basal pexophagy and mitophagy. EMBO Rep. 2018. Jul;19(7). doi:10.15252/embr.201745595. PubMed PMID: 29895712; PubMed Central PMCID: PMCPMC6030704. PubMed DOI PMC

Walter KM, Schonenberger MJ, Trotzmuller M, et al. Hif-2alpha promotes degradation of mammalian peroxisomes by selective autophagy. Cell Metab. 2014. Nov 4;20(5):882–97. doi:10.1016/j.cmet.2014.09.017. PubMed PMID: 25440060. PubMed DOI

Alexander A, Cai SL, Kim J, et al. ATM signals to TSC2 in the cytoplasm to regulate mTORC1 in response to ROS. Proc Natl Acad Sci USA 2010. Feb 16;107:4153–8. doi: 0913860107 [pii] doi:10.1073/pnas.0913860107. PubMed PMID: 20160076; Eng. PubMed DOI PMC

Tripathi DN, Chowdhury R, Trudel LJ, et al. Reactive nitrogen species regulate autophagy through ATM-AMPK-TSC2-mediated suppression of mTORC1. Proc Natl Acad Sci U S A. 2013. Aug 6;110(32):E2950–7. doi:10.1073/pnas.1307736110. PubMed PMID: 23878245; PubMed Central PMCID: PMC3740898. PubMed DOI PMC

Zhang J, Kim J, Alexander A, et al. A tuberous sclerosis complex signalling node at the peroxisome regulates mTORC1 and autophagy in response to ROS. Nat Cell Biol. 2013. Oct;15(10):1186–96. doi:10.1038/ncb2822. PubMed PMID: 23955302; PubMed Central PMCID: PMC3789865. PubMed DOI PMC

Zhang J, Tripathi DN, Jing J, et al. ATM functions at the peroxisome to induce pexophagy in response to ROS. Nat Cell Biol. 2015. Sep 7;17:1259–69. doi:10.1038/ncb3230. PubMed PMID: 26344566. PubMed DOI PMC

D’Eletto M, Farrace MG, Rossin F, et al. Type 2 transglutaminase is involved in the autophagy-dependent clearance of ubiquitinated proteins. Cell Death Differ. 2012. Jul;19(7):1228–38. doi:10.1038/cdd.2012.2. PubMed PMID: 22322858; PubMed Central PMCID: PMC3374086. PubMed DOI PMC

Luiken JJ, van den Berg M, Heikoop JC, et al. Autophagic degradation of peroxisomes in isolated rat hepatocytes. FEBS Lett. 1992. Jun8;304(1):93–7. PubMed PMID: 1618306. PubMed

Nardacci R, Sartori C, Stefanini S.. Selective autophagy of clofibrate-induced rat liver peroxisomes. Cytochemistry and immunocytochemistry on tissue specimens and on fractions obtained by Nycodenz density gradient centrifugation. Cell Mol Biol. 2000. Nov;46(7):1277–90. PubMed PMID: 11075957. PubMed

Yokota S. Formation of auto-phagosomes during degradation of excess peroxisomes induced by administration of dioctyl phthalate [Research Support, Non-U.S. Gov’t]. Eur J Cell Biol. 1993. Jun;61(1):67–80. PubMed PMID: 8223709; eng. PubMed

Huybrechts SJ, Van Veldhoven PP, Brees C, et al. Peroxisome dynamics in cultured mammalian cells [Research Support, Non-U.S. Gov’t]. Traffic. 2009. Nov;10(11):1722–33. doi:10.1111/j.1600-0854.2009.00970.x. PubMed PMID: 19719477; eng. PubMed DOI

Jiang L, Hara-Kuge S, Yamashita S, et al. Peroxin Pex14p is the key component for coordinated autophagic degradation of mammalian peroxisomes by direct binding to LC3-II. Genes Cells. 2015. Jan;20(1):36–49. doi:10.1111/gtc.12198. PubMed PMID: 25358256. PubMed DOI

Fujiki Y, Okumoto K, Mukai S, et al. Peroxisome biogenesis in mammalian cells. Front Physiol. 2014;5:307. doi:10.3389/fphys.2014.00307. PubMed PMID: 25177298; PubMed Central PMCID: PMCPMC4133648. PubMed DOI PMC

Hara-Kuge S, Fujiki Y.. The peroxin Pex14p is involved in LC3-dependent degradation of mammalian peroxisomes [Research Support, Non-U.S. Gov’t]. Exp Cell Res. 2008. Nov 15;314(19):3531–41. doi:10.1016/j.yexcr.2008.09.015. PubMed PMID: 18848543; eng. PubMed DOI

Yamashita S, Abe K, Tatemichi Y, et al. The membrane peroxin PEX3 induces peroxisome-ubiquitination-linked pexophagy. Autophagy. 2014. Sep;10(9):1549–64. doi:10.4161/auto.29329. PubMed PMID: 25007327; PubMed Central PMCID: PMCPMC4206534. PubMed DOI PMC

Yamashita S, Fujiki Y.. Assessing Pexophagy in Mammalian Cells. Methods Mol Biol. 2017;1595:243–248. doi:10.1007/978-1-4939-6937-1_23. PubMed PMID: 28409468. PubMed DOI

Lee JY, Nagano Y, Taylor JP, et al. Disease-causing mutations in parkin impair mitochondrial ubiquitination, aggregation, and HDAC6-dependent mitophagy [Research Support, N.I.H., Extramural]. J Cell Biol. 2010. May 17;189(4):671–9. doi:10.1083/jcb.201001039. PubMed PMID: 20457763; PubMed Central PMCID: PMC2872903. eng. PubMed DOI PMC

Zhou Y, Long Q, Wu H, et al. Topology-dependent, bifurcated mitochondrial quality control under starvation. Autophagy. 2020. Mar;16(3):562–574. doi:10.1080/15548627.2019.1634944. PubMed PMID: 31234709. PubMed DOI PMC

Georgakopoulos ND, Wells G, Campanella M.. The pharmacological regulation of cellular mitophagy. Nat Chem Biol. 2017. Jan 19;13(2):136–146. doi:10.1038/nchembio.2287. PubMed PMID: 28103219. PubMed DOI

Kondapalli C, Kazlauskaite A, Zhang N, et al. PINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating Serine 65. Open Biol. 2012. May;2(5):120080. doi:10.1098/rsob.120080. PubMed PMID: 22724072; PubMed Central PMCID: PMC3376738. PubMed DOI PMC

Yang KC, Ma X, Liu H, et al. Tumor necrosis factor receptor-associated factor 2 mediates mitochondrial autophagy. Circ Heart Fail. 2014. Oct 22;8:175–87. doi:10.1161/CIRCHEARTFAILURE.114.001635. PubMed PMID: 25339503. PubMed DOI PMC

Whitworth AJ, Pallanck LJ.. PINK1/Parkin mitophagy and neurodegeneration-what do we really know in vivo? Curr Opin Genet Dev. 2017. Jun;44:47–53. doi:10.1016/j.gde.2017.01.016. PubMed PMID: 28213158. PubMed DOI

Chan NC, Salazar AM, Pham AH, et al. Broad activation of the ubiquitin-proteasome system by Parkin is critical for mitophagy. Hum Mol Genet. 2011. May 1;20(9):1726–37. doi:10.1093/hmg/ddr048. PubMed PMID: 21296869; PubMed Central PMCID: PMC3071670. eng. PubMed DOI PMC

Martinez A, Lectez B, Ramirez J, et al. Quantitative proteomic analysis of Parkin substrates in Drosophila neurons. Mol Neurodegener. 2017. Apr 11;12(1):29. doi:10.1186/s13024-017-0170-3. PubMed PMID: 28399880; PubMed Central PMCID: PMCPMC5387213. PubMed DOI PMC

Okatsu K, Saisho K, Shimanuki M, et al. p62/SQSTM1 cooperates with Parkin for perinuclear clustering of depolarized mitochondria. Genes Cells. 2010. Aug;15(8):887–900. doi:10.1111/j.1365-2443.2010.01426.x. PubMed PMID: 20604804; PubMed Central PMCID: PMC2970908. eng. PubMed DOI PMC

McWilliams TG, Prescott AR, Montava-Garriga L, et al. Basal mitophagy occurs independently of PINK1 in mouse tissues of high metabolic demand. Cell Metab. 2018. Feb 6;27(2):439–449 e5. doi:10.1016/j.cmet.2017.12.008. PubMed PMID: 29337137; PubMed Central PMCID: PMCPMC5807059. PubMed DOI PMC

Ivatt RM, Sanchez-Martinez A, Godena VK, et al. Genome-wide RNAi screen identifies the Parkinson disease GWAS risk locus SREBF1 as a regulator of mitophagy. Proc Natl Acad Sci U S A. 2014. Jun 10;111(23):8494–9. doi:10.1073/pnas.1321207111. PubMed PMID: 24912190. PubMed DOI PMC

Kim KY, Stevens MV, Akter MH, et al. Parkin is a lipid-responsive regulator of fat uptake in mice and mutant human cells. J Clin Invest. 2011. Sep;121(9):3701–12. doi:10.1172/JCI44736. PubMed PMID: 21865652; PubMed Central PMCID: PMC3171101. PubMed DOI PMC

Klinkenberg M, Gispert S, Dominguez-Bautista JA, et al. Restriction of trophic factors and nutrients induces PARKIN expression. Neurogenetics. 2012. Feb;13(1):9–21. doi:10.1007/s10048-011-0303-8. PubMed PMID: 22028146; PubMed Central PMCID: PMC3274670. PubMed DOI PMC

Parganlija D, Klinkenberg M, Dominguez-Bautista J, et al. Loss of PINK1 impairs stress-induced autophagy and cell survival. PLoS One. 2014;9(4):e95288. doi:10.1371/journal.pone.0095288. PubMed PMID: 24751806; PubMed Central PMCID: PMC3994056. PubMed DOI PMC

Lyamzaev KG, Nepryakhina OK, Saprunova VB, et al. Novel mechanism of elimination of malfunctioning mitochondria (mitoptosis): formation of mitoptotic bodies and extrusion of mitochondrial material from the cell. Biochim Biophys Acta. 2008. Jul-Aug;1777(7–8):817–25. doi:10.1016/j.bbabio.2008.03.027. PubMed PMID: 18433711; eng. PubMed DOI

Davis CH, Kim KY, Bushong EA, et al. Transcellular degradation of axonal mitochondria. Proc Natl Acad Sci U S A. 2014. Jul 1;111(26):9633–8. doi:10.1073/pnas.1404651111. PubMed PMID: 24979790; PubMed Central PMCID: PMC4084443. PubMed DOI PMC

Zhu JH, Gusdon AM, Cimen H, et al. Impaired mitochondrial biogenesis contributes to depletion of functional mitochondria in chronic MPP+ toxicity: dual roles for ERK1/2. Cell Death Dis. 2012. May 24;3:e312. doi:10.1038/cddis.2012.46. PubMed PMID: 22622131; PubMed Central PMCID: PMCPMC3366080. PubMed DOI PMC

Wang KZ, Zhu J, Dagda RK, et al. ERK-mediated phosphorylation of TFAM downregulates mitochondrial transcription: implications for Parkinson’s disease. Mitochondrion. 2014. Jul;17:132–40. doi:10.1016/j.mito.2014.04.008. PubMed PMID: 24768991; PubMed Central PMCID: PMCPMC4134365. PubMed DOI PMC

Ezaki J, Kominami E, Ueno T.. Peroxisome degradation in mammals. IUBMB life. 2011. Nov;63(11):1001–8. doi:10.1002/iub.537. PubMed PMID: 21990012; eng. PubMed DOI

Ishida H, Yoshimoto K, Izumi M, et al. Mobilization of rubisco and stroma-localized fluorescent proteins of chloroplasts to the vacuole by an ATG gene-dependent autophagic process. Plant Physiol. 2008. Sep;148(1):142–55. doi:10.1104/pp.108.122770. PubMed PMID: 18614709; PubMed Central PMCID: PMC2528122. PubMed DOI PMC

Wada S, Ishida H, Izumi M, et al. Autophagy plays a role in chloroplast degradation during senescence in individually darkened leaves. Plant Physiol. 2009. Feb;149(2):885–93. doi:10.1104/pp.108.130013. PubMed PMID: 19074627; PubMed Central PMCID: PMC2633819. PubMed DOI PMC

Izumi M, Ishida H, Nakamura S, et al. Entire photodamaged chloroplasts are transported to the central vacuole by autophagy. Plant Cell. 2017. Feb;29(2):377–394. doi:10.1105/tpc.16.00637. PubMed PMID: 28123106; PubMed Central PMCID: PMCPMC5354188. PubMed DOI PMC

Nakamura S, Hidema J, Sakamoto W, et al. Selective elimination of membrane-damaged chloroplasts via microautophagy. Plant Physiol. 2018. Jul;177(3):1007–1026. doi:10.1104/pp.18.00444. PubMed PMID: 29748433; PubMed Central PMCID: PMCPMC6052986. PubMed DOI PMC

Michaeli S, Honig A, Levanony H, et al. Arabidopsis ATG8-INTERACTING PROTEIN1 is involved in autophagy-dependent vesicular trafficking of plastid proteins to the vacuole. Plant Cell. 2014. Oct;26(10):4084–101. doi:10.1105/tpc.114.129999. PubMed PMID: 25281689; PubMed Central PMCID: PMC4247578. PubMed DOI PMC

Spitzer C, Li F, Buono R, et al. The endosomal protein CHARGED MULTIVESICULAR BODY PROTEIN1 regulates the autophagic turnover of plastids in Arabidopsis. Plant Cell. 2015. Feb 3;27:391–402. doi:10.1105/tpc.114.135939. PubMed PMID: 25649438. PubMed DOI PMC

Azzopardi M, Farrugia G, Balzan R.. Cell-cycle involvement in autophagy and apoptosis in yeast. Mech Ageing Dev. 2017. Jan;161(Pt B):211–224. doi:10.1016/j.mad.2016.07.006. PubMed PMID: 27450768. PubMed DOI

Changou CA, Chen YR, Xing L, et al. Arginine starvation-associated atypical cellular death involves mitochondrial dysfunction, nuclear DNA leakage, and chromatin autophagy. Proc Natl Acad Sci U S A. 2014. Sep 30;111(39):14147–52. doi:10.1073/pnas.1404171111. PubMed PMID: 25122679. PubMed DOI PMC

Yang M, Chen P, Liu J, et al. Clockophagy is a novel selective autophagy process favoring ferroptosis. Sci Adv. 2019. Jul;5(7):eaaw2238. doi:10.1126/sciadv.aaw2238. PubMed PMID: 31355331; PubMed Central PMCID: PMCPMC6656546. PubMed DOI PMC

Scotton C, Bovolenta M, Schwartz E, et al. Deep RNA profiling identified CLOCK and molecular clock genes as pathophysiological signatures in collagen VI myopathy. J Cell Sci. 2016. Apr 15;129(8):1671–84. doi:10.1242/jcs.175927. PubMed PMID: 26945058; PubMed Central PMCID: PMCPMC4852766. PubMed DOI PMC

Smith RE, Farquhar MG.. Lysosome function in the regulation of the secretory process in cells of the anterior pituitary gland. J Cell Biol. 1966. Nov 1;31(2):319–47. PubMed PMID: 19866704; PubMed Central PMCID: PMC2107048. eng. PubMed PMC

Orci L, Junod A, Pictet R, et al. Granulolysis in a cells of endocrine pancreas in spontaneous and experimental diabetes in animals. J Cell Biol. 1968. Aug;38(2):462–6. doi:10.1083/jcb.38.2.462. PubMed PMID: 5664218; PubMed Central PMCID: PMCPMC2107480. PubMed DOI PMC

Orci L, Ravazzola M, Amherdt M, et al. Insulin, not C-peptide (proinsulin), is present in crinophagic bodies of the pancreatic B-cell. J Cell Biol. 1984. Jan;98(1):222–8. doi:10.1083/jcb.98.1.222. PubMed PMID: 6368567; PubMed Central PMCID: PMCPMC2112993. PubMed DOI PMC

Halban PA, Wollheim CB.. Intracellular degradation of insulin stores by rat pancreatic islets in vitro. An alternative pathway for homeostasis of pancreatic insulin content. J Biol Chem. 1980. Jul 10;255(13):6003–6. PubMed PMID: 6993463. PubMed

Csizmadia T, Lorincz P, Hegedus K, et al. Molecular mechanisms of developmentally programmed crinophagy in Drosophila. J Cell Biol. 2018. Jan 2;217(1):361–374. doi:10.1083/jcb.201702145. PubMed PMID: 29066608; PubMed Central PMCID: PMCPMC5748974. PubMed DOI PMC

Pasquier A, Vivot K, Erbs E, et al. Lysosomal degradation of newly formed insulin granules contributes to beta cell failure in diabetes. Nat Commun. 2019. Jul 25;10(1):3312. doi:10.1038/s41467-019-11170-4. PubMed PMID: 31346174; PubMed Central PMCID: PMCPMC6658524. PubMed DOI PMC

Tollenaere MA, Mailand N, Bekker-Jensen S.. Centriolar satellites: key mediators of centrosome functions. Cellular Mol Life Sci.: CMLS. 2015. Jan;72(1):11–23. doi:10.1007/s00018-014-1711-3. PubMed PMID: 25173771. PubMed DOI PMC

Holdgaard SG, Cianfanelli V, Pupo E, et al. Selective autophagy maintains centrosome integrity and accurate mitosis by turnover of centriolar satellites. Nat Commun. 2019. Sep 13;10(1):4176. doi:10.1038/s41467-019-12094-9. PubMed PMID: 31519908; PubMed Central PMCID: PMCPMC6744468. PubMed DOI PMC

Ott C, Konig J, Hohn A, et al. Reduced autophagy leads to an impaired ferritin turnover in senescent fibroblasts. Free Radic Biol Med. 2016. Dec;101:325–333. doi:10.1016/j.freeradbiomed.2016.10.492. PubMed PMID: 27789294. PubMed DOI

Ott C, Konig J, Hohn A, et al. Macroautophagy is impaired in old murine brain tissue as well as in senescent human fibroblasts. Redox Biol. 2016. Dec;10:266–273. doi:10.1016/j.redox.2016.10.015. PubMed PMID: 27825071; PubMed Central PMCID: PMCPMC5099282. PubMed DOI PMC

Asano T, Komatsu M, Yamaguchi-Iwai Y, et al. Distinct mechanisms of ferritin delivery to lysosomes in iron-depleted and iron-replete cells. Mol Cell Biol. 2011. May;31(10):2040–52. doi:10.1128/MCB.01437-10. PubMed PMID: 21444722; PubMed Central PMCID: PMC3133360. PubMed DOI PMC

Bauckman KA, Haller E, Flores I, et al. Iron modulates cell survival in a Ras- and MAPK-dependent manner in ovarian cells. Cell Death Dis. 2013;4:e592. doi:10.1038/cddis.2013.87. PubMed PMID: 23598404; PubMed Central PMCID: PMC3668627. PubMed DOI PMC

Sturm B, Goldenberg H, Scheiber-Mojdehkar B.. Transient increase of the labile iron pool in HepG2 cells by intravenous iron preparations. Eur J Biochem FEBS 2003. Sep;270(18):3731–8. PubMed PMID: 12950256. PubMed

Mancias JD, Wang X, Gygi SP, et al. Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy. Nature. 2014. Mar 30;509:105–9. doi:10.1038/nature13148. PubMed PMID: 24695223. PubMed DOI PMC

Xie Y, Hou W, Song X, et al. Ferroptosis: process and function. Cell Death Differ. 2016. Mar;23(3):369–79. doi:10.1038/cdd.2015.158. PubMed PMID: 26794443; PubMed Central PMCID: PMCPMC5072448. PubMed DOI PMC

Galluzzi L, Vitale I, Aaronson SA, et al. Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018. Cell Death Differ. 2018. Mar;25(3):486–541. . PubMed PMID: 29362479; PubMed Central PMCID: PMCPMC5864239. PubMed PMC

Hou W, Xie Y, Song X, et al. Autophagy promotes ferroptosis by degradation of ferritin. Autophagy. 2016. Aug 2;12(8):1425–8. doi:10.1080/15548627.2016.1187366. PubMed PMID: 27245739; PubMed Central PMCID: PMCPMC4968231. PubMed DOI PMC

Bauckman KA, Mysorekar IU.. Ferritinophagy drives uropathogenic Escherichia coli persistence in bladder epithelial cells. Autophagy. 2016. Mar 22:0. doi:10.1080/15548627.2016.1160176. PubMed PMID: 27002654. PubMed DOI PMC

Dixon SJ, Lemberg KM, Lamprecht MR, et al. Ferroptosis: an iron-dependent form of nonapoptotic cell death. Cell. 2012. May 25;149(5):1060–72. doi:10.1016/j.cell.2012.03.042. PubMed PMID: 22632970; PubMed Central PMCID: PMCPMC3367386. PubMed DOI PMC

Dixon SJ, Patel DN, Welsch M, et al. Pharmacological inhibition of cystine-glutamate exchange induces endoplasmic reticulum stress and ferroptosis. eLife. 2014. May 20;3:e02523. doi:10.7554/eLife.02523. PubMed PMID: 24844246; PubMed Central PMCID: PMCPMC4054777. PubMed DOI PMC

Wu Z, Geng Y, Lu X, et al. Chaperone-mediated autophagy is involved in the execution of ferroptosis. Proc Natl Acad Sci U S A. 2019. Feb 19;116(8):2996–3005. doi:10.1073/pnas.1819728116. PubMed PMID: 30718432; PubMed Central PMCID: PMCPMC6386716. PubMed DOI PMC

Zhang Z, Yao Z, Wang L, et al. Activation of ferritinophagy is required for the RNA-binding protein ELAVL1/HuR to regulate ferroptosis in hepatic stellate cells. Autophagy. 2018;14(12):2083–2103. doi:10.1080/15548627.2018.1503146. PubMed PMID: 30081711. PubMed DOI PMC

Zhang Z, Guo M, Li Y, et al. RNA-binding protein ZFP36/TTP protects against ferroptosis by regulating autophagy signaling pathway in hepatic stellate cells. Autophagy. 2019. Nov 11:1–24. doi:10.1080/15548627.2019.1687985. PubMed PMID: 31679460. PubMed DOI PMC

Buchan JR, Kolaitis RM, Taylor JP, et al. Eukaryotic stress granules are cleared by autophagy and Cdc48/VCP function. Cell. 2013. Jun 20;153(7):1461–74. doi:10.1016/j.cell.2013.05.037. PubMed PMID: 23791177; PubMed Central PMCID: PMC3760148. PubMed DOI PMC

Guo H, Chitiprolu M, Gagnon D, et al. Autophagy supports genomic stability by degrading retrotransposon RNA. Nat Commun. 2014. Nov 4;5:5276. doi:10.1038/ncomms6276. PubMed PMID: 25366815. PubMed DOI

Zhang Y, Yan L, Zhou Z, et al. SEPA-1 mediates the specific recognition and degradation of P granule components by autophagy in C. elegans. Cell. 2009. Jan 23;136(2):308–21. doi:10.1016/j.cell.2008.12.022. PubMed PMID: 19167332; eng. PubMed DOI

Chitiprolu M, Jagow C, Tremblay V, et al. A complex of C9ORF72 and p62 uses arginine methylation to eliminate stress granules by autophagy. Nat Commun. 2018. Jul 18;9(1):2794. doi:10.1038/s41467-018-05273-7. PubMed PMID: 30022074; PubMed Central PMCID: PMCPMC6052026. PubMed DOI PMC

Ganassi M, Mateju D, Bigi I, et al. A surveillance function of the HSPB8-BAG3-HSP70 chaperone complex ensures stress granule integrity and dynamism. Mol Cell. 2016. Sep 1;63(5):796–810. doi:10.1016/j.molcel.2016.07.021. PubMed PMID: 27570075. PubMed DOI

Mateju D, Franzmann TM, Patel A, et al. An aberrant phase transition of stress granules triggered by misfolded protein and prevented by chaperone function. EMBO J. 2017. Jun 14;36(12):1669–1687. doi:10.15252/embj.201695957. PubMed PMID: 28377462; PubMed Central PMCID: PMCPMC5470046. PubMed DOI PMC

Li YR, King OD, Shorter J, et al. Stress granules as crucibles of ALS pathogenesis. J Cell Biol. 2013. Apr 29;201(3):361–72. doi:10.1083/jcb.201302044. PubMed PMID: 23629963; PubMed Central PMCID: PMCPMC3639398. PubMed DOI PMC

Ryu HH, Jun MH, Min KJ, et al. Autophagy regulates amyotrophic lateral sclerosis-linked fused in sarcoma-positive stress granules in neurons. Neurobiol Aging. 2014. Dec;35(12):2822–31. doi:10.1016/j.neurobiolaging.2014.07.026. PubMed PMID: 25216585. PubMed DOI

Nagl W. ‘‘Plastolysomes’ - Plastids involved in the autolysis of the embryo-suspensor in Phaseolus. Zeitschrift fur Pflanzenphysiologie 1977;85:45–51.

Gartner PJ, Nagl W.. Acid phosphatase activity in plastids (plastolysomes) of senescing embryo-suspensor cells. Planta. 1980. Jan;149(4):341–9. doi:10.1007/BF00571168. PubMed PMID: 24306370. PubMed DOI

van Doorn WG, Kirasak K, Sonong A, et al. Do plastids in Dendrobium cv. Lucky Duan petals function similar to auto-phagosomes and autolysosomes? Autophagy. 2011. Jun7(6):584–97. PubMed PMID: 21460624. PubMed

Parra-Vega V, Corral-Martinez P, Rivas-Sendra A, et al. Formation and excretion of autophagic plastids (plastolysomes) in Brassica napus embryogenic microspores. Front Plant Sci. 2015;6:94. doi:10.3389/fpls.2015.00094. PubMed PMID: 25745429; PubMed Central PMCID: PMC4333807. PubMed DOI PMC

Gonzalez-Melendi P, Uyttewaal M, Morcillo CN, et al. A light and electron microscopy analysis of the events leading to male sterility in Ogu-INRA CMS of rapeseed (Brassica napus). J Exp Bot. 2008;59(4):827–38. doi:10.1093/jxb/erm365. PubMed PMID: 18349052. PubMed DOI

Newcomb EH. Fine structure of protein-storing plastids in bean root tips. J Cell Biol. 1967. Apr;33(1):143–63. PubMed PMID: 6033932; PubMed Central PMCID: PMC2107292. PubMed PMC

Singh R, Kaushik S, Wang Y, et al. Autophagy regulates lipid metabolism. Nature. 2009. Apr 30;458(7242):1131–5. doi:10.1038/nature07976. PubMed PMID: 19339967; PubMed Central PMCID: PMC2676208. eng. PubMed DOI PMC

Koenig U, Fobker M, Lengauer B, et al. Autophagy facilitates secretion and protects against degeneration of the Harderian gland. Autophagy. 2015;11(2):298–313. doi:10.4161/15548627.2014.978221. PubMed PMID: 25484081. PubMed DOI PMC

Shi Y, Han JJ, Tennakoon JB, et al. Androgens promote prostate cancer cell growth through induction of autophagy. Mol Endocrinol. 2013. Feb;27(2):280–95. doi:10.1210/me.2012-1260. PubMed PMID: 23250485; PubMed Central PMCID: PMC3683804. PubMed DOI PMC

O’Rourke EJ, Soukas AA, Carr CE, et al. C. elegans major fats are stored in vesicles distinct from lysosome-related organelles. Cell Metab. 2009. Nov;10(5):430–5. doi:10.1016/j.cmet.2009.10.002. PubMed PMID: 19883620; PubMed Central PMCID: PMC2921818. PubMed DOI PMC

Inokuchi-Shimizu S, Park EJ, Roh YS, et al. TAK1-mediated autophagy and fatty acid oxidation prevent hepatosteatosis and tumorigenesis. J Clin Invest. 2014. Aug 1;124(8):3566–78. doi:10.1172/JCI74068. PubMed PMID: 24983318; PubMed Central PMCID: PMC4109552. PubMed DOI PMC

Lee JH, Budanov AV, Talukdar S, et al. Maintenance of metabolic homeostasis by Sestrin2 and Sestrin3. Cell Metab. 2012. Sep 5;16(3):311–21. doi:10.1016/j.cmet.2012.08.004. PubMed PMID: 22958918; PubMed Central PMCID: PMC3687365. PubMed DOI PMC

Settembre C, De Cegli R, Mansueto G, et al. TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop. Nat Cell Biol. 2013. Jun;15(6):647–58. doi:10.1038/ncb2718. PubMed PMID: 23604321; PubMed Central PMCID: PMC3699877. PubMed DOI PMC

Cuervo AM. Preventing lysosomal fat indigestion. Nat Cell Biol. 2013. Jun;15(6):565–7. doi:10.1038/ncb2778. PubMed PMID: 23728462. PubMed DOI

Settembre C, Fraldi A, Medina DL, et al. Signals from the lysosome: a control centre for cellular clearance and energy metabolism. Nat Rev Mol Cell Biol. 2013. May;14(5):283–96. doi:10.1038/nrm3565. PubMed PMID: 23609508. PubMed DOI PMC

Chao X, Wang S, Zhao K, et al. Impaired TFEB-mediated lysosome biogenesis and autophagy promote chronic ethanol-induced liver injury and steatosis in mice. Gastroenterology. 2018. Sep;155(3):865–879 e12. doi:10.1053/j.gastro.2018.05.027. PubMed PMID: 29782848; PubMed Central PMCID: PMCPMC6120772. PubMed DOI PMC

Yadav N, Cheng D, Richard S, et al. CARM1 promotes adipocyte differentiation by coactivating PPARgamma. EMBO Rep. 2008. Feb;9(2):193–8. doi:10.1038/sj.embor.7401151. PubMed PMID: 18188184; PubMed Central PMCID: PMCPMC2246418. PubMed DOI PMC

Liu Y, Wang T, Ji YJ, et al. A C9orf72-CARM1 axis regulates lipid metabolism under glucose starvation-induced nutrient stress. Genes Dev. 2018. Nov 1;32(21–22):1380–1397. doi:10.1101/gad.315564.118. PubMed PMID: 30366907; PubMed Central PMCID: PMCPMC6217731. PubMed DOI PMC

Ugolino J, Ji YJ, Conchina K, et al. Loss of C9orf72 enhances autophagic activity via deregulated mTOR and TFEB signaling. PLoS Genet. 2016. Nov;12(11):e1006443. doi:10.1371/journal.pgen.1006443. PubMed PMID: 27875531; PubMed Central PMCID: PMCPMC5119725. PubMed DOI PMC

Mizielinska S, Isaacs AM.. C9orf72 amyotrophic lateral sclerosis and frontotemporal dementia: gain or loss of function? Curr Opin Neurol. 2014. Oct;27(5):515–23. doi:10.1097/WCO.0000000000000130. PubMed PMID: 25188012; PubMed Central PMCID: PMCPMC4165481. PubMed DOI PMC

Jiang J, Cleveland DW.. Bidirectional transcriptional inhibition as therapy for ALS/FTD caused by repeat expansion in C9orf72. Neuron. 2016. Dec 21;92(6):1160–1163. doi:10.1016/j.neuron.2016.12.008. PubMed PMID: 28009271. PubMed DOI

Fernandez AF, Barcena C, Martinez-Garcia GG, et al. Autophagy couteracts weight gain, lipotoxicity and pancreatic beta-cell death upon hypercaloric pro-diabetic regimens. Cell Death Dis. 2017. Aug 3;8(8):e2970. doi:10.1038/cddis.2017.373. PubMed PMID: 28771229; PubMed Central PMCID: PMCPMC5596561. PubMed DOI PMC

O’Rourke EJ, Kuballa P, Xavier R, et al. omega-6 Polyunsaturated fatty acids extend life span through the activation of autophagy. Genes Dev. 2013. Feb 15;27(4):429–40. doi:10.1101/gad.205294.112. PubMed PMID: 23392608; PubMed Central PMCID: PMCPMC3589559. PubMed DOI PMC

Visvikis O, Ihuegbu N, Labed SA, et al. Innate host defense requires TFEB-mediated transcription of cytoprotective and antimicrobial genes. Immunity. 2014. Jun 19;40(6):896–909. doi:10.1016/j.immuni.2014.05.002. PubMed PMID: 24882217; PubMed Central PMCID: PMCPMC4104614. PubMed DOI PMC

Jeong SJ, Kim S, Park JG, et al. Prdx1 (peroxiredoxin 1) deficiency reduces cholesterol efflux via impaired macrophage lipophagic flux. Autophagy. 2018;14(1):120–133. doi:10.1080/15548627.2017.1327942. PubMed PMID: 28605287; PubMed Central PMCID: PMCPMC5846566. PubMed DOI PMC

Chiang PM, Ling J, Jeong YH, et al. Deletion of TDP-43 down-regulates Tbc1d1, a gene linked to obesity, and alters body fat metabolism. Proc Natl Acad Sci U S A. 2010. Sep 14;107(37):16320–4. doi:10.1073/pnas.1002176107. PubMed PMID: 20660762; PubMed Central PMCID: PMC2941284. PubMed DOI PMC

Heck MV, Azizov M, Stehning T, et al. Dysregulated expression of lipid storage and membrane dynamics factors in Tia1 knockout mouse nervous tissue. Neurogenetics. 2014. May;15(2):135–44. doi:10.1007/s10048-014-0397-x. PubMed PMID: 24659297; PubMed Central PMCID: PMC3994287. PubMed DOI PMC

Popovic D, Akutsu M, Novak I, et al. Rab GTPase-activating proteins in autophagy: regulation of endocytic and autophagy pathways by direct binding to human ATG8 modifiers. Mol Cell Biol. 2012. May;32(9):1733–44. doi:10.1128/MCB.06717-11. PubMed PMID: 22354992; PubMed Central PMCID: PMC3347240. PubMed DOI PMC

Onal G, Kutlu O, Ozer E, et al. Impairment of lipophagy by PNPLA1 mutations causes lipid droplet accumulation in primary fibroblasts of Autosomal Recessive Congenital Ichthyosis patients. J Dermatol Sci. 2019. Jan;93(1):50–57. doi:10.1016/j.jdermsci.2018.11.013. PubMed PMID: 30655104. PubMed DOI

Sathyanarayan A, Mashek MT, Mashek DG.. ATGL promotes autophagy/lipophagy via SIRT1 to control hepatic lipid droplet catabolism. Cell Rep. 2017. Apr 4;19(1):1–9. doi:10.1016/j.celrep.2017.03.026. PubMed PMID: 28380348; PubMed Central PMCID: PMCPMC5396179. PubMed DOI PMC

Schott MB, Weller SG, Schulze RJ, et al. Lipid droplet size directs lipolysis and lipophagy catabolism in hepatocytes. J Cell Biol. 2019. Oct 7;218(10):3320–3335. doi:10.1083/jcb.201803153. PubMed PMID: 31391210; PubMed Central PMCID: PMCPMC6781454. PubMed DOI PMC

Negoita F, Blomdahl J, Wasserstrom S, et al. PNPLA3 variant M148 causes resistance to starvation-mediated lipid droplet autophagy in human hepatocytes. J Cell Biochem. 2019. Jan;120(1):343–356. doi:10.1002/jcb.27378. PubMed PMID: 30171718. PubMed DOI

Tatsumi T, Takayama K, Ishii S, et al. Forced lipophagy reveals that lipid droplets are required for early embryonic development in mouse. Development. 2018. Feb 23;145(4). doi:10.1242/dev.161893. PubMed PMID: 29475974. PubMed DOI

Kaushik S, Cuervo AM.. Degradation of lipid droplet-associated proteins by chaperone-mediated autophagy facilitates lipolysis. Nat Cell Biol. 2015. Jun;17(6):759–70. doi:10.1038/ncb3166. PubMed PMID: 25961502; PubMed Central PMCID: PMCPMC4449813. PubMed DOI PMC

Ma D, Molusky MM, Song J, et al. Autophagy deficiency by hepatic FIP200 deletion uncouples steatosis from liver injury in NAFLD. Mol Endocrinol. 2013. Oct;27(10):1643–54. doi:10.1210/me.2013-1153. PubMed PMID: 23960084; PubMed Central PMCID: PMCPMC4061382. PubMed DOI PMC

Kim KH, Jeong YT, Oh H, et al. Autophagy deficiency leads to protection from obesity and insulin resistance by inducing Fgf21 as a mitokine. Nat Med. 2013. Jan;19(1):83–92. doi:10.1038/nm.3014. PubMed PMID: 23202295. PubMed DOI

Li Y, Chao X, Wang S, et al. Role of mechanistic target of rapamycin and autophagy in alcohol-induced adipose atrophy and liver injury. Am J Pathol. 2020. Jan;190(1):158–175. doi:10.1016/j.ajpath.2019.09.023. PubMed PMID: 31733185; PubMed Central PMCID: PMCPMC6940593. PubMed DOI PMC

Hung YH, Chen LM, Yang JY, et al. Spatiotemporally controlled induction of autophagy-mediated lysosome turnover. Nat Commun. 2013;4:2111. doi:10.1038/ncomms3111. PubMed PMID: 23817530. PubMed DOI

Maejima I, Takahashi A, Omori H, et al. Autophagy sequesters damaged lysosomes to control lysosomal biogenesis and kidney injury. EMBO J. 2013. Aug 28;32(17):2336–47. doi:10.1038/emboj.2013.171. PubMed PMID: 23921551; PubMed Central PMCID: PMC3770333. PubMed DOI PMC

Raben N, Takikita S, Pittis MG, et al. Deconstructing Pompe disease by analyzing single muscle fibers: to see a world in a grain of sand. Autophagy. 2007. Nov-Dec;3(6):546–52. doi:10.4161/auto.4591. PubMed PMID: 17592248. PubMed DOI

Lopez-Jimenez AT, Cardenal-Munoz E, Leuba F, et al. The ESCRT and autophagy machineries cooperate to repair ESX-1-dependent damage at the Mycobacterium-containing vacuole but have opposite impact on containing the infection. PLoS Pathog. 2018. Dec;14(12):e1007501. doi:10.1371/journal.ppat.1007501. PubMed PMID: 30596802; PubMed Central PMCID: PMCPMC6329560. PubMed DOI PMC

Thumm M, Simons M.. Myelinophagy: Schwann cells dine in. J Cell Biol. 2015. Jul 6;210(1):9–10. doi:10.1083/jcb.201506039. PubMed PMID: 26150387; PubMed Central PMCID: PMCPMC4494007. PubMed DOI PMC

Jessen KR, Mirsky R.. The repair Schwann cell and its function in regenerating nerves. J Physiol. 2016. Jul 1;594(13):3521–31. doi:10.1113/JP270874. PubMed PMID: 26864683; PubMed Central PMCID: PMCPMC4929314. PubMed DOI PMC

Jang SY, Shin YK, Park SY, et al. Autophagic myelin destruction by Schwann cells during Wallerian degeneration and segmental demyelination. Glia. 2016. May;64(5):730–42. doi:10.1002/glia.22957. PubMed PMID: 26712109. PubMed DOI

Gomez-Sanchez JA, Carty L, Iruarrizaga-Lejarreta M, et al. Schwann cell autophagy, myelinophagy, initiates myelin clearance from injured nerves. J Cell Biol. 2015. Jul 6;210(1):153–68. doi:10.1083/jcb.201503019. PubMed PMID: 26150392; PubMed Central PMCID: PMCPMC4494002. PubMed DOI PMC

Coccurello R, Nazio F, Rossi C, et al. Effects of caloric restriction on neuropathic pain, peripheral nerve degeneration and inflammation in normometabolic and autophagy defective prediabetic Ambra1 mice. PLoS One. 2018;13(12):e0208596. doi:10.1371/journal.pone.0208596. PubMed PMID: 30532260; PubMed Central PMCID: PMCPMC6287902. PubMed DOI PMC

Haidar M, Timmerman V.. Autophagy as an emerging common pathomechanism in inherited peripheral neuropathies. Front Mol Neurosci. 2017;10:143. doi:10.3389/fnmol.2017.00143. PubMed PMID: 28553203; PubMed Central PMCID: PMCPMC5425483. PubMed DOI PMC

Park YE, Hayashi YK, Bonne G, et al. Autophagic degradation of nuclear components in mammalian cells. Autophagy. 2009. Aug;5(6):795–804. doi:10.4161/auto.8901. PubMed PMID: 19550147. PubMed DOI

Liu ML, Yao MC.. Role of ATG8 and autophagy in programmed nuclear degradation in Tetrahymena thermophila. Eukaryot Cell. 2012. Apr;11(4):494–506. doi:10.1128/EC.05296-11. PubMed PMID: 22366125; PubMed Central PMCID: PMC3318292. PubMed DOI PMC

Akinduro O, Sully K, Patel A, et al. Constitutive Autophagy and Nucleophagy during Epidermal Differentiation. J Invest Dermatol. 2016. Jul;136(7):1460–1470. doi:10.1016/j.jid.2016.03.016. PubMed PMID: 27021405. PubMed DOI

Kvam E, Goldfarb DS.. Nucleus-vacuole junctions and piecemeal microautophagy of the nucleus in S. cerevisiae. Autophagy. 2007. Mar-Apr;3(2):85–92. doi:10.4161/auto.3586. PubMed PMID: 17204844. PubMed DOI

Rello-Varona S, Lissa D, Shen S, et al. Autophagic removal of micronuclei. Cell cycle. 2012. Jan 1;11(1):170–6. doi:10.4161/cc.11.1.18564. PubMed PMID: 22185757. PubMed DOI

Mochida K, Oikawa Y, Kimura Y, et al. Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus. Nature. 2015. Jun 18;522(7556):359–62. doi:10.1038/nature14506. PubMed PMID: 26040717. PubMed DOI

Dou Z, Xu C, Donahue G, et al. Autophagy mediates degradation of nuclear lamina. Nature. 2015. Nov 5;527(7576):105–9. doi:10.1038/nature15548. PubMed PMID: 26524528; PubMed Central PMCID: PMCPMC4824414. PubMed DOI PMC

De Meyer GR, Grootaert MO, Michiels CF, et al. Autophagy in vascular disease. Circ Res. 2015. Jan 30;116(3):468–79. doi:10.1161/CIRCRESAHA.116.303804. PubMed PMID: 25634970. PubMed DOI

Bar-Yosef T, Damri O, Agam G.. Dual role of autophagy in diseases of the central nervous system. Front Cell Neurosci. 2019;13:196. doi:10.3389/fncel.2019.00196. PubMed PMID: 31191249; PubMed Central PMCID: PMCPMC6548059. PubMed DOI PMC

Brown AJ, Jessup W.. Oxysterols and atherosclerosis. Atherosclerosis. 1999. Jan;142(1):1–28. PubMed PMID: 9920502. PubMed

Zarrouk A, Vejux A, Mackrill J, et al. Involvement of oxysterols in age-related diseases and ageing processes. Ageing Res Rev. 2014. Nov;18:148–62. doi:10.1016/j.arr.2014.09.006. PubMed PMID: 25305550. PubMed DOI

He C, Zhu H, Zhang W, et al. 7-Ketocholesterol induces autophagy in vascular smooth muscle cells through Nox4 and Atg4B. Am J Pathol. 2013. Aug;183(2):626–37. doi:10.1016/j.ajpath.2013.04.028. PubMed PMID: 23770348; PubMed Central PMCID: PMC3730774. PubMed DOI PMC

Martinet W, Schrijvers DM, Timmermans JP, et al. Interactions between cell death induced by statins and 7-ketocholesterol in rabbit aorta smooth muscle cells. Br J Pharmacol. 2008. Jul;154(6):1236–46. doi:10.1038/bjp.2008.181. PubMed PMID: 18469840; PubMed Central PMCID: PMC2483392. PubMed DOI PMC

Nury T, Zarrouk A, Ragot K, et al. 7-Ketocholesterol is increased in the plasma of X-ALD patients and induces peroxisomal modifications in microglial cells: Potential roles of 7-ketocholesterol in the pathophysiology of X-ALD. J Steroid Biochem Mol Biol. 2017. May;169:123–136. doi:10.1016/j.jsbmb.2016.03.037 PubMed PMID: 27041118. PubMed DOI

Monier S, Samadi M, Prunet C, et al.Impairment of the cytotoxic and oxidative activities of 7 beta-hydroxycholesterol and 7-ketocholesterol by esterification with oleate. Biochem Biophys Res Commun. 2003. Apr11;303(3):814–24. PubMed PMID: 12670484. PubMed

Nury T, Zarrouk A, Mackrill JJ, et al. Induction of oxiapoptophagy on 158N murine oligodendrocytes treated by 7-ketocholesterol-, 7beta-hydroxycholesterol-, or 24(S)-hydroxycholesterol: Protective effects of alpha-tocopherol and docosahexaenoic acid (DHA; C22:6 n-3). Steroids. 2015. Jul;99(Pt B):194–203. doi:10.1016/j.steroids.2015.02.003. PubMed PMID: 25683890. PubMed DOI

Nury T, Zarrouk A, Vejux A, et al. Induction of oxiapoptophagy, a mixed mode of cell death associated with oxidative stress, apoptosis and autophagy, on 7-ketocholesterol-treated 158N murine oligodendrocytes: impairment by alpha-tocopherol. Biochem Biophys Res Commun. 2014. Apr 11;446(3):714–9. doi:10.1016/j.bbrc.2013.11.081. PubMed PMID: 24299956. PubMed DOI

Sghaier R, Zarrouk A, Nury T, et al. Biotin attenuation of oxidative stress, mitochondrial dysfunction, lipid metabolism alteration and 7beta-hydroxycholesterol-induced cell death in 158N murine oligodendrocytes. Free Radic Res. 2019. May;53(5):535–561. doi:10.1080/10715762.2019.1612891. PubMed PMID: 31039616. PubMed DOI

Vejux A, Abed-Vieillard D, Hajji K, et al. 7-Ketocholesterol and 7beta-hydroxycholesterol: In vitro and animal models used to characterize their activities and to identify molecules preventing their toxicity.Biochem Pharmacol. 2019. Oct 3:113648. doi:10.1016/j.bcp.2019.113648. PubMed PMID: 31586589. PubMed DOI

Zheng K, Li Y, Wang S, et al. Inhibition of autophagosome-lysosome fusion by ginsenoside Ro via the ESR2-NCF1-ROS pathway sensitizes esophageal cancer cells to 5-fluorouracil-induced cell death via the CHEK1-mediated DNA damage checkpoint. Autophagy. 2016. Sep;12(9):1593–613. doi:10.1080/15548627.2016.1192751. PubMed PMID: 27310928; PubMed Central PMCID: PMCPMC5082787. PubMed DOI PMC

Redmann M, Benavides GA, Berryhill TF, et al. Inhibition of autophagy with bafilomycin and chloroquine decreases mitochondrial quality and bioenergetic function in primary neurons. Redox Biol. 2017. Apr;11:73–81. doi:10.1016/j.redox.2016.11.004. PubMed PMID: 27889640; PubMed Central PMCID: PMCPMC5124357. PubMed DOI PMC

Hsu SPC, Kuo JS, Chiang HC, et al. Temozolomide, sirolimus and chloroquine is a new therapeutic combination that synergizes to disrupt lysosomal function and cholesterol homeostasis in GBM cells. Oncotarget. 2018. Jan 23;9(6):6883–6896. doi:10.18632/oncotarget.23855. PubMed PMID: 29467937; PubMed Central PMCID: PMCPMC5805523. PubMed DOI PMC

Bello-Perez M, Pereiro P, Coll J, et al. Zebrafish C-reactive protein isoforms inhibit SVCV replication by blocking autophagy through interactions with cell membrane cholesterol. Sci Rep. 2020. Jan 17;10(1):566. doi:10.1038/s41598-020-57501-0. PubMed PMID: 31953490; PubMed Central PMCID: PMCPMC6969114. PubMed DOI PMC

Marshall RS, Li F, Gemperline DC, et al. Autophagic degradation of the 26s proteasome is mediated by the dual ATG8/ubiquitin receptor RPN10 in arabidopsis. Mol Cell. 2015. Jun 18;58(6):1053–66. doi:10.1016/j.molcel.2015.04.023. PubMed PMID: 26004230. PubMed DOI PMC

Marshall RS, McLoughlin F, Vierstra RD.. Autophagic turnover of inactive 26S proteasomes in yeast is directed by the ubiquitin receptor Cue5 and the Hsp42 chaperone. Cell Rep. 2016. Aug 9;16(6):1717–1732. doi:10.1016/j.celrep.2016.07.015. PubMed PMID: 27477278. PubMed DOI

Ustun S, Hafren A, Liu Q, et al. Bacteria exploit autophagy for proteasome degradation and enhanced virulence in plants. Plant Cell. 2018. Mar;30(3):668–685. doi:10.1105/tpc.17.00815. PubMed PMID: 29500318; PubMed Central PMCID: PMCPMC5894834. PubMed DOI PMC

Waite KA, De-La Mota-Peynado A, Vontz G, et al. Starvation induces proteasome autophagy with different pathways for core and regulatory particles. J Biol Chem. 2016. Feb 12;291(7):3239–53. doi:10.1074/jbc.M115.699124. PubMed PMID: 26670610; PubMed Central PMCID: PMCPMC4751371. PubMed DOI PMC

Nemec AA, Howell LA, Peterson AK, et al. Autophagic clearance of proteasomes in yeast requires the conserved sorting nexin Snx4. J Biol Chem. 2017. Dec 29;292(52):21466–21480. doi:10.1074/jbc.M117.817999. PubMed PMID: 29109144; PubMed Central PMCID: PMCPMC5766950. PubMed DOI PMC

Cohen-Kaplan V, Livneh I, Avni N, et al. p62- and ubiquitin-dependent stress-induced autophagy of the mammalian 26S proteasome. Proc Natl Acad Sci U S A. 2016. Nov 22;113(47):E7490–E7499. doi:10.1073/pnas.1615455113. PubMed PMID: 27791183; PubMed Central PMCID: PMCPMC5127335. PubMed DOI PMC

Marshall RS, Vierstra RD.. Proteasome storage granules protect proteasomes from autophagic degradation upon carbon starvation. eLife. 2018. Apr 6;7. doi:10.7554/eLife.34532. PubMed PMID: 29624167; PubMed Central PMCID: PMCPMC5947986. PubMed DOI PMC

Marshall RS, Hua Z, Mali S, et al. ATG8-binding UIM proteins define a new class of autophagy adaptors and receptors. Cell. 2019. Apr 18;177(3):766–781 e24. doi:10.1016/j.cell.2019.02.009. PubMed PMID: 30955882; PubMed Central PMCID: PMCPMC6810650. PubMed DOI PMC

Marshall RS, Vierstra RD.. Dynamic regulation of the 26s proteasome: from synthesis to degradation. Front Mol Biosci. 2019;6:40. doi:10.3389/fmolb.2019.00040. PubMed PMID: 31231659; PubMed Central PMCID: PMCPMC6568242. PubMed DOI PMC

Li J, Breker M, Graham M, et al. AMPK regulates ESCRT-dependent microautophagy of proteasomes concomitant with proteasome storage granule assembly during glucose starvation. PLoS Genet. 2019. Nov;15(11):e1008387. doi:10.1371/journal.pgen.1008387. PubMed PMID: 31738769; PubMed Central PMCID: PMCPMC6886873. PubMed DOI PMC

Hamasaki M, Noda T, Baba M, et al. Starvation triggers the delivery of the endoplasmic reticulum to the vacuole via autophagy in yeast. Traffic. 2005. Jan;6(1):56–65. doi:10.1111/j.1600-0854.2004.00245.x. PubMed PMID: 15569245. PubMed DOI

Yorimitsu T, Nair U, Yang Z, et al. Endoplasmic reticulum stress triggers autophagy. J Biol Chem. 2006. Oct 6;281(40):30299–304. doi:10.1074/jbc.M607007200. PubMed PMID: 16901900; PubMed Central PMCID: PMC1828866. eng. PubMed DOI PMC

Schuck S, Gallagher CM, Walter P.. ER-phagy mediates selective degradation of endoplasmic reticulum independently of the core autophagy machinery. J Cell Sci. 2014. Sep 15;127(Pt 18):4078–88. doi:10.1242/jcs.154716. PubMed PMID: 25052096; PubMed Central PMCID: PMC4163648. PubMed DOI PMC

Bernales S, Schuck S, Walter P.. ER-phagy: selective autophagy of the endoplasmic reticulum. Autophagy. 2007. May-Jun;3(3):285–7. PubMed PMID: 17351330. PubMed

Bolender RP, Weibel ER.. A morphometric study of the removal of phenobarbital-induced membranes from hepatocytes after cessation of threatment. J Cell Biol. 1973. Mar;56(3):746–61. PubMed PMID: 4569312. PubMed PMC

Grumati P, Dikic I, Stolz A.. ER-phagy at a glance. J Cell Sci. 2018. Sep 3;131(17). doi:10.1242/jcs.217364. PubMed PMID: 30177506. PubMed DOI

Wilkinson S. ER-phagy: shaping up and destressing the endoplasmic reticulum. FEBS J. 2019. Jul;286(14):2645–2663. doi:10.1111/febs.14932. PubMed PMID: 31116513; PubMed Central PMCID: PMCPMC6772018. PubMed DOI PMC

Loi M, Fregno I, Guerra C, et al. Eat it right: ER-phagy and recovER-phagy. Biochem Soc Trans. 2018. Jun 19;46(3):699–706. doi:10.1042/BST20170354. PubMed PMID: 29802216; PubMed Central PMCID: PMCPMC6008593. PubMed DOI PMC

Wilkinson S. Emerging Principles of Selective ER Autophagy. J Mol Biol. 2020. Jan 3;432(1):185–205. doi:10.1016/j.jmb.2019.05.012. PubMed PMID: 31100386; PubMed Central PMCID: PMCPMC6971691. PubMed DOI PMC

Grumati P, Morozzi G, Holper S, et al. Full length RTN3 regulates turnover of tubular endoplasmic reticulum via selective autophagy. eLife. 2017. Jun 15;6. doi:10.7554/eLife.25555. PubMed PMID: 28617241; PubMed Central PMCID: PMCPMC5517149. PubMed DOI PMC

Chen Q, Xiao Y, Chai P, et al. ATL3 Is a tubular ER-phagy receptor for GABARAP-mediated selective autophagy. Curr Biol. 2019. Mar 4;29(5):846–855 e6. doi:10.1016/j.cub.2019.01.041. PubMed PMID: 30773365. PubMed DOI

An H, Ordureau A, Paulo JA, et al. TEX264 is an endoplasmic reticulum-resident ATG8-interacting protein critical for ER remodeling during nutrient stress. Mol Cell. 2019. Jun 6;74(5):891–908 e10. doi:10.1016/j.molcel.2019.03.034. PubMed PMID: 31006537; PubMed Central PMCID: PMCPMC6747008. PubMed DOI PMC

Fumagalli F, Noack J, Bergmann TJ, et al. Corrigendum: Translocon component Sec62 acts in endoplasmic reticulum turnover during stress recovery. Nat Cell Biol. 2016. Dec 23;19(1):76. doi:10.1038/ncb3451. PubMed PMID: 28008182. PubMed DOI

Fumagalli F, Noack J, Bergmann TJ, et al. Translocon component Sec62 acts in endoplasmic reticulum turnover during stress recovery. Nat Cell Biol. 2016. Nov;18(11):1173–1184. doi:10.1038/ncb3423. PubMed PMID: 27749824. PubMed DOI

Smith MD, Harley ME, Kemp AJ, et al. CCPG1 is a non-canonical autophagy cargo receptor essential for ER-phagy and pancreatic ER proteostasis. Dev Cell. 2018. Jan 22;44(2):217–232 e11. doi:10.1016/j.devcel.2017.11.024. PubMed PMID: 29290589; PubMed Central PMCID: PMCPMC5791736. PubMed DOI PMC

Lipatova Z, Segev N. A. role for macro-ER-phagy in ER quality control. PLoS Genet. 2015. Jul;11(7):e1005390. doi:10.1371/journal.pgen.1005390. PubMed PMID: 26181331; PubMed Central PMCID: PMC4504476. PubMed DOI PMC

Fregno I, Molinari M.. Proteasomal and lysosomal clearance of faulty secretory proteins: ER-associated degradation (ERAD) and ER-to-lysosome-associated degradation (ERLAD) pathways. Crit Rev Biochem Mol Biol. 2019. Apr;54(2):153–163. doi:10.1080/10409238.2019.1610351. PubMed PMID: 31084437. PubMed DOI

Fregno I, Fasana E, Bergmann TJ, et al. ER-to-lysosome-associated degradation of proteasome-resistant ATZ polymers occurs via receptor-mediated vesicular transport. EMBO J. 2018. Sep 3;37(17). doi:10.15252/embj.201899259. PubMed PMID: 30076131; PubMed Central PMCID: PMCPMC6120659. PubMed DOI PMC

Forrester A, De Leonibus C, Grumati P, et al. A selective ER-phagy exerts procollagen quality control via a Calnexin-FAM134B complex. EMBO J. 2019. Jan 15;38(2). doi:10.15252/embj.201899847. PubMed PMID: 30559329; PubMed Central PMCID: PMCPMC6331724. PubMed DOI PMC

Cunningham CN, Williams JM, Knupp J, et al. Cells deploy a two-pronged strategy to rectify misfolded proinsulin aggregates. Mol Cell. 2019. Aug 8;75(3):442–456 e4. doi:10.1016/j.molcel.2019.05.011. PubMed PMID: 31176671; PubMed Central PMCID: PMCPMC6688957. PubMed DOI PMC

Cui Y, Parashar S, Zahoor M, et al. A COPII subunit acts with an autophagy receptor to target endoplasmic reticulum for degradation. Science. 2019. Jul 5;365(6448):53–60. doi:10.1126/science.aau9263. PubMed PMID: 31273116. PubMed DOI PMC

Chiramel AI, Best SM.. Role of autophagy in Zika virus infection and pathogenesis. Virus Res. 2018. Aug 2;254:34–40. doi:10.1016/j.virusres.2017.09.006. PubMed PMID: 28899653; PubMed Central PMCID: PMCPMC5844781. PubMed DOI PMC

Moretti J, Roy S, Bozec D, et al. STING senses microbial viability to orchestrate stress-mediated autophagy of the endoplasmic reticulum. Cell. 2017. Nov 2;171(4):809–823 e13. doi:10.1016/j.cell.2017.09.034. PubMed PMID: 29056340; PubMed Central PMCID: PMCPMC5811766. PubMed DOI PMC

Peng Y, Shapiro SL, Banduseela VC, et al. Increased transport of acetyl-CoA into the endoplasmic reticulum causes a progeria-like phenotype. Aging cell. 2018. Oct;17(5):e12820. doi:10.1111/acel.12820. PubMed PMID: 30051577; PubMed Central PMCID: PMCPMC6156544. PubMed DOI PMC

Farrugia MA, Puglielli L.. Nepsilon-lysine acetylation in the endoplasmic reticulum - a novel cellular mechanism that regulates proteostasis and autophagy. J Cell Sci. 2018. Nov 16;131(22). doi:10.1242/jcs.221747. PubMed PMID: 30446507; PubMed Central PMCID: PMCPMC6262770. PubMed DOI PMC

Peng Y, Kim MJ, Hullinger R, et al. Improved proteostasis in the secretory pathway rescues Alzheimer’s disease in the mouse. Brain. 2016. Mar;139(Pt 3):937–52. doi:10.1093/brain/awv385. PubMed PMID: 26787453; PubMed Central PMCID: PMCPMC4805081. PubMed DOI PMC

Omari S, Makareeva E, Roberts-Pilgrim A, et al. Noncanonical autophagy at ER exit sites regulates procollagen turnover. Proc Natl Acad Sci U S A. 2018. Oct 23;115(43):E10099–E10108. doi:10.1073/pnas.1814552115. PubMed PMID: 30287488; PubMed Central PMCID: PMCPMC6205486. PubMed DOI PMC

Kraft C, Deplazes A, Sohrmann M, et al. Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease. Nat Cell Biol. 2008. May;10(5):602–10. doi:10.1038/ncb1723. PubMed PMID: 18391941; eng. PubMed DOI

Ossareh-Nazari B, Nino CA, Bengtson MH, et al. Ubiquitylation by the Ltn1 E3 ligase protects 60S ribosomes from starvation-induced selective autophagy. J Cell Biol. 2014. Mar 17;204(6):909–17. doi:10.1083/jcb.201308139. PubMed PMID: 24616224; PubMed Central PMCID: PMC3998797. PubMed DOI PMC

Derrien B, Baumberger N, Schepetilnikov M, et al. Degradation of the antiviral component ARGONAUTE1 by the autophagy pathway. Proc Natl Acad Sci U S A. 2012. Sep 25;109(39):15942–6. doi:10.1073/pnas.1209487109. PubMed PMID: 23019378; PubMed Central PMCID: PMC3465452. PubMed DOI PMC

Kobayashi H, Shoji K, Kiyokawa K, et al. VCP machinery mediates autophagic degradation of empty Argonaute. Cell Rep. 2019. Jul 30;28(5):1144–1153 e4. doi:10.1016/j.celrep.2019.07.003. PubMed PMID: 31365860. PubMed DOI

Gibbings D, Mostowy S, Jay F, et al. Selective autophagy degrades DICER and AGO2 and regulates miRNA activity. Nat Cell Biol. 2012. Dec;14(12):1314–21. doi:10.1038/ncb2611. PubMed PMID: 23143396; PubMed Central PMCID: PMC3771578. PubMed DOI PMC

Zhang P, Zhang H.. Autophagy modulates miRNA-mediated gene silencing and selectively degrades AIN-1/GW182 in C. elegans. EMBO Rep. 2013. Jun;14(6):568–76. doi:10.1038/embor.2013.53. PubMed PMID: 23619095; PubMed Central PMCID: PMC3674441. PubMed DOI PMC

Fujiwara Y, Kikuchi H, Aizawa S, et al. Direct uptake and degradation of DNA by lysosomes. Autophagy. 2013. Aug;9(8):1167–71. doi:10.4161/auto.24880. PubMed PMID: 23839276; PubMed Central PMCID: PMC3748189. PubMed DOI PMC

Fujiwara Y, Hase K, Wada K, et al. An RNautophagy/DNautophagy receptor, LAMP2C, possesses an arginine-rich motif that mediates RNA/DNA-binding. Biochem Biophys Res Commun. 2015. May 1;460(2):281–6. doi:10.1016/j.bbrc.2015.03.025. PubMed PMID: 25772617. PubMed DOI

Fujiwara Y, Furuta A, Kikuchi H, et al. Discovery of a novel type of autophagy targeting RNA. Autophagy. 2013. Mar;9(3):403–9. doi: 10.4161/auto.23002. PubMed PMID: 23291500; PubMed Central PMCID: PMC3590259. PubMed DOI PMC

Hase K, Fujiwara Y, Kikuchi H, et al. RNautophagy/DNautophagy possesses selectivity for RNA/DNA substrates. Nucleic Acids Res. 2015. Jul 27;43(13):6439–49. doi:10.1093/nar/gkv579. PubMed PMID: 26038313; PubMed Central PMCID: PMC4513860. PubMed DOI PMC

Aizawa S, Contu VR, Fujiwara Y, et al. Lysosomal membrane protein SIDT2 mediates the direct uptake of DNA by lysosomes. Autophagy. 2017. Jan 2;13(1):218–222. doi:10.1080/15548627.2016.1248019. PubMed PMID: 27846365; PubMed Central PMCID: PMCPMC5245770. PubMed DOI PMC

Aizawa S, Fujiwara Y, Contu VR, et al. Lysosomal putative RNA transporter SIDT2 mediates direct uptake of RNA by lysosomes. Autophagy. 2016;12(3):565–78. . PubMed PMID: 27046251; PubMed Central PMCID: PMCPMC4836006. PubMed PMC

Contu VR, Hase K, Kozuka-Hata H, et al. Lysosomal targeting of SIDT2 via multiple YxxPhi motifs is required for SIDT2 function in the process of RNautophagy. J Cell Sci. 2017. Sep 1;130(17):2843–2853. doi:10.1242/jcs.202481. PubMed PMID: 28724756. PubMed DOI

Brown CR, Chiang H-L.. A selective autophagy pathway that degrades gluconeogenic enzymes during catabolite inactivation. Commun Integr Biol. 2009;2(2):177–83. PubMed PMID: 19513275; PubMed Central PMCID: PMC2686377. eng. PubMed PMC

Regelmann J, Schule T, Josupeit FS, et al. Catabolite degradation of fructose-1,6-bisphosphatase in the yeast Saccharomyces cerevisiae: a genome-wide screen identifies eight novel GID genes and indicates the existence of two degradation pathways [Research Support, Non-U.S. Gov’t]. Mol Biol Cell. 2003. Apr;14(4):1652–63. doi:10.1091/mbc.E02-08-0456. PubMed PMID: 12686616; PubMed Central PMCID: PMC153129. eng. PubMed DOI PMC

Schork SM, Thumm M, Wolf DH.. Catabolite inactivation of fructose-1,6-bisphosphatase of Saccharomyces cerevisiae. Degradation occurs via the ubiquitin pathway. J Biol Chem. 1995. Nov 3;270(44):26446–50. PubMed PMID: 7592860; eng. PubMed

Schule T, Rose M, Entian KD, et al. Ubc8p functions in catabolite degradation of fructose-1, 6-bisphosphatase in yeast. EMBO J. 2000. May 15;19(10):2161–7. doi:10.1093/emboj/19.10.2161. PubMed PMID: 10811607; PubMed Central PMCID: PMC384366. eng. PubMed DOI PMC

Hung GC, Brown CR, Wolfe AB, et al. Degradation of the gluconeogenic enzymes fructose-1,6-bisphosphatase and malate dehydrogenase is mediated by distinct proteolytic pathways and signaling events. J Biol Chem. 2004. Nov19;279(47):49138–50. PubMed PMID: 15358789. PubMed

Chiang H-L, Schekman R, Hamamoto S.. Selective uptake of cytosolic, peroxisomal, and plasma membrane proteins into the yeast lysosome for degradation. J Biol Chem. 1996. Apr 26;271(17):9934–41. PubMed PMID: 8626630; eng. PubMed

Huang PH, Chiang H-L.. Identification of novel vesicles in the cytosol to vacuole protein degradation pathway. J Cell Biol. 1997. Feb 24;136(4):803–10. PubMed PMID: 9049246; PubMed Central PMCID: PMC2132494. eng. PubMed PMC

Alibhoy AA, Giardina BJ, Dunton DD, et al. Vid30 is required for the association of Vid vesicles and actin patches in the vacuole import and degradation pathway. Autophagy. 2012;8:29–46. PubMed PMC

Brown CR, Wolfe AB, Cui D, et al. The vacuolar import and degradation pathway merges with the endocytic pathway to deliver fructose-1,6-bisphosphatase to the vacuole for degradation. J Biol Chem. 2008. Sep 19;283(38):26116–27. doi:10.1074/jbc.M709922200. PubMed PMID: 18660504; PubMed Central PMCID: PMC2533773. eng. PubMed DOI PMC

Chiang MC, Chiang H-L.. Vid24p, a novel protein localized to the fructose-1, 6-bisphosphatase-containing vesicles, regulates targeting of fructose-1,6-bisphosphatase from the vesicles to the vacuole for degradation. J Cell Biol. 1998. Mar 23;140(6):1347–56. PubMed PMID: 9508768; PubMed Central PMCID: PMC2132677. eng. PubMed PMC

Vida TA, Emr SD.. A new vital stain for visualizing vacuolar membrane dynamics and endocytosis in yeast. J Cell Biol. 1995. Mar;128(5):779–92. PubMed PMID: 7533169; PubMed Central PMCID: PMC2120394. eng. PubMed PMC

Brown CR, Hung GC, Dunton D, et al. The TOR complex 1 is distributed in endosomes and in retrograde vesicles that form from the vacuole membrane and plays an important role in the vacuole import and degradation pathway. J Biol Chem. 2010. Jul 23;285(30):23359–70. doi: 10.1074/jbc.M109.075143. PubMed PMID: 20457600; PubMed Central PMCID: PMC2906328. eng. PubMed DOI PMC

Brown CR, Dunton D, Chiang H-L.. The vacuole import and degradation pathway utilizes early steps of endocytosis and actin polymerization to deliver cargo proteins to the vacuole for degradation. J Biol Chem. 2010. Jan 8;285(2):1516–28. doi:10.1074/jbc.M109.028241. PubMed PMID: 19892709; PubMed Central PMCID: PMC2801277. eng. PubMed DOI PMC

McLean JE, Wudzinska A, Datan E, et al. Flavivirus NS4A-induced autophagy protects cells against death and enhances virus replication. J Biol Chem. 2011. Jun 24;286(25):22147–59. doi:10.1074/jbc.M110.192500. PubMed PMID: 21511946; PubMed Central PMCID: PMC3121359. eng. PubMed DOI PMC

Lee YR, Lei HY, Liu MT, et al. Autophagic machinery activated by dengue virus enhances virus replication. Virology. 2008. May 10;374(2):240–8. doi:10.1016/j.virol.2008.02.016. PubMed PMID: 18353420. PubMed DOI PMC

Mao Y, Da L, Tang H, et al. Hepatitis B virus X protein reduces starvation-induced cell death through activation of autophagy and inhibition of mitochondrial apoptotic pathway. Biochem Biophys Res Commun. 2011. Nov 11;415(1):68–74. doi:10.1016/j.bbrc.2011.10.013. PubMed PMID: 22020078; eng. PubMed DOI

Orvedahl A, Alexander D, Talloczy Z, et al. HSV-1 ICP34.5 confers neurovirulence by targeting the Beclin 1 autophagy protein [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Cell Host Microbe. 2007. Mar 15;1(1):23–35. doi:10.1016/j.chom.2006.12.001. PubMed PMID: 18005679; eng. PubMed

Alexander DE, Ward SL, Mizushima N, et al. Analysis of the role of autophagy in replication of herpes simplex virus in cell culture. J Virol. 2007. Nov;81(22):12128–34. doi:10.1128/JVI.01356-07. PubMed PMID: 17855538; PubMed Central PMCID: PMC2169004. eng. PubMed DOI PMC

Leib DA, Alexander DE, Cox D, et al. Interaction of ICP34.5 with Beclin 1 modulates herpes simplex virus type 1 pathogenesis through control of CD4+ T-cell responses. J Virol. 2009. Dec;83(23):12164–71. doi:10.1128/JVI.01676-09. PubMed PMID: 19759141; PubMed Central PMCID: PMC2786728. eng. PubMed PMC

Yordy B, Iijima N, Huttner A, et al. A neuron-specific role for autophagy in antiviral defense against herpes simplex virus. Cell Host Microbe. 2012. Sep 13;12(3):334–45. doi:10.1016/j.chom.2012.07.013. PubMed PMID: 22980330; PubMed Central PMCID: PMC3454454. PubMed DOI PMC

Waisner H, Kalamvoki M.. The ICP0 protein of herpes simplex virus 1 (HSV-1) downregulates major autophagy adaptor proteins Sequestosome 1 and Optineurin during the early stages of HSV-1 infection. J Virol. 2019. Nov 1;93(21). doi:10.1128/JVI.01258-19. PubMed PMID: 31375597; PubMed Central PMCID: PMCPMC6803258. PubMed DOI PMC

Liang C, E X, Jung JU. Downregulation of autophagy by herpesvirus Bcl-2 homologs. Autophagy. 2008. Apr;4(3):268–72. PubMed PMID: 17993780. PubMed

Hernaez B, Cabezas M, Munoz-Moreno R, et al. A179L, a new viral Bcl2 homolog targeting Beclin 1 autophagy related protein. Curr Mol Med. 2013. Feb;13(2):305–16. PubMed PMID: 23228131. PubMed

Alonso C, Galindo I, Cuesta-Geijo MA, et al. African swine fever virus-cell interactions: from virus entry to cell survival. Virus Res. 2013. Apr;173(1):42–57. doi:10.1016/j.virusres.2012.12.006. PubMed PMID: 23262167. PubMed DOI PMC

Galindo I, Hernaez B, Diaz-Gil G, et al. A179L, a viral Bcl-2 homologue, targets the core Bcl-2 apoptotic machinery and its upstream BH3 activators with selective binding restrictions for Bid and Noxa. Virology. 2008. Jun 5;375(2):561–72. doi:10.1016/j.virol.2008.01.050. PubMed PMID: 18329683; PubMed Central PMCID: PMC2572728. PubMed DOI PMC

Schein CH. Polyglutamine Repeats in Viruses. Mol Neurobiol. 2019. May;56(5):3664–3675. doi:10.1007/s12035-018-1269-4. PubMed PMID: 30182336; PubMed Central PMCID: PMCPMC6399083. PubMed DOI PMC

Nardacci R, Ciccosanti F, Marsella C, et al. Role of autophagy in HIV infection and pathogenesis. J Intern Med. 2017. May;281(5):422–432. . PubMed PMID: 28139864. PubMed

Leymarie O, Lepont L, Berlioz-Torrent C.. Canonical and Non-Canonical Autophagy in HIV-1 Replication Cycle. Viruses. 2017. Sep 23;9(10). doi:10.3390/v9100270. PubMed PMID: 28946621; PubMed Central PMCID: PMCPMC5691622. PubMed DOI PMC

Nardacci R, Amendola A, Ciccosanti F, et al. Autophagy plays an important role in the containment of HIV-1 in nonprogressor-infected patients. Autophagy. 2014. Jul;10(7):1167–78. doi:10.4161/auto.28678. PubMed PMID: 24813622. PubMed DOI PMC

Moy RH, Gold B, Molleston JM, et al. Antiviral autophagy restrictsRift Valley fever virus infection and is conserved from flies to mammals. Immunity. 2014. Jan 16;40(1):51–65. doi:10.1016/j.immuni.2013.10.020. PubMed PMID: 24374193; PubMed Central PMCID: PMCPMC3951734. PubMed DOI PMC

Sumpter R, Jr., Sirasanagandla S, Fernandez AF, et al. Fanconi Anemia Proteins Function in Mitophagy and Immunity. Cell. 2016. May 5;165(4):867–81. doi:10.1016/j.cell.2016.04.006. PubMed PMID: 27133164; PubMed Central PMCID: PMCPMC4881391. PubMed DOI PMC

Paludan C, Schmid D, Landthaler M, et al. Endogenous MHC class II processing of a viral nuclear antigen after autophagy [Research Support, Non-U.S. Gov’t]. Science. 2005. Jan 28;307(5709):593–6. doi:10.1126/science.1104904. PubMed PMID: 15591165; eng. PubMed DOI

Bhattacharjee S, Bose P, Patel K, et al. Transcriptional and epigenetic modulation of autophagy promotes EBV oncoprotein EBNA3C induced B-cell survival. Cell Death Dis. 2018. May 22;9(6):605. doi:10.1038/s41419-018-0668-9. PubMed PMID: 29789559; PubMed Central PMCID: PMCPMC5964191. PubMed DOI PMC

Lee DY, Sugden B.. The latent membrane protein 1 oncogene modifies B-cell physiology by regulating autophagy. Oncogene. 2008. May 1;27(20):2833–42. doi:10.1038/sj.onc.1210946. PubMed PMID: 18037963. PubMed DOI

Pujals A, Favre L, Pioche-Durieu C, et al. Constitutive autophagy contributes to resistance to TP53-mediated apoptosis in Epstein-Barr virus-positive latency III B-cell lymphoproliferations. Autophagy. 2015;11(12):2275–87. doi:10.1080/15548627.2015.1115939. PubMed PMID: 26565591; PubMed Central PMCID: PMCPMC4835200. PubMed DOI PMC

Fotheringham JA, Raab-Traub N.. Epstein-Barr virus latent membrane protein 2 induces autophagy to promote abnormal acinus formation. J Virol. 2015. Jul;89(13):6940–4. doi:10.1128/JVI.03371-14. PubMed PMID: 25878108; PubMed Central PMCID: PMCPMC4468476. PubMed DOI PMC

Hung CH, Chen LW, Wang WH, et al. Regulation of autophagic activation by Rta of Epstein-Barr virus via the extracellular signal-regulated kinase pathway. J Virol. 2014. Oct;88(20):12133–45. doi:10.1128/JVI.02033-14. PubMed PMID: 25122800; PubMed Central PMCID: PMCPMC4178756. PubMed DOI PMC

McFadden K, Hafez AY, Kishton R, et al. Metabolic stress is a barrier to Epstein-Barr virus-mediated B-cell immortalization. Proc Natl Acad Sci U S A. 2016. Feb 9;113(6):E782–90. doi:10.1073/pnas.1517141113. PubMed PMID: 26802124; PubMed Central PMCID: PMCPMC4760815. PubMed DOI PMC

Montespan C, Marvin SA, Austin S, et al. Multi-layered control of Galectin-8 mediated autophagy during adenovirus cell entry through a conserved PPxY motif in the viral capsid. PLoS Pathog. 2017. Feb;13(2):e1006217. doi:10.1371/journal.ppat.1006217. PubMed PMID: 28192531; PubMed Central PMCID: PMCPMC5325606. PubMed DOI PMC

Hurwitz SN, Cheerathodi MR, Nkosi D, et al. Tetraspanin CD63 bridges autophagic and endosomal processes to regulate exosomal secretion and intracellular signaling of Epstein-Barr Virus LMP1. J Virol. 2018. Mar 1;92(5). doi:10.1128/JVI.01969-17. PubMed PMID: 29212935; PubMed Central PMCID: PMCPMC5809724. PubMed DOI PMC

Panyasrivanit M, Khakpoor A, Wikan N, et al. Co-localization of constituents of the dengue virus translation and replication machinery with amphisomes. J Gen Virol. 2009. Feb;90(Pt 2):448–56. doi:10.1099/vir.0.005355-0. PubMed PMID: 19141455. PubMed DOI

Khakpoor A, Panyasrivanit M, Wikan N, et al. A role for autophagolysosomes in dengue virus 3 production in HepG2 cells. J Gen Virol. 2009. May;90(Pt 5):1093–103. doi:10.1099/vir.0.007914-0. PubMed PMID: 19264601. PubMed DOI

Zhang H, Monken CE, Zhang Y, et al. Cellular autophagy machinery is not required for vaccinia virus replication and maturation. Autophagy. 2006. Apr-Jun;2(2):91–5. PubMed PMID: 16874104; eng. PubMed PMC

Heaton NS, Randall G.. Dengue virus and autophagy. Viruses. 2011. Aug;3(8):1332–41. doi:10.3390/v3081332. PubMed PMID: 21994782; PubMed Central PMCID: PMC3185800. eng. PubMed DOI PMC

Lee YR, Kuo SH, Lin CY, et al. Dengue virus-induced ER stress is required for autophagy activation, viral replication, and pathogenesis both in vitro and in vivo. Sci Rep. 2018. Jan 11;8(1):489. doi:10.1038/s41598-017-18909-3. PubMed PMID: 29323257; PubMed Central PMCID: PMCPMC5765116. PubMed DOI PMC

Dreux M, Gastaminza P, Wieland SF, et al. The autophagy machinery is required to initiate hepatitis C virus replication [Research Support, N.I.H., Extramural]. Proc Natl Acad Sci U S A. 2009. Aug 18;106(33):14046–51. doi:10.1073/pnas.0907344106. PubMed PMID: 19666601; PubMed Central PMCID: PMC2729017. eng. PubMed DOI PMC

Cao B, Parnell LA, Diamond MS, et al. Inhibition of autophagy limits vertical transmission of Zika virus in pregnant mice. J Exp Med. 2017. Aug 7;214(8):2303–2313. doi:10.1084/jem.20170957. PubMed PMID: 28694387; PubMed Central PMCID: PMCPMC5551583. PubMed DOI PMC

Abernathy E, Mateo R, Majzoub K, et al. Differential and convergent utilization of autophagy components by positive-strand RNA viruses. PLoS Biol. 2019. Jan;17(1):e2006926. doi:10.1371/journal.pbio.2006926. PubMed PMID: 30608919; PubMed Central PMCID: PMCPMC6334974. PubMed DOI PMC

Liang Q, Luo Z, Zeng J, et al. Zika virus NS4A and NS4B proteins deregulate Akt-mTOR signaling in human fetal neural stem cells to inhibit neurogenesis and induce autophagy. Cell Stem Cell. 2016. Nov 3;19(5):663–671. doi:10.1016/j.stem.2016.07.019. PubMed PMID: 27524440; PubMed Central PMCID: PMCPMC5144538. PubMed DOI PMC

Nombela I, Requena-Platek R, Morales-Lange B, et al. Rainbow trout red blood cells exposed to viral hemorrhagic septicemia virus up-regulate antigen-processing mechanisms and MHC I&II, CD86, and CD83 antigen-presenting cell markers. Cells. 2019. Apr 27;8(5):386. doi:10.3390/cells8050386. PubMed PMID: 31035565; PubMed Central PMCID: PMCPMC6562805. PubMed DOI PMC

Webster P. Cytoplasmic bacteria and the autophagic pathway [Review]. Autophagy. 2006. Jul-Sep;2(3):159–61. PubMed PMID: 16874112; eng. PubMed

Dubuisson JF, Swanson MS.. Mouse infection by Legionella, a model to analyze autophagy [Research Support, N.I.H., Extramural Review]. Autophagy. 2006. Jul-Sep;2(3):179–82. PubMed PMID: 16874080; PubMed Central PMCID: PMC1774947. eng. PubMed PMC

Jordan TX, Randall G.. Manipulation or capitulation: virus interactions with autophagy. Microbes Infect. 2011. Oct 24;in press. doi:10.1016/j.micinf.2011.09.007. PubMed PMID: 22051604; Eng. PubMed DOI PMC

Knodler LA, Celli J.. Eating the strangers within: host control of intracellular bacteria via xenophagy [Research Support, N.I.H., Intramural]. Cell Microbiol. 2011. Sep;13(9):1319–27. doi:10.1111/j.1462-5822.2011.01632.x. PubMed PMID: 21740500; PubMed Central PMCID: PMC3158265. eng. PubMed DOI PMC

Levine B, Mizushima N, Virgin HW.. Autophagy in immunity and inflammation. Nature. 2011. Jan 20;469(7330):323–35. doi:10.1038/nature09782. PubMed PMID: 21248839; PubMed Central PMCID: PMC3131688. eng. PubMed DOI PMC

Deretic V. Autophagy in immunity and cell-autonomous defense against intracellular microbes. Immunol Rev. 2011. Mar;240(1):92–104. doi:10.1111/j.1600-065X.2010.00995.x. PubMed PMID: 21349088; PubMed Central PMCID: PMC3057454. eng. PubMed DOI PMC

Dong X, Levine B.. Autophagy and viruses: adversaries or allies? J Innate Immun. 2013;5(5):480–93. doi:10.1159/000346388. PubMed PMID: 23391695; PubMed Central PMCID: PMC3790331. PubMed DOI PMC

Cardenal-Munoz E, Barisch C, Lefrancois LH, et al. When dicty met myco, a (Not So) romantic story about one amoeba and its intracellular pathogen. Front Cell Infect Microbiol. 2017;7:529. doi:10.3389/fcimb.2017.00529. PubMed PMID: 29376033; PubMed Central PMCID: PMCPMC5767268. PubMed DOI PMC

Dunn JD, Bosmani C, Barisch C, et al. Eat prey, live: dictyostelium discoideum as a model for cell-autonomous defenses. Front Immunol. 2017;8:1906. doi: 10.3389/fimmu.2017.01906. PubMed PMID: 29354124; PubMed Central PMCID: PMCPMC5758549. PubMed DOI PMC

Leary AY, Savage Z, Tumtas Y, et al. Contrasting and emerging roles of autophagy in plant immunity. Curr Opin Plant Biol. 2019. Dec;52:46–53. doi:10.1016/j.pbi.2019.07.002. PubMed PMID: 31442734. PubMed DOI

Wang C, Symington JW, Mysorekar IU.. ATG16L1 and pathogenesis of urinary tract infections. Autophagy. 2012. Nov;8(11):1693–4. doi:10.4161/auto.21600. PubMed PMID: 22874553; PubMed Central PMCID: PMC3494604. PubMed DOI PMC

Choy A, Roy CR.. Autophagy and bacterial infection: an evolving arms race. Trends Microbiol. 2013. Sep;21(9):451–6. doi:10.1016/j.tim.2013.06.009. PubMed PMID: 23880062; PubMed Central PMCID: PMC3839292. PubMed DOI PMC

Mostowy S, Cossart P.. Bacterial autophagy: restriction or promotion of bacterial replication? Trends Cell Biol. 2012. Jun;22(6):283–91. doi:10.1016/j.tcb.2012.03.006. PubMed PMID: 22555009. PubMed DOI

Andersson AM, Andersson B, Lorell C, et al. Autophagy induction targeting mTORC1 enhances Mycobacterium tuberculosis replication in HIV co-infected human macrophages. Sci Rep. 2016. Jun 15;6:28171. doi:10.1038/srep28171. PubMed PMID: 27302320; PubMed Central PMCID: PMCPMC4908603. PubMed DOI PMC

Dinic M, Lukic J, Djokic J, et al. Lactobacillus fermentum Postbiotic-induced Autophagy as Potential Approach for Treatment of Acetaminophen Hepatotoxicity. Front Microbiol. 2017;8:594. doi:10.3389/fmicb.2017.00594. PubMed PMID: 28428777; PubMed Central PMCID: PMCPMC5382196. PubMed DOI PMC

Kageyama S, Omori H, Saitoh T, et al. The LC3 recruitment mechanism is separate from Atg9L1-dependent membrane formation in the autophagic response against Salmonella [Research Support, Non-U.S. Gov’t]. Mol Biol Cell. 2011. Jul 1;22(13):2290–300. doi:10.1091/mbc.E10-11-0893. PubMed PMID: 21525242; PubMed Central PMCID: PMC3128531. eng. PubMed DOI PMC

Thurston TL, Wandel MP, von Muhlinen N, et al. Galectin 8 targets damaged vesicles for autophagy to defend cells against bacterial invasion. Nature. 2012. Feb 16;482(7385):414–8. doi:10.1038/nature10744. PubMed PMID: 22246324; PubMed Central PMCID: PMC3343631. PubMed DOI PMC

Zheng YT, Shahnazari S, Brech A, et al. The adaptor protein p62/SQSTM1 targets invading bacteria to the autophagy pathway. J Iimmunol. 2009. Nov 1;183(9):5909–16. doi:10.4049/jimmunol.0900441. PubMed PMID: 19812211; eng. PubMed DOI

Thurston TL, Ryzhakov G, Bloor S, et al. The TBK1 adaptor and autophagy receptor NDP52 restricts the proliferation of ubiquitin-coated bacteria. Nat Immunol. 2009. Nov;10(11):1215–21. doi:10.1038/ni.1800. PubMed PMID: 19820708; eng. PubMed DOI

Tumbarello DA, Manna PT, Allen M, et al. The autophagyrReceptor TAX1BP1 and the molecular motor myosin VI are required for clearance of Salmonella Typhimurium by autophagy. PLoS Pathog. 2015;11:e1005174. PubMed PMC

Wild P, Farhan H, McEwan DG, et al. Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth. Science. 2011. Jul 8;333(6039):228–33. doi:10.1126/science.1205405. PubMed PMID: 21617041; eng. PubMed DOI PMC

Lopez-Montero N, Ramos-Marques E, Risco C, et al. Intracellular Salmonella induces aggrephagy of host endomembranes in persistent infections. Autophagy. 2016. Oct 2;12(10):1886–1901. doi:10.1080/15548627.2016.1208888 PubMed PMID: 27485662; PubMed Central PMCID: PMCPMC5079681. PubMed DOI PMC

Benjamin JL, Sumpter R, Jr., Levine B, et al. Intestinal epithelial autophagy is essential for host defense against invasive bacteria. Cell Host Microbe. 2013. Jun 12;13(6):723–34. doi:10.1016/j.chom.2013.05.004. PubMed PMID: 23768496; PubMed Central PMCID: PMCPMC3755484. PubMed DOI PMC

Ammanathan V, Mishra P, Chavalmane AK, et al. Restriction of intracellular Salmonella replication by restoring TFEB-mediated xenophagy. Autophagy. 2019. Nov 19:1–14. doi:10.1080/15548627.2019.1689770. PubMed PMID: 31744366. PubMed DOI PMC

Xu Y, Zhou P, Cheng S, et al. A bacterial effector reveals the V-ATPase-ATG16L1 axis that initiates xenophagy. Cell. 2019. Jul 25;178(3):552–566 e20. doi:10.1016/j.cell.2019.06.007. PubMed PMID: 31327526. PubMed DOI

Zhang H, Wu F, Wang X, et al. The two C. elegans ATG-16 homologs have partially redundant functions in the basal autophagy pathway. Autophagy. 2013. Dec;9(12):1965–74. PubMed PMID: 24185444; PubMed Central PMCID: PMC4028341. PubMed PMC

Fletcher K, Ulferts R, Jacquin E, et al. The WD40 domain of ATG16L1 is required for its non-canonical role in lipidation of LC3 at single membranes. EMBO J. 2018. Feb 15;37(4). doi:10.15252/embj.201797840. PubMed PMID: 29317426; PubMed Central PMCID: PMCPMC5813257. PubMed DOI PMC

Shahnazari S, Brumell JH.. Mechanisms and consequences of bacterial targeting by the autophagy pathway. Curr Opin Microbiol. 2011. Feb;14(1):68–75. doi:10.1016/j.mib.2010.11.001. PubMed PMID: 21112809; eng. PubMed DOI

Klionsky DJ, Eskelinen EL, Deretic V.. Autophagosomes, phagosomes, autolysosomes, phagolysosomes, autophagolysosomes … wait, I’m confused. Autophagy. 2014. Apr;10(4):549–51. doi:10.4161/auto.28448. PubMed PMID: 24657946. PubMed DOI PMC

Li X, He S, Zhou X, et al. Lyn delivers bacteria to lysosomes for eradication through TLR2-initiated autophagy related phagocytosis. PLoS Pathog. 2016. Jan;12(1):e1005363. doi:10.1371/journal.ppat.1005363. PubMed PMID: 26735693; PubMed Central PMCID: PMCPMC4703367. PubMed DOI PMC

Li X, Ye Y, Zhou X, et al. Atg7 enhances host defense against infection via downregulation of superoxide but upregulation of nitric oxide. J Iimmunol. 2015. Feb 1;194(3):1112–21. doi:10.4049/jimmunol.1401958. PubMed PMID: 25535282; PubMed Central PMCID: PMC4409144. PubMed DOI PMC

Ye Y, Tan S, Zhou X, et al. Inhibition of p-IkappaBalpha ubiquitylation by autophagy-related gene 7 to regulate inflammatory responses to bacterial infection. J Infect Dis. 2015. May 28;212:1816–26. doi:10.1093/infdis/jiv301. PubMed PMID: 26022442. PubMed DOI PMC

Yuan K, Huang C, Fox J, et al. Autophagy plays an essential role in the clearance of Pseudomonas aeruginosa by alveolar macrophages. J Cell Sci. 2012. Jan 15;125(Pt 2):507–15. doi:10.1242/jcs.094573. PubMed PMID: 22302984; PubMed Central PMCID: PMC3283879. PubMed DOI PMC

Irving AT, Mimuro H, Kufer TA, et al. The immune receptor NOD1 and kinase RIP2 interact with bacterial peptidoglycan on early endosomes to promote autophagy and inflammatory signaling. Cell Host Microbe. 2014. May 14;15(5):623–35. doi:10.1016/j.chom.2014.04.001. PubMed PMID: 24746552. PubMed DOI

Kaparakis-Liaskos M, Ferrero RL.. Immune modulation by bacterial outer membrane vesicles. Nat Rev Immunol. 2015. Jun;15(6):375–87. doi:10.1038/nri3837. PubMed PMID: 25976515. PubMed DOI

Travassos LH, Carneiro LA, Ramjeet M, et al. Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry. Nat Immunol. 2010. Jan;11(1):55–62. doi:10.1038/ni.1823. PubMed PMID: 19898471; eng. PubMed DOI

Chaudhary A, Kamischke C, Leite M, et al. beta-Barrel outer membrane proteins suppress mTORC2 activation and induce autophagic responses. Sci Signal. 2018. Nov 27;11(558). doi:10.1126/scisignal.aat7493. PubMed PMID: 30482849. PubMed DOI

Hayrabedyan S, Todorova K, Jabeen A, et al. Sertoli cells have a functional NALP3 inflammasome that can modulate autophagy and cytokine production. Sci Rep. 2016. Jan 8;6:18896. doi:10.1038/srep18896. PubMed PMID: 26744177; PubMed Central PMCID: PMCPMC4705529. PubMed DOI PMC

Keestra-Gounder AM, Tsolis RM.. NOD1 and NOD2: Beyond Peptidoglycan Sensing. Trends Immunol. 2017. Oct;38(10):758–767. doi:10.1016/j.it.2017.07.004. PubMed PMID: 28823510; PubMed Central PMCID: PMCPMC5624830. PubMed DOI PMC

Nabatov AA, Hatzis P, Rouschop KM, et al. Hypoxia inducible NOD2 interacts with 3-O-sulfogalactoceramide and regulates vesicular homeostasis. Biochim Biophys Acta. 2013. Nov;1830(11):5277–86. doi:10.1016/j.bbagen.2013.07.017. PubMed PMID: 23880069. PubMed DOI

Casassa AF, Vanrell MC, Colombo MI, et al. Autophagy plays a protective role against Trypanosoma cruzi infection in mice. Virulence. 2019. Dec;10(1):151–165. doi:10.1080/21505594.2019.1584027. PubMed PMID: 30829115; PubMed Central PMCID: PMCPMC6550547. PubMed DOI PMC

Collins CA, De Maziere A, van Dijk S, et al. Atg5-independent sequestration of ubiquitinated mycobacteria [Research Support, Non-U.S. Gov’t]. PLoS Pathog. 2009. May;5(5):e1000430. doi:10.1371/journal.ppat.1000430. PubMed PMID: 19436699; PubMed Central PMCID: PMC2673685. eng. PubMed DOI PMC

Moreau K, Lacas-Gervais S, Fujita N, et al. Autophagosomes can support Yersinia pseudotuberculosis replication in macrophages. Cell Microbiol. 2010. Aug;12(8):1108–23. doi:10.1111/j.1462-5822.2010.01456.x. PubMed PMID: 20180800; eng. PubMed DOI

Chandra P, Ghanwat S, Matta SK, et al. Mycobacterium tuberculosis inhibits RAB7 recruitment to selectively modulate autophagy flux in macrophages. Sci Rep. 2015. Nov 6;5:16320. doi:10.1038/srep16320. PubMed PMID: 26541268; PubMed Central PMCID: PMCPMC4635374. PubMed DOI PMC

Chandra P, Kumar D.. Selective autophagy gets more selective: Uncoupling of autophagy flux and xenophagy flux in Mycobacterium tuberculosis-infected macrophages. Autophagy. 2016;12(3):608–9. doi:10.1080/15548627.2016.1139263. PubMed PMID: 27046255; PubMed Central PMCID: PMCPMC4836011. PubMed DOI PMC

Grasso D, Ropolo A, Re A Lo, et al. Zymophagy, a novel selective autophagy pathway mediated by VMP1-USP9x-p62, prevents pancreatic cell death. J Biol Chem. 2011. Mar 11;286(10):8308–24. doi:10.1074/jbc.M110.197301. PubMed PMID: 21173155; PubMed Central PMCID: PMC3048716. eng. PubMed DOI PMC

Wang S, Ni HM, Chao X, et al. Critical role of TFEB-mediated lysosomal biogenesis in alcohol-induced pancreatitis in mice and humans. Cell Mol Gastroenterol Hepatol. 2020;10(1):59–81. doi:10.1016/j.jcmgh.2020.01.008. PubMed PMID: 31987928; PubMed Central PMCID: PMCPMC7210479. PubMed DOI PMC

Mareninova OA, Hermann K, French SW, et al. Impaired autophagic flux mediates acinar cell vacuole formation and trypsinogen activation in rodent models of acute pancreatitis. J Clin Invest. 2009. Nov;119(11):3340–55. doi:10.1172/JCI38674. PubMed PMID: 19805911; PubMed Central PMCID: PMCPMC2769194. PubMed DOI PMC

Wang S, Ni HM, Chao X, et al. Impaired TFEB-mediated lysosomal biogenesis promotes the development of pancreatitis in mice and is associated with human pancreatitis. Autophagy. 2019. Nov;15(11):1954–1969. doi:10.1080/15548627.2019.1596486. PubMed PMID: 30894069; PubMed Central PMCID: PMCPMC6844531. PubMed DOI PMC

Seglen PO, Gordon PB, Tolleshaug H, et al. Use of [3H]raffinose as a specific probe of autophagic sequestration. Exp Cell Res. 1986. Jan;162(1):273–7. PubMed PMID: 3940229; eng. PubMed

Kopitz J, Kisen GO, Gordon PB, et al. Nonselective autophagy of cytosolic enzymes by isolated rat hepatocytes. J Cell Biol. 1990. Sep;111(3):941–53. PubMed PMID: 2391370; eng. PubMed PMC

Seglen PO, Luhr M, Mills IG, et al. Macroautophagic cargo sequestration assays. Methods. 2015. Mar;75:25–36. doi:10.1016/j.ymeth.2014.12.021. PubMed PMID: 25576638. PubMed DOI

Gordon PB, Seglen PO.. Autophagic sequestration of [14C]sucrose, introduced into rat hepatocytes by reversible electro-permeabilization. Exp Cell Res. 1982. Nov142(1):1–14. PubMed PMID: 7140848. PubMed

Kjos I, Borg Distefano M, Saetre F, et al. Rab7b modulates autophagic flux by interacting with Atg4B. EMBO Rep. 2017. Oct;18(10):1727–1739. doi:10.15252/embr.201744069. PubMed PMID: 28835545; PubMed Central PMCID: PMCPMC5623852. PubMed DOI PMC

Luhr M, Szalai P, Saetre F, et al. A simple cargo sequestration assay for quantitative measurement of nonselective autophagy in cultured cells. Methods Enzymol. 2017;587:351–364. doi:10.1016/bs.mie.2016.09.064. PubMed PMID: 28253965. PubMed DOI

Boland B, Smith DA, Mooney D, et al. Macroautophagy is not directly involved in the metabolism of amyloid precursor protein. J Biol Chem. 2010. Nov 26;285(48):37415–26. doi: 10.1074/jbc.M110.186411. PubMed PMID: 20864542; PubMed Central PMCID: PMC2988347. PubMed DOI PMC

Nair U, Thumm M, Klionsky DJ, et al. GFP-Atg8 protease protection as a tool to monitor autophagosome biogenesis. Autophagy. 2011. Dec 1;7(12):1546–1550. PubMed PMID: 22108003; Eng. PubMed PMC

Plomp PJ, Gordon PB, Meijer AJ, et al. Energy dependence of different steps in the autophagic-lysosomal pathway. J Biol Chem. 1989. Apr 25;264(12):6699–704. PubMed PMID: 2708336; eng. PubMed

Gutierrez MG, Munafo DB, Beron W, et al. Rab7 is required for the normal progression of the autophagic pathway in mammalian cells. J Cell Sci. 2004. Jun1;117(Pt 13):2687–97. PubMed PMID: 15138286; eng. PubMed

Jager S, Bucci C, Tanida I, et al. Role for Rab7 in maturation of late autophagic vacuoles. J Cell Sci. 2004. Sep15;117(Pt 20):4837–48. doi: 10.1242/jcs.01370 jcs.01370 [pii]. PubMed PMID: 15340014; eng. PubMed

Rodriguez-Enriquez S, Kim I, Currin RT, et al. Tracker dyes to probe mitochondrial autophagy (mitophagy) in rat hepatocytes. Autophagy. 2006. Jan-Mar;2(1):39–46. PubMed PMID: 16874071; eng. PubMed PMC

Lorenz H, Hailey DW, Lippincott-Schwartz J.. Fluorescence protease protection of GFP chimeras to reveal protein topology and subcellular localization. Nat Methods. 2006. Mar;3(3):205–10. PubMed PMID: 16489338; eng. PubMed

Korsnes MS, Korsnes R.. Single-cell tracking of A549 lung cancer cells exposed to a marine toxin reveals correlations in pedigree tree profiles. Front Oncol. 2018;8:260. doi:10.3389/fonc.2018.00260. PubMed PMID: 30023341; PubMed Central PMCID: PMCPMC6039982. PubMed DOI PMC

Korsnes MS, Kolstad H, Kleiveland CR, et al. Autophagic activity in BC3H1 cells exposed to yessotoxin. Toxicol In Vitro. 2016. Apr;32:166–80. doi:10.1016/j.tiv.2015.12.010. PubMed PMID: 26743762. PubMed DOI

Takats S, Toth S, Szenci G, et al. Investigating Non-selective autophagy in Drosophila. Methods Mol Biol. 2019;1880:589–600. doi: 10.1007/978-1-4939-8873-0_38. PubMed PMID: 30610724. PubMed DOI

McNeil PL, Murphy RF, Lanni F, et al. A method for incorporating macromolecules into adherent cells. J Cell Biol. 1984. Apr;98(4):1556–64. PubMed PMID: 6201494; eng. PubMed PMC

Kim J, Huang WP, Stromhaug PE, et al. Convergence of multiple autophagy and cytoplasm to vacuole targeting components to a perivacuolar membrane compartment prior to de novo vesicle formation. J Biol Chem. 2002. Jan 4;277(1):763–73. doi:10.1074/jbc.M109134200. PubMed PMID: 11675395; PubMed Central PMCID: PMC2754695. eng. PubMed DOI PMC

Velikkakath AK, Nishimura T, Oita E, et al. Mammalian Atg2 proteins are essential for autophagosome formation and important for regulation of size and distribution of lipid droplets. Mol Biol Cell. 2012. Mar;23(5):896–909. doi:10.1091/mbc.E11-09-0785. PubMed PMID: 22219374; PubMed Central PMCID: PMC3290647. PubMed DOI PMC

Seglen PO, Gordon PB.. Amino acid control of autophagic sequestration and protein degradation in isolated rat hepatocytes. J Cell Biol. 1984. Aug;99(2):435–44. doi:10.1083/jcb.99.2.435. PubMed PMID: 6746735; PubMed Central PMCID: PMCPMC2113269. PubMed DOI PMC

Kovács AL, Laszlo L, Kovács J.. Effect of amino acids and cycloheximide on changes caused by vinblastine, leupeptin and methylamine in the autophagic/lysosomal system of mouse hepatocytes in vivo. Exp Cell Res. 1985. Mar;157(1):83–94. PubMed PMID: 3972014; eng. PubMed

Swanson MS, Byrne BG, Dubuisson JF.. Kinetic analysis of autophagosome formation and turnover in primary mouse macrophages. Methods Enzymol. 2009;452:383–402. doi:10.1016/S0076-6879(08)03623-9. PubMed PMID: 19200894; eng. PubMed DOI

Urban J, Soulard A, Huber A, et al. Sch9 is a major target of TORC1 in Saccharomyces cerevisiae. Mol Cell. 2007. Jun 8;26(5):663–74. doi:10.1016/j.molcel.2007.04.020. PubMed PMID: 17560372; eng. PubMed DOI

Jomain-Baum M, Garber AJ, Farber E, et al. The effect of cycloheximide on the interaction between mitochondrial respiration and gluconeogenesis in guinea pig and rat liver. J Biol Chem. 1973. Mar 10;248(5):1536–43. PubMed PMID: 4348543; eng. PubMed

Garber AJ, Jomain-Baum M, Salganicoff L, et al. The effects of cycloheximide on energy transfer in rat and guinea pig liver mitochondria. J Biol Chem. 1973. Mar 10;248(5):1530–5. PubMed PMID: 4144389; eng. PubMed

Mora R, Dokic I, Kees T, et al. Sphingolipid rheostat alterations related to transformation can be exploited for specific induction of lysosomal cell death in murine and human glioma. Glia. 2010. Aug 15;58(11):1364–83. doi:10.1002/glia.21013. PubMed PMID: 20607862; eng. PubMed DOI

Bright NA, Lindsay MR, Stewart A, et al. The relationship between lumenal and limiting membranes in swollen late endocytic compartments formed after wortmannin treatment or sucrose accumulation. Traffic. 2001. Sep;2(9):631–42. PubMed PMID: 11555417; eng. PubMed

Deter RL. Quantitative characterization of dense body, autophagic vacuole, and acid phosphatase-bearing particle populations during the early phases of glucagon-induced autophagy in rat liver. J Cell Biol. 1971. Mar;48(3):473–89. PubMed PMID: 5553081; eng. PubMed PMC

Deter RL. Analog modeling of glucagon-induced autophagy in rat liver. I. Conceptual and mathematical model of telolysosome-autophagosome-autolysosome interaction. Exp Cell Res. 1975. Aug;94(1):122–6. PubMed PMID: 1193121; eng. PubMed

Deter RL. Analog modeling of glucagon-induced autophagy in rat liver. II. Evaluation of iron labeling as a means for identifying telolysosome, autophagosome and autolysosome populations.Exp Cell Res. 1975. Aug;94(1):127–39. PubMed PMID: 172336; eng. PubMed

Deter RL, Baudhuin P, de Duve C.. Participation of lysosomes in cellular autophagy induced in rat liver by glucagon. J Cell Biol. 1967. Nov;35(2):C11–6. PubMed PMID: 6055998; eng. PubMed PMC

Deter RL, de Duve C.. Influence of glucagon, an inducer of cellular autophagy, on some physical properties of rat liver lysosomes. J Cell Biol. 1967. May;33(2):437–49. PubMed PMID: 4292315; eng. PubMed PMC

Stromhaug PE, Berg TO, Fengsrud M, et al. Purification and characterization of auto-phagosomes from rat hepatocytes. Biochem J. 1998. Oct;15;335(Pt 2):217–24. PubMed PMID: 9761717; PubMed Central PMCID: PMC1219772. eng. PubMed PMC

Deter RL. Electron microscopic evaluation of subcellular fractions obtained by ultracentrifugation. In: Hayat MA, editor. Principles and Techniques of Electron Microscopy. Vol. 3. New York: Van Nostrand Reinhold Co; 1973. p. 199–235.

Marzella L, Ahlberg J, Glaumann H.. Isolation of autophagic vacuoles from rat liver: morphological and biochemical characterization. J Cell Biol. 1982. Apr;93(1):144–54. PubMed PMID: 7068752; eng. PubMed PMC

Wattiaux R, Wattiaux-De Coninck S, Ronveaux-Dupal M-F, et al. Isolation of rat liver lysosomes by isopycnic centrifugation in a metrizamide gradient. J Cell Biol. 1978. Aug;78(2):349–68. PubMed PMID: 211139; eng. PubMed PMC

Rodriguez-Navarro JA, Rodriguez L, Casarejos MJ, et al. Trehalose ameliorates dopaminergic and tau pathology in parkin deleted/tau overexpressing mice through autophagy activation. Neurobiol Dis. 2010. Sep;39(3):423–38. doi:10.1016/j.nbd.2010.05.014. PubMed PMID: 20546895; eng. PubMed DOI

Ge L, Melville D, Zhang M, et al. The ER-Golgi intermediate compartment is a key membrane source for the LC3 lipidation step of autophagosome biogenesis. eLife. 2013. Aug 6;2:e00947. doi:10.7554/eLife.00947. PubMed PMID: 23930225; PubMed Central PMCID: PMCPMC3736544. PubMed DOI PMC

Ge L, Zhang M, Schekman R.. Phosphatidylinositol 3-kinase and COPII generate LC3 lipidation vesicles from the ER-Golgi intermediate compartment. eLife. 2014. Nov 28;3:e04135. doi:10.7554/eLife.04135. PubMed PMID: 25432021; PubMed Central PMCID: PMCPMC4270069. PubMed DOI PMC

Ge L, Wilz L, Schekman R.. Biogenesis of autophagosomal precursors for LC3 lipidation from the ER-Golgi intermediate compartment. Autophagy. 2015;11(12):2372–4. doi:10.1080/15548627.2015.1105422. PubMed PMID: 26565421; PubMed Central PMCID: PMCPMC4835199. PubMed DOI PMC

Shima T, Kirisako H, Nakatogawa H.. COPII vesicles contribute to autophagosomal membranes. J Cell Biol. 2019. May 6;218(5):1503–1510. doi:10.1083/jcb.201809032. PubMed PMID: 30787039; PubMed Central PMCID: PMCPMC6504894. PubMed DOI PMC

Ge L, Zhang M, Kenny SJ, et al. Remodeling of ER-exit sites initiates a membrane supply pathway for autophagosome biogenesis. EMBO Rep. 2017. Sep;18(9):1586–1603. doi:10.15252/embr.201744559. PubMed PMID: 28754694; PubMed Central PMCID: PMCPMC5579361. PubMed DOI PMC

He C, Sumpter R, Jr., Levine B.. Exercise induces autophagy in peripheral tissues and in the brain. Autophagy. 2012. Oct;8(10):1548–51. doi:10.4161/auto.21327. PubMed PMID: 22892563; PubMed Central PMCID: PMC3463459. PubMed DOI PMC

Munoz-Galdeano T, Reigada D, Del Aguila A, et al. Cell specific changes of autophagy in a mouse model of contusive spinal cord injury. Front Cell Neurosci. 2018;12:164. doi:10.3389/fncel.2018.00164. PubMed PMID: 29946241; PubMed Central PMCID: PMCPMC6005838. PubMed DOI PMC

Mizushima N, Yoshimori T, Levine B.. Methods in mammalian autophagy research. Cell. 2010. Feb 5;140(3):313–26. doi:10.1016/j.cell.2010.01.028. PubMed PMID: 20144757; PubMed Central PMCID: PMC2852113. eng. PubMed DOI PMC

Iwai-Kanai E, Yuan H, Huang C, et al. A method to measure cardiac autophagic flux in vivo [Research Support, N.I.H., Extramural]. Autophagy. 2008. Apr;4(3):322–9. PubMed PMID: 18216495; eng. PubMed PMC

Zhu H, Tannous P, Johnstone JL, et al. Cardiac autophagy is a maladaptive response to hemodynamic stress. J Clin Invest. 2007. Jul;117(7):1782–93. doi:10.1172/JCI27523. PubMed PMID: 17607355; PubMed Central PMCID: PMC1890995. eng. PubMed DOI PMC

Castillo K, Valenzuela V, Matus S, et al. Measurement of autophagy flux in the nervous system in vivo. Cell Death Dis. 2013;4:e917. doi:10.1038/cddis.2013.421. PubMed PMID: 24232093; PubMed Central PMCID: PMC3847309. PubMed DOI PMC

Matus S, Valenzuela V, Hetz C.. A new method to measure autophagy flux in the nervous system. Autophagy. 2014. Apr;10(4):710–4. doi:10.4161/auto.28434. PubMed PMID: 24717689; PubMed Central PMCID: PMC4091163. PubMed DOI PMC

Leiva-Rodriguez T, Romeo-Guitart D, Marmolejo-Martinez-Artesero S, et al. ATG5 overexpression is neuroprotective and attenuates cytoskeletal and vesicle-trafficking alterations in axotomized motoneurons. Cell Death Dis. 2018. May 24;9(6):626. doi:10.1038/s41419-018-0682-y. PubMed PMID: 29799519; PubMed Central PMCID: PMCPMC5967323. PubMed DOI PMC

Castillo K, Nassif M, Valenzuela V, et al. Trehalose delays the progression of amyotrophic lateral sclerosis by enhancing autophagy in motoneurons. Autophagy. 2013. Sep;9(9):1308–20. doi:10.4161/auto.25188. PubMed PMID: 23851366. PubMed DOI

Chiarelli R, Agnello M, Roccheri MC.. Sea urchin embryos as a model system for studying autophagy induced by cadmium stress. Autophagy. 2011. Sep 1;7(9):1028–34. PubMed PMID: 21628995; eng. PubMed

Morici G, Agnello M, Spagnolo F, et al. Confocal microscopy study of the distribution, content and activity of mitochondria during Paracentrotus lividus development. J Microsc. 2007. Nov;228(Pt 2):165–73. doi:10.1111/j.1365-2818.2007.01860.x. PubMed PMID: 17970916; eng. PubMed DOI

McWilliams TG, Ganley IG.. Investigating mitophagy and mitochondrial morphology in vivo using mito-QC: A comprehensive guide. Methods Mol Biol. 2019;1880:621–642. doi:10.1007/978-1-4939-8873-0_41. PubMed PMID: 30610727. PubMed DOI

Martinet W, De Meyer GR, Andries L, et al. Detection of autophagy in tissue by standard immunohistochemistry: possibilities and limitations. Autophagy. 2006. Jan-Mar;2(1):55–7. PubMed PMID: 16874065; eng. PubMed

Holt SV, Wyspianska B, Randall KJ, et al. The development of an immunohistochemical method to detect the autophagy-associated protein LC3-II in human tumor xenografts. Toxicol Pathol. 2011. Apr;39(3):516–23. doi:10.1177/0192623310396903. PubMed PMID: 21441228; eng. PubMed DOI

Kimura S, Fujita N, Noda T, et al. Monitoring autophagy in mammalian cultured cells through the dynamics of LC3. Methods Enzymol. 2009;452:1–12. doi:10.1016/S0076-6879(08)03601-X. PubMed PMID: 19200872; eng. PubMed DOI

Dehay B, Bove J, Rodriguez-Muela N, et al. Pathogenic lysosomal depletion in Parkinson’s disease. J Neurosci. 2010. Sep 15;30(37):12535–44. doi:10.1523/JNEUROSCI.1920-10.2010. PubMed PMID: 20844148; eng. PubMed DOI PMC

Daniels BH, McComb RD, Mobley BC, et al. LC3 and p62 as diagnostic markers of drug-induced autophagic vacuolar cardiomyopathy: a study of 3 cases. Am J Surg Pathol. 2013. Jul;37(7):1014–21. doi:10.1097/PAS.0b013e3182863fa8. PubMed PMID: 23681079. PubMed DOI

Hiniker A, Daniels BH, Lee HS, et al. Comparative utility of LC3, p62 and TDP-43 immunohistochemistry in differentiation of inclusion body myositis from polymyositis and related inflammatory myopathies. Acta Neuropathol Commun. 2013;1(1):29. doi:10.1186/2051-5960-1-29. PubMed PMID: 24252466; PubMed Central PMCID: PMC3893502. PubMed DOI PMC

Lee HS, Daniels BH, Salas E, et al. Clinical utility of LC3 and p62 immunohistochemistry in diagnosis of drug-induced autophagic vacuolar myopathies: a case-control study. PLoS One. 2012;7(4):e36221. doi:10.1371/journal.pone.0036221. PubMed PMID: 22558391; PubMed Central PMCID: PMC3338695. PubMed DOI PMC

Lastres-Becker I, Garcia-Yague AJ, Scannevin RH, et al. Repurposing the NRF2 activator dimethyl fumarate as therapy against synucleinopathy in Parkinson’s disease. Antioxid Redox Signal. 2016. Jul 10;25(2):61–77. doi:10.1089/ars.2015.6549. PubMed PMID: 27009601; PubMed Central PMCID: PMCPMC4943471. PubMed DOI PMC

Chung YC, Lim JH, Oh HM, et al. Calcimimetic restores diabetic peripheral neuropathy by ameliorating apoptosis and improving autophagy. Cell Death Dis. 2018. Nov 26;9(12):1163. doi:10.1038/s41419-018-1192-7. PubMed PMID: 30478254; PubMed Central PMCID: PMCPMC6255917. PubMed DOI PMC

Huang HC, Chen L, Zhang HX, et al. Autophagy promotes peripheral nerve regeneration and motor recovery following sciatic nerve crush injury in rats. J Mol Neurosci. 2016. Apr;58(4):416–23. doi:10.1007/s12031-015-0672-9. PubMed PMID: 26738732; PubMed Central PMCID: PMCPMC4829621. PubMed DOI PMC

Hamada K, Terauchi A, Nakamura K, et al. Aberrant calcium signaling by transglutaminase-mediated posttranslational modification of inositol 1,4,5-trisphosphate receptors. Proc Natl Acad Sci U S A. 2014. Sep 23;111(38):E3966–75. doi:10.1073/pnas.1409730111. PubMed PMID: 25201980; PubMed Central PMCID: PMC4183345. PubMed DOI PMC

Rodriguez-Muela N, Koga H, Garcia-Ledo L, et al. Balance between autophagic pathways preserves retinal homeostasis. Aging cell. 2013. Jun;12(3):478–88. doi: 10.1111/acel.12072. PubMed PMID: 23521856; PubMed Central PMCID: PMC3655122. PubMed DOI PMC

Esteban-Martinez L, Boya P.. Autophagic flux determination in vivo and ex vivo. Methods. 2015;75:79–86. PubMed

Gomez-Sintes R, Villarejo-Zori B, Serrano-Puebla A, et al. Standard assays for the study of autophagy in the ex vivo retina. Cells. 2017. Oct 22;6(4). doi:10.3390/cells6040037. PubMed PMID: 29065501; PubMed Central PMCID: PMCPMC5755496. PubMed DOI PMC

McMahon J, Huang X, Yang J, et al. Impaired autophagy in neurons after disinhibition of mammalian target of rapamycin and its contribution to epileptogenesis. J Neurosci. 2012. Nov 7;32(45):15704–14. doi:10.1523/JNEUROSCI.2392-12.2012. PubMed PMID: 23136410; PubMed Central PMCID: PMC3501684. PubMed DOI PMC

Messing L, Decker JM, Joseph M, et al. Cascade of tau toxicity in inducible hippocampal brain slices and prevention by aggregation inhibitors. Neurobiol Aging. 2013. May;34(5):1343–1354. doi: 10.1016/j.neurobiolaging.2012.10.024. PubMed PMID: 23158765; PubMed Central PMCID: PMCPMC4984976. PubMed DOI PMC

Herrando-Grabulosa M, Casas C, Aguilera J.. The C-terminal domain of tetanus toxin protects motoneurons against acute excitotoxic damage on spinal cord organotypic cultures. J Neurochem. 2013. Jan;124(1):36–44. doi: 10.1111/jnc.12062. PubMed PMID: 23106494. PubMed DOI

Follo C, Cheng Y, Richards WG, et al. Autophagy facilitates the release of immunogenic signals following chemotherapy in 3D models of mesothelioma. Mol Carcinog. 2019. Oct;58(10):1754–1769. doi:10.1002/mc.23050. PubMed PMID: 31215708. PubMed DOI

Gomes LC, Di Benedetto G, Scorrano L.. During autophagy mitochondria elongate, are spared from degradation and sustain cell viability. Nat Cell Biol. 2011. May;13(5):589–98. doi:10.1038/ncb2220. PubMed PMID: 21478857; PubMed Central PMCID: PMC3088644. eng. PubMed DOI PMC

Grumati P, Coletto L, Sabatelli P, et al. Autophagy is defective in collagen VI muscular dystrophies, and its reactivation rescues myofiber degeneration.Nat Med. 2010. Nov;16(11):1313–20. doi:10.1038/nm.2247. PubMed PMID: 21037586; eng. PubMed DOI

Zecchini S, Giovarelli M, Perrotta C, et al. Autophagy controls neonatal myogenesis by regulating the GH-IGF1 system through a NFE2L2- and DDIT3-mediated mechanism. Autophagy. 2019. Jan;15(1):58–77. doi:10.1080/15548627.2018.1507439. PubMed PMID: 30081710; PubMed Central PMCID: PMCPMC6287695. PubMed DOI PMC

Bloemberg D, McDonald E, Dulay D, et al. Autophagy is altered in skeletal and cardiac muscle of spontaneously hypertensive rats. Acta Physiol (Oxf). 2014. Feb;210(2):381–91. doi:10.1111/apha.12178. PubMed PMID: 24119246. PubMed DOI

Ogata T, Oishi Y, Higuchi M, et al. Fasting-related autophagic response in slow- and fast-twitch skeletal muscle. Biochem Biophys Res Commun. 2010. Mar 26;394(1):136–40. doi:10.1016/j.bbrc.2010.02.130. PubMed PMID: 20184860. PubMed DOI

Yamada E, Bastie CC, Koga H, et al. Mouse skeletal muscle fiber-type-specific macroautophagy and muscle wasting are regulated by a Fyn/STAT3/Vps34 signaling pathway. Cell Rep. 2012. May 31;1(5):557–69. doi:10.1016/j.celrep.2012.03.014. PubMed PMID: 22745922; PubMed Central PMCID: PMC3383827. PubMed DOI PMC

Pare MF, Baechler BL, Fajardo VA, et al. Effect of acute and chronic autophagy deficiency on skeletal muscle apoptotic signaling, morphology, and function. Biochim Biophys Acta Mol Cell Res. 2017. Apr;1864(4):708–718. doi:10.1016/j.bbamcr.2016.12.015. PubMed PMID: 27993671. PubMed DOI

He C, Bassik MC, Moresi V, et al. Exercise-induced BCL2-regulated autophagy is required for muscle glucose homeostasis. Nature. 2012. Jan 26;481(7382):511–5. doi:10.1038/nature10758. PubMed PMID: 22258505; PubMed Central PMCID: PMC3518436. PubMed DOI PMC

Haspel J, Shaik RS, Ifedigbo E, et al. Characterization of macroautophagic flux in vivo using a leupeptin-based assay [Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Autophagy. 2011. Jun;7(6):629–42. PubMed PMID: 21460622; PubMed Central PMCID: PMC3127049. eng. PubMed PMC

Kominami E, Hashida S, Khairallah EA, et al. Sequestration of cytoplasmic enzymes in an autophagic vacuole-lysosomal system induced by injection of leupeptin. J Biol Chem. 1983. May 25;258(10):6093–100. PubMed PMID: 6133857; eng. PubMed

Bell RM, Mocanu MM, Yellon DM.. Retrograde heart perfusion: the Langendorff technique of isolated heart perfusion. J Mol Cell Cardiol. 2011. Jun50(6):940–50. doi:10.1016/j.yjmcc.2011.02.018. PubMed PMID: 21385587. PubMed DOI

Huang C, Andres AM, Ratliff EP, et al. Preconditioning involves selective mitophagy mediated by Parkin and p62/SQSTM1. PLoS One. 2011;6(6):e20975. doi:10.1371/journal.pone.0020975. PubMed PMID: 21687634; PubMed Central PMCID: PMC3110820. PubMed DOI PMC

Gottlieb RA, Finley KD, Mentzer RM, Jr.. Cardioprotection requires taking out the trash. Basic Res Cardiol. 2009. Mar;104(2):169–80. doi:10.1007/s00395-009-0011-9. PubMed PMID: 19242643; PubMed Central PMCID: PMC3661679. PubMed DOI PMC

Kaludercic N, Maiuri MC, Kaushik S, et al. Comprehensive autophagy evaluation in cardiac diseases models. Cardiovasc Res. 2019. Aug 27. doi:10.1093/cvr/cvz233. PubMed PMID: 31504266. PubMed DOI PMC

Nakashima A, Tsuda S, Kusabiraki T, et al. Current understanding of autophagy in pregnancy. Int J Mol Sci. 2019. May 11;20(9). doi:10.3390/ijms20092342. PubMed PMID: 31083536; PubMed Central PMCID: PMCPMC6539256. PubMed DOI PMC

Oh SY, Roh CR.. Autophagy in the placenta. Obstet Gynecol Sci. 2017. May; 60(3):241–259. doi:10.5468/ogs.2017.60.3.241. PubMed PMID: 28534010; PubMed Central PMCID: PMCPMC5439273. PubMed DOI PMC

Avagliano L, Virgili E, Garo C, et al. Autophagy and human parturition: evaluation of LC3 expression in placenta from spontaneous or medically induced onset of labor. Biomed Res Int. 2013;2013:689768. doi:10.1155/2013/689768. PubMed PMID: 23956998; PubMed Central PMCID: PMC3730383. PubMed DOI PMC

Hung TH, Hsieh TT, Chen SF, et al. Autophagy in the human placenta throughout gestation. PLoS One. 2013;8(12):e83475. doi:10.1371/journal.pone.0083475. PubMed PMID: 24349516; PubMed Central PMCID: PMC3862763. PubMed DOI PMC

Signorelli P, Avagliano L, Virgili E, et al. Autophagy in term normal human placentas. Placenta. 2011. Jun;32(6):482–5. doi:10.1016/j.placenta.2011.03.005. PubMed PMID: 21459442. PubMed DOI

Hung TH, Chen SF, Lo LM, et al. Increased autophagy in placentas of intrauterine growth-restricted pregnancies. PLoS One. 2012;7(7):e40957. doi:10.1371/journal.pone.0040957. PubMed PMID: 22815878; PubMed Central PMCID: PMC3397998. PubMed DOI PMC

Chang YL, Wang TH, Chang SD, et al. Increased autophagy in the placental territory of selective intrauterine growth-restricted monochorionic twins. Prenat Diagn. 2013. Feb;33(2):187–90. doi:10.1002/pd.4040. PubMed PMID: 23288835. PubMed DOI

Oh SY, Choi SJ, Kim KH, et al. Autophagy-related proteins, LC3 and Beclin-1, in placentas from pregnancies complicated by preeclampsia. Reprod Sci. 2008. Nov;15(9):912–20. doi:10.1177/1933719108319159. PubMed PMID: 19050324. PubMed DOI

Avagliano L, Danti L, Doi P, et al. Autophagy in placentas from acidotic newborns: an immunohistochemical study of LC3 expression. Placenta. 2013. Nov;34(11):1091–4. doi:10.1016/j.placenta.2013.09.004. PubMed PMID: 24070620. PubMed DOI

Mellen MA, de la Rosa EJ, Boya P.. Autophagy is not universally required for phosphatidyl-serine exposure and apoptotic cell engulfment during neural development. Autophagy. 2009. Oct;5(7):964–72. PubMed PMID: 19587526; eng. PubMed

Amato R, Catalani E, Dal Monte M, et al. Autophagy-mediated neuroprotection induced by octreotide in an ex vivo model of early diabetic retinopathy. Pharmacol Res. 2018. Feb;128:167–178. doi:10.1016/j.phrs.2017.09.022. PubMed PMID: 28970178. PubMed DOI

Cammalleri M, Locri F, Catalani E, et al. The beta adrenergic receptor blocker propranolol counteracts retinal dysfunction in a mouse model of oxygen induced retinopathy: restoring the balance between apoptosis and autophagy. Front Cell Neurosci. 2017;11:395. doi:10.3389/fncel.2017.00395. PubMed PMID: 29375312; PubMed Central PMCID: PMCPMC5770647. PubMed DOI PMC

Perry CN, Kyoi S, Hariharan N, et al. Novel methods for measuring cardiac autophagy in vivo. Methods Enzymol. 2009;453:325–42. doi:10.1016/S0076-6879(08)04016-0. PubMed PMID: 19216914; PubMed Central PMCID: PMC3658837. PubMed DOI PMC

Munafo DB, Colombo MI.. A novel assay to study autophagy: regulation of autophagosome vacuole size by amino acid deprivation. J Cell Sci. 2001. Oct;114(Pt 20):3619–29. PubMed PMID: 11707514; eng. PubMed

Carloni S, Buonocore G, Balduini W.. Protective role of autophagy in neonatal hypoxia-ischemia induced brain injury. Neurobiol Dis. 2008. Dec;32(3):329–39. doi:10.1016/j.nbd.2008.07.022. PubMed PMID: 18760364. PubMed DOI

Carloni S, Girelli S, Scopa C, et al. Activation of autophagy and Akt/CREB signaling play an equivalent role in the neuroprotective effect of rapamycin in neonatal hypoxia-ischemia. Autophagy. 2010. Apr;6(3):366–77. PubMed PMID: 20168088. PubMed

Niemann A, Baltes J, Elsasser HP.. Fluorescence properties and staining behavior of monodansylpentane, a structural homologue of the lysosomotropic agent monodansylcadaverine. J Histochem Cytochem. 2001. Feb;49(2):177–85. PubMed PMID: 11156686; eng. PubMed

Jung H, Leal-Ekman JS, Lu Q, et al. Atg14 protects the intestinal epithelium from TNF-triggered villus atrophy. Autophagy. 2019. Nov;15(11):1990–2001. doi:10.1080/15548627.2019.1596495. PubMed PMID: 30894050; PubMed Central PMCID: PMCPMC6844524. PubMed DOI PMC

Subirada PV, Paz MC, Ridano ME, et al. Effect of Autophagy Modulators on Vascular, Glial, and Neuronal Alterations in the Oxygen-Induced Retinopathy Mouse Model. Front Cell Neurosci. 2019;13:279. doi:10.3389/fncel.2019.00279. PubMed PMID: 31297049; PubMed Central PMCID: PMCPMC6608561. PubMed DOI PMC

Sarkar C, Jones JW, Hegdekar N, et al. PLA2G4A/cPLA2-mediated lysosomal membrane damage leads to inhibition of autophagy and neurodegeneration after brain trauma. Autophagy. 2020. Mar;16(3):466–485. doi:10.1080/15548627.2019.1628538. PubMed PMID: 31238788. PubMed DOI PMC

Li Y, Jones JW, MCC H, et al. cPLA2 activation contributes to lysosomal defects leading to impairment of autophagy after spinal cord injury. Cell Death Dis. 2019. Jul 11;10(7):531. doi:10.1038/s41419-019-1764-1. PubMed PMID: 31296844; PubMed Central PMCID: PMCPMC6624263. PubMed DOI PMC

Ginet V, Puyal J, Clarke PG, et al. Enhancement of autophagic flux after neonatal cerebral hypoxia-ischemia and its region-specific relationship to apoptotic mechanisms. Am J Pathol. 2009. Nov;175(5):1962–74. doi:10.2353/ajpath.2009.090463. PubMed PMID: 19815706; PubMed Central PMCID: PMC2774060. PubMed DOI PMC

Penas C, Font-Nieves M, Fores J, et al. Autophagy, and BiP level decrease are early key events in retrograde degeneration of motoneurons. Cell Death Differ. 2011. Oct;18(10):1617–27. doi:10.1038/cdd.2011.24. PubMed PMID: 21436843; PubMed Central PMCID: PMC3172115. PubMed DOI PMC

Colacurcio DJ, Nixon RA.. Disorders of lysosomal acidification-The emerging role of v-ATPase in aging and neurodegenerative disease. Ageing Res Rev. 2016. Dec;32:75–88. doi:10.1016/j.arr.2016.05.004. PubMed PMID: 27197071; PubMed Central PMCID: PMCPMC5112157. PubMed DOI PMC

Rodriguez-Muela N, Hernandez-Pinto AM, Serrano-Puebla A, et al. Lysosomal membrane permeabilization and autophagy blockade contribute to photoreceptor cell death in a mouse model of retinitis pigmentosa. Cell Death Differ. 2014. Dec 12. doi:10.1038/cdd.2014.203. PubMed PMID: 25501597. PubMed DOI PMC

Uchiyama Y. Autophagic cell death and its execution by lysosomal cathepsins. Arch Histol Cytol. 2001. Aug;64(3):233–46. PubMed PMID: 11575420; eng. PubMed

Marino ML, Fais S, Djavaheri-Mergny M, et al. Proton pump inhibition induces autophagy as a survival mechanism following oxidative stress in human melanoma cells. Cell Death Dis. 2010. Oct 21;1:e87. doi:10.1038/cddis.2010.67. PubMed PMID: 21368860; PubMed Central PMCID: PMCPMC3035900. PubMed DOI PMC

Udelnow A, Kreyes A, Ellinger S, et al. Omeprazole inhibits proliferation and modulates autophagy in pancreatic cancer cells. PLoS One. 2011;6(5):e20143. doi:10.1371/journal.pone.0020143. PubMed PMID: 21629657; PubMed Central PMCID: PMC3101238. PubMed DOI PMC

McWilliams TG, Barini E, Pohjolan-Pirhonen R, et al. Phosphorylation of Parkin at serine 65 is essential for its activation in vivo. Open Biol. 2018. Nov 7;8(11). doi:10.1098/rsob.180108. PubMed PMID: 30404819; PubMed Central PMCID: PMCPMC6282074. PubMed DOI PMC

Shang D, Wang L, Klionsky DJ, et al. Sex differences in autophagy-mediated diseases: toward precision medicine. Autophagy. 2020. Apr 17:in press. doi:10.1080/15548627.2020.1752511. PubMed PMID: 32264724. PubMed DOI PMC

Weber SM, Levitz SM.. Chloroquine interferes with lipopolysaccharide-induced TNF-alpha gene expression by a nonlysosomotropic mechanism [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S.]. J Iimmunol. 2000. Aug 1;165(3):1534–40. PubMed PMID: 10903761; eng. PubMed

Ryzhikov M, Ehlers A, Steinberg D, et al. Diurnal Rhythms Spatially and Temporally Organize Autophagy. Cell Rep. 2019. Feb 12;26(7):1880–1892 e6. doi:10.1016/j.celrep.2019.01.072. PubMed PMID: 30759397; PubMed Central PMCID: PMCPMC6442472. PubMed DOI PMC

Akagi Y, Isaka Y, Akagi A, et al. Transcriptional activation of a hybrid promoter composed of cytomegalovirus enhancer and beta-actin/beta-globin gene in glomerular epithelial cells in vivo. Kidney Int. 1997. Apr;51(4):1265–9. PubMed PMID: 9083295; eng. PubMed

Kimura T, Takabatake Y, Takahashi A, et al. Autophagy protects the proximal tubule from degeneration and acute ischemic injury. J Am Soc Nephrol. 2011. May;22(5):902–13. doi:10.1681/ASN.2010070705. PubMed PMID: 21493778; PubMed Central PMCID: PMC3083312. eng. PubMed DOI PMC

Hartleben B, Godel M, Meyer-Schwesinger C, et al. Autophagy influences glomerular disease susceptibility and maintains podocyte homeostasis in aging mice. J Clin Invest. 2010. Apr 1;120(4):1084–96. doi:10.1172/JCI39492. PubMed PMID: 20200449; PubMed Central PMCID: PMC2846040. eng. PubMed DOI PMC

Cudjoe EK, Jr., Saleh T, Hawkridge AM, et al. Proteomics insights into autophagy. Proteomics. 2017. Oct;17(20). doi:10.1002/pmic.201700022. PubMed PMID: 28902446. PubMed DOI

Wong YK, Zhang J, Hua ZC, et al. Recent advances in quantitative and chemical proteomics for autophagy studies. Autophagy. 2017. Sep 2;13(9):1472–1486. doi:10.1080/15548627.2017.1313944. PubMed PMID: 28820289; PubMed Central PMCID: PMC5612287. PubMed DOI PMC

McLoughlin F, Augustine RC, Marshall RS, et al. Maize multi-omics reveal roles for autophagic recycling in proteome remodelling and lipid turnover. Nat Plants. 2018. Dec;4(12):1056–1070. doi:10.1038/s41477-018-0299-2. PubMed PMID: 30478358. PubMed DOI

Schneider JL, Suh Y, Cuervo AM.. Deficient chaperone-mediated autophagy in liver leads to metabolic dysregulation. Cell Metab. 2014. Sep 2;20(3):417–32. doi:10.1016/j.cmet.2014.06.009. PubMed PMID: 25043815; PubMed Central PMCID: PMCPMC4156578. PubMed DOI PMC

Le Guerroue F, Eck F, Jung J, et al. Autophagosomal content profiling reveals an LC3C-dependent piecemeal mitophagy pathway. Mol Cell. 2017. Nov 16;68(4):786–796 e6. doi:10.1016/j.molcel.2017.10.029. PubMed PMID: 29149599. PubMed DOI

Zhang T, Shen S, Qu J, et al. Global analysis of cellular protein flux quantifies the selectivity of basal autophagy. Cell Rep. 2016. Mar 15;14(10):2426–39. doi:10.1016/j.celrep.2016.02.040. PubMed PMID: 26947064; PubMed Central PMCID: PMCPMC5470642. PubMed DOI PMC

Mellacheruvu D, Wright Z, Couzens AL, et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods. 2013. Aug;10(8):730–6. doi:10.1038/nmeth.2557. PubMed PMID: 23921808; PubMed Central PMCID: PMCPMC3773500. PubMed DOI PMC

Stryeck S, Birner-Gruenberger R, Madl T.. Integrative metabolomics as emerging tool to study autophagy regulation. Microb Cell. 2017. Jul 13;4(8):240–258. doi:10.15698/mic2017.08.584. PubMed PMID: 28845422; PubMed Central PMCID: PMCPMC5568430. PubMed DOI PMC

Galdieri L, Zhang T, Rogerson D, et al. Protein acetylation and acetyl coenzyme a metabolism in budding yeast. Eukaryot Cell. 2014. Dec;13(12):1472–83. doi:10.1128/EC.00189-14. PubMed PMID: 25326522; PubMed Central PMCID: PMCPMC4248685. PubMed DOI PMC

Hartl FU, Bracher A, Hayer-Hartl M.. Molecular chaperones in protein folding and proteostasis. Nature. 2011. Jul 20;475(7356):324–32. doi:10.1038/nature10317. PubMed PMID: 21776078. PubMed DOI

Bartlett AI, Radford SE.. An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms. Nat Struct Mol Biol. 2009. Jun;16(6):582–8. doi:10.1038/nsmb.1592. PubMed PMID: 19491935. PubMed DOI

Madeo F, Eisenberg T, Buttner S, et al. Spermidine: a novel autophagy inducer and longevity elixir. Autophagy. 2010. Jan;6(1):160–2. doi:10.4161/auto.6.1.10600. PubMed PMID: 20110777. PubMed DOI

Morselli E, Marino G, Bennetzen MV, et al. Spermidine and resveratrol induce autophagy by distinct pathways converging on the acetylproteome. J Cell Biol. 2011. Feb 21;192(4):615–29. doi:10.1083/jcb.201008167. PubMed PMID: 21339330; PubMed Central PMCID: PMCPMC3044119. PubMed DOI PMC

Pietrocola F, Lachkar S, Enot DP, et al. Spermidine induces autophagy by inhibiting the acetyltransferase EP300. Cell Death Differ. 2015. Dec 19;22:509–16. doi:10.1038/cdd.2014.215. PubMed PMID: 25526088. PubMed DOI PMC

Saiki S, Sasazawa Y, Fujimaki M, et al. A metabolic profile of polyamines in parkinson disease: A promising biomarker. Ann Neurol. 2019. Aug;86(2):251–263. doi:10.1002/ana.25516. PubMed PMID: 31155745; PubMed Central PMCID: PMCPMC6772170. PubMed DOI PMC

Gu H, Du J, Carnevale Neto F, et al. Metabolomics method to comprehensively analyze amino acids in different domains. Analyst. 2015. Apr 21;140(8):2726–34. doi10.1039/c4an02386b. PubMed PMID: 25699545; PubMed Central PMCID: PMCPMC4380628. PubMed DOI PMC

Meijer AJ, Lorin S, Blommaart EF, et al. Regulation of autophagy by amino acids and MTOR-dependent signal transduction. Amino Acids. 2015. Oct;47(10):2037–63. doi:10.1007/s00726-014-1765-4. PubMed PMID: 24880909; PubMed Central PMCID: PMCPMC4580722. PubMed DOI PMC

Kofeler HC, Fauland A, Rechberger GN, et al. Mass spectrometry based lipidomics: an overview of technological platforms. Metabolites. 2012. Jan 5;2(1):19–38. doi:10.3390/metabo2010019. PubMed PMID: 24957366; PubMed Central PMCID: PMCPMC3901195. PubMed DOI PMC

Cao Y, Wen J, Li Y, et al. Uric acid and sphingomyelin enhance autophagy in iPS cell-originated cardiomyocytes through lncRNA MEG3/miR-7-5p/EGFR axis. Artif Cells Nanomed Biotechnol. 2019. Dec;47(1):3774–3785. doi:10.1080/21691401.2019.1667817. PubMed PMID: 31559872. PubMed DOI

Li X, Qi J, Zhu Q, et al. The role of androgen in autophagy of granulosa cells from PCOS. Gynecol Endocrinol. 2019. Aug;35(8):669–672. doi:10.1080/09513590.2018.1540567. PubMed PMID: 31056990. PubMed DOI

Qian X, Li X, Cai Q, et al. Phosphoglycerate Kinase 1 Phosphorylates Beclin1 to Induce Autophagy. Mol Cell. 2017. Mar 2;65(5):917–931 e6. doi:10.1016/j.molcel.2017.01.027. PubMed PMID: 28238651; PubMed Central PMCID: PMCPMC5389741. PubMed DOI PMC

Vandrovcova J, Anaya F, Kay V, et al. Disentangling the role of the tau gene locus in sporadic tauopathies. Curr Alzheimer Res. 2010. Dec;7(8):726–34. PubMed PMID: 20704554. PubMed

Chen YS, Chen SD, Wu CL, et al. Induction of sestrin2 as an endogenous protective mechanism against amyloid beta-peptide neurotoxicity in primary cortical culture. Exp Neurol. 2014. Mar;253:63–71. doi:10.1016/j.expneurol.2013.12.009. PubMed PMID: 24368194. PubMed DOI

Ulamek-Koziol M, Kocki J, Bogucka-Kocka A, et al. Autophagy, mitophagy and apoptotic gene changes in the hippocampal CA1 area in a rat ischemic model of Alzheimer’s disease. Pharmacol Rep. 2017. Dec;69(6):1289–1294. doi:10.1016/j.pharep.2017.07.015. PubMed PMID: 29128811. PubMed DOI

Ulamek-Koziol M, Kocki J, Bogucka-Kocka A, et al. Dysregulation of autophagy, mitophagy, and apoptotic genes in the medial temporal lobe cortex in an ischemic model of Alzheimer’s disease. J Alzheimers Dis. 2016. Jul 27;54(1):113–21. doi:10.3233/JAD-160387. PubMed PMID: 27472881; PubMed Central PMCID: PMCPMC5008226. PubMed DOI PMC

Tofaris GK, Spillantini MG.. Physiological and pathological properties of alpha-synuclein. Cell Mol Life Sci. 2007. Sep;64(17):2194–201. doi:10.1007/s00018-007-7217-5. PubMed PMID: 17605001. PubMed DOI PMC

Wanker EE. Protein aggregation and pathogenesis of Huntington’s disease: mechanisms and correlations. Biol Chem. 2000. Sep-Oct;381(9–10):937–42. doi:10.1515/BC.2000.114. PubMed PMID: 11076024. PubMed DOI

Croce KR, Yamamoto A.. A role for autophagy in Huntington’s disease. Neurobiol Dis. 2019. Feb;122:16–22. doi:10.1016/j.nbd.2018.08.010. PubMed PMID: 30149183; PubMed Central PMCID: PMCPMC6364695. PubMed DOI PMC

Sandri M, Coletto L, Grumati P, et al. Misregulation of autophagy and protein degradation systems in myopathies and muscular dystrophies. J Cell Sci. 2013. Dec1;126\(Pt 23):5325–33. doi:10.1242/jcs.114041. PubMed PMID: 24293330. PubMed DOI

Margeta M. Autophagy Defects in Skeletal Myopathies. Annu Rev Pathol. 2020. Jan 24;15:261–285. doi:10.1146/annurev-pathmechdis-012419-032618. PubMed PMID: 31594457. PubMed DOI

Bentmann E, Haass C, Dormann D.. Stress granules in neurodegeneration–lessons learnt from TAR DNA binding protein of 43 kDa and fused in sarcoma. FEBS J. 2013. Sep;280(18):4348–70. doi:10.1111/febs.12287. PubMed PMID: 23587065. PubMed DOI

Simonovitch S, Schmukler E, Masliah E, et al. The effects of APOE4 on mitochondrial dynamics and proteins in vivo. J Alzheimers Dis. 2019;70(3):861–875. doi:10.3233/JAD-190074. PubMed PMID: 31306119. PubMed DOI PMC

Puyal J, Ginet V, Clarke PG.. Multiple interacting cell death mechanisms in the mediation of excitotoxicity and ischemic brain damage: a challenge for neuroprotection. Prog Neurobiol. 2013. Jun;105:24–48. doi:10.1016/j.pneurobio.2013.03.002. PubMed PMID: 23567504. PubMed DOI

Grishchuk Y, Ginet V, Truttmann AC, et al. Beclin 1-independent autophagy contributes to apoptosis in cortical neurons. Autophagy. 2011. Oct;7(10):1115–31. doi:10.4161/auto.7.10.16608. PubMed PMID: 21646862. PubMed DOI

Menzies FM, Fleming A, Caricasole A, et al. Autophagy and neurodegeneration: pathogenic mechanisms and therapeutic opportunities. Neuron. 2017. Mar 8;93(5):1015–1034. doi:10.1016/j.neuron.2017.01.022. PubMed PMID: 28279350. PubMed DOI

Comerota MM, Tumurbaatar B, Krishnan B, et al. Near infrared light treatment reduces synaptic levels of toxic tau oligomers in two transgenic mouse models of human tauopathies. Mol Neurobiol. 2019. May;56(5):3341–3355. doi:10.1007/s12035-018-1248-9. PubMed PMID: 30120733; PubMed Central PMCID: PMCPMC6476871. PubMed DOI PMC

Scarffe LA, Stevens DA, Dawson VL, et al. Parkin and PINK1: much more than mitophagy. Trends in neurosciences. 2014. Jun;37(6):315–324. doi:10.1016/j.tins.2014.03.004. PubMed PMID: 24735649. PubMed DOI PMC

Salminen A, Kaarniranta K, Haapasalo A, et al. Emerging role of p62/sequestosome-1 in the pathogenesis of Alzheimer’s disease. Prog Neurobiol. 2012. Jan;96(1):87–95. doi:10.1016/j.pneurobio.2011.11.005. PubMed PMID: 22138392. PubMed DOI

Seidel K, Brunt ER, de Vos RA, et al. The p62 antibody reveals various cytoplasmic protein aggregates in spinocerebellar ataxia type 6. Clin Neuropathol. 2009. Sep-Oct;28(5):344–9. PubMed PMID: 19788049. PubMed

Harada H, Warabi E, Matsuki T, et al. Deficiency of p62/Sequestosome 1 causes hyperphagia due to leptin resistance in the brain. J Neurosci. 2013. Sep 11;33(37):14767–77. doi:10.1523/JNEUROSCI.2954-12.2013. PubMed PMID: 24027277. PubMed DOI PMC

Merenlender-Wagner A, Malishkevich A, Shemer Z, et al. Autophagy has a key role in the pathophysiology of schizophrenia. Mol Psychiatry. 2015. Dec 24;20:126–32. doi:10.1038/mp.2013.174. PubMed PMID: 24365867. PubMed DOI PMC

Dresner E, Agam G, Gozes I.. Activity-dependent neuroprotective protein (ADNP) expression level is correlated with the expression of the sister protein ADNP2: deregulation in schizophrenia. Eur Neuropsychopharmacol. 2011. May;21(5):355–61. doi:10.1016/j.euroneuro.2010.06.004. PubMed PMID: 20598862. PubMed DOI

Lotze MT, Maranchie J, Appleman L.. Inhibiting autophagy: a novel approach for the treatment of renal cell carcinoma. Cancer J. 2013. Jul-Aug;19(4):341–7. doi:10.1097/PPO.0b013e31829da0d6. PubMed PMID: 23867516. PubMed DOI

Chude CI, Amaravadi RK.. Targeting autophagy in cancer: update on clinical trials and novel inhibitors. Int J Mol Sci. 2017. Jun 16;18(6). doi:10.3390/ijms18061279. PubMed PMID: 28621712; PubMed Central PMCID: PMCPMC5486101. PubMed DOI PMC

Maes H, Kuchnio A, Peric A, et al. Tumor vessel normalization by chloroquine independent of autophagy. Cancer cell. 2014. Aug 11;26(2):190–206. doi:10.1016/j.ccr.2014.06.025. PubMed PMID: 25117709. PubMed DOI

Maycotte P, Aryal S, Cummings CT, et al. Chloroquine sensitizes breast cancer cells to chemotherapy independent of autophagy. Autophagy. 2012. Feb 1;8(2):200–12. doi:10.4161/auto.8.2.18554. PubMed PMID: 22252008; PubMed Central PMCID: PMCPMC3336076. PubMed DOI PMC

Ebrahimi-Fakhari D, Wahlster L, Hoffmann GF, et al. Emerging role of autophagy in pediatric neurodegenerative and neurometabolic diseases. Pediatr Res. 2014. Jan;75(1–2):217–26. doi:10.1038/pr.2013.185. PubMed PMID: 24165736. PubMed DOI

Lee KM, Hwang SK, Lee JA.. Neuronal autophagy and neurodevelopmental disorders. Exp Neurobiol. 2013. Sep;22(3):133–42. doi:10.5607/en.2013.22.3.133. PubMed PMID: 24167408; PubMed Central PMCID: PMC3807000. PubMed DOI PMC

Yasin SA, Ali AM, Tata M, et al. mTOR-dependent abnormalities in autophagy characterize human malformations of cortical development: evidence from focal cortical dysplasia and tuberous sclerosis. Acta Neuropathol. 2013. Aug;126(2):207–18. doi:10.1007/s00401-013-1135-4. PubMed PMID: 23728790. PubMed DOI

Nishino I. Autophagic vacuolar myopathy. Semin Pediatr Neurol. 2006. Jun;13(2):90–5. doi:10.1016/j.spen.2006.06.004. PubMed PMID: 17027858. PubMed DOI

Girolamo F, Lia A, Amati A, et al. Overexpression of autophagic proteins in the skeletal muscle of sporadic inclusion body myositis. Neuropathol Appl Neurobiol. 2013. Dec;39(7):736–49. doi:10.1111/nan.12040. PubMed PMID: 23452291. PubMed DOI

Temiz P, Weihl CC, Pestronk A.. Inflammatory myopathies with mitochondrial pathology and protein aggregates. J Neurol Sci. 2009. Mar 15;278(1–2):25–9. doi:10.1016/j.jns.2008.11.010. PubMed PMID: 19101700. PubMed DOI

Maugeri N, Campana L, Gavina M, et al. Activated platelets present high mobility group box 1 to neutrophils, inducing autophagy and promoting the extrusion of neutrophil extracellular traps. J Thromb Haemost. 2014. Dec;12(12):2074–88. doi:10.1111/jth.12710. PubMed PMID: 25163512. PubMed DOI

Lunemann JD, Schmidt J, Schmid D, et al. Beta-amyloid is a substrate of autophagy in sporadic inclusion body myositis. Ann Neurol. 2007. May;61(5):476–83. doi:10.1002/ana.21115. PubMed PMID: 17469125. PubMed DOI

Screen M, Raheem O, Holmlund-Hampf J, et al. Gene expression profiling in tibial muscular dystrophy reveals unfolded protein response and altered autophagy. PLoS One. 2014;9(3):e90819. doi:10.1371/journal.pone.0090819. PubMed PMID: 24618559; PubMed Central PMCID: PMC3949689. PubMed DOI PMC

Brady S, Squier W, Sewry C, et al. A retrospective cohort study identifying the principal pathological features useful in the diagnosis of inclusion body myositis. BMJ open. 2014;4(4):e004552. doi:10.1136/bmjopen-2013-004552. PubMed PMID: 24776709; PubMed Central PMCID: PMC4010816. PubMed DOI PMC

Yu Z, Ma J, Li X, et al. Autophagy defects and related genetic variations in renal cell carcinoma with eosinophilic cytoplasmic inclusions. Sci Rep. 2018. Jul 2;8(1):9972. doi:10.1038/s41598-018-28369-y. PubMed PMID: 29967346; PubMed Central PMCID: PMCPMC6028630. PubMed DOI PMC

Pan Q, Gao C, Chen Y, et al. Update on the role of autophagy in systemic lupus erythematosus: A novel therapeutic target. Biomed Pharmacother. 2015. Apr;71:190–3. doi:10.1016/j.biopha.2015.02.017. PubMed PMID: 25960235. PubMed DOI

An N, Chen Y, Wang C, et al. Chloroquine autophagic inhibition rebalances Th17/Treg-mediated immunity and ameliorates systemic lupus erythematosus. Cell Physiol Biochem. 2017;44(1):412–422. doi:10.1159/000484955. PubMed PMID: 29141242. PubMed DOI

Alessandri C, Barbati C, Vacirca D, et al. T lymphocytes from patients with systemic lupus erythematosus are resistant to induction of autophagy. FASEB J. 2012. Nov;26(11):4722–32. doi:10.1096/fj.12-206060. PubMed PMID: 22835828; PubMed Central PMCID: PMCPMC3475261. PubMed DOI PMC

Tchetina EV, Poole AR, Zaitseva EM, et al. Differences in Mammalian target of rapamycin gene expression in the peripheral blood and articular cartilages of osteoarthritic patients and disease activity. Arthritis. 2013;2013:461486. doi:10.1155/2013/461486. PubMed PMID: 23864948; PubMed Central PMCID: PMC3707211. PubMed DOI PMC

Mitroulis I, Kourtzelis I, Kambas K, et al. Evidence for the involvement of mTOR inhibition and basal autophagy in familial Mediterranean fever phenotype. Hum Immunol. 2011. Feb;72(2):135–8. doi:10.1016/j.humimm.2010.11.006. PubMed PMID: 21081147. PubMed DOI

Bachetti T, Chiesa S, Castagnola P, et al. Autophagy contributes to inflammation in patients with TNFR-associated periodic syndrome (TRAPS). Ann Rheum Dis. 2013. Jun;72(6):1044–52. doi:10.1136/annrheumdis-2012-201952. PubMed PMID: 23117241. PubMed DOI

Mi S, Li Z, Yang HZ, et al. Blocking IL-17A promotes the resolution of pulmonary inflammation and fibrosis via TGF-beta1-dependent and -independent mechanisms. J Iimmunol. 2011. Sep 15;187(6):3003–14. doi:10.4049/jimmunol.1004081. PubMed PMID: 21841134. PubMed DOI

Liu H, Mi S, Li Z, et al. Interleukin 17A inhibits autophagy through activation of PIK3CA to interrupt the GSK3B-mediated degradation of BCL2 in lung epithelial cells. Autophagy. 2013. May;9(5):730–42. doi:10.4161/auto.24039. PubMed PMID: 23514933; PubMed Central PMCID: PMCPMC3669182. PubMed DOI PMC

Wang K, Zhang T, Lei Y, et al. Identification of ANXA2 (annexin A2) as a specific bleomycin target to induce pulmonary fibrosis by impeding TFEB-mediated autophagic flux. Autophagy. 2018;14(2):269–282. doi:10.1080/15548627.2017.1409405. PubMed PMID: 29172997; PubMed Central PMCID: PMCPMC5902212. PubMed DOI PMC

Remijsen Q, Vanden Berghe T, Wirawan E, et al. Neutrophil extracellular trap cell death requires both autophagy and superoxide generation. Cell Res. 2011. Feb;21(2):290–304. doi:10.1038/cr.2010.150. PubMed PMID: 21060338; PubMed Central PMCID: PMC3193439. PubMed DOI PMC

Mitroulis I, Kambas K, Chrysanthopoulou A, et al. Neutrophil extracellular trap formation is associated with IL-1beta and autophagy-related signaling in gout. PLoS One. 2011;6(12):e29318. doi:10.1371/journal.pone.0029318. PubMed PMID: 22195044; PubMed Central PMCID: PMC3241704. PubMed DOI PMC

Apostolidou E, Skendros P, Kambas K, et al. Neutrophil extracellular traps regulate IL-1beta-mediated inflammation in familial Mediterranean fever. Ann Rheum Dis. 2016. Jan;75(1):269–77. doi:10.1136/annrheumdis-2014-205958. PubMed PMID: 25261578. PubMed DOI

Skendros P, Chrysanthopoulou A, Rousset F, et al. Regulated in development and DNA damage responses 1 (REDD1) links stress with IL-1beta-mediated familial Mediterranean fever attack through autophagy-driven neutrophil extracellular traps. J Allergy Clin Immunol. 2017. Nov;140(5):1378–1387 e13. doi:10.1016/j.jaci.2017.02.021. PubMed PMID: 28342915. PubMed DOI

Papagoras C, Chrysanthopoulou A, Mitsios A, et al. Autophagy inhibition in adult-onset Still’s disease: still more space for hydroxychloroquine? Clin Exp Rheumatol. 2017. Nov-Dec;35Suppl 108(6):133–134. PubMed PMID: 29148405. PubMed

Angelidou I, Chrysanthopoulou A, Mitsios A, et al. REDD1/autophagy pathway is associated with neutrophil-driven IL-1beta inflammatory response in active ulcerative colitis. J Iimmunol. 2018. Jun 15;200(12):3950–3961. doi:10.4049/jimmunol.1701643. PubMed PMID: 29712770. PubMed DOI

Kambas K, Mitroulis I, Apostolidou E, et al. Autophagy mediates the delivery of thrombogenic tissue factor to neutrophil extracellular traps in human sepsis. PLoS One. 2012;7(9):e45427. doi:10.1371/journal.pone.0045427. PubMed PMID: 23029002; PubMed Central PMCID: PMC3446899. PubMed DOI PMC

Stakos DA, Kambas K, Konstantinidis T, et al. Expression of functional tissue factor by neutrophil extracellular traps in culprit artery of acute myocardial infarction. Eur Heart J. 2015. Jun 7;36(22):1405–14. doi:10.1093/eurheartj/ehv007. PubMed PMID: 25660055; PubMed Central PMCID: PMCPMC4458286. PubMed DOI PMC

Chrysanthopoulou A, Kambas K, Stakos D, et al. Interferon lambda1/IL-29 and inorganic polyphosphate are novel regulators of neutrophil-driven thromboinflammation. J Pathol. 2017. Sep;243(1):111–122. doi:10.1002/path.4935. PubMed PMID: 28678391. PubMed DOI

Chrysanthopoulou A, Mitroulis I, Apostolidou E, et al. Neutrophil extracellular traps promote differentiation and function of fibroblasts. J Pathol. 2014. Jul;233(3):294–307. doi:10.1002/path.4359. PubMed PMID: 24740698. PubMed DOI

Maugeri N, Capobianco A, Rovere-Querini P, et al. Platelet microparticles sustain autophagy-associated activation of neutrophils in systemic sclerosis. Sci Transl Med. 2018. Jul 25;10(451). doi:10.1126/scitranslmed.aao3089. PubMed PMID: 30045975. PubMed DOI

Manfredi AA, Rovere-Querini P, D’Angelo A, et al. Low molecular weight heparins prevent the induction of autophagy of activated neutrophils and the formation of neutrophil extracellular traps. Pharmacol Res. 2017. Sep;123:146–156. doi:10.1016/j.phrs.2016.08.008. PubMed PMID: 28161237. PubMed DOI

Dupont N, Jiang S, Pilli M, et al. Autophagy-based unconventional secretory pathway for extracellular delivery of IL-1beta. EMBO J. 2011. Nov30;30(23):4701–11. doi:10.1038/emboj.2011.398. PubMed PMID: 22068051; PubMed Central PMCID: PMC3243609. PubMed DOI PMC

Kambas K, Chrysanthopoulou A, Vassilopoulos D, et al. Tissue factor expression in neutrophil extracellular traps and neutrophil derived microparticles in antineutrophil cytoplasmic antibody associated vasculitis may promote thromboinflammation and the thrombophilic state associated with the disease. Ann Rheum Dis. 2014. Jul 19;73:1854–63. doi:10.1136/annrheumdis-2013-203430. PubMed PMID: 23873874. PubMed DOI

Berton G. Editorial: Gigantism: a new way to prolong neutrophil life. J Leukoc Biol. 2014. Oct;96(4):505–6. doi:10.1189/jlb.3CE0214-107R. PubMed PMID: 25271292. PubMed DOI

Dyugovskaya L, Berger S, Polyakov A, et al. The development of giant phagocytes in long-term neutrophil cultures. J Leukoc Biol. 2014. Oct;96(4):511–21. doi10.1189/jlb.0813437. PubMed PMID: 24577569. PubMed DOI

Masini M, Bugliani M, Lupi R, et al. Autophagy in human type 2 diabetes pancreatic beta cells. Diabetologia. 2009. Jun;52(6):1083–6. doi: 10.1007/s00125-009-1347-2. PubMed PMID: 19367387. PubMed DOI

Mizukami H, Takahashi K, Inaba W, et al. Involvement of oxidative stress-induced DNA damage, endoplasmic reticulum stress, and autophagy deficits in the decline of beta-cell mass in Japanese type 2 diabetic patients. Diabetes care. 2014. Jul;37(7):1966–1974. doi:10.2337/dc13-2018. PubMed PMID: 24705612. PubMed DOI

Kosacka J, Kern M, Kloting N, et al. Autophagy in adipose tissue of patients with obesity and type 2 diabetes. Mol Cell Endocrinol. 2015. Jul 5;409:21–32. doi:10.1016/j.mce.2015.03.015. PubMed PMID: 25818883. PubMed DOI

Stienstra R, Haim Y, Riahi Y, et al. Autophagy in adipose tissue and the beta cell:implications for obesity and diabetes. Diabetologia. 2014. Aug;57(8):1505–16. doi:10.1007/s00125-014-3255-3. PubMed PMID: 24795087. PubMed DOI

Tatsuno K, Yamazaki T, Hanlon D, et al. Extracorporeal photochemotherapy induces bona fide immunogenic cell death. Cell Death Dis. 2019. Aug 2;10(8):578. doi:10.1038/s41419-019-1819-3. PubMed PMID: 31371700; PubMed Central PMCID: PMCPMC6675789. PubMed DOI PMC

Garg AD, Krysko DV, Verfaillie T, et al. A novel pathway combining calreticulin exposure and ATP secretion in immunogenic cancer cell death. EMBO J. 2012. Mar 7;31(5):1062–79. doi:10.1038/emboj.2011.497. PubMed PMID: 22252128; PubMed Central PMCID: PMC3298003. PubMed DOI PMC

Bacellar IO, Tsubone TM, Pavani C, et al. Photodynamic Efficiency: From Molecular Photochemistry to Cell Death. Int J Mol Sci. 2015. Aug 31;16(9):20523–59. doi:10.3390/ijms160920523. PubMed PMID: 26334268; PubMed Central PMCID: PMCPMC4613217. PubMed DOI PMC

Dewaele M, Martinet W, Rubio N, et al. Autophagy pathways activated in response to PDT contribute to cell resistance against ROS damage. J Cell Mol Med. 2011. Jun;15(6):1402–14. doi:10.1111/j.1582-4934.2010.01118.x. PubMed PMID: 20626525; PubMed Central PMCID: PMCPMC4373339. PubMed DOI PMC

Du L, Jiang N, Wang G, et al. Autophagy inhibition sensitizes bladder cancer cells to the photodynamic effects of the novel photosensitizer chlorophyllin e4. J Photochem Photobiol B. 2014. Apr 5;133:1–10. doi:10.1016/j.jphotobiol.2014.02.010. PubMed PMID: 24650577. PubMed DOI

Kessel D, Reiners JJ, Jr.. Effects of combined lysosomal and mitochondrial photodamage in a non-small-cell lung cancer cell line: the role of paraptosis. Photochem Photobiol. 2017. Nov;93(6):1502–1508. doi:10.1111/php.12805. PubMed PMID: 28696570; PubMed Central PMCID: PMCPMC5693656. PubMed DOI PMC

Kessel DH, Price M, Reiners JJ, Jr.. ATG7 deficiency suppresses apoptosis and cell death induced by lysosomal photodamage. Autophagy. 2012. Sep;8(9):1333–41. doi:10.4161/auto.20792. PubMed PMID: 22889762; PubMed Central PMCID: PMCPMC3442880. PubMed DOI PMC

Lihuan D, Jingcun Z, Ning J, et al. Photodynamic therapy with the novel photosensitizer chlorophyllin f induces apoptosis and autophagy in human bladder cancer cells. Lasers Surg Med. 2014. Apr;46(4):319–34. doi:10.1002/lsm.22225. PubMed PMID: 24464873. PubMed DOI

Galluzzi L, Kepp O, Kroemer G.. Enlightening the impact of immunogenic cell death in photodynamic cancer therapy. EMBO J. 2012. Mar 7;31(5):1055–7. doi:10.1038/emboj.2012.2. PubMed PMID: 22252132; PubMed Central PMCID: PMC3298006. PubMed DOI PMC

Panzarini E, Inguscio V, Fimia GM, et al. Rose Bengal Acetate PhotoDynamic Therapy (RBAc-PDT) induces exposure and release of damage-associated molecular patterns (DAMPs) in human HeLa cells. PLoS One 2014;9:e105778. PubMed PMC

Santin G, Bottone MG, Malatesta M, et al. Regulated forms of cell death are induced by the photodynamic action of the fluorogenic substrate, Hypocrellin B-acetate. J Photochem Photobiol B. 2013. Aug 5;125:90–7. doi:10.1016/j.jphotobiol.2013.05.006. PubMed PMID: 23770337. PubMed DOI

Maes H, Rubio N, Garg AD, et al. Autophagy: shaping the tumor microenvironment and therapeutic response. Trends Mol Med. 2013. Jul;19(7):428–46. doi:10.1016/j.molmed.2013.04.005. PubMed PMID: 23714574. PubMed DOI

Garg AD, Krysko DV, Vandenabeele P, et al. The emergence of phox-ER stress induced immunogenic apoptosis. Oncoimmunology. 2012. Aug 1;1(5):786–788. doi:10.4161/onci.19750. PubMed PMID: 22934283; PubMed Central PMCID: PMC3429595. PubMed DOI PMC

Garg AD, Martin S, Golab J, et al. Danger signalling during cancer cell death: origins, plasticity and regulation. Cell Death Differ. 2014. Jan;21(1):26–38. doi:10.1038/cdd.2013.48. PubMed PMID: 23686135; PubMed Central PMCID: PMC3858605. PubMed DOI PMC

Kroemer G, Galluzzi L, Kepp O, et al. Immunogenic cell death in cancer therapy. Annu Rev Immunol. 2013;31:51–72. doi:10.1146/annurev-immunol-032712-100008. PubMed PMID: 23157435. PubMed DOI

Dudek AM, Garg AD, Krysko DV, et al. Inducers of immunogenic cancer cell death. Cytokine Growth Factor Rev. 2013. Aug;24(4):319–33. doi:10.1016/j.cytogfr.2013.01.005. PubMed PMID: 23391812. PubMed DOI

Garg AD, Dudek AM, Ferreira GB, et al. ROS-induced autophagy in cancer cells assists in evasion from determinants of immunogenic cell death. Autophagy. 2013. Sep;9(9):1292–307. doi:10.4161/auto.25399. PubMed PMID: 23800749. PubMed DOI

Yamazaki T, Kirchmair A, Sato A, et al. Mitochondrial DNA drives abscopal responses to radiation that are inhibited by autophagy. Nat Immunol. 2020. Oct;21(10):1160–1171. doi:10.1038/s41590-020-0751-0. PubMed PMID: 32747819. PubMed DOI

Michaud M, Martins I, Sukkurwala AQ, et al. Autophagy-dependent anticancer immune responses induced by chemotherapeutic agents in mice. Science. 2011. Dec 16;334(6062):1573–7. doi:10.1126/science.1208347. PubMed PMID: 22174255. PubMed DOI

Bian S, Sun X, Bai A, et al. P2X7 integrates PI3K/AKT and AMPK-PRAS40-mTOR signaling pathways to mediate tumor cell death. PLoS One. 2013;8(4):e60184. doi:10.1371/journal.pone.0060184. PubMed PMID: 23565201; PubMed Central PMCID: PMC3615040. PubMed DOI PMC

Di Virgilio F. Liaisons dangereuses: P2X(7) and the inflammasome. Trends Pharmacol Sci. 2007. Sep;28(9):465–72. doi:10.1016/j.tips.2007.07.002. PubMed PMID: 17692395. PubMed DOI

Garg AD, Dudek AM, Agostinis P.. Calreticulin surface exposure is abrogated in cells lacking, chaperone-mediated autophagy-essential gene, LAMP2A. Cell Death Dis. 2013;4:e826. doi:10.1038/cddis.2013.372. PubMed PMID: 24091669; PubMed Central PMCID: PMC3824681. PubMed DOI PMC

Poon AH, Chouiali F, Tse SM, et al. Genetic and histologic evidence for autophagy in asthma pathogenesis. J Allergy Clin Immunol. 2012. Feb;129(2):569–71. doi:10.1016/j.jaci.2011.09.035. PubMed PMID: 22040902; PubMed Central PMCID: PMCPMC3268897. PubMed DOI PMC

Martin LJ, Gupta J, Jyothula SS, et al. Functional variant in the autophagy-related 5 gene promotor is associated with childhood asthma. PLoS One. 2012;7(4):e33454. doi:10.1371/journal.pone.0033454. PubMed PMID: 22536318; PubMed Central PMCID: PMCPMC3335039. PubMed DOI PMC

McAlinden KD, Deshpande DA, Ghavami S, et al. Autophagy activation in asthma airways remodeling. Am J Respir Cell Mol Biol. 2019. May;60(5):541–553. doi:10.1165/rcmb.2018-0169OC. PubMed PMID: 30383396; PubMed Central PMCID: PMCPMC6503620. PubMed DOI PMC

Orenstein SJ, Kuo SH, Tasset I, et al. Interplay of LRRK2 with chaperone-mediated autophagy. Nat Neurosci. 2013. Apr;16(4):394–406. doi:10.1038/nn.3350. PubMed PMID: 23455607; PubMed Central PMCID: PMC3609872. PubMed DOI PMC

Napolitano G, Johnson JL, He J, et al. Impairment of chaperone-mediated autophagy leads to selective lysosomal degradation defects in the lysosomal storage disease cystinosis. EMBO Mol Med. 2015. Feb;7(2):158–74. doi:10.15252/emmm.201404223. PubMed PMID: 25586965; PubMed Central PMCID: PMC4328646. PubMed DOI PMC

Venugopal B, Mesires NT, Kennedy JC, et al. Chaperone-mediated autophagy is defective in mucolipidosis type IV. J Cell Physiol. 2009. May;219(2):344–53. doi:10.1002/jcp.21676. PubMed PMID: 19117012. PubMed DOI

Franch HA. Pathways of proteolysis affecting renal cell growth. Curr Opin Nephrol Hypertens. 2002. Jul;11(4):445–50. PubMed PMID: 12105396. PubMed

Sooparb S, Price SR, Shaoguang J, et al. Suppression of chaperone-mediated autophagy in the renal cortex during acute diabetes mellitus. Kidney Int. 2004. Jun;65(6):2135–44. doi:10.1111/j.1523-1755.2004.00639.x, PubMed PMID: 15149326. PubMed DOI

Chen ZH, Kim HP, Sciurba FC, et al. Egr-1 regulates autophagy in cigarette smoke-induced chronic obstructive pulmonary disease. PLoS One. 2008;3(10):e3316. doi:10.1371/journal.pone.0003316. PubMed PMID: 18830406; PubMed Central PMCID: PMC2552992. PubMed DOI PMC

Qaisiya M, Mardesic P, Pastore B, et al. The activation of autophagy protects neurons and astrocytes against bilirubin-induced cytotoxicity. Neurosci Lett. 2017. Nov 20;661:96–103. doi:10.1016/j.neulet.2017.09.056. PubMed PMID: 28965934. PubMed DOI

Wasko MC, Hubert HB, Lingala VB, et al. Hydroxychloroquine and risk of diabetes in patients with rheumatoid arthritis. JAMA. 2007. Jul 11;298(2):187–93. doi:10.1001/jama.298.2.187. PubMed PMID: 17622600. PubMed DOI

Merlini L, Nishino I, Consortium for Autophagy in Muscular D. 201st ENMC International Workshop: Autophagy in muscular dystrophies–translational approach, 1–3 November 2013, Bussum, The Netherlands. Neuromuscular disorders: NMD. 2014 Jun;24(6):546–61. doi: 10.1016/j.nmd.2014.03.009. PubMed PMID: 24746377. PubMed

Wang KZQ, Steer E, Otero PA, et al. PINK1 Interacts with VCP/p97 and Activates PKA to Promote NSFL1C/p47 Phosphorylation and Dendritic Arborization in Neurons. eNeuro. 2018. Nov-Dec;5(6). doi:10.1523/ENEURO.0466-18.2018. PubMed PMID: 30783609; PubMed Central PMCID: PMCPMC6377406. PubMed DOI PMC

Denton D, Kumar S.. Autophagy-dependent cell death. Cell Death Differ. 2019. Mar;26(4):605–616. doi:10.1038/s41418-018-0252-y. PubMed PMID: 30568239; PubMed Central PMCID: PMCPMC6460387. PubMed DOI PMC

Doherty J, Baehrecke EH.. Life, death and autophagy. Nat Cell Biol. 2018. Oct;20(10):1110–1117. doi:10.1038/s41556-018-0201-5. PubMed PMID: 30224761. PubMed DOI PMC

Ramos-Torres A, Bort A, Morell C, et al. The pepper’s natural ingredient capsaicin induces autophagy blockage in prostate cancer cells. Oncotarget. 2016. Jan 12;7(2):1569–83. doi:10.18632/oncotarget.6415. PubMed PMID: 26625315; PubMed Central PMCID: PMCPMC4811481. PubMed DOI PMC

Beaulaton J, Lockshin RA.. Ultrastructural study of the normal degeneration of the intersegmental muscles of Anthereae polyphemus and Manduca sexta (Insecta, Lepidoptera) with particular reference of cellular autophagy. J Morphol. 1977. Oct;154(1):39–57. doi:10.1002/jmor.1051540104. PubMed PMID: 915948; eng. PubMed DOI

Clarke PG. Developmental cell death: morphological diversity and multiple mechanisms. Anatomy and embryology. 1990;181(3):195–213. PubMed PMID: 2186664; eng. PubMed

Assuncao Guimaraes C, Linden R.. Programmed cell deaths. Apoptosis and alternative deathstyles. Eur J Biochem/FEBS. 2004. May;271(9):1638–50. doi:10.1111/j.1432-1033.2004.04084.x. PubMed PMID: 15096203. PubMed DOI

Guimaraes CA, Benchimol M, Amarante-Mendes GP, et al. Alternative programs of cell death in developing retinal tissue. J Biol Chem. 2003. Oct 24;278(43):41938–46. doi:10.1074/jbc.M306547200. PubMed PMID: 12917395. PubMed DOI

Napoletano F, Baron O, Vandenabeele P, et al. Intersections between Regulated Cell Death and Autophagy. Trends Cell Biol. 2019. Apr;29(4):323–338. doi:10.1016/j.tcb.2018.12.007. PubMed PMID: 30665736. PubMed DOI

Baron O, Fanto M.. Karyoptosis: A novel type of cell death caused by chronic autophagy inhibition. Autophagy. 2018;14(4):722–723. doi:10.1080/15548627.2018.1434372. PubMed PMID: 29388501; PubMed Central PMCID: PMCPMC5959325. PubMed DOI PMC

Barthet VJA, Ryan KM.. Autophagy in neurodegeneration: can’t digest it, spit it out! Trends Cell Biol. 2018. Mar;28(3):171–173. doi: 10.1016/j.tcb.2018.01.001. PubMed PMID: 29395716. PubMed DOI

Yu H, Yin S, Zhou S, et al. Magnolin promotes autophagy and cell cycle arrest via blocking LIF/Stat3/Mcl-1 axis in human colorectal cancers. Cell Death Dis. 2018. Jun 13;9(6):702. doi:10.1038/s41419-018-0660-4. PubMed PMID: 29899555; PubMed Central PMCID: PMCPMC5999973. PubMed DOI PMC

Yu H, Qiu Y, Pang X, et al. Lycorine promotes autophagy and apoptosis via TCRP1/Akt/mTOR axis inactivation in human hepatocellular carcinoma. Mol Cancer Ther. 2017. Dec;16(12):2711–2723. doi:10.1158/1535-7163.MCT-17-0498. PubMed PMID: 28974556. PubMed DOI

Richard VR, Beach A, Piano A, et al. Mechanism of liponecrosis, a distinct mode of programmed cell death. Cell cycle. 2014;13(23):3707–26. doi:10.4161/15384101.2014.965003. PubMed PMID: 25483081. PubMed DOI PMC

Sheibani S, Richard VR, Beach A, et al. Macromitophagy, neutral lipids synthesis, and peroxisomal fatty acid oxidation protect yeast from “liponecrosis”, a previously unknown form of programmed cell death. Cell cycle. 2014;13(1):138–47. PubMed PMID: 24196447; PubMed Central PMCID: PMC3925724. PubMed PMC

Tang D, Kang R, Berghe TV, et al. The molecular machinery of regulated cell death. Cell Res. 2019. May;29(5):347–364. doi:10.1038/s41422-019-0164-5. PubMed PMID: 30948788; PubMed Central PMCID: PMCPMC6796845. PubMed DOI PMC

Galluzzi L, Aaronson SA, Abrams J, et al. Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes [Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov’t Review]. Cell Death Differ. 2009. Aug;16(8):1093–107. doi:10.1038/cdd.2009.44. PubMed PMID: 19373242; PubMed Central PMCID: PMC2757140. eng. PubMed DOI PMC

Galluzzi L, Bravo-San Pedro JM, Vitale I, et al. Essential versus accessory aspects of cell death: recommendations of the NCCD 2015. Cell Death Differ. 2015. Jan;22(1):58–73. doi:10.1038/cdd.2014.137. PubMed PMID: 25236395; PubMed Central PMCID: PMC4262782. PubMed DOI PMC

Minina EA, Bozhkov PV, Hofius D.. Autophagy as initiator or executioner of cell death. Trends Plant Sci. 2014. Aug 22. doi:10.1016/j.tplants.2014.07.007. PubMed PMID: 25156061. PubMed DOI

van Doorn WG, Beers EP, Dangl JL, et al. Morphological classification of plant cell deaths. Cell Death Differ. 2011. Aug;18(8):1241–6. doi:10.1038/cdd.2011.36. PubMed PMID: 21494263; PubMed Central PMCID: PMC3172093. eng. PubMed DOI PMC

Kwon SI, Cho HJ, Jung JH, et al. The Rab GTPase RabG3b functions in autophagy and contributes to tracheary element differentiation in Arabidopsis. Plant J Cell Mol Biol 2010. Jul 23;64:151–64. . PubMed PMID: 20659276; Eng. PubMed

Minina EA, Filonova LH, Fukada K, et al. Autophagy and metacaspase determine the mode of cell death in plants. J Cell Biol. 2013. Dec 23;203(6):917–27. doi:10.1083/jcb.201307082. PubMed PMID: 24344187; PubMed Central PMCID: PMC3871426. PubMed DOI PMC

Hofius D, Schultz-Larsen T, Joensen J, et al. Autophagic components contribute to hypersensitive cell death in Arabidopsis. Cell. 2009. May 15;137(4):773–83. doi:10.1016/j.cell.2009.02.036. PubMed PMID: 19450522. PubMed DOI

Giusti C, Tresse E, Luciani MF, et al. Autophagic cell death: analysis in Dictyostelium [Research Support, Non-U.S. Gov’t Review]. Biochim Biophys Acta. 2009. Sep;1793(9):1422–31. doi:10.1016/j.bbamcr.2008.12.005. PubMed PMID: 19133302; eng. PubMed DOI

Luciani MF, Giusti C, Harms B, et al. Atg1 allows second-signaled autophagic cell death in Dictyostelium. Autophagy. 2011. May;7(5):501–8. PubMed PMID: 21301205; eng. PubMed

Uchikawa T, Yamamoto A, Inouye K.. Origin and function of the stalk-cell vacuole in Dictyostelium. Dev Biol. 2011. Apr 1;352(1):48–57. doi:10.1016/j.ydbio.2011.01.014. PubMed PMID: 21256841; eng. PubMed DOI

Sharma D, Otto G, Warren EC, et al. Gamma secretase orthologs are required for lysosomal activity and autophagic degradation in Dictyostelium discoideum, independent of PSEN (presenilin) proteolytic function. Autophagy. 2019. Aug;15(8):1407–1418. doi:10.1080/15548627.2019.1586245. PubMed PMID: 30806144; PubMed Central PMCID: PMCPMC6613883. PubMed DOI PMC

Ludtmann MH, Otto GP, Schilde C, et al. An ancestral non-proteolytic role for presenilin proteins in multicellular development of the social amoeba Dictyostelium discoideum. J Cell Sci. 2014. Apr1;127(Pt 7):1576–84. doi:10.1242/jcs.140939. PubMed PMID: 24463814; PubMed Central PMCID: PMCPMC3970561. PubMed DOI PMC

Denton D, Xu T, Dayan S, et al. Dpp regulates autophagy-dependent midgut removal and signals to block ecdysone production. Cell Death Differ. 2019. Mar;26(4):763–778. doi:10.1038/s41418-018-0154-z. PubMed PMID: 29959404; PubMed Central PMCID: PMCPMC6460390. PubMed DOI PMC

Xu T, Nicolson S, Denton D, et al. Distinct requirements of Autophagy-related genes in programmed cell death. Cell Death Differ. 2015. Nov;22(11):1792–802. . PubMed PMID: 25882046; PubMed Central PMCID: PMCPMC4648326. PubMed PMC

Berry DL, Baehrecke EH.. Growth arrest and autophagy are required for salivary gland cell degradation in Drosophila. Cell. 2007. Dec 14;131(6):1137–48. doi:10.1016/j.cell.2007.10.048. PubMed PMID: 18083103; PubMed Central PMCID: PMC2180345. eng. PubMed DOI PMC

Daish TJ, Mills K, Kumar S.. Drosophila caspase DRONC is required for specific developmental cell death pathways and stress-induced apoptosis. Dev Cell. 2004. Dec;7(6):909–15. doi:10.1016/j.devcel.2004.09.018. PubMed PMID: 15572132. PubMed DOI

Mills K, Daish T, Harvey KF, et al. The Drosophila melanogaster Apaf-1 homologue ARK is required for most, but not all, programmed cell death. J Cell Biol. 2006. Mar 13;172(6):809–15. doi:10.1083/jcb.200512126. PubMed PMID: 16533943; PubMed Central PMCID: PMCPMC2063725. PubMed DOI PMC

Denton D, Aung-Htut MT, Lorensuhewa N, et al. UTX coordinates steroid hormone-mediated autophagy and cell death.Nat Commun. 2013;4:2916. doi:10.1038/ncomms3916. PubMed PMID: 24336022; PubMed Central PMCID: PMCPMC3973156. PubMed DOI PMC

Koenig U, Robenek H, Barresi C, et al. Cell death induced autophagy contributes to terminal differentiation of skin and skin appendages. Autophagy. 2019. Aug 4:1–14. doi:10.1080/15548627.2019.1646552. PubMed PMID: 31379249. PubMed DOI PMC

Jung S, Choe S, Woo H, et al. Autophagic death of neural stem cells mediates chronic stress-induced decline of adult hippocampal neurogenesis and cognitive deficits. Autophagy. 2020. Mar;16(3):512–530. doi:10.1080/15548627.2019.1630222. PubMed PMID: 31234698. PubMed DOI PMC

Zhou B, Liu J, Kang R, et al. Ferroptosis is a type of autophagy-dependent cell death. Semin Cancer Biol. 2019. Mar 14. doi:10.1016/j.semcancer.2019.03.002. PubMed PMID: 30880243. PubMed DOI

Bai Y, Meng L, Han L, et al. Lipid storage and lipophagy regulates ferroptosis. Biochem Biophys Res Commun. 2019. Jan 22;508(4):997–1003. doi:10.1016/j.bbrc.2018.12.039.PubMed PMID: 30545638. PubMed DOI

Song X, Zhu S, Chen P, et al. AMPK-Mediated BECN1 Phosphorylation Promotes Ferroptosis by Directly Blocking System Xc(-) Activity. Curr Biol. 2018. Aug 6;28(15):2388–2399 e5. doi:10.1016/j.cub.2018.05.094. PubMed PMID: 30057310; PubMed Central PMCID: PMCPMC6081251. PubMed DOI PMC

Kang R, Zhu S, Zeh HJ, et al. BECN1 is a new driver of ferroptosis. Autophagy. 2018;14(12):2173–2175. doi:10.1080/15548627.2018.1513758. PubMed PMID: 30145930. PubMed DOI PMC

Gao H, Bai Y, Jia Y, et al. Ferroptosis is a lysosomal cell death process. Biochem Biophys Res Commun. 2018. Sep 10;503(3):1550–1556. doi:10.1016/j.bbrc.2018.07.078. PubMed PMID: 30031610. PubMed DOI

Sperandio S, de Belle I, Bredesen DE.. An alternative, nonapoptotic form of programmed cell death.Proceedings of the National Academy of Sciences of the United States of America. 2000. Dec 19;97(26):14376–81. doi:10.1073/pnas.97.26.14376. PubMed PMID: 11121041; PubMed Central PMCID: PMCPMC18926. PubMed DOI PMC

Kar R, Singha PK, Venkatachalam MA, et al. A novel role for MAP1 LC3 in nonautophagic cytoplasmic vacuolation death of cancer cells. Oncogene. 2009. Jul 16;28(28):2556–68. doi:10.1038/onc.2009.118. PubMed PMID: 19448671; PubMed Central PMCID: PMCPMC2717022. PubMed DOI PMC

Wang WB, Feng LX, Yue QX, et al. Paraptosis accompanied by autophagy and apoptosis was induced by celastrol, a natural compound with influence on proteasome, ER stress and Hsp90. J Cell Physiol. 2012. May;227(5):2196–206. doi:10.1002/jcp.22956. PubMed PMID: 21866552. PubMed DOI

Singha PK, Pandeswara S, Venkatachalam MA, et al. Manumycin A inhibits triple-negative breast cancer growth through LC3-mediated cytoplasmic vacuolation death. Cell Death Dis. 2013. Jan 17;4:e457. doi:10.1038/cddis.2012.192. PubMed PMID: 23328664; PubMed Central PMCID: PMCPMC3563980. PubMed DOI PMC

Ram BM, Ramakrishna G.. Endoplasmic reticulum vacuolation and unfolded protein response leading to paraptosis like cell death in cyclosporine A treated cancer cervix cells is mediated by cyclophilin B inhibition. Biochim Biophys Acta. 2014. Nov;1843(11):2497–512. doi:10.1016/j.bbamcr.2014.06.020. PubMed PMID: 25003316. PubMed DOI

Zheng H, Dong Y, Li L, et al. Novel Benzo[a]quinolizidine Analogs Induce Cancer Cell Death through Paraptosis and Apoptosis. J Med Chem. 2016. May 26;59(10):5063–76. doi:10.1021/acs.jmedchem.6b00484. PubMed PMID: 27077446. PubMed DOI

Mi X, Wang C, Sun C, et al. Xanthohumol induces paraptosis of leukemia cells through p38 mitogen activated protein kinase signaling pathway. Oncotarget. 2017. May 9;8(19):31297–31304. doi:10.18632/oncotarget.16185. PubMed PMID: 28415750; PubMed Central PMCID: PMCPMC5458208. PubMed DOI PMC

Nedungadi D, Binoy A, Pandurangan N, et al. 6-Shogaol induces caspase-independent paraptosis in cancer cells via proteasomal inhibition. Exp Cell Res. 2018. Mar 15;364(2):243–251. doi:10.1016/j.yexcr.2018.02.018. PubMed PMID: 29462602. PubMed DOI

Binoy A, Nedungadi D, Katiyar N, et al. Plumbagin induces paraptosis in cancer cells by disrupting the sulfhydryl homeostasis and proteasomal function. Chem Biol Interact. 2019. Sep 1;310:108733. doi:10.1016/j.cbi.2019.108733. PubMed PMID: 31276663. PubMed DOI

Wang L, Gundelach JH, Bram RJ.. Cycloheximide promotes paraptosis induced by inhibition of cyclophilins in glioblastoma multiforme. Cell Death Dis. 2017. May 18;8(5):e2807. doi: 10.1038/cddis.2017.217. PubMed PMID: 28518150; PubMed Central PMCID: PMCPMC5520731. PubMed DOI PMC

Tsai TL, Wang HC, Hung CH, et al. Wheat germ agglutinin-induced paraptosis-like cell death and protective autophagy is mediated by autophagy-linked FYVE inhibition. Oncotarget. 2017. Oct 31;8(53):91209–91222. doi:10.18632/oncotarget.20436. PubMed PMID: 29207637; PubMed Central PMCID: PMCPMC5710917. PubMed DOI PMC

Zhang C, Jiang Y, Zhang J, et al. 8-p-Hdroxybenzoyl Tovarol Induces Paraptosis Like Cell Death and Protective Autophagy in Human Cervical Cancer HeLa Cells. Int J Mol Sci. 2015. Jul 2;16(7):14979–96. doi:10.3390/ijms160714979. PubMed PMID: 26147427; PubMed Central PMCID: PMCPMC4519883. PubMed DOI PMC

Han H, Chou CC, Li R, et al. Chalcomoracin is a potent anticancer agent acting through triggering Oxidative stress via a mitophagy- and paraptosis-dependent mechanism. Sci Rep. 2018. Jun 22;8(1):9566. doi:10.1038/s41598-018-27724-3. PubMed PMID: 29934599; PubMed Central PMCID: PMCPMC6014977. PubMed DOI PMC

Cadwell K, Debnath J.. Beyond self-eating: The control of nonautophagic functions and signaling pathways by autophagy-related proteins. J Cell Biol. 2018. Mar 5;217(3):813–822. doi:10.1083/jcb.201706157. PubMed PMID: 29237720; PubMed Central PMCID: PMCPMC5839790. PubMed DOI PMC

Galluzzi L, Green DR.. Autophagy-Independent Functions of the Autophagy Machinery. Cell. 2019. Jun 13;177(7):1682–1699. doi:10.1016/j.cell.2019.05.026. PubMed PMID: 31199916. PubMed DOI PMC

Galluzzi L, Vitale I, Abrams JM, et al. Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012. Cell Death Differ. 2011. Jul 15. doi:10.1038/cdd.2011.96. PubMed PMID: 21760595; Eng. PubMed DOI PMC

Kaushik S, Bandyopadhyay U, Sridhar S, et al.Chaperone-mediated autophagy at a glance. J Cell Sci. 2011. Feb 15;124(Pt 4):495–9. doi:124/4/495[pii] doi:10.1242/jcs.073874. PubMed PMID: 21282471; PubMed Central PMCID: PMC3031365. eng. PubMed DOI PMC

Arias E, Cuervo AM.. Chaperone-mediated autophagy in protein quality control. Curr Opinion Cell Biol 2010. Nov 18;23:184–9. doi:S0955-0674(10)00180-8 [pii] doi:10.1016/j.ceb.2010.10.009. PubMed PMID: 21094035; Eng. PubMed DOI PMC

Li W, Dou J, Yang J, et al. Targeting Chaperone-Mediated Autophagy for Disease Therapy. Current Pharmacol Rep. 2018;4:261–275. PubMed PMC

Li W, Yang Q, Mao Z.. Chaperone-mediated autophagy: machinery, regulation and biological consequences. Cell Mol Life Sci. 2011. Mar;68(5):749–63. doi:10.1007/s00018-010-0565-6. PubMed PMID: 20976518. PubMed DOI PMC

Patel B, Cuervo AM.. Methods to study chaperone-mediated autophagy. Methods. 2015. Mar;75:133–40. doi:10.1016/j.ymeth.2015.01.003. PubMed PMID: 25595300; PubMed Central PMCID: PMCPMC4355229. PubMed DOI PMC

Yabu T, Imamura S, Mohammed MS, et al. Differential gene expression of HSC70/HSP70 in yellowtail cells in response to chaperone-mediated autophagy. FEBS J. 2011. Feb;278(4):673–85. doi:10.1111/j.1742-4658.2010.07989.x. PubMed PMID: 21205201. PubMed DOI

Lescat L, Herpin A, Mourot B, et al. CMA restricted to mammals and birds: myth or reality? Autophagy. 2018;14(7):1267–1270. doi:10.1080/15548627.2018.1460021. PubMed PMID: 29929419; PubMed Central PMCID: PMCPMC6103740. PubMed DOI PMC

Mukherjee A, Patel B, Koga H, et al. Selective endosomal microautophagy is starvation-inducible in Drosophila. Autophagy. 2016. Nov;12(11):1984–1999. doi:10.1080/15548627.2016.1208887. PubMed PMID: 27487474; PubMed Central PMCID: PMCPMC5103356. PubMed DOI PMC

Eisermann DJ, Wenzel U, Fitzenberger E.. Inhibition of chaperone-mediated autophagy prevents glucotoxicity in the Caenorhabditis elegans mev-1 mutant by activation of the proteasome. Biochem Biophys Res Commun. 2017. Feb 26;484(1):171–175. doi:10.1016/j.bbrc.2017.01.043. PubMed PMID: 28089866. PubMed DOI

Lescat L, Veron V, Mourot B, et al. Chaperone-Mediated Autophagy in the light of evolution: insight from fish. Mol Biol Evol. 2020. May 21. doi:10.1093/molbev/msaa127. PubMed PMID: 32437540. PubMed DOI

Kirchner P, Bourdenx M, Madrigal-Matute J, et al. Proteome-wide analysis of chaperone-mediated autophagy targeting motifs. PLoS Biol. 2019. May;17(5):e3000301. doi:10.1371/journal.pbio.3000301. PubMed PMID: 31150375; PubMed Central PMCID: PMCPMC6561683 of the submitted manuscript. PubMed DOI PMC

Gough NR, Hatem CL, Fambrough DM.. The family of LAMP-2 proteins arises by alternative splicing from a single gene: characterization of the avian LAMP-2 gene and identification of mammalian homologs of LAMP-2b and LAMP-2c. DNA Cell Biol. 1995. Oct;14(10):863–7. doi:10.1089/dna.1995.14.863. PubMed PMID: 7546292. PubMed DOI

Kaushik S, Cuervo AM.. Methods to monitor chaperone-mediated autophagy [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Methods Enzymol. 2009;452:297–324. doi:10.1016/S0076-6879(08)03619-7. PubMed PMID: 19200890; eng. PubMed DOI PMC

Dice JF. Peptide sequences that target cytosolic proteins for lysosomal proteolysis [Research Support, U.S. Gov’t, P.H.S Review]. Trends Biochem Sci. 1990. Aug;15(8):305–9. PubMed PMID: 2204156; eng. PubMed

Bonhoure A, Vallentin A, Martin M, et al. Acetylation of translationally controlled tumor protein promotes its degradation through chaperone-mediated autophagy. Eur J Cell Biol. 2017. Mar;96(2):83–98. doi:10.1016/j.ejcb.2016.12.002. PubMed PMID: 28110910. PubMed DOI

Ho PW, Leung CT, Liu H, et al. Age-dependent accumulation of oligomeric SNCA/alpha-synuclein from impaired degradation in mutant LRRK2 knockin mouse model of Parkinson disease: role for therapeutic activation of chaperone-mediated autophagy (CMA). Autophagy. 2020. Feb;16(2):347–370. doi:10.1080/15548627.2019.1603545. PubMed PMID: 30983487. PubMed DOI PMC

Cuervo AM, Dice JF, Knecht E.. A population of rat liver lysosomes responsible for the selective uptake and degradation of cytosolic proteins. J Biol Chem. 1997. Feb 28;272(9):5606–15. PubMed PMID: 9038169; eng. PubMed

Cuervo AM, Dice JF.. A receptor for the selective uptake and degradation of proteins by lysosomes [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S.]. Science. 1996. Jul 26;273(5274):501–3. PubMed PMID: 8662539; eng. PubMed

Cuervo AM, Dice JF.. Unique properties of lamp2a compared to other lamp2 isoforms [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S.]. J Cell Sci. 2000. Dec;113:4441–50. PubMed PMID: 11082038; eng. PubMed

Finn PF, Mesires NT, Vine M, et al. Effects of small molecules on chaperone-mediated autophagy. Autophagy. 2005. Oct-Dec;1(3):141–5. PubMed PMID: 16874031; eng. PubMed

Bandyopadhyay U, Kaushik S, Varticovski L, et al. The chaperone-mediated autophagy receptor organizes in dynamic protein complexes at the lysosomal membrane. Mol Cell Biol. 2008. Sep;28(18):5747–63. doi:MCB.02070-07 [pii] doi:10.1128/MCB.02070-07. PubMed PMID: 18644871; PubMed Central PMCID: PMC2546938. eng. PubMed DOI PMC

Aniento F, Emans N, Griffiths G, et al. Cytoplasmic dynein-dependent vesicular transport from early to late endosomes [In Vitro Research Support, Non-U.S. Gov’t]. J Cell Biol. 1993. Dec;123(6 Pt 1):1373–87. PubMed PMID: 8253838; PubMed Central PMCID: PMC2290907. eng. PubMed PMC

Salvador N, Aguado C, Horst M, et al. Import of a cytosolic protein into lysosomes by chaperone-mediated autophagy depends on its folding state [Research Support, Non-U.S. Gov’t]. J Biol Chem. 2000. Sep 1;275(35):27447–56. doi:10.1074/jbc.M001394200. PubMed PMID: 10862611; eng. PubMed DOI

Koga H, Martinez-Vicente M, Macian F, et al. A photoconvertible fluorescent reporter to track chaperone-mediated autophagy [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Nat Commun. 2011;2:386. doi:10.1038/ncomms1393. PubMed PMID: 21750540; eng. PubMed DOI PMC

Sahu R, Kaushik S, Clement CC, et al. Microautophagy of cytosolic proteins by late endosomes [Research Support, N.I.H., Extramural]. Develop cell. 2011. Jan 18; 20(1):131–9. doi: 10.1016/j.devcel.2010.12.003. PubMed PMID: 21238931; PubMed Central PMCID: PMC3025279. eng. PubMed DOI PMC

Wang Y, Martinez-Vicente M, Kruger U, et al. Tau fragmentation, aggregation and clearance: the dual role of lysosomal processing. Hum Mol Genet. 2009. Nov 1;18(21):4153–70. doi:10.1093/hmg/ddp367. PubMed PMID: 19654187; PubMed Central PMCID: PMCPMC2758146. PubMed DOI PMC

Caballero B, Wang Y, Diaz A, et al. Interplay of pathogenic forms of human tau with different autophagic pathways. Aging cell. 2018. Feb;17(1). doi:10.1111/acel.12692. PubMed PMID: 29024336; PubMed Central PMCID: PMCPMC5770880. PubMed DOI PMC

Morozova K, Clement CC, Kaushik S, et al. Structural and Biological Interaction of hsc-70 Protein with Phosphatidylserine in Endosomal Microautophagy. J Biol Chem. 2016. Aug 26;291(35):18096–106. doi:10.1074/jbc.M116.736744. PubMed PMID: 27405763; PubMed Central PMCID: PMCPMC5000059. PubMed DOI PMC

Uytterhoeven V, Lauwers E, Maes I, et al. Hsc70-4 Deforms Membranes to Promote Synaptic Protein Turnover by Endosomal Microautophagy. Neuron. 2015. Nov 18;88(4):735–48. doi:10.1016/j.neuron.2015.10.012. PubMed PMID: 26590345. PubMed DOI

Arndt V, Dick N, Tawo R, et al. Chaperone-assisted selective autophagy is essential for muscle maintenance [Research Support, Non-U.S. Gov’t]. Curr Biol. 2010. Jan 26;20(2):143–8. doi:10.1016/j.cub.2009.11.022. PubMed PMID: 20060297; eng. PubMed DOI

Eskelinen EL, Schmidt CK, Neu S, et al. Disturbed cholesterol traffic but normal proteolytic function in LAMP-1/LAMP-2 double-deficient fibroblasts. Mol Biol Cell. 2004. Jul;15(7):3132–45. doi:10.1091/mbc.E04-02-0103. PubMed PMID: 15121881; PubMed Central PMCID: PMC452571. PubMed DOI PMC

Eskelinen EL, Illert AL, Tanaka Y, et al. Role of LAMP-2 in lysosome biogenesis and autophagy. Mol Biol Cell. 2002. Sep;13(9):3355–68. doi:10.1091/mbc.E02-02-0114. PubMed PMID: 12221139; PubMed Central PMCID: PMC124165. PubMed DOI PMC

Huynh KK, Eskelinen EL, Scott CC, et al. LAMP proteins are required for fusion of lysosomes with phagosomes. EMBO J. 2007. Jan 24;26(2):313–24. doi:10.1038/sj.emboj.7601511. PubMed PMID: 17245426; PubMed Central PMCID: PMC1783450. PubMed DOI PMC

Perez L, McLetchie S, Gardiner GJ, et al. LAMP-2C Inhibits MHC Class II Presentation of Cytoplasmic Antigens by Disrupting Chaperone-Mediated Autophagy. J Iimmunol. 2016. Mar 15; 196(6):2457–65. doi:10.4049/jimmunol.1501476. PubMed PMID: 26856698; PubMed Central PMCID: PMCPMC4779666. PubMed DOI PMC

Perez L, Sinn AL, Sandusky GE, et al. Melanoma LAMP-2C Modulates Tumor Growth and Autophagy. Front Cell Dev Biol. 2018;6:101. doi:10.3389/fcell.2018.00101. PubMed PMID: 30211163; PubMed Central PMCID: PMCPMC6123356. PubMed DOI PMC

Furuta A, Kikuchi H, Fujita H, et al. Property of lysosomal storage disease associated with midbrain pathology in the central nervous system of lamp-2-deficient mice. Am J Pathol. 2015. Jun;185(6):1713–23. doi:10.1016/j.ajpath.2015.02.015. PubMed PMID: 25998250. PubMed DOI

Rothaug M, Stroobants S, Schweizer M, et al. LAMP-2 deficiency leads to hippocampal dysfunction but normal clearance of neuronal substrates of chaperone-mediated autophagy in a mouse model for Danon disease. Acta Neuropathol Commun. 2015;3:6. doi:10.1186/s40478-014-0182-y. PubMed PMID: 25637286; PubMed Central PMCID: PMC4359523. PubMed DOI PMC

Sarparanta J, Jonson PH, Golzio C, et al. Mutations affecting the cytoplasmic functions of the co-chaperone DNAJB6 cause limb-girdle muscular dystrophy. Nat Genet. 2012. Feb 26;44(4):450–5, S1-2. doi:10.1038/ng.1103. PubMed PMID: 22366786; PubMed Central PMCID: PMCPMC3315599. PubMed DOI PMC

Ulbricht A, Eppler FJ, Tapia VE, et al. Cellular mechanotransduction relies on tension-induced and chaperone-assisted autophagy. Curr Biol. 2013. Mar 4;23(5):430–5. doi10.1016/j.cub.2013.01.064. PubMed PMID: 23434281. PubMed DOI

Gamerdinger M, Kaya AM, Wolfrum U, et al. BAG3 mediates chaperone-based aggresome-targeting and selective autophagy of misfolded proteins. EMBO Rep. 2011. Feb;12(2):149–56. doi:10.1038/embor.2010.203. PubMed PMID: 21252941; PubMed Central PMCID: PMCPMC3049430. PubMed DOI PMC

Gamerdinger M, Hajieva P, Kaya AM, et al. Protein quality control during aging involves recruitment of the macroautophagy pathway by BAG3. EMBO J. 2009. Apr 8;28(7):889–901. doi:10.1038/emboj.2009.29. PubMed PMID: 19229298; PubMed Central PMCID: PMCPMC2647772. PubMed DOI PMC

Sturner E, Behl C.. The Role of the Multifunctional BAG3 Protein in Cellular Protein Quality Control and in Disease. Front Mol Neurosci. 2017;10:177. doi:10.3389/fnmol.2017.00177. PubMed PMID: 28680391; PubMed Central PMCID: PMCPMC5478690. PubMed DOI PMC

Cristofani R, Crippa V, Rusmini P, et al. Inhibition of retrograde transport modulates misfolded protein accumulation and clearance in motoneuron diseases. Autophagy. 2017. Aug 3;13(8):1280–1303. doi:10.1080/15548627.2017.1308985. PubMed PMID: 28402699; PubMed Central PMCID: PMCPMC5584856. PubMed DOI PMC

Adriaenssens E, Tedesco B, Mediani L, et al. BAG3 Pro209 mutants associated with myopathy and neuropathy relocate chaperones of the CASA-complex to aggresomes. Sci Rep. 2020. May 29;10(1):8755. doi:10.1038/s41598-020-65664-z. PubMed PMID: 32472079; PubMed Central PMCID: PMCPMC7260189. PubMed DOI PMC

Evangelinos M, Martzoukou O, Chorozian K, et al. BsdA(Bsd2) -dependent vacuolar turnover of a misfolded version of the UapA transporter along the secretory pathway: prominent role of selective autophagy. Mol Microbiol. 2016. Jun;100(5):893–911. doi:10.1111/mmi.13358. PubMed PMID: 26917498. PubMed DOI

Oku M, Sakai Y.. Three Distinct Types of Microautophagy Based on Membrane Dynamics and Molecular Machineries. Bioessays. 2018. Jun;40(6):e1800008. doi:10.1002/bies.201800008. PubMed PMID: 29708272. PubMed DOI

Xie Z, Klionsky DJ.. Autophagosome formation: core machinery and adaptations. Nat Cell Biol. 2007. Oct;9(10):1102–9. doi:10.1038/ncb1007-1102. PubMed PMID: 17909521. PubMed DOI

Mukaiyama H, Baba M, Osumi M, et al. Modification of a ubiquitin-like protein Paz2 conducted micropexophagy through formation of a novel membrane structure. ?Mol Biol Cell 2004. Jan;15(1):58–70. PubMed PMID: 13679515. PubMed PMC

Salum TT, Tsil’mer K, Vikhalemm TE, et al. [Features of temperature dependence of the Na+,K+-ATPase reaction in normal and tumorous brain tissue]. Ukr Biokhim Zh. 1989. Jul-Aug;61(4):65–9. PubMed PMID: 2555948. PubMed

Vevea JD, Garcia EJ, Chan RB, et al. Role for Lipid Droplet Biogenesis and Microlipophagy in Adaptation to Lipid Imbalance in Yeast. Dev Cell. 2015. Dec 7;35(5):584–599. doi:10.1016/j.devcel.2015.11.010. PubMed PMID: 26651293; PubMed Central PMCID: PMCPMC4679156. PubMed DOI PMC

Oku M, Maeda Y, Kagohashi Y, et al. Evidence for ESCRT- and clathrin-dependent microautophagy. J Cell Biol. 2017. Oct 2;216(10):3263–3274. doi:10.1083/jcb.201611029. PubMed PMID: 28838958; PubMed Central PMCID: PMCPMC5626533. PubMed DOI PMC

Chanoca A, Kovinich N, Burkel B, et al. Anthocyanin Vacuolar Inclusions Form by a Microautophagy Mechanism. Plant Cell. 2015. Sep;27(9):2545–59. doi:10.1105/tpc.15.00589. PubMed PMID: 26342015; PubMed Central PMCID: PMCPMC4815043. PubMed DOI PMC

Liu XM, Sun LL, Hu W, et al. ESCRTs Cooperate with a Selective Autophagy Receptor to Mediate Vacuolar Targeting of Soluble Cargos. Mol Cell. 2015. Sep 17;59(6):1035–42. doi:10.1016/j.molcel.2015.07.034. PubMed PMID: 26365378. PubMed DOI

Rahman MA, Terasawa M, Mostofa MG, et al. The TORC1-Nem1/Spo7-Pah1/lipin axis regulates microautophagy induction in budding yeast. Biochem Biophys Res Commun. 2018. Oct 2;504(2):505–512. doi:10.1016/j.bbrc.2018.09.011. PubMed PMID: 30201264. PubMed DOI

Hatakeyama R, De Virgilio C.. TORC1 specifically inhibits microautophagy through ESCRT-0. Curr Genet. 2019. Oct;65(5):1243–1249. doi:10.1007/s00294-019-00982-y. PubMed PMID: 31041524; PubMed Central PMCID: PMCPMC6744375. PubMed DOI PMC

Seo AY, Lau PW, Feliciano D, et al. AMPK and vacuole-associated Atg14p orchestrate mu-lipophagy for energy production and long-term survival under glucose starvation. eLife. 2017. Apr 10;6. doi:10.7554/eLife.21690. PubMed PMID: 28394250; PubMed Central PMCID: PMCPMC5407857. PubMed DOI PMC

Tsuji T, Fujimoto M, Tatematsu T, et al. Niemann-Pick type C proteins promote microautophagy by expanding raft-like membrane domains in the yeast vacuole. eLife. 2017. Jun 7;6. doi:10.7554/eLife.25960. PubMed PMID: 28590904; PubMed Central PMCID: PMCPMC5462540. PubMed DOI PMC

Wang CW, Miao YH, Chang YS.. A sterol-enriched vacuolar microdomain mediates stationary phase lipophagy in budding yeast. J Cell Biol. 2014. Aug 4;206(3):357–66. doi:10.1083/jcb.201404115. PubMed PMID: 25070953; PubMed Central PMCID: PMC4121974. PubMed DOI PMC

Sattler T, Mayer A.. Cell-free reconstitution of microautophagic vacuole invagination and vesicle formation [Research Support, Non-U.S. Gov’t]. J Cell Biol. 2000. Oct 30;151(3):529–38. PubMed PMID: 11062255; PubMed Central PMCID: PMC2185593. eng. PubMed PMC

Thery C, Witwer KW, Aikawa E, et al. Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines. J Extracell Vesicles. 2018;7(1):1535750. doi:10.1080/20013078.2018.1535750. PubMed PMID: 30637094; PubMed Central PMCID: PMCPMC6322352. PubMed DOI PMC

Exosomes Vidal M.: Revisiting their role as “garbage bags”. Traffic. 2019. Nov;20(11):815–828. doi:10.1111/tra.12687. PubMed PMID: 31418976. PubMed DOI

Paglin S, Hollister T, Delohery T, et al. A novel response of cancer cells to radiation involves autophagy and formation of acidic vesicles. Cancer Res. 2001. Jan 15;61(2):439–44. PubMed PMID: 11212227; eng. PubMed

Florez-McClure ML, Linseman DA, Chu CT, et al. The p75 neurotrophin receptor can induce autophagy and death of cerebellar Purkinje neurons. J Neurosci. 2004. May 12;24(19):4498–509. PubMed PMID: 15140920; eng. PubMed PMC

Moriyasu Y, Ohsumi Y.. Autophagy in tobacco suspension-cultured cells in response to sucrose starvation. Plant Physiol. 1996. Aug;111(4):1233–1241. PubMed PMID: 12226358; PubMed Central PMCID: PMC161001. Eng. PubMed PMC

Wolfe DM, Lee JH, Kumar A, et al. Autophagy failure in Alzheimer’s disease and the role of defective lysosomal acidification. Eur J Neurosci. 2013. Jun;37(12):1949–1961. doi:10.1111/ejn.12169. PubMed PMID: 23773064; PubMed Central PMCID: PMC3694736. PubMed DOI PMC

Thome MP, Filippi-Chiela EC, Villodre ES, et al. Ratiometric analysis of Acridine Orange staining in the study of acidic organelles and autophagy. J Cell Sci. 2016. Dec 15;129(24):4622–4632. doi:10.1242/jcs.195057. PubMed PMID: 27875278. PubMed DOI

Bashmail HA, Alamoudi AA, Noorwali A, et al. Thymoquinone synergizes gemcitabine anti-breast cancer activity via modulating its apoptotic and autophagic activities. Sci Rep. 2018. Aug 3;8(1):11674. doi:10.1038/s41598-018-30046-z. PubMed PMID: 30076320; PubMed Central PMCID: PMCPMC6076303. PubMed DOI PMC

Biederbick A, Kern HF, Elsasser HP.. Monodansylcadaverine (MDC) is a specific in vivo marker for autophagic vacuoles. Eur J Cell Biol. 1995. Jan;66(1):3–14. PubMed PMID: 7750517; eng. PubMed

Hoyer-Hansen M, Bastholm L, Mathiasen IS, et al. Vitamin D analog EB1089 triggers dramatic lysosomal changes and Beclin 1-mediated autophagic cell death. Cell Death Differ. 2005. Oct;12(10):1297–309. PubMed PMID: 15905882; eng. PubMed

Fogel JL, Thein TZ, Mariani FV.. Use of LysoTracker to detect programmed cell death in embryos and differentiating embryonic stem cells. J vis exp. 2012. (68). doi:10.3791/4254. PubMed PMID: 23092960; PubMed Central PMCID: PMC3490301. PubMed DOI PMC

Freundt EC, Czapiga M, Lenardo MJ.. Photoconversion of Lysotracker Red to a green fluorescent molecule [Letter Research Support, N.I.H., Intramural]. Cell Res. 2007. Nov;17(11):956–8. doi:10.1038/cr.2007.80. PubMed PMID: 17893709; eng. PubMed DOI

Oeste CL, Seco E, Patton WF, et al. Interactions between autophagic and endo-lysosomal markers in endothelial cells. Histochem Cell Biol. 2013. May;139(5):659–70. doi:10.1007/s00418-012-1057-6. PubMed PMID: 23203316. PubMed DOI

Rubinsztein DC, Gestwicki JE, Murphy LO, et al. Potential therapeutic applications of autophagy. Nat Rev Drug Discov. 2007. Apr;6(4):304–12. PubMed PMID: 17396135; eng. PubMed

Funderburk SF, Wang QJ, Yue Z.. The Beclin 1-VPS34 complex–at the crossroads of autophagy and beyond [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t Review]. Trends Cell Biol. 2010. Jun;20(6):355–62. doi:10.1016/j.tcb.2010.03.002. PubMed PMID: 20356743; eng. PubMed DOI PMC

Levine B, Sinha S, Kroemer G.. Bcl-2 family members: dual regulators of apoptosis and autophagy [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t Review]. Autophagy. 2008. Jul;4(5):600–6. PubMed PMID: 18497563; PubMed Central PMCID: PMC2749577. eng. PubMed PMC

Simonsen A, Tooze SA.. Coordination of membrane events during autophagy by multiple class III PI3-kinase complexes [Review]. J Cell Biol. 2009. Sep 21;186(6):773–82. doi:10.1083/jcb.200907014. PubMed PMID: 19797076; PubMed Central PMCID: PMC2753151. eng. PubMed DOI PMC

Pyo JO, Jang MH, Kwon YK, et al. Essential roles of Atg5 and FADD in autophagic cell death: dissection of autophagic cell death into vacuole formation and cell death [Research Support, Non-U.S. Gov’t]. J Biol Chem. 2005. May 27;280(21):20722–9. doi:10.1074/jbc.M413934200. PubMed PMID: 15778222; eng. PubMed DOI

Petiot A, Ogier-Denis E, Blommaart EF, et al. Distinct classes of phosphatidylinositol 3ʹ-kinases are involved in signaling pathways that control macroautophagy in HT-29 cells. J Biol Chem. 2000. Jan 14;275(2):992–8. PubMed PMID: 10625637; eng. PubMed

Harris J, Hartman M, Roche C, et al. Autophagy controls IL-1beta secretion by targeting pro-IL-1beta for degradation [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. J Biol Chem. 2011. Mar 18;286(11):9587–97. doi:10.1074/jbc.M110.202911. PubMed PMID: 21228274; PubMed Central PMCID: PMC3058966. eng. PubMed DOI PMC

Crisan TO, Plantinga TS, van de Veerdonk FL, et al. Inflammasome-independent modulation of cytokine response by autophagy in human cells [Research Support, Non-U.S. Gov’t]. PLoS One. 2011;6(4):e18666. doi:10.1371/journal.pone.0018666. PubMed PMID: 21490934; PubMed Central PMCID: PMC3072416. eng. PubMed DOI PMC

Kleinnijenhuis J, Oosting M, Plantinga TS, et al. Autophagy modulates the Mycobacterium tuberculosis-induced cytokine response [Research Support, Non-U.S. Gov’t]. Immunology. 2011. Nov;134(3):341–8. doi:10.1111/j.1365-2567.2011.03494.x. PubMed PMID: 21978003; PubMed Central PMCID: PMC3209573. eng. PubMed DOI PMC

Peral de Castro C, Jones SA, Ni Cheallaigh C, et al. Autophagy regulates IL-23 secretion and innate T cell responses through effects on IL-1 secretion. J Iimmunol. 2012. Oct 15;189(8):4144–53. doi:10.4049/jimmunol.1201946. PubMed PMID: 22972933. PubMed DOI

Herbst S, Schaible UE, Schneider BE.. Interferon gamma activated macrophages kill mycobacteria by nitric oxide induced apoptosis. PLoS One. 2011. May 2;6(5):e19105. doi:10.1371/journal.pone.0019105. PubMed PMID: 21559306; PubMed Central PMCID: PMCPMC3085516. PubMed DOI PMC

Dowdle WE, Nyfeler B, Nagel J, et al. Selective VPS34 inhibitor blocks autophagy and uncovers a role for NCOA4 in ferritin degradation and iron homeostasis in vivo. Nat Cell Biol. 2014. Nov;16(11):1069–79. doi:10.1038/ncb3053. PubMed PMID: 25327288. PubMed DOI

Ronan B, Flamand O, Vescovi L, et al. A highly potent and selective Vps34 inhibitor alters vesicle trafficking and autophagy. Nat Chem Biol. 2014. Dec;10(12):1013–9. doi:10.1038/nchembio.1681. PubMed PMID: 25326666. PubMed DOI

Isosaki M. Inhibition of wortmannin activities by amino compounds. Biochem Biophys Res Commun. 2004. Nov 26;324(4):1406–12. doi:10.1016/j.bbrc.2004.09.200. PubMed PMID: 15504370. PubMed DOI

Yuan H, Barnes KR, Weissleder R, et al. Covalent reactions of wortmannin under physiological conditions. Chem Biol. 2007. Mar;14(3):321–8. doi:10.1016/j.chembiol.2007.02.007. PubMed PMID: 17379147. PubMed DOI

Chen J, Chen MX, Fogo AB, et al. mVps34 deletion in podocytes causes glomerulosclerosis by disrupting intracellular vesicle trafficking. J Am Soc Nephrol. 2013. Feb;24(2):198–207. doi:10.1681/ASN.2012010101. PubMed PMID: 23291473; PubMed Central PMCID: PMC3559479. PubMed DOI PMC

Kovács J. Morphometric study of the effect of leupeptin, vinblastine, estron acetate and cycloheximide on the autophagic vacuole-lysosomal compartments in mouse seminal vesicle cells. Virchows Arch B Cell Pathol Incl Mol Pathol. 1983;42(1):83–93. PubMed PMID: 6132491; eng. PubMed

Papadopoulos T, Pfeifer U.. Regression of rat liver autophagic vacuoles by locally applied cycloheximide. Lab Invest. 1986. Jan;54(1):100–7. PubMed PMID: 3941538; eng. PubMed

Rumpelt HJ, Albring M, Thoenes W.. Prevention of D-galactosamine-induced hepatocellular autophagocytosis by cycloheximide. Virchows Arch B Cell Pathol. 1974;16(2):195–203. PubMed PMID: 4216140; eng. PubMed

Kovács AL, Kovács J.. Autophagocytosis in mouse seminal vesicle cells in vitro. Temperature dependence and effects of vinblastine and inhibitors of protein synthesis. Virchows Arch B Cell Pathol Incl Mol Pathol. 1980;32(2):97–104. PubMed PMID: 6102826; eng. PubMed

Rodemann HP, Dittmann K, Toulany M.. Radiation-induced EGFR-signaling and control of DNA-damage repair [Research Support, Non-U.S. Gov’t Review]. Int J Radiat Biol.2007. Nov-Dec;83(11–12):781–91. doi:10.1080/09553000701769970. PubMed PMID: 18058366; eng. PubMed DOI

Chaachouay H, Ohneseit P, Toulany M, et al. Autophagy contributes to resistance of tumor cells to ionizing radiation [Research Support, Non-U.S. Gov’t]. Radiother Oncol. 2011. Jun;99(3):287–92. doi:10.1016/j.radonc.2011.06.002. PubMed PMID: 21722986; eng. PubMed DOI

Apel A, Herr I, Schwarz H, et al. Blocked autophagy sensitizes resistant carcinoma cells to radiation therapy [Research Support, Non-U.S. Gov’t]. Cancer Res. 2008. Mar 1;68(5):1485–94. doi:10.1158/0008-5472.CAN-07-0562. PubMed PMID: 18316613; eng. PubMed DOI

Hounjet J, Habets R, Schaaf MB, et al. The anti-malarial drug chloroquine sensitizes oncogenic NOTCH1 driven human T-ALL to gamma-secretase inhibition. Oncogene. 2019. Jul;38(27):5457–5468. doi:10.1038/s41388-019-0802-x. PubMed PMID: 30967635. PubMed DOI

Eng CH, Yu K, Lucas J, et al. Ammonia derived from glutaminolysis is a diffusible regulator of autophagy [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Sci Signal. 2010;3(119):ra31. doi:10.1126/scisignal.2000911. PubMed PMID: 20424262; eng. PubMed DOI

Seglen PO, Gordon PB.. Effects of lysosomotropic monoamines, diamines, amino alcohols, and other amino compounds on protein degradation and protein synthesis in isolated rat hepatocytes [In Vitro Research Support, Non-U.S. Gov’t]. Mol Pharmacol. 1980. Nov;18(3):468–75. PubMed PMID: 7464813; eng. PubMed

Cheong H, Lindsten T, Wu J, et al. Ammonia-induced autophagy is independent of ULK1/ULK2 kinases [Research Support, N.I.H., Extramural]. Proc Natl Acad Sci U S A. 2011. Jul 5;108(27):11121–6. doi:10.1073/pnas.1107969108. PubMed PMID: 21690395; PubMed Central PMCID: PMC3131371. eng. PubMed DOI PMC

Li Z, Ji X, Wang W, et al. Ammonia Induces Autophagy through Dopamine Receptor D3 and MTOR. PLoS One. 2016;11(4):e0153526. doi:10.1371/journal.pone.0153526. PubMed PMID: 27077655; PubMed Central PMCID: PMCPMC4831814. PubMed DOI PMC

Pellegrini P, Strambi A, Zipoli C, et al. Acidic extracellular pH neutralizes the autophagy-inhibiting activity of chloroquine: implications for cancer therapies. Autophagy. 2014. Apr;10(4):562–71. doi:10.4161/auto.27901. PubMed PMID: 24492472; PubMed Central PMCID: PMC3984580. PubMed DOI PMC

Fischer S, Ronellenfitsch MW, Thiepold AL, et al. Hypoxia enhances the antiglioma cytotoxicity of B10, a glycosylated derivative of betulinic acid. PLoS One. 2014;9(4):e94921. doi: 10.1371/journal.pone.0094921. PubMed PMID: 24743710; PubMed Central PMCID: PMC3990545. PubMed DOI PMC

Gonzalez P, Mader I, Tchoghandjian A, et al. Impairment of lysosomal integrity by B10, a glycosylated derivative of betulinic acid, leads to lysosomal cell death and converts autophagy into a detrimental process. Cell Death Differ. 2012. Aug;19(8):1337–46. doi:10.1038/cdd.2012.10. PubMed PMID: 22343715; PubMed Central PMCID: PMC3392623. PubMed DOI PMC

Potze L, Mullauer FB, Colak S, et al. Betulinic acid-induced mitochondria-dependent cell death is counterbalanced by an autophagic salvage response. Cell Death Dis. 2014;5:e1169. doi:10.1038/cddis.2014.139. PubMed PMID: 24722294. PubMed DOI PMC

Chen Y, Sun R, Wang B.. Monolayer behavior of binary systems of betulinic acid and cardiolipin: thermodynamic analyses of Langmuir monolayers and AFM study of Langmuir-Blodgett monolayers. J Colloid Interface Sci. 2011. Jan 1;353(1):294–300. doi:10.1016/j.jcis.2010.09.019. PubMed PMID: 20888569. PubMed DOI

Gao M, Lau PM, Kong SK.. Mitochondrial toxin betulinic acid induces in vitro eryptosis in human red blood cells through membrane permeabilization. Arch Toxicol. 2014Mar;88(3):755–68. doi:10.1007/s00204-013-1162-x. PubMed PMID: 24241250. PubMed DOI

Milczarek M, Wiktorska K, Mielczarek L, et al. Autophagic cell death and premature senescence: New mechanism of 5-fluorouracil and sulforaphane synergistic anticancer effect in MDA-MB-231 triple negative breast cancer cell line. Food Chem Toxicol. 2018. Jan;111:1–8. doi:10.1016/j.fct.2017.10.056. PubMed PMID: 29104175. PubMed DOI

Hsieh MJ, Chien SY, Lin JT, et al. Polyphyllin G induces apoptosis and autophagy cell death in human oral cancer cells. Phytomedicine. 2016. Dec 1;23(13):1545–1554. doi:10.1016/j.phymed.2016.09.004. PubMed PMID: 27823618. PubMed DOI

Hsieh MJ, Lin CW, Chiou HL, et al. Dehydroandrographolide, an iNOS inhibitor, extracted from Andrographis paniculata (Burm.f.) Nees, induces autophagy in human oral cancer cells. Oncotarget. 2015. Oct 13;6(31):30831–49. doi:10.18632/oncotarget.5036. PubMed PMID: 26356821; PubMed Central PMCID: PMCPMC4741571. PubMed DOI PMC

Law BYK, Mok SWF, Chen J, et al. N-Desmethyldauricine Induces Autophagic Cell Death in Apoptosis-Defective Cells via Ca(2+) Mobilization. Front Pharmacol. 2017;8:388. doi:10.3389/fphar.2017.00388. PubMed PMID: 28670281; PubMed Central PMCID: PMCPMC5472688. PubMed DOI PMC

Wong VK, Li T, Law BY, et al. Saikosaponin-d, a novel SERCA inhibitor, induces autophagic cell death in apoptosis-defective cells. Cell Death Dis. 2013;4:e720. doi:10.1038/cddis.2013.217. PubMed PMID: 23846222; PubMed Central PMCID: PMC3730398. PubMed DOI PMC

Xu SW, Law BY, Mok SW, et al. Autophagic degradation of epidermal growth factor receptor in gefitinib-resistant lung cancer by celastrol. Int J Oncol. 2016. Oct;49(4):1576–88. doi:10.3892/ijo.2016.3644. PubMed PMID: 27498688. PubMed DOI

Tsuyoshi H, Wong VKW, Han Y, et al. Saikosaponin-d, a calcium mobilizing agent, sensitizes chemoresistant ovarian cancer cells to cisplatin-induced apoptosis by facilitating mitochondrial fission and G2/M arrest. Oncotarget. 2017. Nov 21;8(59):99825–99840. doi: 10.18632/oncotarget.21076. PubMed PMID: 29245943; PubMed Central PMCID: PMCPMC5725134. PubMed DOI PMC

Law BY, Chan WK, Xu SW, et al. Natural small-molecule enhancers of autophagy induce autophagic cell death in apoptosis-defective cells. Sci Rep. 2014. Jul 1;4:5510. doi:10.1038/srep05510. PubMed PMID: 24981420; PubMed Central PMCID: PMCPMC4076737. PubMed DOI PMC

Law BY, Mok SW, Chan WK, et al. Hernandezine, a novel AMPK activator induces autophagic cell death in drug-resistant cancers. Oncotarget. 2016. Feb 16;7(7):8090–104. doi:10.18632/oncotarget.6980. PubMed PMID: 26811496; PubMed Central PMCID: PMCPMC4884978. PubMed DOI PMC

Law BYK, Gordillo-Martinez F, Qu YQ, et al. Thalidezine, a novel AMPK activator, eliminates apoptosis-resistant cancer cells through energy-mediated autophagic cell death. Oncotarget. 2017. May 2;8(18):30077–30091. doi:10.18632/oncotarget.15616. PubMed PMID: 28404910; PubMed Central PMCID: PMCPMC5444727. PubMed DOI PMC

Zhou X, Qu YQ, Zheng Z, et al. Novel dauricine derivatives suppress cancer via autophagy-dependent cell death. Bioorg Chem. 2019. Mar;83:450–460. doi:10.1016/j.bioorg.2018.10.074. PubMed PMID: 30448723. PubMed DOI

Wong VKW, Zeng W, Chen J, et al. Tetrandrine, an Activator of Autophagy, Induces Autophagic Cell Death via PKC-alpha Inhibition and mTOR-Dependent Mechanisms. Front Pharmacol. 2017;8:351. doi:10.3389/fphar.2017.00351. PubMed PMID: 28642707; PubMed Central PMCID: PMCPMC5462963. PubMed DOI PMC

Teng JF, Qin DL, Mei QB, et al. Polyphyllin VI, a saponin from Trillium tschonoskii Maxim. induces apoptotic and autophagic cell death via the ROS triggered mTOR signaling pathway in non-small cell lung cancer. Pharmacol Res. 2019. Sep;147:104396. doi:10.1016/j.phrs.2019.104396. PubMed PMID: 31404628. PubMed DOI

Wei P, Zhang L, Lu Y, et al. C60(Nd) nanoparticles enhance chemotherapeutic susceptibility of cancer cells by modulation of autophagy [Research Support, Non-U.S. Gov’t]. Nanotechnology. 2010. Dec 10;21(49):495101. doi:10.1088/0957-4484/21/49/495101. PubMed PMID: 21071824; eng. PubMed DOI

Mohammadinejad R, Moosavi MA, Tavakol S, et al. Necrotic, apoptotic and autophagic cell fates triggered by nanoparticles. Autophagy. 2019. Jan;15(1):4–33. doi:10.1080/15548627.2018.1509171. PubMed PMID: 30160607; PubMed Central PMCID: PMCPMC6287681. PubMed DOI PMC

Lee DH, Goldberg AL.. Proteasome inhibitors: valuable new tools for cell biologists [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S. Review]. Trends Cell Biol. 1998. Oct;8(10):397–403. PubMed PMID: 9789328; eng. PubMed

Mehdi S. Cell-penetrating inhibitors of calpain [Review]. Trends Biochem Sci. 1991. Apr;16(4):150–3. PubMed PMID: 1877091; eng. PubMed

Holen I, Gordon PB, Seglen PO.. Inhibition of hepatocytic autophagy by okadaic acid and other protein phosphatase inhibitors [Research Support, Non-U.S. Gov’t]. Eur J Biochem/FEBS. 1993. Jul 1;215(1):113–22. PubMed PMID: 8393787; eng. PubMed

Sasaki K, Murata M, Yasumoto T, et al. Affinity of okadaic acid to type-1 and type-2A protein phosphatases is markedly reduced by oxidation of its 27-hydroxyl group. Biochem J. 1994. Mar 1;298:259–62. PubMed PMID: 8135728; eng. PubMed PMC

Robinson DG, Albrecht S, Moriyasu Y.. The V-ATPase inhibitors concanamycin A and bafilomycin A lead to Golgi swelling in tobacco BY-2 cells [Research Support, Non-U.S. Gov’t]. Protoplasma. 2004. Dec;224(3–4):255–60. doi:10.1007/s00709-004-0070-6. PubMed PMID: 15614486; eng. PubMed DOI

Zoncu R, Bar-Peled L, Efeyan A, et al. mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H-ATPase [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Science. 2011. Nov 4;334(6056):678–83. doi:10.1126/science.1207056. PubMed PMID: 22053050; PubMed Central PMCID: PMC3211112. eng. PubMed DOI PMC

Zhang CS, Jiang B, Li M, et al. The lysosomal v-ATPase-Ragulator complex is a common activator for AMPK and mTORC1, acting as a switch between catabolism and anabolism. Cell Metab. 2014. Sep 2;20(3):526–40. doi:10.1016/j.cmet.2014.06.014. PubMed PMID: 25002183. PubMed DOI

Wu YC, Wu WK, Li Y, et al. Inhibition of macroautophagy by bafilomycin A1 lowers proliferation and induces apoptosis in colon cancer cells. Biochem Biophys Res Commun. 2009. May 1;382(2):451–6. doi:10.1016/j.bbrc.2009.03.051. PubMed PMID: 19289106; eng. PubMed DOI

Vats S, Manjithaya R.. A reversible autophagy inhibitor blocks autophagosome-lysosome fusion by preventing Stx17 loading onto auto-phagosomes. Mol Biol Cell. 2019. Aug 1;30(17):2283–2295. doi:10.1091/mbc.E18-08-0482. PubMed PMID: 31188703; PubMed Central PMCID: PMCPMC6743457. PubMed DOI PMC

Ostenfeld MS, Hoyer-Hansen M, Bastholm L, et al. Anti-cancer agent siramesine is a lysosomotropic detergent that induces cytoprotective autophagosome accumulation [Research Support, Non-U.S. Gov’t]. Autophagy. 2008. May;4(4):487–99. PubMed PMID: 18305408; eng. PubMed

Amaravadi RK, Yu D, Lum JJ, et al. Autophagy inhibition enhances therapy-induced apoptosis in a Myc-induced model of lymphoma. J Clin Invest. 2007. Jan 18;117:326–36. PubMed PMID: 17235397. PubMed PMC

Garcia-Garcia A, Anandhan A, Burns M, et al. Impairment of Atg5-dependent autophagic flux promotes paraquat- and MPP(+)-induced apoptosis but not rotenone or 6-hydroxydopamine toxicity. Toxicol Sci. 2013. Nov;136(1):166–82. doi:10.1093/toxsci/kft188. PubMed PMID: 23997112; PubMed Central PMCID: PMC3829573. PubMed DOI PMC

Maclean KH, Dorsey FC, Cleveland JL, et al. Targeting lysosomal degradation induces p53-dependent cell death and prevents cancer in mouse models of lymphomagenesis. J Clin Invest. 2008. Jan;118(1):79–88. doi: 10.1172/JCI33700. PubMed PMID: 18097482; PubMed Central PMCID: PMC2148253. PubMed DOI PMC

Poole B, Ohkuma S.. Effect of weak bases on the intralysosomal pH in mouse peritoneal macrophages. J Cell Biol. 1981. Sep;90(3):665–9. PubMed PMID: 6169733; PubMed Central PMCID: PMC2111912. PubMed PMC

Matsuoka K, Higuchi T, Maeshima M, et al. A vacuolar-type H+-ATPase in a nonvacuolar organelle is required for the sorting of soluble vacuolar protein precursors in tobacco cells. Plant Cell. 1997. Apr;9(4):533–546. doi:10.1105/tpc.9.4.533. PubMed PMID: 12237363; PubMed Central PMCID: PMC156937. Eng. PubMed DOI PMC

Yano K, Yanagisawa T, Mukae K, et al. Dissection of autophagy in tobacco BY-2 cells under sucrose starvation conditions using the vacuolar H(+)-ATPase inhibitor concanamycin A and the autophagy-related protein Atg8. Plant Signal Behav. 2015;10(11):e1082699. doi:10.1080/15592324.2015.1082699. PubMed PMID: 26368310; PubMed Central PMCID: PMCPMC4883836. PubMed DOI PMC

Arstila AU, Nuuja IJ, Trump BF.. Studies on cellular autophagocytosis. Vinblastine-induced autophagy in the rat liver. Exp Cell Res. 1974. Aug;87(2):249–52. PubMed PMID: 4415937; eng. PubMed

Hirsimaki Y, Arstila AU, Trump BF.. Autophagocytosis: in vitro induction by microtuble poisons. Exp Cell Res. 1975. Apr;92(1):11–4. PubMed PMID: 1169154; eng. PubMed

Réz G, Fellinger E, Reti M, et al. Time course of quantitative morphological changes of the autophagic-lysosomal compartment of murine seminal vesicle epithelial cells under the influence of vinblastine. J Submicrosc Cytol Pathol. 1990. Oct;22(4):529–34. PubMed PMID: 2282639; eng. PubMed

Oliva O, Réz G, Pálfia Z, et al. Dynamics of vinblastine-induced autophagocytosis in murine pancreatic acinar cells: influence of cycloheximide post-treatments. Exp Mol Pathol. 1992. Feb;56(1):76–86. PubMed PMID: 1547871; eng. PubMed

Dominguez-Martin E, Cardenal-Munoz E, King JS, et al. Methods to Monitor and Quantify Autophagy in the Social Amoeba Dictyostelium discoideum. Cells. 2017. Jul 3;6(3). doi:10.3390/cells6030018. PubMed PMID: 28671610; PubMed Central PMCID: PMCPMC5617964. PubMed DOI PMC

Mejlvang J, Olsvik H, Svenning S, et al. Starvation induces rapid degradation of selective autophagy receptors by endosomal microautophagy. J Cell Biol. 2018. Oct 1;217(10):3640–3655. doi:10.1083/jcb.201711002. PubMed PMID: 30018090; PubMed Central PMCID: PMCPMC6168274. PubMed DOI PMC

Feldman ME, Apsel B, Uotila A, et al. Active-site inhibitors of mTOR target rapamycin-resistant outputs of mTORC1 and mTORC2 [Research Support, Non-U.S. Gov’t]. PLoS Biol. 2009. Feb 10;7(2):e38. doi:10.1371/journal.pbio.1000038. PubMed PMID: 19209957; PubMed Central PMCID: PMC2637922. eng. PubMed DOI PMC

Fleming A, Noda T, Yoshimori T, et al. Chemical modulators of autophagy as biological probes and potential therapeutics [Research Support, Non-U.S. Gov’t Review]. Nat Chem Biol. 2011. Jan;7(1):9–17. doi:10.1038/nchembio.500. PubMed PMID: 21164513; eng. PubMed DOI

Yu K, Toral-Barza L, Shi C, et al. Biochemical, cellular, and in vivo activity of novel ATP-competitive and selective inhibitors of the mammalian target of rapamycin. Cancer Res. 2009. Aug 1;69(15):6232–40. doi:10.1158/0008-5472.CAN-09-0299. PubMed PMID: 19584280; eng. PubMed DOI

Chresta CM, Davies BR, Hickson I, et al. AZD8055 is a potent, selective, and orally bioavailable ATP-competitive mammalian target of rapamycin kinase inhibitor with in vitro and in vivo antitumor activity. Cancer Res. 2010. Jan 1;70(1):288–98. doi:10.1158/0008-5472.CAN-09-1751. PubMed PMID: 20028854; eng. PubMed DOI

Roscic A, Baldo B, Crochemore C, et al. Induction of autophagy with catalytic mTOR inhibitors reduces huntingtin aggregates in a neuronal cell model [Research Support, Non-U.S. Gov’t]. J Neurochem. 2011. Oct;119(2):398–407. doi:10.1111/j.1471-4159.2011.07435.x. PubMed PMID: 21854390; eng. PubMed DOI

Fan QW, Cheng C, Hackett C, et al. Akt and autophagy cooperate to promote survival of drug-resistant glioma [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Sci Signal. 2010;3(147):ra81. doi:10.1126/scisignal.2001017. PubMed PMID: 21062993; PubMed Central PMCID: PMC3001107. eng. PubMed DOI PMC

Yang L, Li P, Fu S, et al. Defective hepatic autophagy in obesity promotes ER stress and causes insulin resistance [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Cell Metab. 2010. Jun 9;11(6):467–78. doi:10.1016/j.cmet.2010.04.005. PubMed PMID: 20519119; PubMed Central PMCID: PMC2881480. eng. PubMed DOI PMC

Yamamoto A, Yue Z.. Autophagy and its normal and pathogenic States in the brain. Annu Rev Neurosci. 2014. Jul 8;37:55–78. doi:10.1146/annurev-neuro-071013-014149. PubMed PMID: 24821313. PubMed DOI

Tsvetkov AS, Miller J, Arrasate M, et al. A small-molecule scaffold induces autophagy in primary neurons and protects against toxicity in a Huntington disease model [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Proc Natl Acad Sci U S A. 2010. Sep 28;107(39):16982–7. doi:10.1073/pnas.1004498107. PubMed PMID: 20833817; PubMed Central PMCID: PMC2947884. eng. PubMed DOI PMC

Williams A, Sarkar S, Cuddon P, et al. Novel targets for Huntington’s disease in an mTOR-independent autophagy pathway [Research Support, Non-U.S. Gov’t]. Nat Chem Biol. 2008. May;4(5):295–305. doi:10.1038/nchembio.79. PubMed PMID: 18391949; PubMed Central PMCID: PMC2635566. eng. PubMed DOI PMC

Palomo GM, Cerrato T, Gargini R, et al. Silencing of frataxin gene expression triggers p53-dependent apoptosis in human neuron-like cells [Research Support, Non-U.S. Gov’t]. Hum Mol Genet. 2011. Jul 15;20(14):2807–22. doi:10.1093/hmg/ddr187. PubMed PMID: 21531789; eng. PubMed DOI

Bolinches-Amoros A, Molla B, Pla-Martin D, et al. Mitochondrial dysfunction induced by frataxin deficiency is associated with cellular senescence and abnormal calcium metabolism. Front Cell Neurosci. 2014;8:124. doi:10.3389/fncel.2014.00124. PubMed PMID: 24860428; PubMed Central PMCID: PMC4026758. PubMed DOI PMC

Sakagami H, Kawase M, Wakabayashi H, et al. Factors that affect the type of cell death induced by chemicals. Autophagy. 2007. Sep-Oct;3(5):493–5. PubMed PMID: 17611389; eng. PubMed

Doelling JH, Walker JM, Friedman EM, et al. The APG8/12-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S. Research Support, U.S. Gov’t, P.H.S.]. J Biol Chem. 2002. Sep 6;277(36):33105–14. doi:10.1074/jbc.M204630200. PubMed PMID: 12070171; eng. PubMed DOI

Fimia GM, Stoykova A, Romagnoli A, et al. Ambra1 regulates autophagy and development of the nervous system. Nature. 2007. Jun 28;447(7148):1121–5. PubMed PMID: 17589504; eng. PubMed

Kuma A, Hatano M, Matsui M, et al. The role of autophagy during the early neonatal starvation period. Nature. 2004. Dec 23;432(7020):1032–6. PubMed PMID: 15525940; eng. PubMed

Hwang S, Maloney NS, Bruinsma MW, et al. Nondegradative role of Atg5-Atg12/Atg16L1 autophagy protein complex in antiviral activity of interferon gamma. Cell Host Microbe. 2012. Apr 19;11(4):397–409. doi:10.1016/j.chom.2012.03.002. PubMed PMID: 22520467; PubMed Central PMCID: PMC3348177. PubMed DOI PMC

Zhu H, Wu H, Liu X, et al. Regulation of autophagy by a beclin 1-targeted microRNA, miR-30a, in cancer cells [Research Support, N.I.H., Extramural Research Support, U.S. Gov’t, Non-P.H.S.]. Autophagy. 2009. Aug;5(6):816–23. PubMed PMID: 19535919; eng. PubMed PMC

Hamacher-Brady A, Brady NR, Logue SE, et al. Response to myocardial ischemia/reperfusion injury involves Bnip3 and autophagy. Cell Death Differ. 2007. Jan;14(1):146–57. PubMed PMID: 16645637; eng. PubMed

Poeck H, Besch R, Maihoefer C, et al. 5ʹ-Triphosphate-siRNA: turning gene silencing and Rig-I activation against melanoma [Research Support, Non-U.S. Gov’t]. Nat Med. 2008. Nov;14(11):1256–63. doi:10.1038/nm.1887. PubMed PMID: 18978796; eng. PubMed DOI

Delgado MA, Elmaoued RA, Davis AS, et al. Toll-like receptors control autophagy [Research Support, N.I.H., Extramural]. EMBO J. 2008. Apr 9;27(7):1110–21. doi:10.1038/emboj.2008.31. PubMed PMID: 18337753; PubMed Central PMCID: PMC2323261. eng. PubMed DOI PMC

Pua HH, Dzhagalov I, Chuck M, et al. A critical role for the autophagy gene Atg5 in T cell survival and proliferation [Research Support, N.I.H., Extramural]. J Exp Med. 2007. Jan 22;204(1):25–31. doi:10.1084/jem.20061303. PubMed PMID: 17190837; PubMed Central PMCID: PMC2118420. eng. PubMed DOI PMC

Miller BC, Zhao Z, Stephenson LM, et al. The autophagy gene ATG5 plays an essential role in B lymphocyte development [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Autophagy. 2008. Apr;4(3):309–14. PubMed PMID: 18188005; eng. PubMed

Lee JS, Li Q, Lee JY, et al. FLIP-mediated autophagy regulation in cell death control [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Nat Cell Biol. 2009. Nov;11(11):1355–62. doi:10.1038/ncb1980. PubMed PMID: 19838173; PubMed Central PMCID: PMC2802862. eng. PubMed DOI PMC

Kyei GB, Dinkins C, Davis AS, et al. Autophagy pathway intersects with HIV-1 biosynthesis and regulates viral yields in macrophages [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. J Cell Biol. 2009. Jul 27;186(2):255–68. doi:10.1083/jcb.200903070. PubMed PMID: 19635843; PubMed Central PMCID: PMC2717652. eng. PubMed DOI PMC

Choy A, Dancourt J, Mugo B, et al. The Legionella effector RavZ inhibits host autophagy through irreversible Atg8 deconjugation. Science. 2012. Nov 23;338(6110):1072–6. doi:10.1126/science.1227026. PubMed PMID: 23112293; PubMed Central PMCID: PMCPMC3682818. PubMed DOI PMC

Kwon DH, Kim S, Jung YO, et al. The 1:2 complex between RavZ and LC3 reveals a mechanism for deconjugation of LC3 on the phagophore membrane. Autophagy. 2017. Jan 2;13(1):70–81. doi:10.1080/15548627.2016.1243199. PubMed PMID: 27791457; PubMed Central PMCID: PMCPMC5240826. PubMed DOI PMC

David S, Rusniok C, Mentasti M, et al. Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently. Genome Res. 2016. Nov;26(11):1555–1564. doi:10.1101/gr.209536.116. PubMed PMID: 27662900; PubMed Central PMCID: PMCPMC5088597. PubMed DOI PMC

Gomez-Valero L, Buchrieser C.. Intracellular parasitism, the driving force of evolution of Legionella pneumophila and the genus Legionella. Genes Immun. 2019. May;20(5):394–402. doi:10.1038/s41435-019-0074-z. PubMed PMID: 31053752. PubMed DOI

Rolando M, Escoll P, Nora T, et al. Legionella pneumophila S1P-lyase targets host sphingolipid metabolism and restrains autophagy. Proc Natl Acad Sci U S A. 2016. Feb 16;113(7):1901–1906. doi:10.1073/pnas.1522067113. PubMed PMID: 26831115; PubMed Central PMCID: PMCPMC4763766. PubMed DOI PMC

Kimball SR, Siegfried BA, Jefferson LS.. Glucagon represses signaling through the mammalian target of rapamycin in rat liver by activating AMP-activated protein kinase. J Biol Chem. 2004. Dec 24;279(52):54103–9. PubMed PMID: 15494402; eng. PubMed

Blommaart EF, Luiken JJ, Blommaart PJ, et al. Phosphorylation of ribosomal protein S6 is inhibitory for autophagy in isolated rat hepatocytes. J Biol Chem 1995. Feb 3;270(5):2320–6. PubMed PMID: 7836465. PubMed

Klionsky DJ, Meijer AJ, Codogno P, et al. Autophagy and p70S6 kinase. Autophagy. 2005. Apr;1(1):59–61. PubMed PMID: 16874035. PubMed

Noda T, Ohsumi Y.. Tor, a phosphatidylinositol kinase homologue, controls autophagy in yeast. J Biol Chem 1998. Feb 13;273(7):3963–6. PubMed PMID: 9461583. PubMed

Sarkar S, Floto RA, Berger Z, et al. Lithium induces autophagy by inhibiting inositol monophosphatase. J Cell Biol 2005. Sep 26;170(7):1101–11. PubMed PMID: 16186256. PubMed PMC

Renna M, Jimenez-Sanchez M, Sarkar S, et al. Chemical inducers of autophagy that enhance the clearance of mutant proteins in neurodegenerative diseases. J Biol Chem. 2010. Apr 9;285(15):11061–7. doi:10.1074/jbc.R109.072181. PubMed PMID: 20147746; PubMed Central PMCID: PMC2856980. PubMed DOI PMC

Zhang L, Yu J, Pan H, et al. Small molecule regulators of autophagy identified by an image-based high-throughput screen. Proc Natl Acad Sci USA. 2007;104:19023–19028. PubMed PMC

Shin SY, Lee KS, Choi YK, et al. The antipsychotic agent chlorpromazine induces autophagic cell death by inhibiting the Akt/mTOR pathway in human U-87MG glioma cells. Carcinogenesis. 2013. Sep;34(9):2080–9. doi:10.1093/carcin/bgt169. PubMed PMID: 23689352. PubMed DOI

Wu CH, Bai LY, Tsai MH, et al. Pharmacological exploitation of the phenothiazine antipsychotics to develop novel antitumor agents-A drug repurposing strategy. Sci Rep. 2016. Jun 9;6:27540. doi:10.1038/srep27540. PubMed PMID: 27277973; PubMed Central PMCID: PMCPMC4899727. PubMed DOI PMC

Chu CW, Ko HJ, Chou CH, et al. Thioridazine Enhances P62-Mediated Autophagy and Apoptosis Through Wnt/beta-Catenin Signaling Pathway in Glioma Cells. Int J Mol Sci. 2019. Jan 22;20(3). doi:10.3390/ijms20030473. PubMed PMID: 30678307; PubMed Central PMCID: PMCPMC6386927. PubMed DOI PMC

Medeiros HCD, Colturato-Kido C, Ferraz LS, et al. AMPK activation induced by promethazine increases NOXA expression and Beclin-1 phosphorylation and drives autophagy-associated apoptosis in chronic myeloid leukemia. Chem Biol Interact. 2020. Jan 5;315:108888. doi:10.1016/j.cbi.2019.108888. PubMed PMID: 31682805. PubMed DOI

Decuypere JP, Welkenhuyzen K, Luyten T, et al. Ins(1,4,5)P3 receptor-mediated Ca2+ signaling and autophagy induction are interrelated. Autophagy. 2011. Dec;7(12):1472–89. doi:10.4161/auto.7.12.17909. PubMed PMID: 22082873; PubMed Central PMCID: PMCPMC3327615. PubMed DOI PMC

Hoyer-Hansen M, Bastholm L, Szyniarowski P, et al. Control of macroautophagy by calcium, calmodulin-dependent kinase kinase-[b], and Bcl-2 [Research Support, Non-U.S. Gov’t]. Mol Cell. 2007. Jan 26;25(2):193–205. doi:10.1016/j.molcel.2006.12.009. PubMed PMID: 17244528; eng. PubMed DOI

Decuypere JP, Kindt D, Luyten T, et al. mTOR-Controlled Autophagy Requires Intracellular Ca(2+) Signaling. PLoS One. 2013;8(4):e61020. doi:10.1371/journal.pone.0061020. PubMed PMID: 23565295; PubMed Central PMCID: PMC3614970. PubMed DOI PMC

Kary C. Liver autophagy’s sweet side. Nat Cell Biol. 2018. Mar;20(3):224. doi:10.1038/s41556-018-0059-6. PubMed PMID: 29476155. PubMed DOI

Szalai P, Parys JB, Bultynck G, et al. Nonlinear relationship between ER Ca(2+) depletion versus induction of the unfolded protein response, autophagy inhibition, and cell death. Cell Calcium. 2018. Dec;76:48–61. doi:10.1016/j.ceca.2018.09.005. PubMed PMID: 30261424. PubMed DOI

Wong VKW, Qiu C, Xu SW, et al. Ca(2+) signalling plays a role in celastrol-mediated suppression of synovial fibroblasts of rheumatoid arthritis patients and experimental arthritis in rats. Br J Pharmacol. 2019. Aug;176(16):2922–2944. doi:10.1111/bph.14718. PubMed PMID: 31124139; PubMed Central PMCID: PMCPMC6637043. PubMed DOI PMC

Qu YQ, Gordillo-Martinez F, Law BYK, et al. 2-Aminoethoxydiphenylborane sensitizes anti-tumor effect of bortezomib via suppression of calcium-mediated autophagy. Cell Death Dis. 2018. Mar 2;9(3):361. doi:10.1038/s41419-018-0397-0. PubMed PMID: 29500417; PubMed Central PMCID: PMCPMC5834458. PubMed DOI PMC

Decuypere JP, Bultynck G, Parys JB.. A dual role for Ca(2+) in autophagy regulation. Cell Calcium 2011;50:242–50. PubMed

Luyten T, Welkenhuyzen K, Roest G, et al. Resveratrol-induced autophagy is dependent on IP3Rs and on cytosolic Ca(2). Biochim Biophys Acta Mol Cell Res. 2017. Jun;1864(6):947–956. doi:10.1016/j.bbamcr.2017.02.013. PubMed PMID: 28254579. PubMed DOI

Roest G, Hesemans E, Welkenhuyzen K, et al. The ER Stress Inducer l-Azetidine-2-Carboxylic Acid Elevates the Levels of Phospho-eIF2alpha and of LC3-II in a Ca(2+)-Dependent Manner. Cells. 2018. Nov 30;7(12). doi:10.3390/cells7120239. PubMed PMID: 30513588; PubMed Central PMCID: PMCPMC6316609. PubMed DOI PMC

Tuncer S, Sade-Memisoglu A, Keskus AG, et al. Enhanced expression of HNF4alpha during intestinal epithelial differentiation is involved in the activation of ER stress. FEBS J. 2020. Jun;287(12):2504–2523. doi:10.1111/febs.15152. PubMed PMID: 31762160. PubMed DOI

Bootman MD, Chehab T, Bultynck G, et al. The regulation of autophagy by calcium signals: Do we have a consensus? Cell Calcium. 2018. Mar;70:32–46. doi:10.1016/j.ceca.2017.08.005. PubMed PMID: 28847414. PubMed DOI

Pereira GJ, Antonioli M, Hirata H, et al. Glutamate induces autophagy via the two-pore channels in neural cells. Oncotarget. 2017. Feb 21;8(8):12730–12740. doi:10.18632/oncotarget.14404. PubMed PMID: 28055974; PubMed Central PMCID: PMCPMC5355049. PubMed DOI PMC

Pereira GJ, Hirata H, Fimia GM, et al. Nicotinic acid adenine dinucleotide phosphate (NAADP) regulates autophagy in cultured astrocytes [Research Support, Non-U.S. Gov’t]. J Biol Chem. 2011. Aug 12;286(32):27875–81. doi:10.1074/jbc.C110.216580. PubMed PMID: 21610076; PubMed Central PMCID: PMC3151033. eng. PubMed DOI PMC

Cang C, Zhou Y, Navarro B, et al. mTOR regulates lysosomal ATP-sensitive two-pore Na(+) channels to adapt to metabolic state. Cell. 2013. Feb 14;152(4):778–90. doi: 10.1016/j.cell.2013.01.023. PubMed PMID: 23394946; PubMed Central PMCID: PMC3908667. PubMed DOI PMC

Ogunbayo OA, Duan J, Xiong J, et al. mTORC1 controls lysosomal Ca(2+) release through the two-pore channel TPC2. Sci Signal. 2018. Apr 10;11(525). doi: 10.1126/scisignal.aao5775. PubMed PMID: 29636391; PubMed Central PMCID: PMCPMC6055479. PubMed DOI PMC

Sun X, Yang Y, Zhong XZ, et al. A negative feedback regulation of MTORC1 activity by the lysosomal Ca(2+) channel MCOLN1 (mucolipin 1) using a CALM (calmodulin)-dependent mechanism. Autophagy. 2018;14(1):38–52. doi:10.1080/15548627.2017.1389822. PubMed PMID: 29460684; PubMed Central PMCID: PMCPMC5846559. PubMed DOI PMC

Medina DL, Di Paola S, Peluso I, et al. Lysosomal calcium signalling regulates autophagy through calcineurin and TFEB. Nat Cell Biol. 2015. Mar;17(3):288–99. doi:10.1038/ncb3114. PubMed PMID: 25720963. PubMed DOI PMC

Bootman MD, Bultynck G.. Fundamentals of cellular calcium signaling: a primer. Cold Spring Harb Perspect Biol. 2020. Jan 2;12(1). doi:10.1101/cshperspect.a038802. PubMed PMID: 31427372. PubMed DOI PMC

Smith NA, Kress BT, Lu Y, et al. Fluorescent Ca(2+) indicators directly inhibit the Na,K-ATPase and disrupt cellular functions. Sci Signal. 2018. Jan 30;11(515). doi:10.1126/scisignal.aal2039. PubMed PMID: 29382785; PubMed Central PMCID: PMCPMC6190706. PubMed DOI PMC

Bootman MD, Allman S, Rietdorf K, et al. Deleterious effects of calcium indicators within cells; an inconvenient truth. Cell Calcium. 2018. Jul;73:82–87. doi:10.1016/j.ceca.2018.04.005. PubMed PMID: 29689523. PubMed DOI

Shoji-Kawata S, Sumpter R, Leveno M, et al. Identification of a candidate therapeutic autophagy-inducing peptide. Nature. 2013. Feb 14;494(7436):201–6. doi:10.1038/nature11866. PubMed PMID: 23364696; PubMed Central PMCID: PMC3788641. PubMed DOI PMC

Su M, Mei Y, Sanishvili R, et al. Targeting gamma-herpesvirus 68 Bcl-2-mediated down-regulation of autophagy. J Biol Chem. 2014. Mar 21;289(12):8029–40. doi:10.1074/jbc.M113.515361. PubMed PMID: 24443581; PubMed Central PMCID: PMC3961636. PubMed DOI PMC

Winter G, Hazan R, Bakalinsky AT, et al. Caffeine induces macroautophagy and confers a cytocidal effect on food spoilage yeast in combination with benzoic acid [Research Support, Non-U.S. Gov’t]. Autophagy. 2008. Jan;4(1):28–36. PubMed PMID: 17952024; eng. PubMed

Saiki S, Sasazawa Y, Imamichi Y, et al. Caffeine induces apoptosis by enhancement of autophagy via PI3K/Akt/mTOR/p70S6K inhibition. Autophagy. 2011. Feb;7(2):176–87. PubMed PMID: 21081844; PubMed Central PMCID: PMC3039768. PubMed PMC

Tsabar M, Eapen VV, Mason JM, et al. Caffeine impairs resection during DNA break repair by reducing the levels of nucleases Sae2 and Dna2. Nucleic Acids Res. 2015. Aug 18;43(14):6889–901. doi:10.1093/nar/gkv520. PubMed PMID: 26019182; PubMed Central PMCID: PMC4538808. PubMed DOI PMC

Fu J, Shao CJ, Chen FR, et al. Autophagy induced by valproic acid is associated with oxidative stress in glioma cell lines. Neuro Oncol. 2010. Apr;12(4):328–40. doi:10.1093/neuonc/nop005. PubMed PMID: 20308311; PubMed Central PMCID: PMC2940599. PubMed DOI PMC

Robert T, Vanoli F, Chiolo I, et al. HDACs link the DNA damage response, processing of double-strand breaks and autophagy. Nature. 2011. Mar 3;471(7336):74–9. doi:10.1038/nature09803. PubMed PMID: 21368826; PubMed Central PMCID: PMC3935290. PubMed DOI PMC

Bartholomew CR, Suzuki T, Du Z, et al. Ume6 transcription factor is part of a signaling cascade that regulates autophagy. Proc Natl Acad Sci U S A. 2012. Jul 10;109(28):11206–10. doi:10.1073/pnas.1200313109. PubMed PMID: 22733735; PubMed Central PMCID: PMC3396506. PubMed DOI PMC

Yi C, Ma M, Ran L, et al. Function and molecular mechanism of acetylation in autophagy regulation. Science. 2012. Apr 27;336(6080):474–7. doi:10.1126/science.1216990. PubMed PMID: 22539722. PubMed DOI

Koukourakis MI, Giatromanolaki A, Fylaktakidou K, et al. SMER28 is a mTOR-independent small molecule enhancer of autophagy that protects mouse bone marrow and liver against radiotherapy. Invest New Drugs. 2018. Oct;36(5):773–781. doi:10.1007/s10637-018-0566-0. PubMed PMID: 29387992. PubMed DOI

Xie N, Zhong L, Liu L, et al. Autophagy contributes to dasatinib-induced myeloid differentiation of human acute myeloid leukemia cells. Biochem Pharmacol. 2014. May 1;89(1):74–85. doi:10.1016/j.bcp.2014.02.019. PubMed PMID: 24607273. PubMed DOI

Romeo-Guitart D, Fores J, Herrando-Grabulosa M, et al. Neuroprotective Drug for Nerve Trauma Revealed Using Artificial Intelligence. Sci Rep. 2018. Jan 30;8(1):1879. doi:10.1038/s41598-018-19767-3. PubMed PMID: 29382857; PubMed Central PMCID: PMCPMC5790005. PubMed DOI PMC

Romeo-Guitart D, Leiva-Rodriguez T, Fores J, et al. Improved Motor Nerve Regeneration by SIRT1/Hif1a-Mediated Autophagy. Cells. 2019. Oct 30;8(11). doi:10.3390/cells8111354. PubMed PMID: 31671642; PubMed Central PMCID: PMCPMC6912449. PubMed DOI PMC

Romeo-Guitart D, Fores J, Navarro X, et al. Boosted regeneration and reduced denervated muscle atrophy by neuroheal in a pre-clinical model of lumbar root avulsion with delayed reimplantation. Sci Rep. 2017. Sep 20;7(1):12028. doi:10.1038/s41598-017-11086-3. PubMed PMID: 28931824; PubMed Central PMCID: PMCPMC5607317. PubMed DOI PMC

Romeo-Guitart D, Leiva-Rodriguez T, Espinosa-Alcantud M, et al. SIRT1 activation with neuroheal is neuroprotective but SIRT2 inhibition with AK7 is detrimental for disconnected motoneurons. Cell Death Dis. 2018. May 1;9(5):531. doi:10.1038/s41419-018-0553-6. PubMed PMID: 29748539; PubMed Central PMCID: PMCPMC5945655. PubMed DOI PMC

Mishra P, Rai S, Manjithaya R.. A novel dual luciferase based high throughput assay to monitor autophagy in real time in yeast S. cerevisiae. Biochem Biophys Rep. 2017. Sep;11:138–146. doi:10.1016/j.bbrep.2017.07.008. PubMed PMID: 28955778; PubMed Central PMCID: PMCPMC5614714. PubMed DOI PMC

Gama JB, Ohlmeier S, Martins TG, et al. Proteomic analysis of the action of the Mycobacterium ulcerans toxin mycolactone: targeting host cells cytoskeleton and collagen. PLoS Negl Trop Dis. 2014. Aug;8(8):e3066. doi:10.1371/journal.pntd.0003066. PubMed PMID: 25101965; PubMed Central PMCID: PMCPMC4125307. PubMed DOI PMC

Ogbechi J, Hall BS, Sbarrato T, et al. Inhibition of Sec61-dependent translocation by mycolactone uncouples the integrated stress response from ER stress, driving cytotoxicity via translational activation of ATF4. Cell Death Dis. 2018. Mar 14;9(3):397. doi:10.1038/s41419-018-0427-y. PubMed PMID: 29540678; PubMed Central PMCID: PMCPMC5852046. PubMed DOI PMC

Hall BS, Hill K, McKenna M, et al. The pathogenic mechanism of the Mycobacterium ulcerans virulence factor, mycolactone, depends on blockade of protein translocation into the ER. PLoS Pathog. 2014. Apr;10(4):e1004061. doi:10.1371/journal.ppat.1004061. PubMed PMID: 24699819; PubMed Central PMCID: PMCPMC3974873. PubMed DOI PMC

Capela C, Dossou AD, Silva-Gomes R, et al. Genetic variation in autophagy-related genes influences the risk and phenotype of buruli ulcer. PLoS Negl Trop Dis. 2016. Apr;10(4):e0004671. doi:10.1371/journal.pntd.0004671. PubMed PMID: 27128681; PubMed Central PMCID: PMCPMC4851401. PubMed DOI PMC

Qi X, Man SM, Malireddi RK, et al. Cathepsin B modulates lysosomal biogenesis and host defense against Francisella novicida infection. J Exp Med. 2016. Sep 19;213(10):2081–97. doi:10.1084/jem.20151938. PubMed PMID: 27551156; PubMed Central PMCID: PMCPMC5030800. PubMed DOI PMC

Katagiri N, Kuroda T, Kishimoto H, et al. The nucleolar protein nucleophosmin is essential for autophagy induced by inhibiting Pol I transcription. Sci Rep. 2015;5:8903. doi:10.1038/srep08903. PubMed PMID: 25754892; PubMed Central PMCID: PMC4354046. PubMed DOI PMC

Kreiner G, Bierhoff H, Armentano M, et al. A neuroprotective phase precedes striatal degeneration upon nucleolar stress. Cell Death Differ. 2013. Nov;20(11):1455–64. doi:10.1038/cdd.2013.66. PubMed PMID: 23764776; PubMed Central PMCID: PMC3792439. PubMed DOI PMC

Pfister AS. Emerging role of the nucleolar stress response in autophagy. Front Cell Neurosci. 2019;13:156. doi:10.3389/fncel.2019.00156. PubMed PMID: 31114481; PubMed Central PMCID: PMCPMC6503120. PubMed DOI PMC

Dannheisig DP, Beck E, Calzia E, et al. Loss of Peter Pan (PPAN) Affects Mitochondrial Homeostasis and Autophagic Flux. Cells. 2019. Aug 14;8(8). doi:10.3390/cells8080894. PubMed PMID: 31416196; PubMed Central PMCID: PMCPMC6721654. PubMed DOI PMC

Furuya N, Liang XH, Levine B.. Autophagy and cancer. In: Klionsky DJ, editor. Autophagy. Georgetown, TX: Landes Bioscience; 2004. p. 241–255.

de Medina P, Paillasse MR, Segala G, et al. Importance of cholesterol and oxysterols metabolism in the pharmacology of tamoxifen and other AEBS ligands. Chem Phys Lipids. 2011;164(6):432–7. doi:10.1016/j.chemphyslip.2011.05.005. PubMed PMID: 21641337. PubMed DOI

de Medina P, Payre B, Boubekeur N, et al. Ligands of the antiestrogen-binding site induce active cell death and autophagy in human breast cancer cells through the modulation of cholesterol metabolism [Research Support, Non-U.S. Gov’t]. Cell Death Differ. 2009. Oct;16(10):1372–84. doi:10.1038/cdd.2009.62. PubMed PMID: 19521424; eng. PubMed DOI

Sarkar S, Perlstein EO, Imarisio S, et al. Small molecules enhance autophagy and reduce toxicity in Huntington’s disease models. Nat Chem Biol. 2007. Jun;3(6):331–8. PubMed PMID: 17486044; eng. PubMed PMC

Savolainen MH, Richie CT, Harvey BK, et al. The beneficial effect of a prolyl oligopeptidase inhibitor, KYP-2047, on alpha-synuclein clearance and autophagy in A30P transgenic mouse. Neurobiol Dis. 2014. Aug;68:1–15. doi:10.1016/j.nbd.2014.04.003. PubMed PMID: 24746855. PubMed DOI PMC

Svarcbahs R, Julku U, Kilpelainen T, et al. New tricks of prolyl oligopeptidase inhibitors - A common drug therapy for several neurodegenerative diseases. Biochem Pharmacol. 2019. Mar;161:113–120. doi:10.1016/j.bcp.2019.01.013. PubMed PMID: 30660495. PubMed DOI

Svarcbahs R, Julku UH, Norrbacka S, et al. Removal of prolyl oligopeptidase reduces alpha-synuclein toxicity in cells and in vivo. Sci Rep. 2018. Jan 24;8(1):1552. doi:10.1038/s41598-018-19823-y. PubMed PMID: 29367610; PubMed Central PMCID: PMCPMC5784134. PubMed DOI PMC

Sarkar S, Davies JE, Huang Z, et al. Trehalose, a novel mTOR-independent autophagy enhancer, accelerates the clearance of mutant huntingtin and [a]-synuclein [Research Support, Non-U.S. Gov’t]. J Biol Chem. 2007. Feb 23;282(8):5641–52. doi:10.1074/jbc.M609532200. PubMed PMID: 17182613; eng. PubMed DOI

Kruger U, Wang Y, Kumar S, et al. Autophagic degradation of tau in primary neurons and its enhancement by trehalose. Neurobiol Aging. 2012. Dec 12;33:2291–305. doi:10.1016/j.neurobiolaging.2011.11.009. PubMed PMID: 22169203; Eng. PubMed DOI

Rusmini P, Cortese K, Crippa V, et al. Trehalose induces autophagy via lysosomal-mediated TFEB activation in models of motoneuron degeneration. Autophagy. 2019. Apr;15(4):631–651. doi:10.1080/15548627.2018.1535292. PubMed PMID: 30335591; PubMed Central PMCID: PMCPMC6526812. PubMed DOI PMC

Tien NT, Karaca I, Tamboli IY, et al. Trehalose Alters Subcellular Trafficking and the Metabolism of the Alzheimer-associated Amyloid Precursor Protein. J Biol Chem. 2016. May 13;291(20):10528–40. doi:10.1074/jbc.M116.719286. PubMed PMID: 26957541; PubMed Central PMCID: PMCPMC4865903. PubMed DOI PMC

Yoon YS, Cho ED, Jung Ahn W, et al. Is trehalose an autophagic inducer? Unraveling the roles of non-reducing disaccharides on autophagic flux and alpha-synuclein aggregation. Cell Death Dis. 2017. Oct 5;8(10):e3091. doi:10.1038/cddis.2017.501. PubMed PMID: 28981090; PubMed Central PMCID: PMCPMC5682667. PubMed DOI PMC

Kruse KB, Brodsky JL, McCracken AA.. Characterization of an ERAD gene as VPS30/ATG6 reveals two alternative and functionally distinct protein quality control pathways: one for soluble Z variant of human alpha-1 proteinase inhibitor (A1PiZ) and another for aggregates of A1PiZ. Mol Biol Cell. 2006. Jan;17(1):203–12. doi:10.1091/mbc.e04-09-0779. PubMed PMID: 16267277; PubMed Central PMCID: PMCPMC1345659. PubMed DOI PMC

Gossner G, Choi M, Tan L, et al. Genistein-induced apoptosis and autophagocytosis in ovarian cancer cells. Gynecol Oncol. 2007. Apr;105(1):23–30. doi:10.1016/j.ygyno.2006.11.009. PubMed PMID: 17234261. PubMed DOI

Nakamura Y, Yogosawa S, Izutani Y, et al. A combination of indol-3-carbinol and genistein synergistically induces apoptosis in human colon cancer HT-29 cells by inhibiting Akt phosphorylation and progression of autophagy. Mol Cancer. 2009. Nov 12;8:100. doi:10.1186/1476-4598-8-100. PubMed PMID: 19909554; PubMed Central PMCID: PMCPMC2784428. PubMed DOI PMC

Prietsch RF, Monte LG, da Silva FA, et al. Genistein induces apoptosis and autophagy in human breast MCF-7 cells by modulating the expression of proapoptotic factors and oxidative stress enzymes. Mol Cell Biochem. 2014. May;390(1–2):235–42. doi:10.1007/s11010-014-1974-x. PubMed PMID: 24573886. PubMed DOI

Suzuki R, Kang Y, Li X, et al. Genistein potentiates the antitumor effect of 5-Fluorouracil by inducing apoptosis and autophagy in human pancreatic cancer cells. Anticancer Res. 2014. Sep;34(9):4685–92. PubMed PMID: 25202045; PubMed Central PMCID: PMCPMC4240628. PubMed PMC

Castro L, Gao X, Moore AB, et al. A High Concentration of Genistein Induces Cell Death in Human Uterine Leiomyoma Cells by Autophagy. Expert Opin Environ Biol. 2016;5(Suppl 1). doi:10.4172/2325-9655.S1-003. PubMed PMID: 27512718; PubMed Central PMCID: PMCPMC4976942. PubMed DOI PMC

Pierzynowska K, Gaffke L, Hac A, et al. Correction of huntington’s disease phenotype by genistein-induced autophagy in the cellular model. Neuromolecular Med. 2018. Mar;20(1):112–123. doi:10.1007/s12017-018-8482-1. PubMed PMID: 29435951; PubMed Central PMCID: PMCPMC5834590. PubMed DOI PMC

Pierzynowska K, Podlacha M, Gaffke L, et al. Autophagy-dependent mechanism of genistein-mediated elimination of behavioral and biochemical defects in the rat model of sporadic Alzheimer’s disease. Neuropharmacology. 2019. Apr;148:332–346. doi:10.1016/j.neuropharm.2019.01.030. PubMed PMID: 30710571. PubMed DOI

Pierzynowska K, Gaffke L, Cyske Z, et al. Autophagy stimulation as a promising approach in treatment of neurodegenerative diseases. Metab Brain Dis. 2018. Aug;33(4):989–1008. doi:10.1007/s11011-018-0214-6. PubMed PMID: 29542037; PubMed Central PMCID: PMCPMC6060747. PubMed DOI PMC

Pierzynowska K, Gaffke L, Podlacha M, et al. Mucopolysaccharidosis and autophagy: controversies on the contribution of the process to the pathogenesis and possible therapeutic applications. Neuromolecular Med. 2019. Aug 1. doi:10.1007/s12017-019-08559-1. PubMed PMID: 31372809. PubMed DOI PMC

Moskot M, Montefusco S, Jakobkiewicz-Banecka J, et al. The phytoestrogen genistein modulates lysosomal metabolism and transcription factor EB (TFEB) activation. J Biol Chem. 2014. Jun 13;289(24):17054–69. doi:10.1074/jbc.M114.555300. PubMed PMID: 24770416; PubMed Central PMCID: PMCPMC4059147. PubMed DOI PMC

Lee KY, Kim JR, Choi HC.. Genistein-induced LKB1-AMPK activation inhibits senescence of VSMC through autophagy induction. Vascul Pharmacol. 2016. Jun;81:75–82. doi:10.1016/j.vph.2016.02.007. PubMed PMID: 26924458. PubMed DOI

Zhang H, Yang X, Pang X, et al. Genistein protects against ox-LDL-induced senescence through enhancing SIRT1/LKB1/AMPK-mediated autophagy flux in HUVECs. Mol Cell Biochem. 2019. May;455(1–2): 127–134. doi:10.1007/s11010-018-3476-8. PubMed PMID: 30443855. PubMed DOI

Bai X, Bai A, Honda JR, et al. Alpha-1-Antitrypsin Enhances Primary Human Macrophage Immunity Against Non-tuberculous Mycobacteria. Front Immunol. 2019;10:1417. doi:10.3389/fimmu.2019.01417. PubMed PMID: 31293581; PubMed Central PMCID: PMCPMC6606736. PubMed DOI PMC

Bai X, Feldman NE, Chmura K, et al. Inhibition of nuclear factor-kappa B activation decreases survival of Mycobacterium tuberculosis in human macrophages. PLoS One. 2013;8(4):e61925. doi:10.1371/journal.pone.0061925. PubMed PMID: 23634218; PubMed Central PMCID: PMCPMC3636238. PubMed DOI PMC

Hilchie AL, Wuerth K, Hancock RE.. Immune modulation by multifaceted cationic host defense (antimicrobial) peptides. Nat Chem Biol. 2013. Dec;9(12):761–8. doi:10.1038/nchembio.1393. PubMed PMID: 24231617. PubMed DOI

Alonso S, Pethe K, Russell DG, et al. Lysosomal killing of Mycobacterium mediated by ubiquitin-derived peptides is enhanced by autophagy. Proc Natl Acad Sci U S A. 2007. Apr 3;104(14):6031–6. doi:10.1073/pnas.0700036104. PubMed PMID: 17389386; PubMed Central PMCID: PMCPMC1851611. PubMed DOI PMC

Ponpuak M, Davis AS, Roberts EA, et al. Delivery of cytosolic components by autophagic adaptor protein p62 endows auto-phagosomes with unique antimicrobial properties [Research Support, N.I.H., Extramural]. Immunity. 2010. Mar 26;32(3):329–41. doi:10.1016/j.immuni.2010.02.009. PubMed PMID: 20206555; PubMed Central PMCID: PMC2846977. eng. PubMed DOI PMC

Bera A, Singh S, Nagaraj R, et al. Induction of autophagic cell death in Leishmania donovani by antimicrobial peptides. Mol Biochem Parasitol. 2003. Mar;127(1):23–35. doi:10.1016/s0166-6851(02)00300-6. PubMed PMID: 12615333. PubMed DOI

Rekha RS, Rao Muvva SS, Wan M, et al. Phenylbutyrate induces LL-37-dependent autophagy and intracellular killing of Mycobacterium tuberculosis in human macrophages. Autophagy. 2015;11(9):1688–99. doi:10.1080/15548627.2015.1075110. PubMed PMID: 26218841; PubMed Central PMCID: PMCPMC4590658. PubMed DOI PMC

Koshkina NV, Briggs K, Palalon F, et al. Autophagy and enhanced chemosensitivity in experimental pancreatic cancers induced by noninvasive radiofrequency field treatment. Cancer. 2014. Feb 15;120(4):480–91. doi:10.1002/cncr.28453. PubMed PMID: 24496866; PubMed Central PMCID: PMC3916783. PubMed DOI PMC

Suresh SN, Chavalmane AK, Pillai M, et al. Modulation of Autophagy by a Small Molecule Inverse Agonist of ERRalpha Is Neuroprotective. Front Mol Neurosci. 2018;11:109. doi:10.3389/fnmol.2018.00109. PubMed PMID: 29686608; PubMed Central PMCID: PMCPMC5900053. PubMed DOI PMC

Vicencio JM, Ortiz C, Criollo A, et al. The inositol 1,4,5-trisphosphate receptor regulates autophagy through its interaction with Beclin 1 [Research Support, Non-U.S. Gov’t]. Cell Death Differ. 2009. Jul;16(7):1006–17. doi:10.1038/cdd.2009.34. PubMed PMID: 19325567; eng. PubMed DOI

Dayan F, Bilton RL, Laferriere J, et al. Activation of HIF-1alpha in exponentially growing cells via hypoxic stimulation is independent of the Akt/mTOR pathway [Research Support, Non-U.S. Gov’t]. J Cell Physiol. 2009. Jan;218(1):167–74. doi:10.1002/jcp.21584. PubMed PMID: 18781596; eng. PubMed DOI

Yamashita S, Yurimoto H, Murakami D, et al. Lag-phase autophagy in the methylotrophic yeast Pichia pastoris [Research Support, Non-U.S. Gov’t]. Genes Cells Devot Mol Cell Mech 2009. Jul;14(7):861–70. doi:10.1111/j.1365-2443.2009.01316.x. PubMed PMID: 19549169; eng. PubMed DOI

van Zutphen T, Baerends RJ, Susanna KA, et al. Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis [Research Support, Non-U.S. Gov’t]. BMC genomics. 2010;11:1. doi:10.1186/1471-2164-11-1. PubMed PMID: 20044946; PubMed Central PMCID: PMC2827406. eng. PubMed DOI PMC

Moriyasu Y, Hattori M, Jauh G-Y, et al. Alpha tonoplast intrinsic protein is specifically associated with vacuole membrane involved in an autophagic process [Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. Plant Cell Physiol. 2003. Aug;44(8):795–802. PubMed PMID: 12941871; eng. PubMed

Inoue Y, Suzuki T, Hattori M, et al. AtATG genes, homologs of yeast autophagy genes, are involved in constitutive autophagy in Arabidopsis root tip cells [Research Support, Non-U.S. Gov’t]. Plant Cell Physiol. 2006. Dec;47(12):1641–52. doi:10.1093/pcp/pcl031. PubMed PMID: 17085765; eng. PubMed DOI

Yano K, Suzuki T, Moriyasu Y.. Constitutive autophagy in plant root cells [Comment]. Autophagy. 2007. Jul-Aug;3(4):360–2. PubMed PMID: 17426438; eng. PubMed

Gordon PB, Kisen GO, Kovacs AL, et al. Experimental characterization of the autophagic-lysosomal pathway in isolated rat hepatocytes. Biochem Soc Symp. 1989;55:129–43. PubMed PMID: 2619764; eng. PubMed

Poli A, Gordon PB, Schwarze PE, et al. Effects of insulin and anchorage on hepatocytic protein metabolism and amino acid transport. J Cell Sci. 1981. Apr;48:1–18. PubMed PMID: 7024288; eng. PubMed

Schliess F, Reissmann R, Reinehr R, et al. Involvement of integrins and Src in insulin signaling toward autophagic proteolysis in rat liver. J Biol Chem. 2004. May 14;279(20):21294–301. PubMed PMID: 14985360; eng. PubMed

vom Dahl S, Stoll B, Gerok W, et al. Inhibition of proteolysis by cell swelling in the liver requires intact microtubular structures. Biochem J. 1995. Jun 1;308(Pt 2):529–36. PubMed PMID: 7772037; eng. PubMed PMC

vom Dahl S, Dombrowski F, Schmitt M, et al. Cell hydration controls autophagosome formation in rat liver in a microtubule-dependent way downstream from p38MAPK activation. Biochem J. 2001. Feb 15;354(Pt 1):31–6. PubMed PMID: 11171076; eng. PubMed PMC

Shyu YJ, Liu H, Deng X, et al. Identification of new fluorescent protein fragments for bimolecular fluorescence complementation analysis under physiological conditions. BioTechniques. 2006. Jan;40(1):61–6. PubMed PMID: 16454041. PubMed

Colson YL, Grinstaff MW.. Biologically responsive polymeric nanoparticles for drug delivery. Adv Mater. 2012. Jul 24;24(28):3878–86. doi:10.1002/adma.201200420. PubMed PMID: 22988558. PubMed DOI

Stern ST, Adiseshaiah PP, Crist RM.. Autophagy and lysosomal dysfunction as emerging mechanisms of nanomaterial toxicity. Part Fibre Toxicol. 2012. Jun 14;9:20. doi:10.1186/1743-8977-9-20. PubMed PMID: 22697169; PubMed Central PMCID: PMCPMC3441384. PubMed DOI PMC

Anozie UC, Dalhaimer P.. Molecular links among non-biodegradable nanoparticles, reactive oxygen species, and autophagy. Adv Drug Deliv Rev. 2017. Dec 1;122:65–73. doi:10.1016/j.addr.2017.01.001. PubMed PMID: 28065863. PubMed DOI

Gallud A, Kloditz K, Ytterberg J, et al. Cationic gold nanoparticles elicit mitochondrial dysfunction: a multi-omics study. Sci Rep. 2019. Mar 13;9(1):4366. doi:10.1038/s41598-019-40579-6. PubMed PMID: 30867451; PubMed Central PMCID: PMCPMC6416392. PubMed DOI PMC

Hulea L, Markovic Z, Topisirovic I, et al. Biomedical Potential of mTOR Modulation by Nanoparticles. Trends Biotechnol. 2016. May;34(5):349–353. doi:10.1016/j.tibtech.2016.01.005. PubMed PMID: 26900005. PubMed DOI

Trudeau KM, Colby AH, Zeng J, et al. Lysosome acidification by photoactivated nanoparticles restores autophagy under lipotoxicity. J Cell Biol. 2016. Jul 4;214(1):25–34. doi:10.1083/jcb.201511042. PubMed PMID: 27377248; PubMed Central PMCID: PMCPMC4932370. PubMed DOI PMC

Zeng J, Shirihai OS, Grinstaff MW.. Degradable Nanoparticles Restore Lysosomal pH and Autophagic Flux in Lipotoxic Pancreatic Beta Cells. Adv Healthc Mater. 2019. Jun;8(12):e1801511. doi:10.1002/adhm.201801511. PubMed PMID: 30698920. PubMed DOI

Zeng J, Martin A, Han X, et al. Biodegradable PLGA nanoparticles restore lysosomal acidity and protect neural PC-12 cells against mitochondrial toxicity. Ind Eng Chem Res. 2019;58:13910–13917. PubMed PMC

Bourdenx M, Daniel J, Genin E, et al. Nanoparticles restore lysosomal acidification defects: Implications for Parkinson and other lysosomal-related diseases. Autophagy. 2016;12(3):472–83. doi:10.1080/15548627.2015.1136769. PubMed PMID: 26761717; PubMed Central PMCID: PMCPMC4835967. PubMed DOI PMC

Sadhu A, Ghosh I, Moriyasu Y, et al. Role of cerium oxide nanoparticle-induced autophagy as a safeguard to exogenous H2O2-mediated DNA damage in tobacco BY-2 cells. Mutagenesis. 2018. Apr 13;33(2):161–177. doi: 10.1093/mutage/gey004. PubMed PMID: 29506140. PubMed DOI

Liu Y, Yu H, Zhang X, et al. The protective role of autophagy in nephrotoxicity induced by bismuth nanoparticles through AMPK/mTOR pathway. Nanotoxicology. 2018. Aug;12(6):586–601. doi:10.1080/17435390.2018.1466932. PubMed PMID: 29732938. PubMed DOI

Tomic S, Janjetovic K, Mihajlovic D, et al. Graphene quantum dots suppress proinflammatory T cell responses via autophagy-dependent induction of tolerogenic dendritic cells. Biomaterials. 2017. Nov;146:13–28. doi:10.1016/j.biomaterials.2017.08.040. PubMed PMID: 28892752. PubMed DOI

Markovic ZM, Ristic BZ, Arsikin KM, et al. Graphene quantum dots as autophagy-inducing photodynamic agents. Biomaterials. 2012. Oct;33(29):7084–92. doi:10.1016/j.biomaterials.2012.06.060. PubMed PMID: 22795854. PubMed DOI

Moosavi MA, Sharifi M, Ghafary SM, et al. Photodynamic N-TiO2 nanoparticle treatment induces controlled ROS-mediated autophagy and terminal differentiation of leukemia cells. Sci Rep. 2016. Oct 4;6:34413. doi:10.1038/srep34413. PubMed PMID: 27698385; PubMed Central PMCID: PMCPMC5048164. PubMed DOI PMC

Liu R, Colby AH, Gilmore D, et al. Nanoparticle tumor localization, disruption of autophagosomal trafficking, and prolonged drug delivery improve survival in peritoneal mesothelioma. Biomaterials. 2016. Sep;102:175–86. doi:10.1016/j.biomaterials.2016.06.031. PubMed PMID: 27343465; PubMed Central PMCID: PMCPMC4948582. PubMed DOI PMC

Wu L, Zhang Y, Zhang C, et al. Tuning cell autophagy by diversifying carbon nanotube surface chemistry. ACS Nano. 2014. Mar 25;8(3):2087–99. doi:10.1021/nn500376w. PubMed PMID: 24552177; PubMed Central PMCID: PMCPMC5586106. PubMed DOI PMC

Zhang Y, Zheng F, Yang T, et al. Tuning the autophagy-inducing activity of lanthanide-based nanocrystals through specific surface-coating peptides. Nat Mater. 2012. Sep;11(9):817–26. doi:10.1038/nmat3363. PubMed PMID: 22797828. PubMed DOI

Seleverstov O, Zabirnyk O, Zscharnack M, et al. Quantum dots for human mesenchymal stem cells labeling. A size-dependent autophagy activation. Nano Lett. 2006. Dec;6(12):2826–32. PubMed PMID: 17163713; eng. PubMed

Zabirnyk O, Yezhelyev M, Seleverstov O.. Nanoparticles as a novel class of autophagy activators. Autophagy. 2007. May-Jun;3(3):278–81. doi:10.4161/auto.3916. PubMed PMID: 17351332. PubMed DOI

Cohignac V, Landry MJ, Ridoux A, et al. Carbon nanotubes, but not spherical nanoparticles, block autophagy by a shape-related targeting of lysosomes in murine macrophages. Autophagy. 2018;14(8):1323–1334. doi:10.1080/15548627.2018.1474993. PubMed PMID: 29938576; PubMed Central PMCID: PMCPMC6103705. PubMed DOI PMC

Ma X, Wu Y, Jin S, et al. Gold nanoparticles induce autophagosome accumulation through size-dependent nanoparticle uptake and lysosome impairment. ACS Nano 2011. Nov 22;5(11):8629–39. doi:10.1021/nn202155y. PubMed PMID: 21974862. PubMed DOI

Zhang JQ, Zhou W, Zhu SS, et al. Persistency of enlarged autolysosomes underscores nanoparticle-induced autophagy in hepatocytes. Small. 2017. Feb;13(7). doi:10.1002/smll.201602876. PubMed PMID: 27925395. PubMed DOI

Wang J, Li Y, Duan J, et al. Silica nanoparticles induce autophagosome accumulation via activation of the EIF2AK3 and ATF6 UPR pathways in hepatocytes. Autophagy. 2018;14(7):1185–1200. doi:10.1080/15548627.2018.1458174. PubMed PMID: 29940794; PubMed Central PMCID: PMCPMC6103719. PubMed DOI PMC

Liu HL, Zhang YL, Yang N, et al. A functionalized single-walled carbon nanotube-induced autophagic cell death in human lung cells through Akt-TSC2-mTOR signaling. Cell Death Dis. 2011. May 19;2:e159. doi:10.1038/cddis.2011.27. PubMed PMID: 21593791; PubMed Central PMCID: PMCPMC3122114. PubMed DOI PMC

Chen GY, Meng CL, Lin KC, et al. Graphene oxide as a chemosensitizer: diverted autophagic flux, enhanced nuclear import, elevated necrosis and improved antitumor effects. Biomaterials. 2015. Feb;40:12–22. doi:10.1016/j.biomaterials.2014.11.034. PubMed PMID: 25498801. PubMed DOI

Ha SW, Weitzmann MN, Beck GR, Jr.. Bioactive silica nanoparticles promote osteoblast differentiation through stimulation of autophagy and direct association with LC3 and p62. ACS Nano. 2014. Jun 24;8(6):5898–910. doi:10.1021/nn5009879. PubMed PMID: 24806912; PubMed Central PMCID: PMCPMC4076025. PubMed DOI PMC

Lin YX, Qiao SL, Wang Y, et al. An in situ intracellular self-assembly strategy for quantitatively and temporally monitoring autophagy. ACS Nano. 2017. Feb 28;11(2):1826–1839. doi:10.1021/acsnano.6b07843. PubMed PMID: 28112893. PubMed DOI

Lin YX, Wang Y, Qiao SL, et al.“In vivo self-assembled” nanoprobes for optimizing autophagy-mediated chemotherapy. Biomaterials. 2017. Oct;141:199–209. doi:10.1016/j.biomaterials.2017.06.042. PubMed PMID: 28689116. PubMed DOI

Choi KM, Nam HY, Na JH, et al. A monitoring method for Atg4 activation in living cells using peptide-conjugated polymeric nanoparticles. Autophagy. 2011. Sep;7(9):1052–62. doi:10.4161/auto.7.9.16451. PubMed PMID: 21610316. PubMed DOI

Neumann S, Pucadyil TJ, Schmid SL.. Analyzing membrane remodeling and fission using supported bilayers with excess membrane reservoir. Nat Protoc. 2013. Jan;8(1):213–22. doi:10.1038/nprot.2012.152. PubMed PMID: 23288321; PubMed Central PMCID: PMCPMC4753780. PubMed DOI PMC

Hervas JH, Landajuela A, Anton Z, et al. Human ATG3 binding to lipid bilayers: role of lipid geometry, and electric charge. Sci Rep. 2017. Nov 15;7(1):15614. doi:10.1038/s41598-017-15057-6. PubMed PMID: 29142222; PubMed Central PMCID: PMCPMC5688168. PubMed DOI PMC

King JS, Veltman DM, Insall RH.. The induction of autophagy by mechanical stress. Autophagy. 2011. Dec 1;7(12):1490–9. PubMed PMID: 22024750; Eng. PubMed PMC

Grodzki AC, Giulivi C, Lein PJ.. Oxygen tension modulates differentiation and primary macrophage functions in the human monocytic THP-1 cell line. PLoS One. 2013;8(1):e54926. doi:10.1371/journal.pone.0054926. PubMed PMID: 23355903; PubMed Central PMCID: PMCPMC3552948. PubMed DOI PMC

Roberts R, Al-Jamal WT, Whelband M, et al. Autophagy and formation of tubulovesicular auto-phagosomes provide a barrier against nonviral gene delivery. Autophagy. 2013. May;9(5):667–82. doi:10.4161/auto.23877. PubMed PMID: 23422759; PubMed Central PMCID: PMC3669178. PubMed DOI PMC

Kovacs AL, Zhang H.. Role of autophagy in Caenorhabditis elegans. FEBS Lett. 2010. Apr 2;584(7):1335–41. doi:10.1016/j.febslet.2010.02.002. PubMed PMID: 20138173; eng. PubMed DOI

Wu F, Li Y, Wang F, et al. Differential function of the two Atg4 homologues in the aggrephagy pathway in Caenorhabditis elegans. J Biol Chem. 2012. Aug 24;287(35):29457–67. doi:10.1074/jbc.M112.365676. PubMed PMID: 22767594; PubMed Central PMCID: PMC3436130. PubMed DOI PMC

Morselli E, Maiuri MC, Markaki M, et al. Caloric restriction and resveratrol promote longevity through the Sirtuin-1-dependent induction of autophagy. Cell Death Dis. 2010;1:e10. doi:10.1038/cddis.2009.8. PubMed PMID: 21364612; PubMed Central PMCID: PMC3032517. eng. PubMed DOI PMC

Samara C, Syntichaki P, Tavernarakis N.. Autophagy is required for necrotic cell death in Caenorhabditis elegans. Cell Death Differ. 2008. Jan;15(1):105–12. doi:10.1038/sj.cdd.4402231. PubMed PMID: 17901876; eng. PubMed DOI

Alberti A, Michelet X, Djeddi A, et al. The autophagosomal protein LGG-2 acts synergistically with LGG-1 in dauer formation and longevity in C. elegans. Autophagy. 2010. Jul 5;6(5):622–633. PubMed PMID: 20523114; Eng. PubMed

Kang C, You YJ, Avery L.. Dual roles of autophagy in the survival of Caenorhabditis elegans during starvation. Genes Dev. 2007. Sep 1;21(17):2161–71. PubMed PMID: 17785524; eng. PubMed PMC

Evans TC. Transformation and microinjection. Pasadena, CA: WormBook; 2006.

Chapin HC, Okada M, Merz AJ, et al. Tissue-specific autophagy responses to aging and stress in C. elegans. Aging (Albany NY). 2015. Jun;7(6):419–34. doi:10.18632/aging.100765. PubMed PMID: 26142908; PubMed Central PMCID: PMCPMC4505168. PubMed DOI PMC

Springhorn A, Hoppe T.. Western blot analysis of the autophagosomal membrane protein LGG-1/LC3 in Caenorhabditis elegans. Methods Enzymol 2019;619:319–336. doi:10.1016/bs.mie.2018.12.034. PubMed PMID: 30910027. PubMed DOI

Tasdemir E, Maiuri MC, Galluzzi L, et al. Regulation of autophagy by cytoplasmic p53. Nat Cell Biol. 2008. Jun;10(6):676–87. doi:10.1038/ncb1730. PubMed PMID: 18454141; PubMed Central PMCID: PMC2676564. PubMed DOI PMC

Tavernarakis N, Pasparaki A, Tasdemir E, et al. The effects of p53 on whole organism longevity are mediated by autophagy. Autophagy. 2008. Oct;4(7):870–3. PubMed PMID: 18728385; eng. PubMed

Schiavi A, Torgovnick A, Kell A, et al. Autophagy induction extends lifespan and reduces lipid content in response to frataxin silencing in C. elegans. Exp Gerontol. 2013. Feb;48(2):191–201. doi:10.1016/j.exger.2012.12.002. PubMed PMID: 23247094; PubMed Central PMCID: PMC3572394. PubMed DOI PMC

Palikaras K, Lionaki E, Tavernarakis N.. Coordination of mitophagy and mitochondrial biogenesis during ageing in C. elegans. Nature. 2015. May 28;521(7553):525–8. doi:10.1038/nature14300. PubMed PMID: 25896323. PubMed DOI

Fostel JL, Benner Coste L, Jacobson LA.. Degradation of transgene-coded and endogenous proteins in the muscles of Caenorhabditis elegans. Biochem Biophys Res Commun. 2003. Dec 5;312(1):173–7. doi:10.1016/j.bbrc.2003.09.248. PubMed PMID: 14630038. PubMed DOI

Lehmann S, Shephard F, Jacobson LA, et al. Integrated control of protein degradation in C. elegans muscle. Worm. 2012. Jul 1;1(3):141–50. doi:10.4161/worm.20465. PubMed PMID: 23457662; PubMed Central PMCID: PMCPMC3583358. PubMed DOI PMC

Etheridge T, Oczypok EA, Lehmann S, et al. Calpains mediate integrin attachment complex maintenance of adult muscle in Caenorhabditis elegans. PLoS Genet. 2012. Jan;8(1):e1002471. doi:10.1371/journal.pgen.1002471. PubMed PMID: 22253611; PubMed Central PMCID: PMCPMC3257289. PubMed DOI PMC

Szewczyk NJ, Hartman JJ, Barmada SJ, et al. Genetic defects in acetylcholine signalling promote protein degradation in muscle cells of Caenorhabditis elegans. J Cell Sci. 2000. Jun;113 (Pt 11):2003–10. PubMed PMID: 10806111. PubMed

Gaffney CJ, Shephard F, Chu J, et al. Degenerin channel activation causes caspase-mediated protein degradation and mitochondrial dysfunction in adult C. elegans muscle. J Cachexia Sarcopenia Muscle. 2016. May;7(2):181–92. doi:10.1002/jcsm.12040. PubMe;d PMID: 27493871; PubMed Central PMCID: PMCPMC4864282. PubMed DOI PMC

Lehmann S, Bass JJ, Szewczyk NJ.. Knockdown of the C. elegans kinome identifies kinases required for normal protein homeostasis, mitochondrial network structure, and sarcomere structure in muscle. Cell Commun Signal. 2013. Sep 23;11:71. doi:10.1186/1478-811X-11-71. PubMed PMID: 24060339; PubMed Central PMCID: PMCPMC3849176. PubMed DOI PMC

Lehmann S, Bass JJ, Barratt TF, et al. Functional phosphatome requirement for protein homeostasis, networked mitochondria, and sarcomere structure in C. elegans muscle. J Cachexia Sarcopenia Muscle. 2017. Aug;8(4):660–672. doi:10.1002/jcsm.12196. PubMed PMID: 28508547; PubMed Central PMCID: PMCPMC5566650. PubMed DOI PMC

Chang JT, Kumsta C, Hellman AB, et al. Spatiotemporal regulation of autophagy during Caenorhabditis elegans aging. eLife. 2017. Jul 4;6. doi:10.7554/eLife.18459. PubMed PMID: 28675140; PubMed Central PMCID: PMCPMC5496740. PubMed DOI PMC

Brown WR, Hubbard SJ, Tickle C, et al. The chicken as a model for large-scale analysis of vertebrate gene function [Research Support, Non-U.S. Gov’t Review]. Nat Rev Genet. 2003. Feb;4(2):87–98. doi:10.1038/nrg998. PubMed PMID: 12560806; eng. PubMed DOI

Mellen MA, de la Rosa EJ, Boya P.. The autophagic machinery is necessary for removal of cell corpses from the developing retinal neuroepithelium. Cell Death Differ. 2008. Aug;15(8):1279–90. doi:10.1038/cdd.2008.40. PubMed PMID: 18369370; eng. PubMed DOI

Aburto MR, Sanchez-Calderon H, Hurle JM, et al. Early otic development depends on autophagy for apoptotic cell clearance and neural differentiation. Cell Death Dis. 2012;3:e394. doi:10.1038/cddis.2012.132. PubMed PMID: 23034329; PubMed Central PMCID: PMC3481121. PubMed DOI PMC

Wang L, Rodrigues NA, Wu Y, et al. Pleiotropic action of AP-1 in v-Src-transformed cells. J Virol. 2011. Jul;85(13):6725–35. doi:10.1128/JVI.01013-10. PubMed PMID: 21507983; PubMed Central PMCID: PMC3126506. PubMed DOI PMC

Baba TW, Giroir BP, Humphries EH.. Cell lines derived from avian lymphomas exhibit two distinct phenotypes. Virology. 1985. Jul 15;144(1):139–51. PubMed PMID: 2998040; eng. PubMed

Perez-Martin M, Perez-Perez ME, Lemaire SD, et al. Oxidative stress contributes to autophagy induction in response to endoplasmic reticulum stress in chlamydomonas reinhardtii. Plant Physiol. 2014. Oct;166(2):997–1008. doi:10.1104/pp.114.243659. PubMed PMID: 25143584. PubMed DOI PMC

Perez-Perez ME, Couso I, Crespo JL.. Carotenoid deficiency triggers autophagy in the model green alga Chlamydomonas reinhardtii. Autophagy. 2012. Mar;8(3):376–88. doi:10.4161/auto.18864. PubMed PMID: 22302003. PubMed DOI

Tran QG, Yoon HR, Cho K, et al. Dynamic interactions between auto-phagosomes and lipid droplets in chlamydomonas reinhardtii. Cells. 2019. Aug 28;8(9). doi:10.3390/cells8090992. PubMed PMID: 31466295; PubMed Central PMCID: PMCPMC6769876. PubMed DOI PMC

Couso I, Perez-Perez ME, Martinez-Force E, et al. Autophagic flux is required for the synthesis of triacylglycerols and ribosomal protein turnover in Chlamydomonas. J Exp Bot. 2018. Mar 14;69(6):1355–1367. doi:10.1093/jxb/erx372. PubMed PMID: 29053817; PubMed Central PMCID: PMCPMC6018900. PubMed DOI PMC

Heredia-Martinez LG, Andres-Garrido A, Martinez-Force E, et al. Chloroplast Damage Induced by the Inhibition of Fatty Acid Synthesis Triggers Autophagy in Chlamydomonas. Plant Physiol. 2018. Nov;178(3):1112–1129. doi:10.1104/pp.18.00630. PubMed PMID: 30181343; PubMed Central PMCID: PMCPMC6236622. PubMed DOI PMC

Xu T, Kumar S, Denton D.. Characterization of autophagic responses in drosophila melanogaster. Methods Enzymol. 2017;588:445–465. doi:10.1016/bs.mie.2016.09.089. PubMed PMID: 28237115. PubMed DOI

Mulakkal NC, Nagy P, Takats S, et al. Autophagy in Drosophila: from historical studies to current knowledge. Biomed Res Int. 2014;2014:273473. doi:10.1155/2014/273473. PubMed PMID: 24949430; PubMed Central PMCID: PMCPMC4052151. PubMed DOI PMC

Lorincz P, Mauvezin C, Juhasz G.. Exploring Autophagy in Drosophila. Cells. 2017. Jul 12;6(3). doi:10.3390/cells6030022. PubMed PMID: 28704946; PubMed Central PMCID: PMCPMC5617968. PubMed DOI PMC

Zhang P, Holowatyj AN, Roy T, et al. An SH3PX1-dependent endocytosis-autophagy network restrains intestinal stem cell proliferation by counteracting EGFR-ERK signaling. Dev Cell. 2019. May 20;49(4):574–589 e5. doi:10.1016/j.devcel.2019.03.029. PubMed PMID: 31006650; PubMed Central PMCID: PMCPMC6542281. PubMed DOI PMC

Nelson C, Baehrecke EH.. Autophagy and cell death in the fly. Methods Enzymol. 2014;545:181–99. doi:10.1016/B978-0-12-801430-1.00008-1. PubMed PMID: 25065891. PubMed DOI

Mauvezin C, Ayala C, Braden CR, et al. Assays to monitor autophagy in Drosophila. Methods. 2014. Jun 15;68(1):134–9. doi:10.1016/j.ymeth.2014.03.014. PubMed PMID: 24667416; PubMed Central PMCID: PMC4048785. PubMed DOI PMC

Neisch AL, Neufeld TP, Hays TS.. A STRIPAK complex mediates axonal transport of auto-phagosomes and dense core vesicles through PP2A regulation. J Cell Biol. 2017. Feb;216(2):441–461. doi:10.1083/jcb.201606082. PubMed PMID: 28100687; PubMed Central PMCID: PMCPMC5294782. PubMed DOI PMC

Denton D, Chang TK, Nicolson S, et al. Relationship between growth arrest and autophagy in midgut programmed cell death in Drosophila. Cell Death Differ. 2012. Aug;19(8):1299–307. doi:10.1038/cdd.2012.43. PubMed PMID: 22555456; PubMed Central PMCID: PMCPMC3392632. PubMed DOI PMC

Shelly S, Lukinova N, Bambina S, et al. Autophagy is an essential component of Drosophila immunity against vesicular stomatitis virus [Research Support, N.I.H., Extramural]. Immunity. 2009. Apr 17;30(4):588–98. doi:10.1016/j.immuni.2009.02.009. PubMed PMID: 19362021; PubMed Central PMCID: PMC2754303. eng. PubMed DOI PMC

Juhasz G, Hill JH, Yan Y, et al. The class III PI(3)K Vps34 promotes autophagy and endocytosis but not TOR signaling in Drosophila. J Cell Biol. 2008. May 19;181(4):655–66. doi:10.1083/jcb.200712051. PubMed PMID: 18474623; PubMed Central PMCID: PMC2386105. PubMed DOI PMC

Nagy P, Hegedus K, Pircs K, et al. Different effects of Atg2 and Atg18 mutations on Atg8a and Atg9 trafficking during starvation in Drosophila. FEBS Lett. 2014. Jan 31;588(3):408–13. doi:10.1016/j.febslet.2013.12.012. PubMed PMID: 24374083; PubMed Central PMCID: PMCPMC3928829. PubMed DOI PMC

Shravage BV, Hill JH, Powers CM, et al. Atg6 is required for multiple vesicle trafficking pathways and hematopoiesis in Drosophila. Development. 2013. Mar;140(6):1321–9. doi:10.1242/dev.089490. PubMed PMID: 23406899; PubMed Central PMCID: PMC3585664. PubMed DOI PMC

Melani M, Valko A, Romero NM, et al. Zonda is a novel early component of the autophagy pathway in Drosophila. Mol Biol Cell. 2017. Nov 1;28(22):3070–3081. doi:10.1091/mbc.E16-11-0767. PubMed PMID: 28904211; PubMed Central PMCID: PMCPMC5662263. PubMed DOI PMC

Nezis IP, Shravage BV, Sagona AP, et al. Autophagic degradation of dBruce controls DNA fragmentation in nurse cells during late Drosophila melanogaster oogenesis [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. J Cell Biol. 2010. Aug 23;190(4):523–31. doi:10.1083/jcb.201002035. PubMed PMID: 20713604; PubMed Central PMCID: PMC2928014. eng. PubMed DOI PMC

Robin M, Issa AR, Santos CC, et al. Drosophila p53 integrates the antagonism between autophagy and apoptosis in response to stress. Autophagy. 2019. May;15(5):771–784. doi:10.1080/15548627.2018.1558001. PubMed PMID: 30563404; PubMed Central PMCID: PMCPMC6526837. PubMed DOI PMC

Kim M, Semple I, Kim B, et al. Drosophila Gyf/GRB10 interacting GYF protein is an autophagy regulator that controls neuron and muscle homeostasis. Autophagy. 2015. Aug 3;11(8):1358–72. doi:10.1080/15548627.2015.1063766. PubMed PMID: 26086452. PubMed DOI PMC

Pircs K, Nagy P, Varga A, et al. Advantages and limitations of different p62-based assays for estimating autophagic activity in Drosophila. PLoS One. 2012;7(8):e44214. doi:10.1371/journal.pone.0044214. PubMed PMID: 22952930; PubMed Central PMCID: PMC3432079. PubMed DOI PMC

Wyers F, Dru P, Simonet B, et al. Immunological cross-reactions and interactions between the Drosophila melanogaster ref(2)P protein and sigma rhabdovirus proteins. J Virol. 1993. Jun; 67(6):3208–16. PubMed PMID: 7684462; PubMed Central PMCID: PMCPMC237660. PubMed PMC

Hindle S, Afsari F, Stark M, et al. Dopaminergic expression of the Parkinsonian gene LRRK2-G2019S leads to non-autonomous visual neurodegeneration, accelerated by increased neural demands for energy. Hum Mol Genet. 2013. Jun 1; 22(11):2129–40. doi:10.1093/hmg/ddt061. PubMed PMID: 23396536; PubMed Central PMCID: PMC3652415. PubMed DOI PMC

Anding AL, Baehrecke EH.. Vps15 is required for stress induced and developmentally triggered autophagy and salivary gland protein secretion in Drosophila. Cell Death Differ. 2014. Oct 24. doi:10.1038/cdd.2014.174. PubMed PMID: 25342466. PubMed DOI PMC

Hou YC, Chittaranjan S, Barbosa SG, et al. Effector caspase Dcp-1 and IAP protein Bruce regulate starvation-induced autophagy during Drosophila melanogaster oogenesis [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S.]. J Cell Biol. 2008. Sep 22;182(6):1127–39. doi:10.1083/jcb.200712091. PubMed PMID: 18794330; PubMed Central PMCID: PMC2542474. eng. PubMed DOI PMC

Tusco R, Jacomin AC, Jain A, et al. Kenny mediates selective autophagic degradation of the IKK complex to control innate immune responses. Nat Commun. 2017. Nov 2;8(1):1264. doi:10.1038/s41467-017-01287-9. PubMed PMID: 29097655; PubMed Central PMCID: PMCPMC5668318. PubMed DOI PMC

Marinkovic D, Zhang X, Yalcin S, et al. Foxo3 is required for the regulation of oxidative stress in erythropoiesis. J Clin Invest. 2007. Aug;117(8):2133–44. doi:10.1172/JCI31807. PubMed PMID: 17671650; PubMed Central PMCID: PMC1934587. PubMed DOI PMC

McIver SC, Kang YA, DeVilbiss AW, et al. The exosome complex establishes a barricade to erythroid maturation. Blood. 2014. Oct 2;124(14):2285–97. doi:10.1182/blood-2014-04-571083. PubMed PMID: 25115889; PubMed Central PMCID: PMC4183988. PubMed DOI PMC

Fujiwara T, O’Geen H, Keles S, et al. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol Cell. 2009. Nov 25;36(4):667–81. doi:10.1016/j.molcel.2009.11.001. PubMed PMID: 19941826; PubMed Central PMCID: PMC2784893. PubMed DOI PMC

Welch JJ, Watts JA, Vakoc CR, et al. Global regulation of erythroid gene expression by transcription factor GATA-1. Blood. 2004. Nov 15;104(10):3136–47. doi:10.1182/blood-2004-04-1603. PubMed PMID: 15297311. PubMed DOI

Yu M, Riva L, Xie H, et al. Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Mol Cell. 2009. Nov 25;36(4):682–95. doi:10.1016/j.molcel.2009.11.002. PubMed PMID: 19941827; PubMed Central PMCID: PMC2800995. PubMed DOI PMC

Kundu M, Lindsten T, Yang CY, et al. Ulk1 plays a critical role in the autophagic clearance of mitochondria and ribosomes during reticulocyte maturation. Blood. 2008. Aug 15; 112(4):1493–502. doi:10.1182/blood-2008-02-137398. PubMed PMID: 18539900; PubMed Central PMCID: PMC2515143. PubMed DOI PMC

Mortensen M, Ferguson DJ, Edelmann M, et al. Loss of autophagy in erythroid cells leads to defective removal of mitochondria and severe anemia in vivo. Proc Natl Acad Sci U S A. 2010. Jan 12; 107(2):832–7. doi:10.1073/pnas.0913170107. PubMed PMID: 20080761; PubMed Central PMCID: PMC2818953. PubMed DOI PMC

Sandoval H, Thiagarajan P, Dasgupta SK, et al. Essential role for Nix in autophagic maturation of erythroid cells. Nature. 2008. Jul 10;454(7201):232–5. doi:10.1038/nature07006. PubMed PMID: 18454133; PubMed Central PMCID: PMC2570948. PubMed DOI PMC

Schweers RL, Zhang J, Randall MS, et al. NIX is required for programmed mitochondrial clearance during reticulocyte maturation. Proc Natl Acad Sci U S A. 2007. Dec 4;104(49):19500–5. doi: 0708818104 [pii] doi:10.1073/pnas.0708818104. PubMed PMID: 18048346; PubMed Central PMCID: PMC2148318. eng. PubMed DOI PMC

Zhang X, Camprecios G, Rimmele P, et al. FOXO3-mTOR metabolic cooperation in the regulation of erythroid cell maturation and homeostasis. Am J Hematol. 2014. Oct;89(10):954–63. doi:10.1002/ajh.23786. PubMed PMID: 24966026; PubMed Central PMCID: PMCPMC4201594. PubMed DOI PMC

Lithanatudom P, Wannatung T, Leecharoenkiat A, et al. Enhanced activation of autophagy in beta-thalassemia/Hb E erythroblasts during erythropoiesis. Ann Hematol. 2011. Jul;90(7):747–58. doi: 10.1007/s00277-010-1152-5. PubMed PMID: 21221583. PubMed DOI

Lupo F, Tibaldi E, Matte A, et al. A new molecular link between defective autophagy and erythroid abnormalities in chorea-acanthocytosis. Blood. 2016. Dec 22;128(25):2976–2987. doi:10.1182/blood-2016-07-727321. PubMed PMID: 27742708; PubMed Central PMCID: PMCPMC5179337. PubMed DOI PMC

Beneduce E, Matte A, De Falco L, et al. Fyn kinase is a novel modulator of erythropoietin signaling and stress erythropoiesis. Am J Hematol. 2019. Jan;94(1):10–20. doi:10.1002/ajh.25295. PubMed PMID: 30252956. PubMed DOI PMC

Josefsen L, Droce A, Sondergaard TE, et al. Autophagy provides nutrients for nonassimilating fungal structures and is necessary for plant colonization but not for infection in the necrotrophic plant pathogen Fusarium gaminearum. Autophagy. 2012;8:326–37. PubMed

Nadal M, Gold SE.. The autophagy genes ATG8 and ATG1 affect morphogenesis and pathogenicity in Ustilago maydis. Mol Plant Pathol. 2010. Jul;11(4):463–78. doi:10.1111/j.1364-3703.2010.00620.x. PubMed PMID: 20618705; eng. PubMed DOI PMC

Pollack JK, Harris SD, Marten MR.. Autophagy in filamentous fungi [Research Support, U.S. Gov’t, Non-P.H.S Review]. Fungal Genet biol FG & B. 2009. Jan;46(1):1–8. doi:10.1016/j.fgb.2008.10.010. PubMed PMID: 19010432; eng. PubMed DOI

Richie DL, Fuller KK, Fortwendel J, et al. Unexpected link between metal ion deficiency and autophagy in Aspergillus fumigatus [Research Support, N.I.H., Extramural]. Eukaryot Cell. 2007. Dec;6(12):2437–47. doi:10.1128/EC.00224-07. PubMed PMID: 17921348; PubMed Central PMCID: PMC2168250. eng. PubMed DOI PMC

Voigt O, Poggeler S.. Self-eating to grow and kill: autophagy in filamentous ascomycetes. Appl Microbiol Biotechnol. 2013. Nov;97(21):9277–90. doi:10.1007/s00253-013-5221-2. PubMed PMID: 24077722. PubMed DOI

Kim Y, Islam N, Moss BJ, et al. Autophagy induced by rapamycin and carbon-starvation have distinct proteome profiles in Aspergillus nidulans. Biotechnol Bioeng. 2011. Nov;108(11):2705–15. doi:10.1002/bit.23223. PubMed PMID: 21618477. PubMed DOI

Ren W, Zhang Z, Shao W, et al. The autophagy-related gene BcATG1 is involved in fungal development and pathogenesis in Botrytis cinerea. Mol Plant Pathol. 2017. Feb;18(2):238–248. doi:10.1111/mpp.12396. PubMed PMID: 26972592; PubMed Central PMCID: PMCPMC6638273. PubMed DOI PMC

Pinan-Lucarre B, Balguerie A, Clave C.. Accelerated cell death in Podospora autophagy mutants [Research Support, Non-U.S. Gov’t]. Eukaryot Cell. 2005. Nov;4(11):1765–74. doi:10.1128/EC.4.11.1765-1774.2005. PubMed PMID: 16278443; PubMed Central PMCID: PMC1287858. eng. PubMed DOI PMC

Deng YZ, Naqvi NI.. A vacuolar glucoamylase, Sga1, participates in glycogen autophagy for proper asexual differentiation in Magnaporthe oryzae. Autophagy. 2010. May;6(4):455–61. doi:10.4161/auto.6.4.11736. PubMed PMID: 20383057. PubMed DOI

Deng YZ, Ramos-Pamplona M, Naqvi NI.. Autophagy-assisted glycogen catabolism regulates asexual differentiation in Magnaporthe oryzae. Autophagy. 2009. Jan;5(1):33–43. PubMed PMID: 19115483. PubMed

Ren W, Liu N, Sang C, et al. The Autophagy Gene BcATG8 Regulates the Vegetative Differentiation and Pathogenicity of Botrytis cinerea. Appl Environ Microbiol. 2018. Jun 1;84(11). doi:10.1128/AEM.02455-17. PubMed PMID: 29572212; PubMed Central PMCID: PMCPMC5960959. PubMed DOI PMC

Knuppertz L, Hamann A, Pampaloni F, et al. Identification of autophagy as a longevity-assurance mechanism in the aging model Podospora anserina. Autophagy. 2014. May;10(5):822–34. doi:10.4161/auto.28148. PubMed PMID: 24584154. PubMed DOI PMC

Asakura M, Ninomiya S, Sugimoto M, et al. Atg26-mediated pexophagy is required for host invasion by the plant pathogenic fungus Colletotrichum orbiculare [Research Support, Non-U.S. Gov’t]. Plant Cell. 2009. Apr;21(4):1291–304. doi:10.1105/tpc.108.060996. PubMed PMID: 19363139; PubMed Central PMCID: PMC2685618. eng. PubMed DOI PMC

Liu XH, Lu JP, Zhang L, et al. Involvement of a Magnaporthe grisea serine/threonine kinase gene, MgATG1, in appressorium turgor and pathogenesis [Research Support, Non-U.S. Gov’t]. Eukaryot Cell. 2007. Jun;6(6):997–1005. doi:10.1128/EC.00011-07. PubMed PMID: 17416896; PubMed Central PMCID: PMC1951528. eng. PubMed DOI PMC

Nguyen LN, Bormann J, Le GT, et al. Autophagy-related lipase FgATG15 of Fusarium graminearum is important for lipid turnover and plant infection [Research Support, Non-U.S. Gov’t]. Fungal Genet biol FG & B. 2011. Mar;48(3):217–24. doi:10.1016/j.fgb.2010.11.004. PubMed PMID: 21094265; eng. PubMed DOI

Duan Z, Chen Y, Huang W, et al. Linkage of autophagy to fungal development, lipid storage and virulence in Metarhizium robertsii. Autophagy. 2013. Apr;9(4):538–49. doi:10.4161/auto.23575. PubMed PMID: 23380892; PubMed Central PMCID: PMC3627669. PubMed DOI PMC

Sun G, Qi X, Wilson RA.. A Feed-Forward Subnetwork Emerging from Integrated TOR- and cAMP/PKA-Signaling Architecture Reinforces Magnaporthe oryzae Appressorium Morphogenesis. Mol Plant Microbe Interact. 2019. May;32(5):593–607. doi:10.1094/MPMI-10-18-0287-R. PubMed PMID: 30431400. PubMed DOI

Sun G, Elowsky C, Li G, et al. TOR-autophagy branch signaling via Imp1 dictates plant-microbe biotrophic interface longevity. PLoS Genet. 2018. Nov;14(11):e1007814. doi:10.1371/journal.pgen.1007814. PubMed PMID: 30462633; PubMed Central PMCID: PMCPMC6281275. PubMed DOI PMC

Yin Z, Chen C, Yang J, et al. Histone acetyltransferase MoHat1 acetylates autophagy-related proteins MoAtg3 and MoAtg9 to orchestrate functional appressorium formation and pathogenicity in Magnaporthe oryzae. Autophagy. 2019. Jul;15(7):1234–1257. doi:10.1080/15548627.2019.1580104. PubMed PMID: 30776962; PubMed Central PMCID: PMCPMC6613890. PubMed DOI PMC

Yin Z, Feng W, Chen C, et al. Shedding light on autophagy coordinating with cell wall integrity signaling to govern pathogenicity of Magnaporthe oryzae. Autophagy. 2019. Jul 24:1–17. doi:10.1080/15548627.2019.1644075. PubMed PMID: 31313634. PubMed DOI PMC

Deng YZ, Ramos-Pamplona M, Naqvi NI.. Methods for functional analysis of macroautophagy in filamentous fungi [Research Support, Non-U.S. Gov’t]. Methods Enzymol. 2008;451:295–310. doi:10.1016/S0076-6879(08)03220-5. PubMed PMID: 19185728; eng. PubMed DOI

Kershaw MJ, Talbot NJ.. Genome-wide functional analysis reveals that infection-associated fungal autophagy is necessary for rice blast disease.Proc Natl Acad Sci U S A. 2009. Sep 15;106(37):15967–72. doi:10.1073/pnas.0901477106. PubMed PMID: 19717456; PubMed Central PMCID: PMC2747227. PubMed DOI PMC

Liu TB, Liu XH, Lu JP, et al. The cysteine protease MoAtg4 interacts with MoAtg8 and is required for differentiation and pathogenesis in Magnaporthe oryzae. Autophagy. 2010. Jan;6(1):74–85. PubMed PMID: 19923912. PubMed

Peñalva MA, Galindo A, Abenza JF, et al. Searching for gold beyond mitosis: Mining intracellular membrane traffic in Aspergillus nidulans. Cell Logist. 2012. Jan 1;2(1):2–14. doi:10.4161/cl.19304. PubMed PMID: 22645705; PubMed Central PMCID: PMC3355971. PubMed DOI PMC

Pinar M, Peñalva MA.. Aspergillus nidulans BapH is a RAB11 effector that connects membranes in the Spitzenkorper with basal autophagy. Mol Microbiol. 2017. Nov;106(3):452–468. doi:10.1111/mmi.13777. PubMed PMID: 28857357. PubMed DOI

Lipatova Z, Belogortseva N, Zhang XQ, et al. Regulation of selective autophagy onset by a Ypt/Rab GTPase module. Proc Natl Acad Sci U S A. 2012. May 1;109(18):6981–6. doi:10.1073/pnas.1121299109. PubMed PMID: 22509044; PubMed Central PMCID: PMC3344974. PubMed DOI PMC

Lynch-Day MA, Bhandari D, Menon S, et al. Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy. Proc Natl Acad Sci U S A. 2010. Apr 27;107(17):7811–6. doi: 1000063107 [pii] doi:10.1073/pnas.1000063107. PubMed PMID: 20375281; PubMed Central PMCID: PMC2867920. eng. PubMed DOI PMC

Deng Y, Qu Z, Naqvi NI.. The role of snx41-based pexophagy in magnaporthe development. PLoS One. 2013;8(11):e79128. doi: 10.1371/journal.pone.0079128. PubMed PMID: 24302988; PubMed Central PMCID: PMC3841179. PubMed DOI PMC

Zhong K, Li X, Le X, et al. MoDnm1 dynamin mediating peroxisomal and mitochondrial fission in complex with MoFis1 and MoMdv1 is important for development of functional appressorium in Magnaporthe oryzae. PLoS Pathog. 2016. Aug;12(8):e1005823. doi:10.1371/journal.ppat.1005823. PubMed PMID: 27556292; PubMed Central PMCID: PMCPMC4996533. PubMed DOI PMC

Zhu XM, Liang S, Shi HB, et al. VPS9 domain-containing proteins are essential for autophagy and endocytosis in Pyricularia oryzae. Environ Microbiol. 2018. Apr;20(4):1516–1530. doi:10.1111/1462-2920.14076. PubMed PMID: 29468804. PubMed DOI

Li X, Gao C, Li L, et al. MoEnd3 regulates appressorium formation and virulence through mediating endocytosis in rice blast fungus Magnaporthe oryzae. PLoS Pathog. 2017. Jun;13(6):e1006449. doi:10.1371/journal.ppat.1006449. PubMed PMID: 28628655; PubMed Central PMCID: PMCPMC5491321. PubMed DOI PMC

Piggott N, Cook MA, Tyers M, et al. Genome-wide fitness profiles reveal a requirement for autophagy during yeast fermentation. Genes Genomes Genetics. 2011;1:353–367. PubMed PMC

Cebollero E, Gonzalez R.. Induction of autophagy by second-fermentation yeasts during elaboration of sparkling wines. Appl Environ Microbiol. 2006. Jun;72(6):4121–7. doi:10.1128/AEM.02920-05. PubMed PMID: 16751523; PubMed Central PMCID: PMC1489611. eng. PubMed DOI PMC

Marks VD, Ho Sui SJ, Erasmus D, et al. Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response [Research Support, Non-U.S. Gov’t]. FEMS Yeast Res. 2008. Feb;8(1):35–52. doi:10.1111/j.1567-1364.2007.00338.x. PubMed PMID: 18215224; eng. PubMed DOI PMC

Mendes-Ferreira A, Sampaio-Marques B, Barbosa C, et al. Accumulation of non-superoxide anion reactive oxygen species mediates nitrogen-limited alcoholic fermentation by Saccharomyces cerevisiae. Appl Environ Microbiol. 2010. Dec;76(24):7918–24. doi:10.1128/AEM.01535-10. PubMed PMID: 20952643; PubMed Central PMCID: PMC3008223. eng. PubMed DOI PMC

Rossignol T, Dulau L, Julien A, et al. Genome-wide monitoring of wine yeast gene expression during alcoholic fermentation. Yeast. 2003. Dec;20(16):1369–85. doi:10.1002/yea.1046. PubMed PMID: 14663829; eng. PubMed DOI

Teixeira MC, Raposo LR, Mira NP, et al. Genome-wide identification of Saccharomyces cerevisiae genes required for maximal tolerance to ethanol [Research Support, Non-U.S. Gov’t]. Appl Environ Microbiol. 2009. Sep;75(18):5761–72. doi:10.1128/AEM.00845-09. PubMed PMID: 19633105; PubMed Central PMCID: PMC2747848. eng. PubMed DOI PMC

Yoshikawa K, Tanaka T, Furusawa C, et al. Comprehensive phenotypic analysis for identification of genes affecting growth under ethanol stress in Saccharomyces cerevisiae. FEMS Yeast Res. 2009. Feb;9(1):32–44. doi:10.1111/j.1567-1364.2008.00456.x. PubMed PMID: 19054128; eng. PubMed DOI

Hazan R, Levine A, Abeliovich H.. Benzoic acid, a weak organic acid food preservative, exerts specific effects on intracellular membrane trafficking pathways in Saccharomyces cerevisiae. Appl Environ Microbiol. 2004. Aug;70(8):4449–57. doi:10.1128/AEM.70.8.4449-4457.2004. PubMed PMID: 15294772; PubMed Central PMCID: PMC492424. eng. PubMed DOI PMC

Singletary K, Milner J.. Diet, autophagy, and cancer: a review [Review]. Cancer Epidemiol Biomarkers Prev. 2008. Jul;17(7):1596–610. doi:10.1158/1055-9965.EPI-07-2917. PubMed PMID: 18628411; eng. PubMed DOI

Su CL, Chen FN, Won SJ.. Involvement of apoptosis and autophagy in reducing mouse hepatoma ML-1 cell growth in inbred BALB/c mice by bacterial fermented soybean products. Food Chem Toxicol. 2011. Jan;49(1):17–24. doi:10.1016/j.fct.2010.08.017. PubMed PMID: 20732379; eng. PubMed DOI

Abeliovich H, Gonzalez R.. Autophagy in food biotechnology. Autophagy. 2009. Oct;5(7):925–9. PubMed PMID: 19556866; eng. PubMed

Berger B, Abdalla FC, Cruz-Landim C.. Effect of narcosis with CO2 on the ovarian development in queens of Apis mellifera (Hymenoptera, Apini). Sociobiology. 2005;45:261–70.

ECM Silva-Zacarin, Tomaino GA, Brocheto-Braga MR, et al. Programmed cell death in the larval salivary glands of Apis mellifera (Hymenoptera, Apidae). J Biosci. 2007. Mar;32(2):309–28. PubMed PMID: 17435323; eng. PubMed

Gregorc A, Bowen ID.. Programmed cell death in the honey-bee (Apis mellifera L.) larvae midgut. Cell Biol Int. 1997. Mar;21(3):151–8. doi:10.1006/cbir.1997.0127. PubMed PMID: 9151991; eng. PubMed DOI

Navajas M, Migeon A, Alaux C, et al. Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection. BMC genomics. 2008;9:301. doi:10.1186/1471-2164-9-301. PubMed PMID: 18578863; PubMed Central PMCID: PMC2447852. eng. PubMed DOI PMC

Kimura T, Takabatake Y, Takahashi A, et al. Chloroquine in cancer therapy: a double-edged sword of autophagy. Cancer Res. 2013. Jan 1;73(1):3–7. doi:10.1158/0008-5472.CAN-12-2464. PubMed PMID: 23288916. PubMed DOI

Takahashi A, Kimura T, Takabatake Y, et al. Autophagy guards against cisplatin-induced acute kidney injury. Am J Pathol. 2012. Feb;180(2):517–25. doi:10.1016/j.ajpath.2011.11.001. PubMed PMID: 22265049. PubMed DOI

Rodriguez A, Gomez-Ambrosi J, Catalan V, et al. The ghrelin O-acyltransferase-ghrelin system reduces TNF-alpha-induced apoptosis and autophagy in human visceral adipocytes. Diabetologia. 2012. Nov;55(11):3038–50. doi:10.1007/s00125-012-2671-5. PubMed PMID: 22869322. PubMed DOI

Ramachandran N, Munteanu I, Wang P, et al. VMA21 deficiency prevents vacuolar ATPase assembly and causes autophagic vacuolar myopathy. Acta Neuropathol. 2013. Mar;125(3):439–57. doi:10.1007/s00401-012-1073-6. PubMed PMID: 23315026. PubMed DOI

Colasanti T, Vomero M, Alessandri C, et al. Role of alpha-synuclein in autophagy modulation of primary human T lymphocytes. Cell Death Dis. 2014;5:e1265. doi:10.1038/cddis.2014.211. PubMed PMID: 24874737; PubMed Central PMCID: PMC4047919. PubMed DOI PMC

Spruessel A, Steimann G, Jung M, et al. Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision. BioTechniques. 2004. Jun;36(6):1030–7. PubMed PMID: 15211754; eng. PubMed

Espina V, Edmiston KH, Heiby M, et al. A portrait of tissue phosphoprotein stability in the clinical tissue procurement process. Mol Cell Proteomics. 2008. Oct;7(10):1998–2018. doi:10.1074/mcp.M700596-MCP200. PubMed PMID: 18667411; PubMed Central PMCID: PMC2559936. eng. PubMed DOI PMC

Barth S, Glick D, Macleod KF.. Autophagy: assays and artifacts. J Pathol. 2010. Jun;221(2):117–24. doi:10.1002/path.2694. PubMed PMID: 20225337; PubMed Central PMCID: PMC2989884. eng. PubMed DOI PMC

Domart MC, Esposti DD, Sebagh M, et al. Concurrent induction of necrosis, apoptosis, and autophagy in ischemic preconditioned human livers formerly treated by chemotherapy. J Hepatol. 2009. Nov;51(5):881–9. doi:10.1016/j.jhep.2009.06.028. PubMed PMID: 19765849. PubMed DOI

Vanhorebeek I, Gunst J, Derde S, et al. Insufficient activation of autophagy allows cellular damage to accumulate in critically ill patients. J Clin Endocrinol Metab. 2011. Apr;96(4):E633–45. doi:10.1210/jc.2010-2563. PubMed PMID: 21270330; eng. PubMed DOI

Jahania SM, Sengstock D, Vaitkevicius P, et al. Activation of the homeostatic intracellular repair response during cardiac surgery. J Am Coll Surg. 2013. Apr;216(4):719–26; discussion 726–9. doi:10.1016/j.jamcollsurg.2012.12.034. PubMed PMID: 23415552; PubMed Central PMCID: PMC3724756. PubMed DOI PMC

Singh KK, Yanagawa B, Quan A, et al. Autophagy gene fingerprint in human ischemia and reperfusion. J Thorac Cardiovasc Surg. 2014. Mar;147(3):1065–1072 e1. doi:10.1016/j.jtcvs.2013.04.042. PubMed PMID: 23778083. PubMed DOI

Gao F, Li G, Liu C, et al. Autophagy regulates testosterone synthesis by facilitating cholesterol uptake in Leydig cells. J Cell Biol. 2018. Jun 4;217(6):2103–2119. doi:10.1083/jcb.201710078. PubMed PMID: 29618492; PubMed Central PMCID: PMCPMC5987723. PubMed DOI PMC

Nyman E, Brannmark C, Palmer R, et al. A hierarchical whole-body modeling approach elucidates the link between in vitro insulin signaling and in vivo glucose homeostasis. J Biol Chem. 2011. Jul 22;286(29):26028–41. doi:10.1074/jbc.M110.188987. PubMed PMID: 21572040; PubMed Central PMCID: PMC3138269. eng. PubMed DOI PMC

Faraj J, Bodas M, Pehote G, et al. Novel cystamine-core dendrimer-formulation rescues DeltaF508-CFTR and inhibits Pseudomonas aeruginosa infection by augmenting autophagy. Expert Opin Drug Deliv. 2019. Feb;16(2):177–186. doi:10.1080/17425247.2019.1575807. PubMed PMID: 30732491. PubMed DOI

Shrestha CL, Assani KD, Rinehardt H, et al. Cysteamine-mediated clearance of antibiotic-resistant pathogens in human cystic fibrosis macrophages. PLoS One. 2017;12(10):e0186169. doi:10.1371/journal.pone.0186169. PubMed PMID: 28982193; PubMed Central PMCID: PMCPMC5642023. PubMed DOI PMC

Brockman SM, Bodas M, Silverberg D, et al. Dendrimer-based selective autophagy-induction rescues DeltaF508-CFTR and inhibits Pseudomonas aeruginosa infection in cystic fibrosis. PLoS One. 2017;12(9):e0184793. doi:10.1371/journal.pone.0184793. PubMed PMID: 28902888; PubMed Central PMCID: PMCPMC5597233. PubMed DOI PMC

Krause K, Kopp BT, Tazi MF, et al. The expression of Mirc1/Mir17-92 cluster in sputum samples correlates with pulmonary exacerbations in cystic fibrosis patients. J Cyst Fibros. 2018. Jul;17(4):454–461. doi:10.1016/j.jcf.2017.11.005. PubMed PMID: 29241629; PubMed Central PMCID: PMCPMC5995663. PubMed DOI PMC

Assani K, Shrestha CL, Rinehardt H, et al. AR-13 reduces antibiotic-resistant bacterial burden in cystic fibrosis phagocytes and improves cystic fibrosis transmembrane conductance regulator function. J Cyst Fibros. 2019. Sep;18(5):622–629. doi:10.1016/j.jcf.2018.10.010. PubMed PMID: 30366849. PubMed DOI

Buzgariu W, Chera S, Galliot B.. Methods to investigate autophagy during starvation and regeneration in hydra. Methods Enzymol. 2008;451:409–37. doi:10.1016/S0076-6879(08)03226-6. PubMed PMID: 19185734; eng. PubMed DOI

Chera S, de Rosa R, Miljkovic-Licina M, et al. Silencing of the hydra serine protease inhibitor Kazal1 gene mimics the human SPINK1 pancreatic phenotype. J Cell Sci. 2006. Mar 1;119(Pt 5):846–57. doi:10.1242/jcs.02807. PubMed PMID: 16478786; eng. PubMed DOI

Galliot B. Autophagy and self-preservation: a step ahead from cell plasticity?. Autophagy. 2006. Jul-Sep;2(3):231–3. PubMed PMID: 16874084; eng. PubMed

Chera S, Buzgariu W, Ghila L, et al. Autophagy in Hydra: a response to starvation and stress in early animal evolution. Biochim Biophys Acta. 2009. Sep;1793(9):1432–43. doi:10.1016/j.bbamcr.2009.03.010. PubMed PMID: 19362111; eng. PubMed DOI

Dixit NS, Shravage BV, Ghaskadbi S.. Identification and characterization of the autophagy-related genes Atg12 and Atg5 in hydra. . 2017;61(6–7):389–395. doi:10.1387/ijdb.160461sg. PubMed PMID: 28695958. PubMed DOI

Tiscornia G, Vivas EL, Izpisua Belmonte JC.. Diseases in a dish: modeling human genetic disorders using induced pluripotent cells. Nat Med. 2011. Dec;17(12):1570–6. doi:10.1038/nm.2504. PubMed PMID: 22146428. PubMed DOI

Karagiannis P, Takahashi K, Saito M, et al. Induced pluripotent stem cells and their use in human models of disease and development. Physiol Rev. 2019. Jan 1;99(1):79–114. doi:10.1152/physrev.00039.2017. PubMed PMID: 30328784. PubMed DOI

Schondorf DC, Aureli M, McAllister FE, et al. iPSC-derived neurons from GBA1-associated Parkinson’s disease patients show autophagic defects and impaired calcium homeostasis. Nat Commun. 2014. Jun 6;5:4028. doi:10.1038/ncomms5028. PubMed PMID: 24905578. PubMed DOI

di Domenico A, Carola G, Calatayud C, et al. Patient-specific iPSC-derived astrocytes contribute to non-cell-autonomous neurodegeneration in Parkinson’s disease. Stem Cell Reports. 2019. Feb 12;12(2):213–229. doi:10.1016/j.stemcr.2018.12.011. PubMed PMID: 30639209; PubMed Central PMCID: PMCPMC6372974. PubMed DOI PMC

Marrone L, Drexler HCA, Wang J, et al. FUS pathology in ALS is linked to alterations in multiple ALS-associated proteins and rescued by drugs stimulating autophagy. Acta Neuropathol. 2019. Jul;138(1):67–84. doi:10.1007/s00401-019-01998-x. PubMed PMID: 30937520; PubMed Central PMCID: PMCPMC6570784. PubMed DOI PMC

Seibler P, Burbulla LF, Dulovic M, et al. Iron overload is accompanied by mitochondrial and lysosomal dysfunction in WDR45 mutant cells. Brain. 2018. Oct 1;141(10):3052–3064. doi:10.1093/brain/awy230. PubMed PMID: 30169597. PubMed DOI PMC

Lin DS, Huang YW, Ho CS, et al. Oxidative insults and mitochondrial DNA mutation promote enhanced autophagy and mitophagy compromising cell viability in pluripotent cell model of mitochondrial disease. Cells. 2019. Jan 17;8(1). doi:10.3390/cells8010065. PubMed PMID: 30658448; PubMed Central PMCID: PMCPMC6356288. PubMed DOI PMC

Gilkerson RW, De Vries RL, Lebot P, et al. Mitochondrial autophagy in cells with mtDNA mutations results from synergistic loss of transmembrane potential and mTORC1 inhibition. Hum Mol Genet. 2012. Mar 1;21(5):978–90. doi:10.1093/hmg/ddr529. PubMed PMID: 22080835; PubMed Central PMCID: PMCPMC3277306. PubMed DOI PMC

Kwon Y, Kim JW, Jeoung JA, et al. Autophagy is pro-senescence when seen in close-up, but anti-senescence in long-shot. Mol Cells. 2017. Sep 30;40(9):607–612. doi:10.14348/molcells.2017.0151. PubMed PMID: 28927262; PubMed Central PMCID: PMCPMC5638768. PubMed DOI PMC

Sala-Mercado JA, Wider J, Undyala VV, et al. Profound cardioprotection with chloramphenicol succinate in the swine model of myocardial ischemia-reperfusion injury. Circulation. 2010. Sep 14;122(11 Suppl):S179–84. doi:10.1161/CIRCULATIONAHA.109.928242. PubMed PMID: 20837911; eng. PubMed DOI PMC

Botting KJ, McMillen IC, Forbes H, et al. Chronic hypoxemia in late gestation decreases cardiomyocyte number but does not change expression of hypoxia-responsive genes. J Am Heart Assoc. 2014. Aug;3(4). doi:10.1161/JAHA.113.000531. PubMed PMID: 25085511; PubMed Central PMCID: PMC4310356. PubMed DOI PMC

Wang KC, Brooks DA, Summers-Pearce B, et al. Low birth weight activates the renin-angiotensin system, but limits cardiac angiogenesis in early postnatal life. Physiol Rep. 2015. Feb 1;3(2). doi:10.14814/phy2.12270. PubMed PMID: 25649246; PubMed Central PMCID: PMC4393187. PubMed DOI PMC

Zhang S, Regnault TR, Barker PL, et al. Placental adaptations in growth restriction. Nutrients. 2015. Jan;7(1):360–89. doi:10.3390/nu7010360. PubMed PMID: 25580812; PubMed Central PMCID: PMC4303845. PubMed DOI PMC

Derde S, Vanhorebeek I, Guiza F, et al. Early parenteral nutrition evokes a phenotype of autophagy deficiency in liver and skeletal muscle of critically ill rabbits. Endocrinology. 2012. May;153(5):2267–76. doi:10.1210/en.2011-2068. PubMed PMID: 22396453. PubMed DOI

Gunst J, Derese I, Aertgeerts A, et al. Insufficient autophagy contributes to mitochondrial dysfunction, organ failure, and adverse outcome in an animal model of critical illness. Crit Care Med. 2013. Jan;41(1):182–94. doi:10.1097/CCM.0b013e3182676657. PubMed PMID: 23222264. PubMed DOI

Hermans G, Casaer MP, Clerckx B, et al. Effect of tolerating macronutrient deficit on the development of intensive-care unit acquired weakness: a subanalysis of the EPaNIC trial. Lancet Respir Med. 2013. Oct;1(8):621–9. doi:10.1016/S2213-2600(13)70183-8. PubMed PMID: 24461665. PubMed DOI

Lopez-Alonso I, Aguirre A, Gonzalez-Lopez A, et al. Impairment of autophagy decreases ventilator-induced lung injury by blockade of the NF-kappaB pathway. Am J Physiol Lung Cell Mol Physiol. 2013. Jun 15;304(12):L844–52. doi:10.1152/ajplung.00422.2012. PubMed PMID: 23585228. PubMed DOI

Sun Y, Li C, Shu Y, et al. Inhibition of autophagy ameliorates acute lung injury caused by avian influenza A H5N1 infection. Sci Signal. 2012. Feb 21;5(212):ra16. doi:10.1126/scisignal.2001931. PubMed PMID: 22355189. PubMed DOI

Liu Y, Xue X, Zhang H, et al. Neuronal-targeted TFEB rescues dysfunction of the autophagy-lysosomal pathway and alleviates ischemic injury in permanent cerebral ischemia. Autophagy. 2019. Mar;15(3):493–509. doi:10.1080/15548627.2018.1531196. PubMed PMID: 30304977; PubMed Central PMCID: PMCPMC6351122. PubMed DOI PMC

Zhang X, Yan H, Yuan Y, et al. Cerebral ischemia-reperfusion-induced autophagy protects against neuronal injury by mitochondrial clearance. Autophagy. 2013. Sep;9(9):1321–33. doi:10.4161/auto.25132. PubMed PMID: 23800795. PubMed DOI

Wen YD, Sheng R, Zhang LS, et al. Neuronal injury in rat model of permanent focal cerebral ischemia is associated with activation of autophagic and lysosomal pathways. Autophagy. 2008. Aug;4(6):762–9. doi:10.4161/auto.6412. PubMed PMID: 18567942. PubMed DOI

Ginet V, Spiehlmann A, Rummel C, et al. Involvement of autophagy in hypoxic-excitotoxic neuronal death. Autophagy. 2014. May;10(5):846–60. doi:10.4161/auto.28264. PubMed PMID: 24674959; PubMed Central PMCID: PMCPMC5119065. PubMed DOI PMC

Belibi F, Zafar I, Ravichandran K, et al. Hypoxia-inducible factor-1alpha (HIF-1alpha) and autophagy in polycystic kidney disease (PKD). Am J Physiol Renal Physiol. 2011. May;300(5):F1235–43. doi:10.1152/ajprenal.00348.2010. PubMed PMID: 21270095; PubMed Central PMCID: PMC3094047. PubMed DOI PMC

Gukovskaya AS, Gorelick FS, Groblewski GE, et al. Recent insights into the pathogenic mechanism of pancreatitis: role of acinar cell organelle disorders. Pancreas. 2019. Apr;48(4):459–470. doi:10.1097/MPA.0000000000001298. PubMed PMID: 30973461; PubMed Central PMCID: PMCPMC6461375. PubMed DOI PMC

Sobolewska A, Motyl T, Gajewska M.. Role and regulation of autophagy in the development of acinar structures formed by bovine BME-UV1 mammary epithelial cells. Eur J Cell Biol. 2011. Oct;90(10):854–64. doi:10.1016/j.ejcb.2011.06.007. PubMed PMID: 21868124; eng. PubMed DOI

Motyl T, Gajewska M, Zarzynska J, et al. Regulation of autophagy in bovine mammary epithelial cells. Autophagy. 2007. Sep-Oct;3(5):484–6. PubMed PMID: 17592247; eng. PubMed

Sobolewska A, Gajewska M, Zarzynska J, et al. IGF-I, EGF, and sex steroids regulate autophagy in bovine mammary epithelial cells via the mTOR pathway. Eur J Cell Biol. 2009. Feb;88(2):117–30. doi:10.1016/j.ejcb.2008.09.004. PubMed PMID: 19013662; eng. PubMed DOI

Tettamanti G, Casartelli M.. Cell death during complete metamorphosis. Philos Trans R Soc London, Ser B. 2019. Oct 14;374(1783):20190065. doi:10.1098/rstb.2019.0065. PubMed PMID: 31438818; PubMed Central PMCID: PMCPMC6711292. PubMed DOI PMC

Facey CO, Lockshin RA.. The execution phase of autophagy associated PCD during insect metamorphosis. Apoptosis. 2010. Jun;15(6):639–52. doi: 10.1007/s10495-010-0499-3. PubMed PMID: 20405221; eng. PubMed DOI

Malagoli D, Abdalla FC, Cao Y, et al. Autophagy and its physiological relevance in arthropods: Current knowledge and perspectives. Autophagy. 2010. Jul 1;6(5):575–88. PubMed PMID: 20458176; Eng. PubMed

Mpakou VE, Nezis IP, Stravopodis DJ, et al. Programmed cell death of the ovarian nurse cells during oogenesis of the silkmoth Bombyx mori [Research Support, Non-U.S. Gov’t]. Dev Growth Differ. 2006. Sep;48(7):419–28. doi:10.1111/j.1440-169X.2006.00878.x. PubMed PMID: 16961589; eng. PubMed DOI

Mpakou VE, Nezis IP, Stravopodis DJ, et al. Different modes of programmed cell death during oogenesis of the silkmoth Bombyx mori [Research Support, Non-U.S. Gov’t]. Autophagy. 2008. Jan;4(1):97–100. PubMed PMID: 17986869; eng. PubMed

Sumithra P, Britto CP, Krishnan M.. Modes of cell death in the pupal perivisceral fat body tissue of the silkworm Bombyx mori L. Cell Tissue Res. 2010. Feb;339(2):349–58. doi:10.1007/s00441-009-0898-3. PubMed PMID: 19949813; eng. PubMed DOI

Tettamanti G, Grimaldi A, Casartelli M, et al. Programmed cell death and stem cell differentiation are responsible for midgut replacement in Heliothis virescens during prepupal instar. Cell Tissue Res. 2007. Nov;330(2):345–59. doi:10.1007/s00441-007-0449-8. PubMed PMID: 17661086; eng. PubMed DOI

Romanelli D, Casartelli M, Cappellozza S, et al. Roles and regulation of autophagy and apoptosis in the remodelling of the lepidopteran midgut epithelium during metamorphosis. Sci Rep. 2016. Sep 9;6:32939. doi:10.1038/srep32939. PubMed PMID: 27609527; PubMed Central PMCID: PMCPMC5016986. PubMed DOI PMC

Khoa DB, Takeda M.. Expression of autophagy 8 (Atg8) and its role in the midgut and other organs of the greater wax moth, Galleria mellonella, during metamorphic remodelling and under starvation. Insect Mol Biol. 2012. Oct;21(5):473–87. doi:10.1111/j.1365-2583.2012.01152.x. PubMed PMID: 22830988. PubMed DOI

Gai Z, Zhang X, Islam M, et al. Characterization of Atg8 in lepidopteran insect cells. Arch Insect Biochem Physiol 2013;84:57–77. PubMed

Dai Y, Li K, Wu W, et al. Steroid hormone 20-hydroxyecdysone induces the transcription and complex assembly of V-ATPases to facilitate autophagy in Bombyx mori. Insect Biochem Mol Biol. 2020. Jan;116:103255. doi:10.1016/j.ibmb.2019.103255. PubMed PMID: 31654713. PubMed DOI

Wu W, Luo M, Li K, et al. Cholesterol derivatives induce dephosphorylation of the histone deacetylases Rpd3/HDAC1 to upregulate autophagy. Autophagy. 2020. Feb 12:1–17. doi:10.1080/15548627.2020.1725376. PubMed PMID: 32013726. PubMed DOI PMC

Goncu E, Parlak O.. Some autophagic and apoptotic features of programmed cell death in the anterior silk glands of the silkworm, Bombyx mori. Autophagy. 2008. Nov;4(8):1069–72. PubMed PMID: 18838861; eng. PubMed

Zhou S, Zhou Q, Liu Y, et al. Two Tor genes in the silkworm Bombyx mori. Insect Mol Biol. 2010. Dec;19(6):727–35. doi:10.1111/j.1365-2583.2010.01026.x. PubMed PMID: 20609020; eng. PubMed DOI

Zhang X, Hu ZY, Li WF, et al. Systematic cloning and analysis of autophagy-related genes from the silkworm Bombyx mori. BMC Mol Biol. 2009;10:50. doi:10.1186/1471-2199-10-50. ]. PubMed DOI PMC

Romanelli D, Casati B, Franzetti E, et al. A molecular view of autophagy in Lepidoptera. Biomed Res Int. 2014;2014:902315. doi:10.1155/2014/902315. PubMed PMID: 25143951; PubMed Central PMCID: PMC4124216. PubMed DOI PMC

Li Q, Deng X, Huang Z, et al. Expression of autophagy-related genes in the anterior silk gland of the silkworm (Bombyx mori) during metamorphosis. Can J Zool 2011;89:1019–26.

Casati B, Terova G, Cattaneo AG, et al. Molecular cloning, characterization and expression analysis of ATG1 in the silkworm, Bombyx mori. Gene. 2012. Dec 15;511(2):326–37. doi:10.1016/j.gene.2012.09.086. PubMed PMID: 23041082. PubMed DOI

Godefroy N, Hoa C, Tsokanos F, et al. Identification of autophagy genes in Ciona intestinalis: a new experimental model to study autophagy mechanism. Autophagy. 2009. Aug;5(6):805–15. PubMed PMID: 19502774. PubMed

Martinand-Mari C, Vacelet J, Nickel M, et al. Cell death and renewal during prey capture and digestion in the carnivorous sponge Asbestopluma hypogea (Porifera: Poecilosclerida). J Exp Biol. 2012. Nov 15;215\(Pt 22):3937–43. doi:10.1242/jeb.072371. PubMed PMID: 22899530. PubMed DOI

Jackson DJ, Worheide G.. Symbiophagy and biomineralization in the “living fossil” Astrosclera willeyana. Autophagy 2014. Mar;10(3):408–15. doi:10.4161/auto.27319. PubMed PMID: 24343243; PubMed Central PMCID: PMC4077880. PubMed DOI PMC

Galasso C, D’Aniello S, Sansone C, et al. Identification of cell death genes in sea urchin paracentrotus lividus and their expression patterns during embryonic development. Genome Biol Evol. 2019. Feb 1;11(2):586–596. doi:10.1093/gbe/evz020. PubMed PMID: 30698765; PubMed Central PMCID: PMCPMC6394757. PubMed DOI PMC

Moore MN, Allen JI, McVeigh A, et al. Lysosomal and autophagic reactions as predictive indicators of environmental impact in aquatic animals. Autophagy. 2006. Jul-Sep;2(3):217–20. doi:10.4161/auto.2663. PubMed PMID: 16874099. PubMed DOI

Sforzini S, Moore MN, Oliveri C, et al. Role of mTOR in autophagic and lysosomal reactions to environmental stressors in molluscs. Aquat Toxicol. 2018. Feb;195:114–128. doi:10.1016/j.aquatox.2017.12.014. PubMed PMID: 29306034. PubMed DOI

Moreau P, Moreau K, Segarra A, et al. Autophagy plays an important role in protecting Pacific oysters from OsHV-1 and Vibrio aestuarianus infections. Autophagy. 2015;11(3):516–26. doi:10.1080/15548627.2015.1017188. PubMed PMID: 25714877; PubMed Central PMCID: PMCPMC4502751. PubMed DOI PMC

Balbi T, Cortese K, Ciacci C, et al. Autophagic processes in Mytilus galloprovincialis hemocytes: Effects of Vibrio tapetis. Fish Shellfish Immunol. 2018. Feb;73:66–74. doi:10.1016/j.fsi.2017.12.003. PubMed PMID: 29208501. PubMed DOI

Tanguy M, Gauthier-Clerc S, Pellerin J, et al. The immune response of Mytilus edulis hemocytes exposed to Vibrio splendidus LGP32 strain: A transcriptomic attempt at identifying molecular actors. Fish Shellfish Immunol. 2018. Mar;74:268–280. doi:10.1016/j.fsi.2017.12.038. PubMed PMID: 29305989. PubMed DOI

Wang L, Song X, Song L.. The oyster immunity. Dev Comp Immunol. 2018. Mar;80:99–118. doi:10.1016/j.dci.2017.05.025. PubMed PMID: 28587860. PubMed DOI

Fuess LE, Pinzon CJ, Weil E, et al. Life or death: disease-tolerant coral species activate autophagy following immune challenge. Proc Biol Sci. 2017. Jun 14;284(1856). doi:10.1098/rspb.2017.0771. PubMed PMID: 28592676; PubMed Central PMCID: PMCPMC5474081. PubMed DOI PMC

Zhao MR, Meng C, Xie XL, et al. Characterization of microRNAs by deep sequencing in red claw crayfish Cherax quadricarinatus haematopoietic tissue cells after white spot syndrome virus infection. Fish Shellfish Immunol. 2016. Dec;59:469–483. doi:10.1016/j.fsi.2016.11.012. PubMed PMID: 27825947. PubMed DOI

He Y, Sun Y, Zhang X.. Noncoding miRNAs bridge virus infection and host autophagy in shrimp in vivo. FASEB J. 2017. Jul;31(7):2854–2868. doi:10.1096/fj.201601141RR. PubMed PMID: 28330853. PubMed DOI

Yang W, Liu C, Xu Q, et al. Beclin-1 is involved in the regulation of antimicrobial peptides expression in Chinese mitten crab Eriocheir sinensis. Fish Shellfish Immunol. 2019. Jun;89:207–216. doi:10.1016/j.fsi.2019.03.065. PubMed PMID: 30936045. PubMed DOI

Wang M, Lee JS, Li Y.. Global proteome profiling of a marine copepod and the mitigating effect of ocean acidification on mercury toxicity after multigenerational exposure. Environ Sci Technol. 2017. May 16;51(10):5820–5831. doi:10.1021/acs.est.7b01832. PubMed PMID: 28414453. PubMed DOI

Sforzini S, Oliveri C, Barranger A, et al. Effects of fullerene C60 in blue mussels: Role of mTOR in autophagy related cellular/tissue alterations. Chemosphere. 2019. Dec 23;246:125707. doi:10.1016/j.chemosphere.2019.125707. PubMed PMID: 31891845. PubMed DOI

Thome RG, Santos HB, Arantes FP, et al. Dual roles for autophagy during follicular atresia in fish ovary. Autophagy. 2009. Jan; 5(1):117–9. PubMed PMID: 19011378; eng. PubMed

Santos HB, Thome RG, Arantes FP, et al. Ovarian follicular atresia is mediated by heterophagy, autophagy, and apoptosis in Prochilodus argenteus and Leporinus taeniatus. Theriogenology 2008. Dec;70(9):1449–60. doi:10.1016/j.theriogenology.2008.06.091. PubMed PMID: 18701155; eng. PubMed DOI

Santos HB, Sato Y, Moro L, et al. Relationship among follicular apoptosis, integrin beta1 and collagen type IV during early ovarian regression in the teleost Prochilodus argenteus after induced spawning. Cell Tissue Res. 2008. Apr;332(1):159–70. doi:10.1007/s00441-007-0540-1. PubMed PMID: 18193286; eng. PubMed DOI

Santos HB, Rizzo E, Bazzoli N, et al. Ovarian regression and apoptosis in the South American teleost Leporinus taeniatus Lutken (Characiformes, Anostomidae) from the São Francisco Basin. 2005;67:1446–1459.

Couve E, Schmachtenberg O.. Autophagic activity and aging in human odontoblasts. J Dent Res. 2011. Apr;90(4):523–8. doi:10.1177/0022034510393347. PubMed PMID: 21212314; eng. PubMed DOI

Zhuang H, Hu D, Singer D, et al. Local anesthetics induce autophagy in young permanent tooth pulp cells. Cell Death Discov. 2015;1:15024. doi:10.1038/cddiscovery.2015.24. PubMed PMID: 27551457; PubMed Central PMCID: PMCPMC4979463. PubMed DOI PMC

An Y, Liu W, Xue P, et al. Increased autophagy is required to protect periodontal ligament stem cells from apoptosis in inflammatory microenvironment. J Clin Periodontol. 2016. Jul;43(7):618–25. doi:10.1111/jcpe.12549. PubMed PMID: 26990245. PubMed DOI

Vescarelli E, Pilloni A, Dominici F, et al. Autophagy activation is required for myofibroblast differentiation during healing of oral mucosa. J Clin Periodontol. 2017. Oct;44(10):1039–1050. doi:10.1111/jcpe.12767. PubMed PMID: 28646601. PubMed DOI

Olson PD, Tkach VV.. Advances and trends in the molecular systematics of the parasitic Platyhelminthes. Adv Parasitol. 2005;60:165–243. doi:10.1016/S0065-308X(05)60003-6. PubMed PMID: 16230104. PubMed DOI

Collins JJ, 3rd. Platyhelminthes. Curr Biol. 2017. Apr 3;27(7):R252–R256. doi:10.1016/j.cub.2017.02.016. PubMed PMID: 28376328. PubMed DOI

Threadgold LT, Arme C.. Electron microscope studies of Fasciola hepatica. XI. Autophagy and parenchymal cell function. Exp Parasitol. 1974. Jun;35(3):389–405. doi:10.1016/0014-4894(74)90045-9. PubMed PMID: 4363771. PubMed DOI

Bogitsh BJ. Cytochemistry of gastrodermal autophagy following starvation in Schistosoma mansoni. J Parasitol. 1975. Apr;61(2):237–48. PubMed PMID: 1127552. PubMed

Clarkson J, Erasmus DA.. Schistosoma mansoni: an in vivo study of drug-induced autophagy in the gastrodermis. J Helminthol. 1984. Mar;58(1):59–68. doi:10.1017/s0022149x00028066. PubMed PMID: 6325532. PubMed DOI

Richards KS, Arme C, Bridges JF.. Echinococcus granulosus equinus: variation in the germinal layer of murine hydatids and evidence of autophagy. Parasitology. 1984. Aug;89(Pt 1):35–47. doi: 10.1017/s0031182000001116. PubMed PMID: 6472884. PubMed DOI

McCullough JS, Fairweather I.. The structure, composition, formation and possible functions of calcareous corpuscles in Trilocularia acanthiaevulgaris Olsson 1867 (Cestoda, Tetraphyllidea). Parasitol Res. 1987;74(2):175–82. doi:10.1007/bf00536030. PubMed PMID: 3438298. PubMed DOI

Ogata M, Hino S, Saito A, et al. Autophagy is activated for cell survival after endoplasmic reticulum stress. Mol Cell Biol. 2006. Dec;26(24):9220–31. doi:10.1128/MCB.01453-06. PubMed PMID: 17030611; PubMed Central PMCID: PMCPMC1698520. PubMed DOI PMC

Ahn CS, Kim JG, Bae YA, et al. Fasciclin-calcareous corpuscle binary complex mediated protein-protein interactions in Taenia solium metacestode. Parasit Vectors. 2017. Sep 20;10(1):438. doi:10.1186/s13071-017-2359-2. PubMed PMID: 28931431; PubMed Central PMCID: PMCPMC5606126. PubMed DOI PMC

Loos JA, Caparros PA, Nicolao MC, et al. Identification and pharmacological induction of autophagy in the larval stages of Echinococcus granulosus: an active catabolic process in calcareous corpuscles. Int J Parasitol. 2014. Jun;44(7):415–27. doi:10.1016/j.ijpara.2014.02.007. PubMed PMID: 24703869. PubMed DOI

Berriman M, Haas BJ, LoVerde PT, et al. The genome of the blood fluke Schistosoma mansoni. Nature. 2009. Jul 16;460(7253):352–8. doi:10.1038/nature08160. PubMed PMID: 19606141; PubMed Central PMCID: PMCPMC2756445. PubMed DOI PMC

Tsai IJ, Zarowiecki M, Holroyd N, et al. The genomes of four tapeworm species reveal adaptations to parasitism. Nature. 2013. Apr 4;496(7443):57–63. doi10.1038/nature12031. PubMed PMID: 23485966; PubMed Central PMCID: PMCPMC3964345. PubMed DOI PMC

Zheng H, Zhang W, Zhang L, et al. The genome of the hydatid tapeworm Echinococcus granulosus. Nat Genet. 2013. Oct;45(10):1168–75. doi:10.1038/ng.2757. PubMed PMID: 24013640. PubMed DOI

International Helminth Genomes C. Comparative genomics of the major parasitic worms. Nat Genet. 2019. Jan;51(1):163–174. doi:10.1038/s41588-018-0262-1. PubMed PMID: 30397333; PubMed Central PMCID: PMCPMC6349046. PubMed DOI PMC

Cumino AC, Lamenza P, Denegri GM.. Identification of functional FKB protein in Echinococcus granulosus: its involvement in the protoscolicidal action of rapamycin derivates and in calcium homeostasis. Int J Parasitol. 2010. May;40(6):651–61. doi:10.1016/j.ijpara.2009.11.011. PubMed PMID: 20005877. PubMed DOI

Loos JA, Nicolao MC, Cumino AC.. Metformin promotes autophagy in Echinococcus granulosus larval stage. Mol Biochem Parasitol. 2018. Sep;224:61–70. doi:10.1016/j.molbiopara.2018.07.003. PubMed PMID: 30017657. PubMed DOI

Nicolao MC, Loos JA, Rodriguez Rodrigues C, et al. Bortezomib initiates endoplasmic reticulum stress, elicits autophagy and death in Echinococcus granulosus larval stage. PLoS One. 2017;12(8):e0181528. doi:10.1371/journal.pone.0181528. PubMed PMID: 28817601; PubMed Central PMCID: PMCPMC5560652. PubMed DOI PMC

Gonzalez-Estevez C. Autophagy in freshwater planarians. Methods Enzymol. 2008;451:439–65. doi:10.1016/S0076-6879(08)03227-8. PubMed PMID: 19185735; eng. PubMed DOI

Gonzalez-Estevez C, Felix DA, Aboobaker AA, et al. Gtdap-1 promotes autophagy and is required for planarian remodeling during regeneration and starvation. Proc Natl Acad Sci U S A. 2007. Aug 14;104(33):13373–8. doi:10.1073/pnas.0703588104. PubMed PMID: 17686979; PubMed Central PMCID: PMC1948951. eng. PubMed DOI PMC

Toyooka K, Moriyasu Y, Goto Y, et al. Protein aggregates are transported to vacuoles by a macroautophagic mechanism in nutrient-starved plant cells. Autophagy. 2006. Apr-Jun;2(2):96–106. PubMed PMID: 16874101; eng. PubMed

Corral-Martinez P, Parra-Vega V, Segui-Simarro JM.. Novel features of Brassica napus embryogenic microspores revealed by high pressure freezing and freeze substitution: evidence for massive autophagy and excretion-based cytoplasmic cleaning. J Exp Bot. 2013. Jul;64(10):3061–75. doi:10.1093/jxb/ert151. PubMed PMID: 23761486. PubMed DOI

Le Bars R, Marion J, Le Borgne R, et al. ATG5 defines a phagophore domain connected to the endoplasmic reticulum during autophagosome formation in plants. Nat Commun. 2014;5:4121. doi:10.1038/ncomms5121. PubMed PMID: 24947672. PubMed DOI

Shin KD, Lee HN, Chung T.. A revised assay for monitoring autophagic flux in Arabidopsis thaliana reveals involvement of AUTOPHAGY-RELATED9 in autophagy. Mol Cells. 2014. May;37(5):399–405. doi:10.14348/molcells.2014.0042. PubMed PMID: 24805779; PubMed Central PMCID: PMC4044311. PubMed DOI PMC

Wojciechowska N, Smugarzewska I, Marzec-Schmidt K, et al. Occurrence of autophagy during pioneer root and stem development in Populus trichocarpa. Planta. 2019. Dec;250(6):1789–1801. doi:10.1007/s00425-019-03265-5. PubMed PMID: 31451904. PubMed DOI

Wojciechowska N, Marzec-Schmidt K, Kalemba EM, et al. Autophagy counteracts instantaneous cell death during seasonal senescence of the fine roots and leaves in Populus trichocarpa. BMC Plant Biol. 2018. Oct 29;18(1):260. doi:10.1186/s12870-018-1439-6. PubMed PMID: 30373512; PubMed Central PMCID: PMCPMC6206944. PubMed DOI PMC

Svenning S, Lamark T, Krause K, et al. Plant NBR1 is a selective autophagy substrate and a functional hybrid of the mammalian autophagic adapters NBR1 and p62/SQSTM1. Autophagy. 2011. Sep 1;7(9):993–1010. PubMed PMID: 21606687; Eng. PubMed PMC

Zientara-Rytter K, Lukomska J, Moniuszko G, et al. Identification and functional analysis of Joka2, a tobacco member of the family of selective autophagy cargo receptors. Autophagy. 2011. Oct 1;7(10):1145–58. PubMed PMID: 21670587; Eng. PubMed PMC

Minina EA, Sanchez-Vera V, Moschou PN, et al. Autophagy mediates caloric restriction-induced lifespan extension in Arabidopsis. Aging cell. 2013. Apr;12(2):327–9. doi:10.1111/acel.12048. PubMed PMID: 23331488. PubMed DOI

Farmer LM, Rinaldi MA, Young PG, et al. Disrupting autophagy restores peroxisome function to an Arabidopsis lon2 mutant and reveals a role for the LON2 protease in peroxisomal matrix protein degradation. Plant Cell. 2013. Oct;25(10):4085–100. doi:10.1105/tpc.113.113407. PubMed PMID: 24179123; PubMed Central PMCID: PMC3877801. PubMed DOI PMC

Shibata M, Oikawa K, Yoshimoto K, et al. Highly oxidized peroxisomes are selectively degraded via autophagy in Arabidopsis. Plant Cell. 2013. Dec;25(12):4967–83. doi:10.1105/tpc.113.116947. PubMed PMID: 24368788; PubMed Central PMCID: PMCPMC3903999. PubMed DOI PMC

Fahy D, Sanad M, Duscha K, et al. Impact of salt stress, cell death, and autophagy on peroxisomes: quantitative and morphological analyses using small fluorescent probe N-BODIPY. Sci Rep. 2017. Feb 1;7:39069. doi:10.1038/srep39069. PubMed PMID: 28145408; PubMed Central PMCID: PMCPMC5286434. PubMed DOI PMC

Landrum M, Smertenko A, Edwards R, et al. BODIPY probes to study peroxisome dynamics in vivo. Plant J. 2010. May;62(3):529–38. doi:10.1111/j.1365-313X.2010.04153.x. PubMed PMID: 20113442. PubMed DOI

Eapen D, Barroso ML, Campos ME, et al. A no hydrotropic response root mutant that responds positively to gravitropism in Arabidopsis. Plant Physiol. 2003. Feb;131(2):536–46. doi:10.1104/pp.011841. PubMed PMID: 12586878; PubMed Central PMCID: PMCPMC166830. PubMed DOI PMC

Jimenez-Nopala G, Salgado-Escobar AE, Cevallos-Porta D, et al. Autophagy mediates hydrotropic response in Arabidopsis thaliana roots. Plant Sci. 2018. Jul;272:1–13. doi:10.1016/j.plantsci.2018.03.026. PubMed PMID: 29807580. PubMed DOI

van Doorn WG, Papini A.. Ultrastructure of autophagy in plant cells: a review. Autophagy. 2013. Dec;9(12):1922–36. doi:10.4161/auto.26275. PubMed PMID: 24145319. PubMed DOI

Dagdas YF, Belhaj K, Maqbool A, et al. An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor. eLife. 2016. Jan 14;5. doi:10.7554/eLife.10856. PubMed PMID: 26765567; PubMed Central PMCID: PMCPMC4775223. PubMed DOI PMC

Dagdas YF, Pandey P, Tumtas Y, et al. Host autophagy machinery is diverted to the pathogen interface to mediate focal defense responses against the Irish potato famine pathogen. eLife. 2018. Jun 22;7. doi:10.7554/eLife.37476. PubMed PMID: 29932422; PubMed Central PMCID: PMCPMC6029844. PubMed DOI PMC

Moriyasu Y, Inoue Y.. Use of protease inhibitors for detecting autophagy in plants. Methods Enzymol. 2008;451:557–80. doi:10.1016/S0076-6879(08)03232-1. PubMed PMID: 19185740. PubMed DOI

Takatsuka C, Inoue Y, Matsuoka K, et al. 3-methyladenine inhibits autophagy in tobacco culture cells under sucrose starvation conditions. Plant Cell Physiol 2004. Mar;45(3):265–74. PubMed PMID: 15047874. PubMed

Besteiro S, Brooks CF, Striepen B, et al. Autophagy protein Atg3 is essential for maintaining mitochondrial integrity and for normal intracellular development of Toxoplasma gondii tachyzoites. PLoS Pathog. 2011;7(12):e1002416. PubMed PMC

Calvo-Garrido J, Carilla-Latorre S, Kubohara Y, et al. Autophagy in Dictyostelium: genes and pathways, cell death and infection. Autophagy. 2010. Aug;6(6):686–701. PubMed PMID: 20603609; eng. PubMed

Tung SM, Unal C, Ley A, et al. Loss of Dictyostelium ATG9 results in a pleiotropic phenotype affecting growth, development, phagocytosis and clearance and replication of Legionella pneumophila. Cell Microbiol. 2010. Jun;12(6):765–80. doi:10.1111/j.1462-5822.2010.01432.x. PubMed PMID: 20070309; eng. PubMed DOI

0Bozzaro S, Eichinger L.. The professional phagocyte Dictyostelium discoideum as a model host for bacterial pathogens. Curr Drug Targets. 2011. Jun;12(7):942–54. PubMed PMID: 21366522; eng. PubMed PMC

Schlegel M, Hülsmann N.. Protists – A textbook example for a paraphyletic taxon. Org Divers Evol 2007;7:166–172.

Kitamura K, Kishi-Itakura C, Tsuboi T, et al. Autophagy-related Atg8 localizes to the apicoplast of the human malaria parasite Plasmodium falciparum. PLoS One. 2012;7(8):e42977. doi:10.1371/journal.pone.0042977. PubMed PMID: 22900071; PubMed Central PMCID: PMC3416769. PubMed DOI PMC

Barquilla A, Crespo JL, Navarro M.. Rapamycin inhibits trypanosome cell growth by preventing TOR complex 2 formation. Proc Natl Acad Sci U S A. 2008. Sep 23;105(38):14579–84. doi:10.1073/pnas.0802668105. PubMed PMID: 18796613; PubMed Central PMCID: PMC2567229. eng. PubMed DOI PMC

Vanrell MC, Losinno AD, Cueto JA, et al. The regulation of autophagy differentially affects Trypanosoma cruzi metacyclogenesis. PLoS Negl Trop Dis. 2017. Nov;11(11):e0006049. doi:10.1371/journal.pntd.0006049. PubMed PMID: 29091711; PubMed Central PMCID: PMCPMC5683653. PubMed DOI PMC

Li FJ, He CY.. Acidocalcisome is required for autophagy in Trypanosoma brucei. Autophagy. 2014;10(11):1978–88. doi:10.4161/auto.36183. PubMed PMID: 25484093; PubMed Central PMCID: PMCPMC4502762. PubMed DOI PMC

Hain AU, Bartee D, Sanders NG, et al. Identification of an Atg8-Atg3 protein-protein interaction inhibitor from the medicines for Malaria Venture Malaria Box active in blood and liver stage Plasmodium falciparum parasites. J Med Chem. 2014. Jun 12;57(11):4521–31. doi:10.1021/jm401675a. PubMed PMID: 24786226; PubMed Central PMCID: PMC4059259. PubMed DOI PMC

Hain AU, Weltzer RR, Hammond H, et al. Structural characterization and inhibition of the Plasmodium Atg8-Atg3 interaction. J Struct Biol. 2012. Dec;180(3):551–62. doi:10.1016/j.jsb.2012.09.001. PubMed PMID: 22982544; PubMed Central PMCID: PMC3496014. PubMed DOI PMC

Navale R, Atul, Allanki AD, et al. Characterization of the autophagy marker protein Atg8 reveals atypical features of autophagy in Plasmodium falciparum. PLoS One. 2014;9(11):e113220. doi:10.1371/journal.pone.0113220. PubMed PMID: 25426852; PubMed Central PMCID: PMC4245143. PubMed DOI PMC

Parussini F, Coppens I, Shah PP, et al. Cathepsin L occupies a vacuolar compartment and is a protein maturase within the endo/exocytic system of Toxoplasma gondii. Mol Microbiol. 2010. Jun;76(6):1340–57. doi:10.1111/j.1365-2958.2010.07181.x. PubMed PMID: 20444089; PubMed Central PMCID: PMCPMC2909120. PubMed DOI PMC

Miranda K, Pace DA, Cintron R, et al. Characterization of a novel organelle in Toxoplasma gondii with similar composition and function to the plant vacuole. Mol Microbiol. 2010. Jun;76(6):1358–75. doi:10.1111/j.1365-2958.2010.07165.x. PubMed PMID: 20398214; PubMed Central PMCID: PMCPMC2907454. PubMed DOI PMC

Nguyen HM, El Hajj H, El Hajj R, et al. Toxoplasma gondii autophagy-related protein ATG9 is crucial for the survival of parasites in their host. Cell Microbiol. 2017. Jun;19(6). doi:10.1111/cmi.12712. PubMed PMID: 27992947. PubMed DOI

Di Cristina M, Dou Z, Lunghi M, et al. Toxoplasma depends on lysosomal consumption of auto-phagosomes for persistent infection. Nat Microbiol. 2017. Jun 19;2:17096. doi:10.1038/nmicrobiol.2017.96. PubMed PMID: 28628099; PubMed Central PMCID: PMCPMC5527684. PubMed DOI PMC

Kannan G, Di Cristina M, Schultz AJ, et al. Role of toxoplasma gondii chloroquine resistance transporter in bradyzoite viability and digestive vacuole maintenance. mBio. 2019. Aug 6;10(4). doi:10.1128/mBio.01324-19. PubMed PMID: 31387907; PubMed Central PMCID: PMCPMC6686041. PubMed DOI PMC

Morais P, Lamas J, Sanmartin ML, et al. Resveratrol induces mitochondrial alterations, autophagy and a cryptobiosis-like state in scuticociliates. Protist. 2009. Nov;160(4):552–64. doi:10.1016/j.protis.2009.04.004. PubMed PMID: 19640787; eng. PubMed DOI

Yakisich JS, Kapler GM.. The effect of phosphoinositide 3-kinase inhibitors on programmed nuclear degradation in Tetrahymena and fate of surviving nuclei. Cell Death Differ. 2004. Oct;11(10):1146–9. doi:10.1038/sj.cdd.4401473. PubMed PMID: 15257301; eng. PubMed DOI

Akematsu T, Pearlman RE, Endoh H.. Gigantic macroautophagy in programmed nuclear death of Tetrahymena thermophila [Research Support, Non-U.S. Gov’t]. Autophagy. 2010. Oct;6(7):901–11. doi:10.4161/auto.6.7.13287. PubMed PMID: 20798592; PubMed Central PMCID: PMC3039737. eng. PubMed DOI PMC

Schoijet AC, Miranda K, Girard-Dias W, et al. A Trypanosoma cruzi phosphatidylinositol 3-kinase (TcVps34) is involved in osmoregulation and receptor-mediated endocytosis. J Biol Chem. 2008. Nov 14;283(46):31541–50. doi:10.1074/jbc.M801367200. PubMed PMID: 18801733; PubMed Central PMCID: PMCPMC2581564. PubMed DOI PMC

Thorgaard GH, Bailey GS, Williams D, et al. Status and opportunities for genomics research with rainbow trout. Comp Biochem Physiol Part B Biochem Mol Bio. 2002. Dec;133(4):609–46. PubMed PMID: 12470823; eng. PubMed

Govoroun M, Le Gac F, Guiguen Y.. Generation of a large scale repertoire of Expressed Sequence Tags (ESTs) from normalised rainbow trout cDNA libraries. BMC genomics. 2006;7:196. doi:10.1186/1471-2164-7-196. PubMed PMID: 16887034; PubMed Central PMCID: PMC1564016. eng. PubMed DOI PMC

Rexroad CE, III, Lee Y, Keele JW, et al. Sequence analysis of a rainbow trout cDNA library and creation of a gene index. Cytogenet Genome Res. 2003;102(1–4): 347–54. doi:10.1159/000075773. PubMed PMID: 14970727; eng. PubMed DOI

Rise ML, von Schalburg KR, Brown GD, et al. Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res. 2004. Mar;14(3):478–90. doi:10.1101/gr.1687304. PubMed PMID: 14962987; PubMed Central PMCID: PMC353236. eng. PubMed DOI PMC

Salem M, Rexroad CE, III, Wang J, et al. Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC genomics. 2010;11:564. doi:10.1186/1471-2164-11-564. PubMed PMID: 20942956; PubMed Central PMCID: PMC3091713. eng. PubMed DOI PMC

Seiliez I, Gabillard J-C, Riflade M, et al. Amino acids downregulate the expression of several autophagy-related genes in rainbow trout myoblasts. Autophagy. 2012;8:364–75. PubMed

Seiliez I, Gabillard JC, Skiba-Cassy S, et al. An in vivo and in vitro assessment of TOR signaling cascade in rainbow trout (Oncorhynchus mykiss). Am J Physiol Regul Integr Comp Physiol. 2008. Jul;295(1):R329–35. doi:10.1152/ajpregu.00146.2008. PubMed PMID: 18434442; eng. PubMed DOI

Polakof S, Panserat S, Craig PM, et al. The metabolic consequences of hepatic AMP-kinase phosphorylation in rainbow trout. PLoS One. 2011;6(5):e20228. doi:10.1371/journal.pone.0020228. PubMed PMID: 21625448; PubMed Central PMCID: PMC3098864. eng. PubMed DOI PMC

Frost LS, Mitchell CH, Boesze-Battaglia K.. Autophagy in the eye: implications for ocular cell health. Exp Eye Res. 2014. Jul;124:56–66. doi:10.1016/j.exer.2014.04.010. PubMed PMID: 24810222; PubMed Central PMCID: PMCPMC4156154. eng. PubMed DOI PMC

Muniz-Feliciano L, Doggett TA, Zhou Z, et al. RUBCN/rubicon and EGFR regulate lysosomal degradative processes in the retinal pigment epithelium (RPE) of the eye. Autophagy. 2017;13(12):2072–2085. doi:10.1080/15548627.2017.1380124. PubMed PMID: 28933590; PubMed Central PMCID: PMCPMC5788552. eng. PubMed DOI PMC

Zhang Y, Cross SD, Stanton JB, et al. Early AMD-like defects in the RPE and retinal degeneration in aged mice with RPE-specific deletion of Atg5 or Atg7. Mol Vis. 2017;23:228–241. PubMed PMID: 28465655; PubMed Central PMCID: PMCPMC5398883. eng. PubMed PMC

Zhao C, Yasumura D, Li X, et al. mTOR-mediated dedifferentiation of the retinal pigment epithelium initiates photoreceptor degeneration in mice. J Clin Invest. 2011. Jan;121(1):369–83. doi:10.1172/jci44303. PubMed PMID: 21135502; PubMed Central PMCID: PMCPMC3007156. eng. PubMed DOI PMC

Huang J, Gu S, Chen M, et al. Abnormal mTORC1 signaling leads to retinal pigment epithelium degeneration. Theranostics. 2019;9(4):1170–1180. doi:10.7150/thno.26281. PubMed PMID: 30867823; PubMed Central PMCID: PMCPMC6401408. PubMed DOI PMC

Frost LS, Dhingra A, Reyes-Reveles J, et al. The Use of DQ-BSA to Monitor the Turnover of Autophagy-Associated Cargo. Methods Enzymol. 2017;587:43–54. doi:10.1016/bs.mie.2016.09.052. PubMed PMID: 28253971; PubMed Central PMCID: PMCPMC5338641. eng. PubMed DOI PMC

Frost LS, Lopes VS, Bragin A, et al. The contribution of melanoregulin to microtubule-associated protein 1 light chain 3 (LC3) associated phagocytosis in retinal pigment epithelium. Mol Neurobiol. 2015. Dec;52(3):1135–1151. doi:10.1007/s12035-014-8920-5. PubMed PMID: 25301234; PubMed Central PMCID: PMCPMC5531606. eng. PubMed DOI PMC

Dhingra A, Bell BA, Peachey NS, et al. Microtubule-associated protein 1 light chain 3B, (LC3B) is necessary to maintain lipid-mediated homeostasis in the retinal pigment epithelium. Front Cell Neurosci. 2018;12:351. doi:10.3389/fncel.2018.00351. PubMed PMID: 30349463; PubMed Central PMCID: PMCPMC6186781. eng. PubMed DOI PMC

Baltazar GC, Guha S, Lu W, et al. Acidic nanoparticles are trafficked to lysosomes and restore an acidic lysosomal pH and degradative function to compromised ARPE-19 cells. PLoS One. 2012;7(12):e49635. doi:10.1371/journal.pone.0049635. PubMed PMID: 23272048; PubMed Central PMCID: PMCPMC3525582. eng. PubMed DOI PMC

Guha S, Liu J, Baltazar G, et al. Rescue of compromised lysosomes enhances degradation of photoreceptor outer segments and reduces lipofuscin-like autofluorescence in retinal pigmented epithelial cells. Adv Exp Med Biol. 2014;801:105–11. doi:10.1007/978-1-4614-3209-8_14.PubMed PMID: 24664687; PubMed Central PMCID: PMCPMC4163923. eng. PubMed DOI PMC

Lu W, Campagno KE, Tso HY, et al. Oral delivery of the P2Y12 receptor antagonist ticagrelor prevents loss of photoreceptors in an ABCA4-/- mouse model of retinal degeneration. Invest Ophthalmol Vis Sci. 2019. Jul 1;60(8):3046–3053. doi:10.1167/iovs.19-27241. PubMed PMID: 31319418; PubMed Central PMCID: PMCPMC6640265. eng. PubMed DOI PMC

Lu W, Gomez NM, Lim JC, et al. The P2Y12 receptor antagonist ticagrelor reduces lysosomal pH and autofluorescence in retinal pigmented epithelial cells from the ABCA4(-/-) mouse model of retinal degeneration. Front Pharmacol. 2018;9:242. doi:10.3389/fphar.2018.00242. PubMed PMID: 29725296; PubMed Central PMCID: PMCPMC5917064. eng. PubMed DOI PMC

Li Z, Li H, Xu X, et al. Haploinsufficiency of GCP4 induces autophagy and leads to photoreceptor degeneration due to defective spindle assembly in retina. Cell Death Differ. 2020. Feb;27(2):556–572. doi:10.1038/s41418-019-0371-0. PubMed PMID: 31209365. PubMed DOI PMC

Xu X, Shang D, Cheng H, et al. Gene essentiality of Tubgcp4: dosage effect and autophagy regulation in retinal photoreceptors. Autophagy. 2019. Oct;15(10):1834–1837. doi:10.1080/15548627.2019.1647023. PubMed PMID: 31345090; PubMed Central PMCID: PMCPMC6735468. PubMed DOI PMC

Ruggiero L, Connor MP, Chen J, et al. Diurnal, localized exposure of phosphatidylserine by rod outer segment tips in wild-type but not Itgb5-/- or Mfge8-/- mouse retina. Proc Natl Acad Sci U S A. 2012. May 22;109(21):8145–8. doi:10.1073/pnas.1121101109. PubMed PMID: 22566632; PubMed Central PMCID: PMCPMC3361434. eng. PubMed DOI PMC

Ferguson TA, Green DR.. Autophagy and phagocytosis converge for better vision. Autophagy. 2014. Jan;10(1):165–7. doi:10.4161/auto.26735. PubMed PMID: 24220227; PubMed Central PMCID: PMC4028322. PubMed DOI PMC

Kim JY, Zhao H, Martinez J, et al. Noncanonical autophagy promotes the visual cycle. Cell. 2013. Jul 18;154(2):365–76. doi:10.1016/j.cell.2013.06.012. PubMed PMID: 23870125; PubMed Central PMCID: PMCPMC3744125. eng. PubMed DOI PMC

Dhingra A, Alexander D, Reyes-Reveles J, et al. Microtubule-Associated Protein 1 Light Chain 3 (LC3) Isoforms in RPE and Retina. Adv Exp Med Biol. 2018;1074:609–616. doi:10.1007/978-3-319-75402-4_74. PubMed PMID: 29721994; eng. PubMed DOI

Yu B, Egbejimi A, Dharmat R, et al. Phagocytosed photoreceptor outer segments activate mTORC1 in the retinal pigment epithelium. Sci Signal. 2018. May 29;11(532). doi:10.1126/scisignal.aag3315. PubMed PMID: 29844054; PubMed Central PMCID: PMCPMC6198651. PubMed DOI PMC

Bhattacharya S, Yin J, Winborn CS, et al. Prominin-1 is a novel regulator of autophagy in the human retinal pigment epithelium. Invest Ophthalmol Vis Sci. 2017. Apr 1;58(4):2366–2387. doi:10.1167/iovs.16-21162. PubMed PMID: 28437526; PubMed Central PMCID: PMCPMC5403116. PubMed DOI PMC

Chiarelli R, Agnello M, Bosco L, et al. Sea urchin embryos exposed to cadmium as an experimental model for studying the relationship between autophagy and apoptosis. Mar Environ Res. 2014. Feb;93:47–55. doi:10.1016/j.marenvres.2013.06.001. PubMed PMID: 23838188. PubMed DOI

Umemiya R, Matsuo T, Hatta T, et al. Cloning and characterization of an autophagy-related gene, ATG12, from the three-host tick Haemaphysalis longicornis. Insect Biochem Mol Biol. 2007. Sep;37(9):975–84. doi:10.1016/j.ibmb.2007.05.006. PubMed PMID: 17681237; eng. PubMed DOI

Kawano S, Umemiya-Shirafuji R, Boldbaatar D, et al. Cloning and characterization of the autophagy-related gene 6 from the hard tick, Haemaphysalis longicornis. Parasitol Res. 2011;109(5):1341–9. doi:10.1007/s00436-011-2429-x. PubMed DOI

Umemiya-Shirafuji R, Galay RL, Maeda H, et al. Expression analysis of autophagy-related genes in the hard tick Haemaphysalis longicornis. Vet Parasitol. 2014. Mar 17;201(1–2): 169–75. doi:10.1016/j.vetpar.2014.01.024. PubMed PMID: 24556037. PubMed DOI

Umemiya-Shirafuji R, Matsuo T, Liao M, et al. Increased expression of ATG genes during nonfeeding periods in the tick Haemaphysalis longicornis. Autophagy. 2010. May 16;6(4):473–81. PubMed PMID: 20404490; Eng. PubMed

de la Fuente J, Kocan KM, Almazan C, et al. RNA interference for the study and genetic manipulation of ticks. Trends Parasitol. 2007. Sep;23(9):427–33. doi:10.1016/j.pt.2007.07.002. PubMed PMID: 17656154. PubMed DOI

Ayllón N, Villar V, Galindo RC, et al. Systems biology of tissue-specific response to Anaplasma phagocytophilum reveals differentiated apoptosis in the tick vector Ixodes scapularis. PLoS Genet. 2015;11(3):e1005120. PubMed PMC

Genomic Resources Development C, Contreras M, de la Fuente J, et al. Genomic resources notes accepted 1 April 2014–31 May 2014. Mol Ecol Resour. 2014. Sep;14(5):1095. doi:10.1111/1755-0998.12298. PubMed PMID: 24976445. PubMed DOI

Lee E, Koo Y, Ng A, et al. Autophagy is essential for cardiac morphogenesis during vertebrate development. Autophagy. 2014. Apr;10(4):572–87. doi:10.4161/auto.27649. PubMed PMID: 24441423; PubMed Central PMCID: PMC4091146. PubMed DOI PMC

Sasaki T, Lian S, Qi J, et al. Aberrant autolysosomal regulation is linked to the induction of embryonic senescence: differential roles of Beclin 1 and p53 in vertebrate Spns1 deficiency. PLoS Genet. 2014. Jun;10(6):e1004409. doi:10.1371/journal.pgen.1004409. PubMed PMID: 24967584; PubMed Central PMCID: PMC4072523. PubMed DOI PMC

Varga M, Fodor E, Vellai T.. Autophagy in zebrafish. Methods. 2015. Mar;75:172–80. doi:10.1016/j.ymeth.2014.12.004. PubMed PMID: 25498006. PubMed DOI

Komoike Y, Shimojima K, Liang JS, et al. A functional analysis of GABARAP on 17p13.1 by knockdown zebrafish. J Hum Genet. 2010. Mar;55(3):155–62. doi:10.1038/jhg.2010.1. PubMed PMID: 20111057; eng. PubMed DOI

Hu Z, Zhang J, Zhang Q.. Expression pattern and functions of autophagy-related gene atg5 in zebrafish organogenesis. Autophagy. 2011. Dec;7(12):1514–27. doi:10.4161/auto.7.12.18040. PubMed PMID: 22082871; PubMed Central PMCID: PMCPMC3288024. PubMed DOI PMC

Mans LA, Querol Cano L, van Pelt J, et al. The tumor suppressor LKB1 regulates starvation-induced autophagy under systemic metabolic stress. Sci Rep. 2017. Aug 4;7(1):7327. doi:10.1038/s41598-017-07116-9. PubMed PMID: 28779098; PubMed Central PMCID: PMCPMC5544676. PubMed DOI PMC

Masud S, Prajsnar TK, Torraca V, et al. Macrophages target Salmonella by Lc3-associated phagocytosis in a systemic infection model. Autophagy. 2019. May;15(5):796–812. doi:10.1080/15548627.2019.1569297. PubMed PMID: 30676840; PubMed Central PMCID: PMCPMC6526873. PubMed DOI PMC

Dowling JJ, Low SE, Busta AS, et al. Zebrafish MTMR14 is required for excitation-contraction coupling, developmental motor function and the regulation of autophagy. Hum Mol Genet. 2010. Jul 1;19(13):2668–81. doi:10.1093/hmg/ddq153. PubMed PMID: 20400459; PubMed Central PMCID: PMC2883342. eng. PubMed DOI PMC

Makky K, Tekiela J, Mayer AN.. Target of rapamycin (TOR) signaling controls epithelial morphogenesis in the vertebrate intestine. Dev Biol. 2007. Mar 15;303(2):501–13. doi:10.1016/j.ydbio.2006.11.030. PubMed PMID: 17222402; PubMed Central PMCID: PMC2715143. eng. PubMed DOI PMC

Schulte-Merker S, Stainier DY.. Out with the old, in with the new: reassessing morpholino knockdowns in light of genome editing technology. Development. 2014. Aug;141(16):3103–4. doi:10.1242/dev.112003. PubMed PMID: 25100652. PubMed DOI

Stainier DYR, Raz E, Lawson ND, et al. Guidelines for morpholino use in zebrafish. PLoS Genet. 2017. Oct;13(10):e1007000. doi:10.1371/journal.pgen.1007000. PubMed PMID: 29049395; PubMed Central PMCID: PMCPMC5648102. PubMed DOI PMC

Lai JKH, Gagalova KK, Kuenne C, et al. Induction of interferon-stimulated genes and cellular stress pathways by morpholinos in zebrafish. Dev Biol. 2019. Oct 1;454(1):21–28. doi:10.1016/j.ydbio.2019.06.008. PubMed PMID: 31201802; PubMed Central PMCID: PMCPMC6717701. PubMed DOI PMC

Mastrodonato V, Beznoussenko G, Mironov A, et al. A genetic model of CEDNIK syndrome in zebrafish highlights the role of the SNARE protein Snap29 in neuromotor and epidermal development. Sci Rep. 2019. Feb 4;9(1):1211. doi:10.1038/s41598-018-37780-4. PubMed PMID: 30718891; PubMed Central PMCID: PMCPMC6361908. PubMed DOI PMC

Zhang R, Varela M, Vallentgoed W, et al. The selective autophagy receptors Optineurin and p62 are both required for zebrafish host resistance to mycobacterial infection. PLoS Pathog. 2019. Feb;15(2):e1007329. doi:10.1371/journal.ppat.1007329. PubMed PMID: 30818338; PubMed Central PMCID: PMCPMC6413957. PubMed DOI PMC

Meneghetti G, Skobo T, Chrisam M, et al. The epg5 knockout zebrafish line: a model to study Vici syndrome. Autophagy. 2019. Aug;15(8):1438–1454. doi:10.1080/15548627.2019.1586247. PubMed PMID: 30806141; PubMed Central PMCID: PMCPMC6613882. PubMed DOI PMC

Liu K, Petree C, Requena T, et al. Expanding the CRISPR toolbox in zebrafish for studying development and disease. Front Cell Dev Biol. 2019;7:13. doi:10.3389/fcell.2019.00013. PubMed PMID: 30886848; PubMed Central PMCID: PMCPMC6409501. PubMed DOI PMC

Hernandez-Moreno D, Blazquez M, Andreu-Sanchez O, et al. Acute hazard of biocides for the aquatic environmental compartment from a life-cycle perspective. Sci Total Environ. 2019. Mar 25;658:416–423. doi:10.1016/j.scitotenv.2018.12.186. PubMed PMID: 30579199. PubMed DOI

Moreau K, Fleming A, Imarisio S, et al. PICALM modulates autophagy activity and tau accumulation. Nat Commun. 2014;5:4998. doi:10.1038/ncomms5998. PubMed PMID: 25241929; PubMed Central PMCID: PMC4199285. PubMed DOI PMC

Zhang Y, Nguyen DT, Olzomer EM, et al. Rescue of Pink1 Deficiency by Stress-Dependent Activation of Autophagy. Cell Chem Biol. 2017. Apr 20;24(4):471–480 e4. doi:10.1016/j.chembiol.2017.03.005. PubMed PMID: 28366621. PubMed DOI

Ruparelia AA, McKaige EA, Williams C, et al. Metformin rescues muscle function in BAG3 myofibrillar myopathy models, 2021 Autophagy, in press. doi:10.1080/15548627.2020.1833500. PubMed DOI PMC

Ruparelia AA, Oorschot V, Ramm G, et al. FLNC myofibrillar myopathy results from impaired autophagy and protein insufficiency. Hum Mol Genet. 2016. Jun 1;25(11):2131–2142. doi:10.1093/hmg/ddw080. PubMed PMID: 26969713. PubMed DOI

Ruparelia AA, Oorschot V, Vaz R, et al. Zebrafish models of BAG3 myofibrillar myopathy suggest a toxic gain of function leading to BAG3 insufficiency. Acta Neuropathol. 2014. Dec;128(6):821–33. doi:10.1007/s00401-014-1344-5. PubMed PMID: 25273835. PubMed DOI

Mostowy S, Boucontet L, Mazon Moya MJ, et al. The zebrafish as a new model for the in vivo study of Shigella flexneri interaction with phagocytes and bacterial autophagy. PLoS Pathog. 2013;9(9):e1003588. doi:10.1371/journal.ppat.1003588. PubMed PMID: 24039575; PubMed Central PMCID: PMC3764221. PubMed DOI PMC

van der Vaart M, Korbee CJ, Lamers GE, et al. The DNA damage-regulated autophagy modulator DRAM1 links mycobacterial recognition via TLP-MYD88 to authophagic defense. Cell Host Microbe. 2014. Jun 11;15(6):753–67. doi:10.1016/j.chom.2014.05.005. PubMed PMID: 24922577. PubMed DOI

Espin-Palazon R, Martinez-Lopez A, Roca FJ, et al. TNFalpha impairs rhabdoviral clearance by inhibiting the host autophagic antiviral response. PLoS Pathog. 2016. Jun;12(6):e1005699. doi:10.1371/journal.ppat.1005699. PubMed PMID: 27351838; PubMed Central PMCID: PMCPMC4924823. PubMed DOI PMC

Li YC, Zhang MQ, Zhang JP.. Opposite effects of two human ATG10 isoforms on replication of a HCV sub-genomic replicon are mediated via regulating autophagy flux in zebrafish. Front Cell Infect Microbiol. 2018;8:109. doi:10.3389/fcimb.2018.00109. PubMed PMID: 29670865; PubMed Central PMCID: PMCPMC5893791. PubMed DOI PMC

Garcia-Valtanen P, Ortega-Villaizan Mdel M, Martinez-Lopez A, et al. Autophagy-inducing peptides from mammalian VSV and fish VHSV rhabdoviral G glycoproteins (G) as models for the development of new therapeutic molecules. Autophagy. 2014. Sep;10(9):1666–80. doi:10.4161/auto.29557. PubMed PMID: 25046110; PubMed Central PMCID: PMCPMC4206542. PubMed DOI PMC

Varga M, Sass M, Papp D, et al. Autophagy is required for zebrafish caudal fin regeneration. Cell Death Differ. 2014. Apr;21(4):547–56. doi:10.1038/cdd.2013.175. PubMed PMID: 24317199; PubMed Central PMCID: PMC3950318. PubMed DOI PMC

Benato F, Skobo T, Gioacchini G, et al. Ambra1 knockdown in zebrafish leads to incomplete development due to severe defects in organogenesis. Autophagy. 2013. Apr;9(4):476–95. doi:10.4161/auto.23278. PubMed PMID: 23348054; PubMed Central PMCID: PMC3627665. PubMed DOI PMC

Skobo T, Benato F, Grumati P, et al. Zebrafish ambra1a and ambra1b knockdown impairs skeletal muscle development. PLoS One. 2014;9(6):e99210. doi:10.1371/journal.pone.0099210. PubMed PMID: 24922546; PubMed Central PMCID: PMC4055674. PubMed DOI PMC

Driever W, Rangini Z.. Characterization of a cell line derived from zebrafish (Brachydanio rerio) embryos. In Vitro Cell Dev Biol Anim. 1993. Sep;29A(9):749–54. doi:10.1007/bf02631432. PubMed PMID: 8407719. PubMed DOI

Liu L, Zhu B, Wu S, et al. Spring viraemia of carp virus induces autophagy for necessary viral replication. Cell Microbiol. 2015. Apr;17(4):595–605. doi:10.1111/cmi.12387. PubMed PMID: 25376386. PubMed DOI

Bello-Perez M, Falco A, Novoa B, et al. Hydroxycholesterol binds and enhances the anti-viral activities of zebrafish monomeric c-reactive protein isoforms. PLoS One. 2019;14(1):e0201509. doi:10.1371/journal.pone.0201509. PubMed PMID: 30653529; PubMed Central PMCID: PMCPMC6336239. PubMed DOI PMC

Mizushima N. Methods for monitoring autophagy using GFP-LC3 transgenic mice. Methods Enzymol. 2009;452:13–23. doi:10.1016/S0076-6879(08)03602-1. PubMed PMID: 19200873. PubMed DOI

Herb M, Gluschko A, Schramm M.. LC3-associated phagocytosis - The highway to hell for phagocytosed microbes. Semin Cell Dev Biol. 2019. Apr 29. doi:10.1016/j.semcdb.2019.04.016. PubMed PMID: 31029766. PubMed DOI

Sil P, Muse G, Martinez J.. A ravenous defense: canonical and non-canonical autophagy in immunity. Curr Opin Immunol. 2018. Feb;50:21–31. doi:10.1016/j.coi.2017.10.004. PubMed PMID: 29125936; PubMed Central PMCID: PMCPMC5857463. PubMed DOI PMC

Henault J, Martinez J, Riggs JM, et al. Noncanonical autophagy is required for type I interferon secretion in response to DNA-immune complexes. Immunity. 2012. Dec 14;37(6):986–97. doi:10.1016/j.immuni.2012.09.014. PubMed PMID: 23219390; PubMed Central PMCID: PMC3786711. PubMed DOI PMC

Santarino IB, Viegas MS, Domingues NS, et al. Involvement of the p62/NRF2 signal transduction pathway on erythrophagocytosis. Sci Rep. 2017. Jul 19;7(1):5812. doi:10.1038/s41598-017-05687-1. PubMed PMID: 28724916; PubMed Central PMCID: PMCPMC5517431. PubMed DOI PMC

Fazeli G, Wehman AM.. Safely removing cell debris with LC3-associated phagocytosis. Biol Cell. 2017. Oct;109(10):355–363. doi:10.1111/boc.201700028. PubMed PMID: 28755428. PubMed DOI

Fazeli G, Stetter M, Lisack JN, et al. C. elegans blastomeres clear the corpse of the second polar body by LC3-associated phagocytosis. Cell Rep. 2018. May 15;23(7):2070–2082. doi:10.1016/j.celrep.2018.04.043. PubMed PMID: 29768205. PubMed DOI

Abnave P, Mottola G, Gimenez G, et al. Screening in planarians identifies MORN2 as a key component in LC3-associated phagocytosis and resistance to bacterial infection. Cell Host Microbe. 2014. Sep 10;16(3):338–50. doi:10.1016/j.chom.2014.08.002. PubMed PMID: 25211076. PubMed DOI

Varma H, Gangadhar NM, Letso RR, et al. Identification of a small molecule that induces ATG5-and-cathepsin-l-dependent cell death and modulates polyglutamine toxicity. Exp Cell Res. 2013. Jul 15;319(12):1759–73. doi:10.1016/j.yexcr.2013.03.019. PubMed PMID: 23588206; PubMed Central PMCID: PMC3700633. PubMed DOI PMC

Jacquin E, Leclerc-Mercier S, Judon C, et al. Pharmacological modulators of autophagy activate a parallel noncanonical pathway driving unconventional LC3 lipidation. Autophagy. 2017. May 4;13(5):854–867. doi:10.1080/15548627.2017.1287653. PubMed PMID: 28296541; PubMed Central PMCID: PMCPMC5446083. PubMed DOI PMC

Jiang P, Mizushima N.. LC3- and p62-based biochemical methods for the analysis of autophagy progression in mammalian cells. Methods. 2015. Mar;75:13–8. doi:10.1016/j.ymeth.2014.11.021. PubMed PMID: 25484342. PubMed DOI

Yang CS, Lee JS, Rodgers M, et al. Autophagy protein Rubicon mediates phagocytic NADPH oxidase activation in response to microbial infection or TLR stimulation. Cell Host Microbe. 2012. Mar 15;11(3):264–76. doi:10.1016/j.chom.2012.01.018. PubMed PMID: 22423966; PubMed Central PMCID: PMCPMC3616771. PubMed DOI PMC

Martinez J, Cunha LD, Park S, et al. Noncanonical autophagy inhibits the autoinflammatory, lupus-like response to dying cells. Nature. 2016. May 5;533(7601):115–9. doi:10.1038/nature17950. PubMed PMID: 27096368; PubMed Central PMCID: PMCPMC4860026. PubMed DOI PMC

Heckmann BL, Teubner BJW, Tummers B, et al. LC3-associated endocytosis facilitates beta-amyloid clearance and mitigates neurodegeneration in murine Alzheimer’s disease. Cell. 2019. Jul 25;178(3):536–551 e14. doi:10.1016/j.cell.2019.05.056. PubMed PMID: 31257024; PubMed Central PMCID: PMCPMC6689199. PubMed DOI PMC

Rai S, Arasteh M, Jefferson M, et al. The ATG5-binding and coiled coil domains of ATG16L1 maintain autophagy and tissue homeostasis in mice independently of the WD domain required for LC3-associated phagocytosis. Autophagy. 2019. Apr;15(4):599–612. doi:10.1080/15548627.2018.1534507. PubMed PMID: 30403914; PubMed Central PMCID: PMCPMC6526875. PubMed DOI PMC

Kong-Hap MA, Mouammine A, Daher W, et al. Regulation of ATG8 membrane association by ATG4 in the parasitic protist Toxoplasma gondii. Autophagy. 2013. Sep;9(9):1334–48. doi:10.4161/auto.25189. PubMed PMID: 23748741. PubMed DOI

Jayabalasingham B, Voss C, Ehrenman K, et al. Characterization of the ATG8-conjugation system in 2 Plasmodium species with special focus on the liver stage: possible linkage between the apicoplastic and autophagic systems? Autophagy. 2014. Feb;10(2):269–84. doi:10.4161/auto.27166. PubMed PMID: 24342964. PubMed DOI PMC

Tomlins AM, Ben-Rached F, Williams RA, et al. Plasmodium falciparum ATG8 implicated in both autophagy and apicoplast formation. Autophagy. 2013. Oct;9(10):1540–52. doi:10.4161/auto.25832. PubMed PMID: 24025672. PubMed DOI

Mizushima N, Sahani MH.. ATG8 localization in apicomplexan parasites: apicoplast and more? Autophagy. 2014. Sep;10(9):1487–94. doi:10.4161/auto.32183. PubMed PMID: 25102412. PubMed DOI PMC

Voss C, Ehrenman K, Mlambo G, et al. Overexpression of Plasmodium berghei ATG8 by Liver Forms Leads to Cumulative Defects in Organelle Dynamics and to Generation of Noninfectious Merozoites. mBio. 2016. Jun 28;7(3). doi:10.1128/mBio.00682-16. PubMed PMID: 27353755; PubMed Central PMCID: PMCPMC4937212. PubMed DOI PMC

Leveque MF, Berry L, Cipriano MJ, et al. autophagy-related protein ATG8 has a noncanonical function for apicoplast inheritance in Toxoplasma gondii. mBio. 2015. Oct 27;6(6):e01446–15. doi:10.1128/mBio.01446-15. PubMed PMID: 26507233; PubMed Central PMCID: PMCPMC4626856. PubMed DOI PMC

Nguyen HM, Liu S, Daher W, et al. Characterisation of two Toxoplasma PROPPINs homologous to Atg18/WIPI suggests they have evolved distinct specialised functions. PLoS One. 2018;13(4):e0195921. doi:10.1371/journal.pone.0195921. PubMed PMID: 29659619; PubMed Central PMCID: PMCPMC5901921. PubMed DOI PMC

Bansal P, Tripathi A, Thakur V, et al. Autophagy-related protein ATG18 regulates apicoplast biogenesis in apicomplexan parasites. mBio. 2017. Oct 31;8(5). doi:10.1128/mBio.01468-17. PubMed PMID: 29089429; PubMed Central PMCID: PMCPMC5666157. PubMed DOI PMC

Park S, Choi J, Biering SB, et al. Targeting by AutophaGy proteins (TAG): Targeting of IFNG-inducible GTPases to membranes by the LC3 conjugation system of autophagy. Autophagy. 2016. Jul 2;12(7):1153–67. doi:10.1080/15548627.2016.1178447. PubMed PMID: 27172324; PubMed Central PMCID: PMCPMC4990996. PubMed DOI PMC

Sasai M, Sakaguchi N, Ma JS, et al. Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense. Nat Immunol. 2017. Aug;18(8):899–910. doi:10.1038/ni.3767. PubMed PMID: 28604719. PubMed DOI

Haldar AK, Piro AS, Pilla DM, et al. The E2-like conjugation enzyme Atg3 promotes binding of IRG and Gbp proteins to Chlamydia- and Toxoplasma-containing vacuoles and host resistance. PLoS One. 2014;9(1):e86684. doi:10.1371/journal.pone.0086684. PubMed PMID: 24466199; PubMed Central PMCID: PMC3895038. PubMed DOI PMC

Ohshima J, Lee Y, Sasai M, et al. Role of mouse and human autophagy proteins in IFN-gamma-induced cell-autonomous responses against Toxoplasma gondii. J Iimmunol. 2014. Apr 1;192(7):3328–35. doi:10.4049/jimmunol.1302822. PubMed PMID: 24563254. PubMed DOI

Zhao YO, Khaminets A, Hunn JP, et al. Disruption of the Toxoplasma gondii parasitophorous vacuole by IFNgamma-inducible immunity-related GTPases (IRG proteins) triggers necrotic cell death. PLoS Pathog. 2009. Feb;5(2):e1000288. doi:10.1371/journal.ppat.1000288. PubMed PMID: 19197351; PubMed Central PMCID: PMC2629126. PubMed DOI PMC

Meunier E, Dick MS, Dreier RF, et al. Caspase-11 activation requires lysis of pathogen-containing vacuoles by IFN-induced GTPases. Nature. 2014. May 15;509(7500):366–70. doi:10.1038/nature13157. PubMed PMID: 24739961. PubMed DOI

Taguchi Y, Imaoka K, Kataoka M, et al. Yip1A, a novel host factor for the activation of the IRE1 pathway of the unfolded protein response during Brucella infection. PLoS Pathog. 2015. Mar;11(3):e1004747. doi:10.1371/journal.ppat.1004747. PubMed PMID: 25742138; PubMed Central PMCID: PMC4350842. PubMed DOI PMC

Starr T, Child R, Wehrly TD, et al. Selective subversion of autophagy complexes facilitates completion of the Brucella intracellular cycle. Cell Host Microbe. 2012. Jan 19;11(1):33–45. doi:10.1016/j.chom.2011.12.002. PubMed PMID: 22264511; PubMed Central PMCID: PMC3266535. PubMed DOI PMC

Manjithaya R, Anjard C, Loomis WF, et al. Unconventional secretion of Pichia pastoris Acb1 is dependent on GRASP protein, peroxisomal functions, and autophagosome formation. J Cell Biol. 2010. Feb 22;188(4):537–46. doi:10.1083/jcb.200911149. PubMed PMID: 20156962; PubMed Central PMCID: PMCPMC2828923. PubMed DOI PMC

Duran JM, Anjard C, Stefan C, et al. Unconventional secretion of Acb1 is mediated by auto-phagosomes. J Cell Biol. 2010. Feb 22;188(4):527–36. doi:jcb.200911154 [pii] doi:10.1083/jcb. 200911154. PubMed PMID: 20156967; PubMed Central PMCID: PMC2828925. eng. PubMed PMC

Zhang M, Kenny SJ, Ge L, et al. Translocation of interleukin-1beta into a vesicle intermediate in autophagy-mediated secretion. eLife. 2015. Nov 2;4. doi:10.7554/eLife.11205. PubMed PMID: 26523392; PubMed Central PMCID: PMCPMC4728131. PubMed DOI PMC

Gee HY, Noh SH, Tang BL, et al. Rescue of DeltaF508-CFTR trafficking via a GRASP-dependent unconventional secretion pathway. Cell. 2011. Sep 2;146(5):746–60. doi:10.1016/j.cell.2011.07.021. PubMed PMID: 21884936. PubMed DOI

Curwin AJ, Brouwers N, Alonso YAM, et al. ESCRT-III drives the final stages of CUPS maturation for unconventional protein secretion. eLife. 2016. Apr 26;5. doi:10.7554/eLife.16299. PubMed PMID: 27115345; PubMed Central PMCID: PMCPMC4868542. PubMed DOI PMC

Noh SH, Gee HY, Kim Y, et al. Specific autophagy and ESCRT components participate in the unconventional secretion of CFTR. Autophagy. 2018;14(10):1761–1778. doi:10.1080/15548627.2018.1489479. PubMed PMID: 29969945; PubMed Central PMCID: PMCPMC6135621. PubMed DOI PMC

Robinson SM, Tsueng G, Sin J, et al. Coxsackievirus B exits the host cell in shed microvesicles displaying autophagosomal markers. PLoS Pathog. 2014. Apr;10(4):e1004045. doi:10.1371/journal.ppat.1004045. PubMed PMID: 24722773; PubMed Central PMCID: PMCPMC3983045. PubMed DOI PMC

Nowag H, Guhl B, Thriene K, et al. Macroautophagy proteins assist epstein barr virus production and get incorporated into the virus particles. EBioMedicine. 2014. Dec;1(2–3):116–25. doi:10.1016/j.ebiom.2014.11.007. PubMed PMID: 26137519; PubMed Central PMCID: PMCPMC4457436. PubMed DOI PMC

Chen YH, Du W, Hagemeijer MC, et al. Phosphatidylserine vesicles enable efficient en bloc transmission of enteroviruses. Cell. 2015. Feb 12;160(4):619–630. doi:10.1016/j.cell.2015.01.032. PubMed PMID: 25679758; PubMed Central PMCID: PMCPMC6704014. PubMed DOI PMC

Mehta P, Henault J, Kolbeck R, et al. Noncanonical autophagy: one small step for LC3, one giant leap for immunity. Curr Opin Immunol. 2014. Feb;26:69–75. doi:10.1016/j.coi.2013.10.012. PubMed PMID: 24556403. PubMed DOI

Scarlatti F, Maffei R, Beau I, et al. Non-canonical autophagy: an exception or an underestimated form of autophagy? Autophagy. 2008. Nov 16;4(8):1083–5. doi:7068 [pii]. PubMed PMID: 18849663; eng. PubMed

Takeshita F, Kobiyama K, Miyawaki A, et al. The non-canonical role of Atg family members as suppressors of innate antiviral immune signaling. Autophagy. 2008. Jan;4(1):67–9. PubMed PMID: 17921696. PubMed

Deretic V, Jiang S, Dupont N.. Autophagy intersections with conventional and unconventional secretion in tissue development, remodeling and inflammation. Trends Cell Biol. 2012. Aug;22(8):397–406. doi:10.1016/j.tcb.2012.04.008. PubMed PMID: 22677446; PubMed Central PMCID: PMC3408825. PubMed DOI PMC

Cleyrat C, Darehshouri A, Steinkamp MP, et al. Mpl traffics to the cell surface through conventional and unconventional routes. Traffic. 2014. Sep;15(9):961–82. doi:10.1111/tra.12185. PubMed PMID: 24931576; PubMed Central PMCID: PMC4141020. PubMed DOI PMC

Hughes T, Rusten TE.. Origin and evolution of self-consumption: autophagy. Adv Exp Med Biol. 2007;607:111–8. doi:10.1007/978-0-387-74021-8_9. PubMed PMID: 17977463. PubMed DOI

Kiel JA. Autophagy in unicellular eukaryotes. Philos Trans R Soc London, Ser B. 2010. Mar 12;365(1541):819–30. doi:10.1098/rstb.2009.0237. PubMed PMID: 20124347; PubMed Central PMCID: PMC2817228. PubMed DOI PMC

Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997. Sep 1;25(17):3389–402. PubMed PMID: 9254694; PubMed Central PMCID: PMC146917. PubMed PMC

Pertsemlidis A, Fondon JW, III.. Having a BLAST with bioinformatics (and avoiding BLASTphemy). Genome Biol. 2001;2(10):REVIEWS2002. PubMed PMID: 11597340; PubMed Central PMCID: PMC138974. PubMed PMC

Rost B. Twilight zone of protein sequence alignments. Protein Eng. 1999. Feb;12(2):85–94. PubMed PMID: 10195279. PubMed

Duszenko M, Ginger ML, Brennand A, et al. Autophagy in protists. Autophagy. 2011. Feb;7(2):127–58. PubMed PMID: 20962583; PubMed Central PMCID: PMC3039767. eng. PubMed PMC

Rigden DJ, Michels PA, Ginger ML.. Autophagy in protists: Examples of secondary loss, lineage-specific innovations, and the conundrum of remodeling a single mitochondrion. Autophagy. 2009. Aug;5(6):784–94. PubMed PMID: 19483474. PubMed

Katsani KR, Irimia M, Karapiperis C, et al. Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins. Sci Rep. 2014;4:4655. doi:10.1038/srep04655. PubMed PMID: 24722254; PubMed Central PMCID: PMC3983603. PubMed DOI PMC

Mei Y, Su M, Soni G, et al. Intrinsically disordered regions in autophagy proteins. Proteins. 2014. Apr;82(4):565–78. doi:10.1002/prot.24424. PubMed PMID: 24115198; PubMed Central PMCID: PMC3949125. PubMed DOI PMC

Promponas VJ, Ouzounis CA, Iliopoulos I.. Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. Brief Bioinform. 2014. May;15(3):443–54. doi:10.1093/bib/bbs072. PubMed PMID: 23220349; PubMed Central PMCID: PMC4017328. PubMed DOI PMC

Promponas VJ, Iliopoulos I, Ouzounis CA.. Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure. Stand Genomic Sci. 2015;10:108. doi:10.1186/s40793-015-0101-2. PubMed PMID: 26594309; PubMed Central PMCID: PMCPMC4653902. PubMed DOI PMC

Deng W, Ma L, Zhang Y, et al. THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy. Autophagy. 2018;14(2):296–310. doi:10.1080/15548627.2017.1402990. PubMed PMID: 29157087; PubMed Central PMCID: PMCPMC5902229. PubMed DOI PMC

Chen LL, Wang YB, Song JX, et al. Phosphoproteome-based kinase activity profiling reveals the critical role of MAP2K2 and PLK1 in neuronal autophagy. Autophagy. 2017;13(11):1969–1980. doi:10.1080/15548627.2017.1371393. PubMed PMID: 28933595; PubMed Central PMCID: PMCPMC5788482. PubMed DOI PMC

Zhang Y, Xie Y, Liu W, et al. DeepPhagy: a deep learning framework for quantitatively measuring autophagy activity in Saccharomyces cerevisiae. Autophagy. 2019. Jun 20:1–15. doi:10.1080/15548627.2019.1632622. PubMed PMID: 31204567. PubMed DOI PMC

Li S, Shui K, Zhang Y, et al. CGDB: a database of circadian genes in eukaryotes. Nucleic Acids Res. 2017. Jan 4;45(D1):D397–D403. doi:10.1093/nar/gkw1028. PubMed PMID: 27789706; PubMed Central PMCID: PMCPMC5210527. PubMed DOI PMC

Homma K, Suzuki K, Sugawara H.. The Autophagy Database: an all-inclusive information resource on autophagy that provides nourishment for research. Nucleic Acids Res. 2011. Jan;39(Database issue):D986–90. doi:10.1093/nar/gkq995. PubMed PMID: 20972215; PubMed Central PMCID: PMC3013813. PubMed DOI PMC

Turei D, Foldvari-Nagy L, Fazekas D, et al. Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. Autophagy. 2015;11(1):155–65. doi:10.4161/15548627.2014.994346. PubMed PMID: 25635527. PubMed DOI PMC

Birgisdottir AB, Lamark T, Johansen T.. The LIR motif - crucial for selective autophagy. J Cell Sci. 2013. Aug1;126(Pt 15):3237–47. doi:10.1242/jcs.126128. PubMed PMID: 23908376. PubMed DOI

Wild P, McEwan DG, Dikic I.. The LC3 interactome at a glance. J Cell Sci. 2014. Jan1;127(Pt 1):3–9. doi:10.1242/jcs.140426. PubMed PMID: 24345374. PubMed DOI

Noda NN, Ohsumi Y, Inagaki F.. Atg8-family interacting motif crucial for selective autophagy. FEBS Lett. 2010. Jan 17;584:1379–85. doi:S0014-5793(10)00037-2 [pii] doi:10.1016/j.febslet.2010.01.018. PubMed PMID: 20083108; Eng. PubMed DOI

Kalvari I, Tsompanis S, Mulakkal NC, et al. iLIR: A web resource for prediction of Atg8-family interacting proteins. Autophagy. 2014. May;10(5):913–25. doi:10.4161/auto.28260. PubMed PMID: 24589857. PubMed DOI PMC

Dosztanyi Z, Meszaros B, Simon I.. ANCHOR: web server for predicting protein binding regions in disordered proteins. Bioinformatics. 2009. Oct 15;25(20):2745–6. doi:10.1093/bioinformatics/btp518. PubMed PMID: 19717576; PubMed Central PMCID: PMC2759549. PubMed DOI PMC

Xie Q, Tzfadia O, Levy M, et al. hfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms. Autophagy. 2016. May 3;12(5):876–87. doi:10.1080/15548627.2016.1147668. PubMed PMID: 27071037; PubMed Central PMCID: PMCPMC4854547. PubMed DOI PMC

Jacomin AC, Samavedam S, Promponas V, et al. iLIR database: A web resource for LIR motif-containing proteins in eukaryotes. Autophagy. 2016. Oct 2;12(10):1945–1953. doi:10.1080/15548627.2016.1207016. PubMed PMID: 27484196; PubMed Central PMCID: PMCPMC5079668. PubMed DOI PMC

Jacomin AC, Samavedam S, Charles H, et al. iLIR@viral: A web resource for LIR motif-containing proteins in viruses. Autophagy. 2017. Oct 3;13(10):1782–1789. doi:10.1080/15548627.2017.1356978. PubMed PMID: 28806134; PubMed Central PMCID: PMCPMC5640201. PubMed DOI PMC

Dinkel H, Van Roey K, Michael S, et al. The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Res. 2014. Jan;42(Database issue):D259–66. doi: 10.1093/nar/gkt1047. PubMed PMID: 24214962; PubMed Central PMCID: PMC3964949. PubMed DOI PMC

Di Rita A, Peschiaroli A, P DA, et al. HUWE1 E3 ligase promotes PINK1/PARKIN-independent mitophagy by regulating AMBRA1 activation via IKKalpha. Nat Commun. 2018. Sep 14;9(1):3755. doi:10.1038/s41467-018-05722-3. PubMed PMID: 30217973; PubMed Central PMCID: PMCPMC6138665. PubMed DOI PMC

Jatana N, Ascher DB, Pires DEV, et al. Human LC3 and GABARAP subfamily members achieve functional specificity via specific structural modulations. Autophagy. 2020. Feb;16(2):239–255. doi:10.1080/15548627.2019.1606636. PubMed PMID: 30982432; PubMed Central PMCID: PMCPMC6984608. PubMed DOI PMC

Wu D, Huang Y, Kang JJ, et al. ncRDeathDB: a comprehensive bioinformatics resource for deciphering network organization of the ncRNA-mediated cell death system. Autophagy. 2015;11:1917–26. PubMed PMC

Li Y, Zhuang L, Wang Y, et al. Connect the dots: a systems level approach for analyzing the miRNA-mediated cell death network. Autophagy. 2013. Mar;9(3):436–9. doi:10.4161/auto.23096. PubMed PMID: 23322033; PubMed Central PMCID: PMC3590271. PubMed DOI PMC

Xu J, Li YH.. miRDeathDB: a database bridging microRNAs and the programmed cell death. Cell Death Differ. 2012. Sep;19(9):1571. doi:10.1038/cdd.2012.87. PubMed PMID: 22743998; PubMed Central PMCID: PMC3422482. PubMed DOI PMC

Xu J, Wang Y, Tan X, et al. MicroRNAs in autophagy and their emerging roles in crosstalk with apoptosis. Autophagy. 2012. Jun;8(6):873–82. doi:10.4161/auto.19629. PubMed PMID: 22441107; PubMed Central PMCID: PMC3427253. PubMed DOI PMC

Delaney JR, Patel CB, Willis KM, et al. Haploinsufficiency networks identify targetable patterns of allelic deficiency in low mutation ovarian cancer. Nat Commun. 2017. Feb 15;8:14423. doi:10.1038/ncomms14423. PubMed PMID: 28198375; PubMed Central PMCID: PMCPMC5316854. PubMed DOI PMC

Kaushik S, Cuervo AM.. The coming of age of chaperone-mediated autophagy. Nat Rev Mol Cell Biol. 2018. Jun;19(6):365–381. doi:10.1038/s41580-018-0001-6. PubMed PMID: 29626215; PubMed Central PMCID: PMCPMC6399518. PubMed DOI PMC

Dice JF, Chiang HL, Spencer EP, et al. Regulation of catabolism of microinjected ribonuclease A. Identification of residues 7–11 as the essential pentapeptide. J Biol Chem. 1986. May 25;261(15):6853–9. PubMed PMID: 3700419. PubMed

Morone D, Marazza A, Bergmann TJ, et al. Deep learning approach for quantification of organelles and misfolded polypeptide delivery within degradative compartments. Mol Biol Cell. 2020. Jul 1;31(14):1512–1524. doi:10.1091/mbc.E20-04-0269. PubMed PMID: 32401604. PubMed DOI PMC

Börlin CS, Lang V, Hamacher-Brady A, et al. Agent-based modeling of autophagy reveals emergent regulatory behavior of spatio-temporal autophagy dynamics. Cell Commun Signal. 2014. Sep 10;12:56. doi:10.1186/s12964-014-0056-8. PubMed PMID: 25214434; PubMed Central PMCID: PMCPMC4172826. PubMed DOI PMC

Martin KR, Barua D, Kauffman AL, et al. Computational model for autophagic vesicle dynamics in single cells. Autophagy. 2013. Jan;9(1):74–92. doi:10.4161/auto.22532. PubMed PMID: 23196898; PubMed Central PMCID: PMC3542220. PubMed DOI PMC

Rubinsztein DC, Codogno P, Levine B.. Autophagy modulation as a potential therapeutic target for diverse diseases. Nat Rev Drug Discov. 2012. Sep;11(9):709–30. doi:10.1038/nrd3802. PubMed PMID: 22935804; PubMed Central PMCID: PMCPMC3518431. PubMed DOI PMC

Perelson AS. Modelling viral and immune system dynamics. Nat Rev Immunol. 2002. Jan;2(1):28–36. doi:10.1038/nri700. PubMed PMID: 11905835. PubMed DOI

Kapuy O, Vinod PK, Mandl J, et al. A cellular stress-directed bistable switch controls the crosstalk between autophagy and apoptosis. Mol BioSyst. 2013. Feb 2;9(2):296–306. doi:10.1039/c2mb25261a. PubMed PMID: 23223525. PubMed DOI

Liu B, Oltvai ZN, Bayir H, et al. Quantitative assessment of cell fate decision between autophagy and apoptosis. Sci Rep. 2017. Dec 14;7(1):17605. doi:10.1038/s41598-017-18001-w. PubMed PMID: 29242632; PubMed Central PMCID: PMCPMC5730598. PubMed DOI PMC

Tavassoly I, Parmar J, Shajahan-Haq AN, et al. Dynamic modeling of the interaction between autophagy and apoptosis in mammalian cells. CPT Pharmacometrics Syst Pharmacol. 2015. Apr;4(4):263–72. doi:10.1002/psp4.29. PubMed PMID: 26225250; PubMed Central PMCID: PMC4429580. PubMed DOI PMC

Han K, Kim J, Choi M.. Autophagy mediates phase transitions from cell death to life. Heliyon. 2015. Sep;1(1):e00027. doi:ARTN e00027 doi:10.1016/j.heliyon.2015.e00027. PubMed PMID: WOS:000432001200001; English. PubMed DOI PMC

Jin H, Lei J.. A hybrid model of molecular regulation and population dynamics for yeast autophagy. J Theor Biol. 2016. Aug 7;402:45–53. doi:10.1016/j.jtbi.2016.04.019. PubMed PMID: 27103581. PubMed DOI

Szymańska P, Martin KR, MacKeigan JP, et al. Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1. PLoS One. 2015;10(3):e0116550. doi:10.1371/journal.pone.0116550. PubMed PMID: 25761126; PubMed Central PMCID: PMCPMC4356596. PubMed DOI PMC

Bolliet V, Labonne J, Olazcuaga L, et al. Modeling of autophagy-related gene expression dynamics during long term fasting in European eel (Anguilla anguilla). Sci Rep. 2017. Dec 20;7(1):17896. doi:10.1038/s41598-017-18164-6. PubMed PMID: 29263413; PubMed Central PMCID: PMCPMC5738402. PubMed DOI PMC

Dalmasso G, Marin Zapata PA, Brady NR, et al. Agent-based modeling of mitochondria links sub-cellular dynamics to cellular homeostasis and heterogeneity. PLoS One. 2017;12(1):e0168198. doi:10.1371/journal.pone.0168198. PubMed PMID: 28060865; PubMed Central PMCID: PMCPMC5217980. PubMed DOI PMC

Hoffman TE, Barnett KJ, Wallis L, et al. A multimethod computational simulation approach for investigating mitochondrial dynamics and dysfunction in degenerative aging. Aging cell. 2017. Dec;16(6):1244–1255. doi:10.1111/acel.12644. PubMed PMID: WOS:000418387600004; English. PubMed DOI PMC

Brown AI, Rutenberg AD.. A model of autophagy size selectivity by receptor clustering on peroxisomes. 2. 2017. May 19;5:14. doi: ARTN 14 doi:10.3389/fphy.2017.00014. PubMed PMID: WOS:000403720300001; English. DOI

Shirin A, Klickstein IS, Feng S, et al. Prediction of optimal drug schedules for controlling autophagy. Sci Rep. 2019. Feb 5;9(1):1428. doi:10.1038/s41598-019-38763-9. PubMed PMID: 30723233; PubMed Central PMCID: PMCPMC6363771. PubMed DOI PMC

Munsky B, Hlavacek WS, Tsimring LS, editors. Quantitative Biology: Theory, Computational Methods, and Models. Cambridge, MA: The MIT Press; 2018.

Bergmann FT, Hoops S, Klahn B, et al. COPASI and its applications in biotechnology. J Biotechnol. 2017. Nov 10;261:215–220. doi:10.1016/j.jbiotec.2017.06.1200. PubMed PMID: 28655634; PubMed Central PMCID: PMCPMC5623632. PubMed DOI PMC

Binder B, Goede A, Berndt N, et al. A conceptual mathematical model of the dynamic self-organisation of distinct cellular organelles. PLoS One. 2009. Dec 30;4(12):e8295. doi:10.1371/journal.pone.0008295. PubMed PMID: 20041124; PubMed Central PMCID: PMCPMC2795802. PubMed DOI PMC

Chylek LA, Harris LA, Tung C-S, et al. Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdiscip Rev Syst Biol Med. 2014. Jan-Feb;6(1):13–36. doi:10.1002/wsbm.1245. PubMed PMID: 24123887; PubMed Central PMCID: PMCPMC3947470. PubMed DOI PMC

Kapuy O, Papp D, Vellai T, et al. Systems-Level Feedbacks of NRF2 Controlling Autophagy upon Oxidative Stress Response. Antioxidants (Basel). 2018. Mar 5;7(3). doi:10.3390/antiox7030039. PubMed PMID: 29510589; PubMed Central PMCID: PMCPMC5874525. PubMed DOI PMC

Kapuy O, Vinod PK, Banhegyi G.. mTOR inhibition increases cell viability via autophagy induction during endoplasmic reticulum stress - An experimental and modeling study. FEBS Open Bio. 2014;4:704–13. doi:10.1016/j.fob.2014.07.006. PubMed PMID: 25161878; PubMed Central PMCID: PMCPMC4141208. PubMed DOI PMC

Schwartz-Roberts JL, Cook KL, Chen C, et al. Interferon regulatory factor-1 signaling regulates the switch between autophagy and apoptosis to determine breast cancer cell fate. Cancer Res. 2015. Mar 15;75(6):1046–55. doi:10.1158/0008-5472.CAN-14-1851. PubMed PMID: 25576084; PubMed Central PMCID: PMCPMC4359953. PubMed DOI PMC

Ouzounoglou E, Kalamatianos D, Emmanouilidou E, et al. In silico modeling of the effects of alpha-synuclein oligomerization on dopaminergic neuronal homeostasis. BMC Syst Biol. 2014. May 13;8:54. doi:10.1186/1752-0509-8-54. PubMed PMID: 24885905; PubMed Central PMCID: PMCPMC4062111. PubMed DOI PMC

Holczer M, Marton M, Kurucz A, et al. A Comprehensive Systems Biological Study of Autophagy-Apoptosis Crosstalk during Endoplasmic Reticulum Stress. Biomed Res Int. 2015;2015:319589. doi:10.1155/2015/319589. PubMed PMID: 25984530; PubMed Central PMCID: PMCPMC4423012. PubMed DOI PMC

Petri C. Kommunikation mit Automaten. Technische Universitat Darmstadt, Germany: 1962.

Scheidel J, Amstein L, Ackermann J, et al. In Silico Knockout Studies of Xenophagic Capturing of Salmonella. PLoS Comput Biol. 2016. Dec;12(12):e1005200. doi:10.1371/journal.pcbi.1005200. PubMed PMID: 27906974; PubMed Central PMCID: PMCPMC5131900. PubMed DOI PMC

Janes KA, Chandran PL, Ford RM, et al. An engineering design approach to systems biology. Integr Biol. 2017. Jul 17;9(7):574–583. doi:10.1039/c7ib00014f. PubMed PMID: 28590470; PubMed Central PMCID: PMCPMC6534349. PubMed DOI PMC

Gunawardena J. Models in biology: ‘accurate descriptions of our pathetic thinking’. BMC Biol. 2014. Apr 30;12:29. doi:10.1186/1741-7007-12-29. PubMed PMID: 24886484; PubMed Central PMCID: PMCPMC4005397. PubMed DOI PMC

Lander AD. The edges of understanding. BMC Biol. 2010. Apr 12;8:40. doi:10.1186/1741-7007-8-40. PubMed PMID: 20385033; PubMed Central PMCID: PMCPMC2864098. PubMed DOI PMC

Tyson JJ, Novák B.. Models in biology: lessons from modeling regulation of the eukaryotic cell cycle. BMC Biol. 2015. Jul 1;13:46. doi:10.1186/s12915-015-0158-9. PubMed PMID: 26129844; PubMed Central PMCID: PMCPMC4486427. PubMed DOI PMC

Hucka M, Bergmann FT, Hoops S, et al. The Systems Biology Markup Language (SBML): language specification for Level 3 Version 1 Core. J Integr Bioinform. 2015. Sep 4;12(2):266. doi:10.2390/biecoll-jib-2015-266. PubMed PMID: 26528564; PubMed Central PMCID: PMCPMC5451324. PubMed DOI PMC

Zhang F, Meier-Schellersheim M.. SBML Level 3 package: Multistate, Multicomponent and Multicompartment Species, Version 1, Release 1. J Integr Bioinform. 2018. Apr 20;15(1):20170077. doi:10.1515/jib-2017-0077. PubMed PMID: 29676994; PubMed Central PMCID: PMCPMC6167033. PubMed DOI PMC

Ewald R, Uhrmacher AM.. SESSL: a domain-specific language for simulation experiments. Acm T Model Comput S. 2014. Feb;24(2):11. doi: Artn 11 doi:10.1145/2567895. PubMed PMID: WOS:000334526100005; English. DOI

Waltemath D, Adams R, Bergmann FT, et al. Reproducible computational biology experiments with SED-ML—the Simulation Experiment Description Markup Language. BMC Syst Biol. 2011. Dec 15;5:198. doi:10.1186/1752-0509-5-198. PubMed PMID: 22172142; PubMed Central PMCID: PMCPMC3292844. PubMed DOI PMC

Chelliah V, Juty N, Ajmera I, et al. BioModels: ten-year anniversary. Nucleic Acids Res. 2015. Jan;43(Database issue):D542–8. doi:10.1093/nar/gku1181. PubMed PMID: 25414348; PubMed Central PMCID: PMCPMC4383975. PubMed DOI PMC

Azeloglu EU, Iyengar R.. Good practices for building dynamical models in systems biology. Sci Signal. 2015. Apr 7;8(371):fs8. doi:10.1126/scisignal.aab0880. PubMed PMID: 25852187. PubMed DOI

Gutenkunst RN, Waterfall JJ, Casey FP, et al. Universally sloppy parameter sensitivities in systems biology models. PLOS Comput Biol. 2007. Oct;3(10):1871–78. doi:10.1371/journal.pcbi.0030189. PubMed PMID: 17922568; PubMed Central PMCID: PMCPMC2000971. PubMed DOI PMC

Kirk PDW, Babtie AC, Stumpf MPH.. Systems biology (un)certainties. Science. 2015. Oct 23;350(6259):386–8. doi:10.1126/science.aac9505. PubMed PMID: 26494748. PubMed DOI

Wilkinson DJ. Bayesian methods in bioinformatics and computational systems biology. Brief Bioinform. 2007. Mar;8(2):109–16. doi:10.1093/bib/bbm007. PubMed PMID: 17430978. PubMed DOI

Kreutz C, Raue A, Kaschek D, et al. Profile likelihood in systems biology. FEBS J. 2013. Jun;280(11):2564–71. doi:10.1111/febs.12276. PubMed PMID: 23581573. PubMed DOI

Hellerstein JL, Gu S, Choi K, et al. Recent advances in biomedical simulations: a manifesto for model engineering. F1000Res. 2019;8:261. doi:10.12688/f1000research.15997.1. PubMed PMID: 30881691; PubMed Central PMCID: PMCPMC6406177. PubMed DOI PMC

Medley JK, Goldberg AP, Karr JR.. Guidelines for reproducibly building and simulating systems biology models. IEEE Trans Biomed Eng. 2016. Oct;63(10):2015–20. doi:10.1109/TBME.2016.2591960. PubMed PMID: 27429432; PubMed Central PMCID: PMCPMC5131863. PubMed DOI PMC

Alon U. An Introduction to Systems Biology: Design Principles of Biological Circuits, Second Edition. 2nd Edition ed. Boca Raton, FL: Chapman and Hall/CRC; 2019.

Voit EO. A First Course in Systems Biology. 2nd Edition ed. New York: Garland Science; 2017.

Resnekov O, Munsky B, Hlavacek WS.. Perspective on the q-bio Summer School and Conference: 2007–2014 and beyond. Quant Biol. 2014. Mar 1;2(1):54–58. doi:10.1007/s40484-014-0029-3. PubMed PMID: 27595041; PubMed Central PMCID: PMCPMC5008235. PubMed DOI PMC

Knorr RL, Dimova R, Lipowsky R.. Curvature of double-membrane organelles generated by changes in membrane size and composition. PLoS One. 2012;7(3):e32753. doi:10.1371/journal.pone.0032753. PubMed PMID: 22427874; PubMed Central PMCID: PMCPMC3299685. PubMed DOI PMC

Agudo-Canalejo J, Knorr RL.. Formation of auto-phagosomes coincides with relaxation of membrane curvature. Methods Mol Biol. 2019;1880:173–188. doi:10.1007/978-1-4939-8873-0_10. PubMed PMID: 30610696. PubMed DOI

Klionsky DJ, Baehrecke EH, Brumell JH, et al. A comprehensive glossary of autophagy-related molecules and processes (2nd) edition). Autophagy. 2011. Nov 1;7(11):1273–94. PubMed PMID: 21997368; Eng. PubMed PMC

Klionsky DJ, Codogno P, Cuervo AM, et al. A comprehensive glossary of autophagy-related molecules and processes. Autophagy. 2010. May 16;6(4):438–448. PubMed PMID: 20484971; Eng. PubMed PMC

Moosavi MA, Haghi A, Rahmati M, et al. Phytochemicals as potent modulators of autophagy for cancer therapy. Cancer Lett. 2018. Jun 28;424:46–69. doi:10.1016/j.canlet.2018.02.030. PubMed PMID: 29474859. PubMed DOI

Quintana M, Bilbao A, Comas-Barcelo J, et al. Identification of benzo[cd]indol-2(1H)-ones as novel Atg4B inhibitors via a structure-based virtual screening and a novel AlphaScreen assay. Eur J Med Chem. 2019. Sep 15;178:648–666. doi:10.1016/j.ejmech.2019.05.086. PubMed PMID: 31226656. PubMed DOI

Santo L, Hideshima T, Kung AL, et al. Preclinical activity, pharmacodynamic, and pharmacokinetic properties of a selective HDAC6 inhibitor, ACY-1215, in combination with bortezomib in multiple myeloma. Blood. 2012. Mar 15;119(11):2579–89. doi:10.1182/blood-2011-10-387365. PubMed PMID: 22262760; PubMed Central PMCID: PMCPMC3337713. PubMed DOI PMC

Garcia-Echeverria C. Allosteric and ATP-competitive kinase inhibitors of mTOR for cancer treatment. Bioorg Med Chem Lett. 2010. Aug 1;20(15):4308–12. doi:10.1016/j.bmcl.2010.05.099. PubMed PMID: 20561789. PubMed DOI

Rosich L, Xargay-Torrent S, Lopez-Guerra M, et al. Counteracting autophagy overcomes resistance to everolimus in mantle cell lymphoma. clin cancer res off j am assoc cancer res. 2012. Oct 1;18(19):5278–89. doi:10.1158/1078-0432.CCR-12-0351. PubMed PMID: 22879389. PubMed DOI

Booth L, Roberts JL, Ecroyd H, et al. AR-12 inhibits multiple chaperones concomitant with stimulating autophagosome formation collectively preventing virus replication. J Cell Physiol. 2016. Oct;231(10):2286–302. doi:10.1002/jcp.25431. PubMed PMID: 27187154; PubMed Central PMCID: PMCPMC6327852. PubMed DOI PMC

Anguiano J, Garner TP, Mahalingam M, et al. Chemical modulation of chaperone-mediated autophagy by retinoic acid derivatives. Nat Chem Biol. 2013. Jun;9(6):374–82. doi:10.1038/nchembio.1230. PubMed PMID: 23584676; PubMed Central PMCID: PMC3661710. PubMed DOI PMC

De Mei C, Ercolani L, Parodi C, et al.Dual inhibition of REV-ERBbeta and autophagy as a novel pharmacological approach to induce cytotoxicity in cancer cells. Oncogene. 2015. May 14;34(20):2597–608. doi:10.1038/onc.2014.203. PubMed PMID: 25023698. PubMed DOI PMC

Li M, Sala V, De Santis MC, et al. Phosphoinositide 3-kinase gamma inhibition protects from anthracycline cardiotoxicity and reduces tumor growth. Circulation. 2018. Aug 14;138(7):696–711. doi:10.1161/CIRCULATIONAHA.117.030352. PubMed PMID: 29348263. PubMed DOI

Fujita N, Hayashi-Nishino M, Fukumoto H, et al. An Atg4B mutant hampers the lipidation of LC3 paralogues and causes defects in autophagosome closure. Mol Biol Cell. 2008. Nov;19(11):4651–9. doi:10.1091/mbc.E08-03-0312. PubMed PMID: 18768752; PubMed Central PMCID: PMC2575160. eng. PubMed DOI PMC

Robke L, Laraia L, Carnero Corrales MA, et al. Phenotypic identification of a novel autophagy inhibitor chemotype targeting lipid kinase VPS34. Angew Chem Int Ed Engl. 2017. Jul 3;56(28):8153–8157. doi:10.1002/anie.201703738. PubMed PMID: 28544137. PubMed DOI

Zhuang X, Wang H, Lam SK, et al. A BAR-domain protein SH3P2, which binds to phosphatidylinositol 3-phosphate and ATG8, regulates autophagosome formation in Arabidopsis. Plant Cell. 2013. Nov;25(11):4596–615. doi:10.1105/tpc.113.118307. PubMed PMID: 24249832; PubMed Central PMCID: PMCPMC3875738. PubMed DOI PMC

Ansari MY, Ahmad N, Haqqi TM.. Butein activates autophagy through AMPK/TSC2/ULK1/mTOR pathway to inhibit IL-6 expression in IL-1beta stimulated human chondrocytes. Cell Physiol Biochem. 2018;49(3):932–946. doi:10.1159/000493225. PubMed PMID: 30184535. PubMed DOI

Lyamzaev KG, Tokarchuk AV, Panteleeva AA, et al. Induction of autophagy by depolarization of mitochondria. Autophagy. 2018;14(5):921–924. doi:10.1080/15548627.2018.1436937. PubMed PMID: 29458285; PubMed Central PMCID: PMCPMC6070013. PubMed DOI PMC

Filadi R, Pizzo P.. Defective autophagy and Alzheimer’s disease: is calcium the key? Neural Regen Res. 2019. Dec;14(12):2081–2082. doi:10.4103/1673-5374.262584. PubMed PMID: 31397341; PubMed Central PMCID: PMCPMC6788238. PubMed DOI PMC

Williams RS, Cheng L, Mudge AW, et al. A common mechanism of action for three mood-stabilizing drugs. Nature. 2002. May 16;417(6886):292–5. doi:10.1038/417292a. PubMed PMID: 12015604. PubMed DOI

Parzych K, Saavedra-Garcia P, Valbuena GN, et al. The coordinated action of VCP/p97 and GCN2 regulates cancer cell metabolism and proteostasis during nutrient limitation. Oncogene. 2019. Apr;38(17):3216–3231. doi:10.1038/s41388-018-0651-z. PubMed PMID: 30626938; PubMed Central PMCID: PMCPMC6756015. PubMed DOI PMC

Anderson DJ, Le Moigne R, Djakovic S, et al. Targeting the AAA ATPase p97 as an approach to treat cancer through disruption of protein homeostasis. Cancer cell. 2015. Nov 9;28(5):653–665. doi:10.1016/j.ccell.2015.10.002. PubMed PMID: 26555175; PubMed Central PMCID: PMCPMC4941640. PubMed DOI PMC

Kane MS, Paris A, Codron P, et al. Current mechanistic insights into the CCCP-induced cell survival response. Biochem Pharmacol. 2018. Feb;148:100–110. doi:10.1016/j.bcp.2017.12.018. PubMed PMID: 29277693. PubMed DOI

Mattar P, Bravo-Sagua R, Tobar N, et al. Autophagy mediates calcium-sensing receptor-induced TNFalpha production in human preadipocytes. Biochim Biophys Acta Mol Basis Dis. 2018. Nov;1864(11):3585–3594. doi:10.1016/j.bbadis.2018.08.020. PubMed PMID: 30251678. PubMed DOI

Lim JH, Kim HW, Kim MY, et al. Cinacalcet-mediated activation of the CaMKKbeta-LKB1-AMPK pathway attenuates diabetic nephropathy in db/db mice by modulation of apoptosis and autophagy. Cell Death Dis. 2018. Feb 15;9(3):270. doi:10.1038/s41419-018-0324-4. PubMed PMID: 29449563; PubMed Central PMCID: PMCPMC5833853. PubMed DOI PMC

Vanrell MC, Cueto JA, Barclay JJ, et al. Polyamine depletion inhibits the autophagic response modulating Trypanosoma cruzi infectivity. Autophagy. 2013. Jul;9(7):1080–93. doi:10.4161/auto.24709. PubMed PMID: 23697944; PubMed Central PMCID: PMC3722317. PubMed DOI PMC

D’Eliseo D, Di Renzo L, Santoni A, et al. Docosahexaenoic acid (DHA) promotes immunogenic apoptosis in human multiple myeloma cells, induces autophagy and inhibits STAT3 in both tumor and dendritic cells. Genes Cancer. 2017. Jan;8(1–2): 426–437. doi:10.18632/genesandcancer.131. PubMed PMID: 28435516; PubMed Central PMCID: PMCPMC5396621. PubMed DOI PMC

Jing K, Song KS, Shin S, et al. Docosahexaenoic acid induces autophagy through p53/AMPK/mTOR signaling and promotes apoptosis in human cancer cells harboring wild-type p53. Autophagy. 2011. Nov;7(11):1348–58. doi:10.4161/auto.7.11.16658. PubMed PMID: 21811093; PubMed Central PMCID: PMCPMC3242799. PubMed DOI PMC

Mildenberger J, Johansson I, Sergin I, et al. N-3 PUFAs induce inflammatory tolerance by formation of KEAP1-containing SQSTM1/p62-bodies and activation of NFE2L2. Autophagy. 2017. Oct 3;13(10):1664–1678. doi:10.1080/15548627.2017.1345411. PubMed PMID: 28820283; PubMed Central PMCID: PMCPMC5640206. PubMed DOI PMC

Zhou X, Yue GG, Chan AM, et al. Eriocalyxin B, a novel autophagy inducer, exerts anti-tumor activity through the suppression of Akt/mTOR/p70S6K signaling pathway in breast cancer. Biochem Pharmacol. 2017. Oct 15;142:58–70. doi:10.1016/j.bcp.2017.06.133. PubMed PMID: 28669564. PubMed DOI

Yamamura T, Ohsaki Y, Suzuki M, et al. Inhibition of Niemann-Pick-type C1-like1 by ezetimibe activates autophagy in human hepatocytes and reduces mutant alpha1-antitrypsin Z deposition. Hepatology. 2014. Apr;59(4):1591–9. doi:10.1002/hep.26930. PubMed PMID: 24214142. PubMed DOI

Kim SH, Kim G, Han DH, et al. Ezetimibe ameliorates steatohepatitis via AMP activated protein kinase-TFEB-mediated activation of autophagy and NLRP3 inflammasome inhibition. Autophagy. 2017Oct 3;13(10):1767–1781. doi:10.1080/15548627.2017.1356977. PubMed PMID: 28933629; PubMed Central PMCID: PMCPMC5640190. PubMed DOI PMC

Liu FT, Yang YJ, Wu JJ, et al. Fasudil, a Rho kinase inhibitor, promotes the autophagic degradation of A53T alpha-synuclein by activating the JNK 1/Bcl-2/beclin 1 pathway. Brain Res. 2016. Feb 1;1632:9–18. doi:10.1016/j.brainres.2015.12.002. PubMed PMID: 26683082. PubMed DOI

Gao H, Hou F, Dong R, et al. Rho-Kinase inhibitor fasudil suppresses high glucose-induced H9c2 cell apoptosis through activation of autophagy. Cardiovasc Ther. 2016. Oct;34(5):352–9. doi:10.1111/1755-5922.12206. PubMed PMID: 27333569. PubMed DOI

Koch JC, Tonges L, Barski E, et al. ROCK2 is a major regulator of axonal degeneration, neuronal death and axonal regeneration in the CNS. Cell Death Dis. 2014. May 15;5:e1225. doi:10.1038/cddis.2014.191. PubMed PMID: 24832597; PubMed Central PMCID: PMCPMC4047920. PubMed DOI PMC

Prieto-Dominguez N, Garcia-Mediavilla MV, Sanchez-Campos S, et al. Autophagy as a molecular target of flavonoids underlying their protective effects in human disease. Curr Med Chem. 2018;25(7):814–838. doi:10.2174/0929867324666170918125155. PubMed PMID: 28925866. PubMed DOI

Zheng Q, Li Z, Zhou S, et al. Heparin-binding hemagglutinin of mycobacterium tuberculosis is an inhibitor of autophagy. Front Cell Infect Microbiol. 2017;7:33. doi:10.3389/fcimb.2017.00033. PubMed PMID: 28224118; PubMed Central PMCID: PMCPMC5293787. PubMed DOI PMC

Song W, Zukor H, Liberman A, et al. Astroglial heme oxygenase-1 and the origin of corpora amylacea in aging and degenerating neural tissues. Exp Neurol. 2014. Apr;254:78–89. doi:10.1016/j.expneurol.2014.01.006. PubMed PMID: 24440642; PubMed Central PMCID: PMC4020524. PubMed DOI PMC

Song W, Zukor H, Lin SH, et al. Unregulated brain iron deposition in transgenic mice over-expressing HMOX1 in the astrocytic compartment. J Neurochem. 2012. Oct;123(2):325–36. doi:10.1111/j.1471-4159.2012.07914.x. PubMed PMID: 22881289. PubMed DOI

Garcia-Martinez JM, Moran J, Clarke RG, et al. Ku-0063794 is a specific inhibitor of the mammalian target of rapamycin (mTOR). Biochem J. 2009. Jul 1;421(1):29–42. doi:10.1042/BJ20090489. PubMed PMID: 19402821; PubMed Central PMCID: PMC2708931. eng. PubMed DOI PMC

Bosc D, Vezenkov L, Bortnik S, et al. A new quinoline-based chemical probe inhibits the autophagy-related cysteine protease ATG4B. Sci Rep. 2018. Aug 3;8(1):11653. doi:10.1038/s41598-018-29900-x. PubMed PMID: 30076329; PubMed Central PMCID: PMCPMC6076261. PubMed DOI PMC

San-Miguel B, Crespo I, Sanchez DI, et al. Melatonin inhibits autophagy and endoplasmic reticulum stress in mice with carbon tetrachloride-induced fibrosis. J Pineal Res. 2015. Sep;59(2):151–62. doi:10.1111/jpi.12247. PubMed PMID: 25958928. PubMed DOI

Ordoñez R, Fernandez A, Prieto-Dominguez N, et al. Ceramide metabolism regulates autophagy and apoptotic cell death induced by melatonin in liver cancer cells. J Pineal Res. 2015. Sep;59(2):178–89. doi:10.1111/jpi.12249. PubMed PMID: 25975536; PubMed Central PMCID: PMCPMC4523438. PubMed DOI PMC

San-Miguel B, Crespo I, Vallejo D, et al. Melatonin modulates the autophagic response in acute liver failure induced by the rabbit hemorrhagic disease virus. J Pineal Res. 2014. Apr;56(3):313–21. doi:10.1111/jpi.12124. PubMed PMID: 24499270. PubMed DOI PMC

Kanamori H, Naruse G, Yoshida A, et al. Metformin enhances autophagy and provides cardioprotection in delta-sarcoglycan deficiency-induced dilated cardiomyopathy. Circ Heart Fail. 2019. Apr;12(4):e005418. doi:10.1161/CIRCHEARTFAILURE.118.005418. PubMed PMID: 30922066. PubMed DOI

Wang Y, Yang Z, Zheng G, et al. Metformin promotes autophagy in ischemia/reperfusion myocardium via cytoplasmic AMPKalpha1 and nuclear AMPKalpha2 pathways. Life Sci. 2019. May 15;225:64–71. doi:10.1016/j.lfs.2019.04.002. PubMed PMID: 30953640. PubMed DOI

Zilinyi R, Czompa A, Czegledi A, et al. The cardioprotective effect of metformin in doxorubicin-induced cardiotoxicity: the role of autophagy. Molecules. 2018. May 15;23(5). doi:10.3390/molecules23051184. PubMed PMID: 29762537; PubMed Central PMCID: PMCPMC6100061. PubMed DOI PMC

Pal R, Xiong Y, Sardiello M.. Abnormal glycogen storage in tuberous sclerosis complex caused by impairment of mTORC1-dependent and -independent signaling pathways. Proc Natl Acad Sci U S A. 2019. Feb 19;116(8):2977–2986 . doi:10.1073/pnas.1812943116. PubMed PMID: 30728291; PubMed Central PMCID: PMCPMC6386676. PubMed DOI PMC

Soucy TA, Smith PG, Milhollen MA, et al. An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer. Nature. 2009. Apr 9;458(7239):732–6. doi:10.1038/nature07884. PubMed PMID: 19360080. PubMed DOI

Luo Z, Yu G, Lee HW, et al. The Nedd8-activating enzyme inhibitor MLN4924 induces autophagy and apoptosis to suppress liver cancer cell growth. Cancer Res. 2012. Jul 1;72(13):3360–71. doi:10.1158/0008-5472.CAN-12-0388. PubMed PMID: 22562464. PubMed DOI

Serra V, Markman B, Scaltriti M, et al. NVP-BEZ235, a dual PI3K/mTOR inhibitor, prevents PI3K signaling and inhibits the growth of cancer cells with activating PI3K mutations. Cancer Res. 2008. Oct 1;68(19):8022–30. doi:10.1158/0008-5472.CAN-08-1385. PubMed PMID: 18829560; eng. PubMed DOI

Liu TJ, Koul D, LaFortune T, et al. NVP-BEZ235, a novel dual phosphatidylinositol 3-kinase/mammalian target of rapamycin inhibitor, elicits multifaceted antitumor activities in human gliomas. Mol Cancer Ther. 2009. Aug;8(8):2204–10. doi:10.1158/1535-7163. MCT-09-0160. PubMed PMID: 19671762; PubMed Central PMCID: PMC2752877. eng. PubMed PMC

Wang F, Bonam SR, Schall N, et al. Blocking nuclear export of HSPA8 after heat shock stress severely alters cell survival. Sci Rep. 2018. Nov 14;8(1):16820. doi:10.1038/s41598-018-34887-6. PubMed PMID: 30429537; PubMed Central PMCID: PMCPMC6235846. PubMed DOI PMC

Page N, Schall N, Strub JM, et al. The spliceosomal phosphopeptide P140 controls the lupus disease by interacting with the HSC70 protein and via a mechanism mediated by gammadelta T cells. PLoS One. 2009;4(4):e5273. doi:10.1371/journal.pone.0005273. PubMed PMID: 19390596; PubMed Central PMCID: PMCPMC2669294. PubMed DOI PMC

Macri C, Wang F, Tasset I, et al. Modulation of deregulated chaperone-mediated autophagy by a phosphopeptide. Autophagy. 2015;11(3):472–86. doi:10.1080/15548627.2015.1017179. PubMed PMID: 25719862; PubMed Central PMCID: PMCPMC4502742. PubMed DOI PMC

Jabir MS, Sulaiman GM, Taqi ZJ, et al. Iraqi propolis increases degradation of IL-1beta and NLRC4 by autophagy following Pseudomonas aeruginosa infection. Microbes Infect. 2018. Feb;20(2):89–100. doi:10.1016/j.micinf.2017.10.007. PubMed PMID: 29104144. PubMed DOI

Pirola L, Frojdo S.. Resveratrol: one molecule, many targets. IUBMB life. 2008. May;60(5):323–32. doi:10.1002/iub.47. PubMed PMID: 18421779. PubMed DOI

Vingtdeux V, Giliberto L, Zhao H, et al. AMP-activated protein kinase signaling activation by resveratrol modulates amyloid-beta peptide metabolism. J Biol Chem. 2010. Mar 19;285(12):9100–13. doi:10.1074/jbc.M109.060061. PubMed PMID: 20080969; PubMed Central PMCID: PMC2838330. eng. PubMed DOI PMC

Puissant A, Auberger P.. AMPK- and p62/SQSTM1-dependent autophagy mediate Resveratrol-induced cell death in chronic myelogenous leukemia. Autophagy. 2010. Jul 1;6(5):655–7. PubMed PMID: 20458181; Eng. PubMed

Vingtdeux V, Chandakkar P, Zhao H, et al. Novel synthetic small-molecule activators of AMPK as enhancers of autophagy and amyloid-[b] peptide degradation. FASEB J. 2011. Jan;25(1):219–31. doi:10.1096/fj.10-167361. PubMed PMID: 20852062; PubMed Central PMCID: PMC3005419. eng. PubMed DOI PMC

Dyczynski M, Yu Y, Otrocka M, et al. Targeting autophagy by small molecule inhibitors of vacuolar protein sorting 34 (Vps34) improves the sensitivity of breast cancer cells to Sunitinib. Cancer Lett. 2018. Oct 28;435:32–43. doi:10.1016/j.canlet.2018.07.028. PubMed PMID: 30055290. PubMed DOI

Tang F, Hu P, Yang Z, et al. SBI0206965, a novel inhibitor of Ulk1, suppresses non-small cell lung cancer cell growth by modulating both autophagy and apoptosis pathways. Oncol Rep. 2017. Jun;37(6):3449–3458. doi:10.3892/or.2017.5635. PubMed PMID: 28498429. PubMed DOI

Dite TA, Langendorf CG, Hoque A, et al. AMP-activated protein kinase selectively inhibited by the type II inhibitor SBI-0206965. J Biol Chem. 2018. Jun 8;293(23):8874–8885. doi:10.1074/jbc.RA118.003547. PubMed PMID: 29695504; PubMed Central PMCID: PMCPMC5995511. PubMed DOI PMC

Rodriguez-Hernandez MA, Gonzalez R, de la Rosa AJ, et al. Molecular characterization of autophagic and apoptotic signaling induced by sorafenib in liver cancer cells. J Cell Physiol. 2018. Jan;234(1):692–708. doi:10.1002/jcp.26855. PubMed PMID: 30132846. PubMed DOI

Liu J, Xia H, Kim M, et al. Beclin1 controls the levels of p53 by regulating the deubiquitination activity of USP10 and USP13. Cell. 2011. Sep 30;147(1):223–34. doi:10.1016/j.cell.2011.08.037. PubMed PMID: 21962518; PubMed Central PMCID: PMC3441147. PubMed DOI PMC

Milczarek M, Wiktorska K, Mielczarek L, et al. Corrigendum to ‘Autophagic cell death and premature senescence: New mechanism of 5-fluorouracil and sulforaphane synergistic anticancer effect in MDA-MB-231 triple negative breast cancer cell line’ Food Chem Toxicol. Food Chem Toxicol. 111 (2018) 1–8. 2018. Aug;118:972. doi:10.1016/j.fct.2018.04.037. PubMed PMID: 29731172. PubMed DOI

Yang F, Wang F, Liu Y, et al. Sulforaphane induces autophagy by inhibition of HDAC6-mediated PTEN activation in triple negative breast cancer cells. Life Sci. 2018. Nov 15;213:149–157. doi:10.1016/j.lfs.2018.10.034. PubMed PMID: 30352240. PubMed DOI

Liu Y, Shoji-Kawata S, Sumpter RM, Jr., et al. Autosis is a Na+,K+-ATPase-regulated form of cell death triggered by autophagy-inducing peptides, starvation, and hypoxia-ischemia. Proc Natl Acad Sci U S A. 2013. Dec 17;110(51):20364–71. doi:10.1073/pnas.1319661110. PubMed PMID: 24277826; PubMed Central PMCID: PMC3870705. PubMed DOI PMC

Gordon PB, Holen I, Fosse M, et al. Dependence of hepatocytic autophagy on intracellularly sequestered calcium [In Vitro Research Support, Non-U.S. Gov’t]. J Biol Chem. 1993. Dec 15;268(35):26107–12. PubMed PMID: 8253727; eng. PubMed

Ganley IG, Wong PM, Gammoh N, et al. Distinct autophagosomal-lysosomal fusion mechanism revealed by thapsigargin-induced autophagy arrest. Mol Cell. 2011. Jun 24;42(6):731–43. doi:10.1016/j.molcel.2011.04.024. PubMed PMID: 21700220; PubMed Central PMCID: PMC3124681. eng. PubMed DOI PMC

Zhang L, Dai F, Cui L, et al. Novel role for TRPC4 in regulation of macroautophagy by a small molecule in vascular endothelial cells. Biochim Biophys Acta. 2015. Feb;1853(2):377–87. doi:10.1016/j.bbamcr.2014.10.030. PubMed PMID: 25476892. PubMed DOI

Rodrigues D, Viotto AC, Checchia R, et al. Mechanism of Aloe Vera extract protection against UVA: shelter of lysosomal membrane avoids photodamage. Photochem Photobiol Sci Off J Eur Photochem Assoc Eur Soc Photobiol. 2016. Mar;15(3):334–50. doi:10.1039/c5pp00409h. PubMed PMID: 26815913. PubMed DOI

Casarejos MJ, Solano RM, Gomez A, et al. The accumulation of neurotoxic proteins, induced by proteasome inhibition, is reverted by trehalose, an enhancer of autophagy, in human neuroblastoma cells. Neurochem Int. 2011. Mar;58(4):512–20. doi:10.1016/j.neuint.2011.01.008. PubMed PMID: 21232572; eng. PubMed DOI

Fernandez-Estevez MA, Casarejos MJ, Lopez Sendon J, et al. Trehalose reverses cell malfunction in fibroblasts from normal and Huntington’s disease patients caused by proteosome inhibition. PLoS One. 2014;9(2):e90202. doi:10.1371/journal.pone.0090202. PubMed PMID: 24587280; PubMed Central PMCID: PMCPMC3934989. PubMed DOI PMC

Lotfi P, Tse DY, Di Ronza A, et al. Trehalose reduces retinal degeneration, neuroinflammation and storage burden caused by a lysosomal hydrolase deficiency. Autophagy. 2018;14(8):1419–1434. doi:10.1080/15548627.2018.1474313. PubMed PMID: 29916295; PubMed Central PMCID: PMCPMC6103706. PubMed DOI PMC

Carpenter JE, Jackson W, Benetti L, et al. Autophagosome formation during varicella-zoster virus Infection following endoplasmic reticulum stress and the unfolded protein response. J Virol. 2011. Sep;85(18):9414–24. doi:10.1128/JVI.00281-11. PubMed PMID: 21752906; eng. PubMed DOI PMC

Lu Y, Dong S, Hao B, et al. Vacuolin-1 potently and reversibly inhibits autophagosome-lysosome fusion by activating RAB5A. Autophagy. 2014;10(11):1895–905. doi:10.4161/auto.32200. PubMed PMID: 25483964; PubMed Central PMCID: PMC4502727. PubMed DOI PMC

Donohue E, Tovey A, Vogl AW, et al. Inhibition of autophagosome formation by the benzoporphyrin derivative verteporfin. J Biol Chem 2011;286:7290–7300. PubMed PMC

de Munck E, Palomo V, Munoz-Saez E, et al. Small GSK-3 Inhibitor Shows Efficacy in a Motor Neuron Disease Murine Model Modulating Autophagy. PLoS One. 2016;11(9):e0162723. doi:10.1371/journal.pone.0162723. PubMed PMID: 27631495; PubMed Central PMCID: PMCPMC5025054. PubMed DOI PMC

Bago R, Malik N, Munson MJ, et al. Characterization of VPS34-IN1, a selective inhibitor of Vps34, reveals that the phosphatidylinositol 3-phosphate-binding SGK3 protein kinase is a downstream target of class III phosphoinositide 3-kinase. Biochem J. 2014. Nov 1;463(3):413–27. doi:10.1042/BJ20140889. PubMed PMID: 25177796; PubMed Central PMCID: PMCPMC4209782. PubMed DOI PMC

Korsnes MS. Yessotoxin as a tool to study induction of multiple cell death pathways. Toxins (Basel). 2012. Jul;4(7):568–79. doi:10.3390/toxins4070568. PubMed PMID: 22852069; PubMed Central PMCID: PMCPMC3407893. PubMed DOI PMC

Kijanska M, Dohnal I, Reiter W, et al. Activation of Atg1 kinase in autophagy by regulated phosphorylation. Autophagy. 2010. Nov;6(8):1168–78. PubMed PMID: 20953146. PubMed

Papinski D, Schuschnig M, Reiter W, et al. Early steps in autophagy depend on direct phosphorylation of Atg9 by the Atg1 kinase. Mol Cell. 2014. Feb 6;53(3):471–83. doi:10.1016/j.molcel.2013.12.011. PubMed PMID: 24440502; PubMed Central PMCID: PMC3978657. PubMed DOI PMC

Weerasekara VK, Panek DJ, Broadbent DG, et al. Metabolic-stress-induced rearrangement of the 14-3-3zeta interactome promotes autophagy via a ULK1- and AMPK-regulated 14-3-3zeta interaction with phosphorylated Atg9. Mol Cell Biol. 2014. Dec;34(24):4379–88. doi:10.1128/MCB.00740-14. PubMed PMID: 25266655; PubMed Central PMCID: PMCPMC4248729. PubMed DOI PMC

Kamada Y, Yoshino K, Kondo C, et al. Tor directly controls the Atg1 kinase complex to regulate autophagy. Mol Cell Biol. 2010. Feb;30(4):1049–58. doi: 10.1128/MCB.01344-09. PubMed PMID: 19995911; PubMed Central PMCID: PMC2815578. PubMed DOI PMC

Stephan JS, Yeh YY, Ramachandran V, et al. The Tor and PKA signaling pathways independently target the Atg1/Atg13 protein kinase complex to control autophagy. Proc Natl Acad Sci U S A. 2009. Oct 6;106(40):17049–54. doi:10.1073/pnas.0903316106. PubMed PMID: 19805182; PubMed Central PMCID: PMC2761351. PubMed DOI PMC

Wold MS, Lim J, Lachance V, et al. ULK1-mediated phosphorylation of ATG14 promotes autophagy and is impaired in Huntington’s disease models. Mol Neurodegener. 2016. Dec 9;11(1):76. doi: 10.1186/s13024-016-0141-0. PubMed PMID: 27938392; PubMed Central PMCID: PMCPMC5148922. PubMed DOI PMC

Wei Y, An Z, Zou Z, et al. The stress-responsive kinases MAPKAPK2/MAPKAPK3 activate starvation-induced autophagy through Beclin 1 phosphorylation. eLife. 2015;4. doi:10.7554/eLife.05289. PubMed PMID: 25693418; PubMed Central PMCID: PMC4337728. PubMed DOI PMC

Vega-Rubin-de-Celis S, Zou Z, Fernandez AF, et al. Increased autophagy blocks HER2-mediated breast tumorigenesis. Proc Natl Acad Sci U S A. 2018. Apr 17;115(16):4176–4181. doi:10.1073/pnas.1717800115. PubMed PMID: 29610308; PubMed Central PMCID: PMCPMC5910832. PubMed DOI PMC

Wang BJ, Her GM, Hu MK, et al. ErbB2 regulates autophagic flux to modulate the proteostasis of APP-CTFs in Alzheimer’s disease. Proc Natl Acad Sci U S A. 2017. Apr 11;114(15):E3129–E3138. doi:10.1073/pnas.1618804114. PubMed PMID: 28351972; PubMed Central PMCID: PMCPMC5393216. PubMed DOI PMC

Kratter IH, Zahed H, Lau A, et al. Serine 421 regulates mutant huntingtin toxicity and clearance in mice. J Clin Invest. 2016. Sep 1;126(9):3585–97. doi:10.1172/JCI80339. PubMed PMID: 27525439; PubMed Central PMCID: PMCPMC5004962. PubMed DOI PMC

Nave BT, Ouwens M, Withers DJ, et al. Mammalian target of rapamycin is a direct target for protein kinase B: identification of a convergence point for opposing effects of insulin and amino-acid deficiency on protein translation. Biochem J. 1999. Dec1;344Pt 2:427–31. PubMed PMID: 10567225; PubMed Central PMCID: PMC1220660. PubMed PMC

Peterson RT, Beal PA, Comb MJ, et al. FKBP12-rapamycin-associated protein (FRAP) autophosphorylates at serine 2481 under translationally repressive conditions. J Biol Chem 2000. Mar10;275(10):7416–23. PubMed PMID: 10702316. PubMed

Nicot AS, Lo Verso F, Ratti F, et al. Phosphorylation of NBR1 by GSK3 modulates protein aggregation. Autophagy. 2014. Jun;10(6):1036–53. doi:10.4161/auto.28479. PubMed PMID: 24879152; PubMed Central PMCID: PMC4091167. PubMed DOI PMC

Rosner M, Fuchs C, Siegel N, et al. Functional interaction of mammalian target of rapamycin complexes in regulating mammalian cell size and cell cycle. Hum Mol Genet. 2009. Sep 1;18(17):3298–310. doi:10.1093/hmg/ddp271. PubMed PMID: 19505958; PubMed Central PMCID: PMC2722991. PubMed DOI PMC

Shin S, Wolgamott L, Yu Y, et al. Glycogen synthase kinase (GSK)-3 promotes p70 ribosomal protein S6 kinase (p70S6K) activity and cell proliferation. Proc Natl Acad Sci U S A. 2011. Nov 22;108(47):E1204–13. doi:10.1073/pnas.1110195108. PubMed PMID: 22065737; PubMed Central PMCID: PMC3223461. PubMed DOI PMC

Cheng X, Ma X, Ding X, et al. Pacer mediates the function of class III PI3K and HOPS complexes in autophagosome maturation by engaging Stx17. Mol Cell. 2017. Mar 16;65(6):1029–1043 e5. doi:10.1016/j.molcel.2017.02.010. PubMed PMID: 28306502. PubMed DOI

Ro SH, Semple IA, Park H, et al. Sestrin2 promotes Unc-51-like kinase 1 mediated phosphorylation of p62/sequestosome-1. FEBS J. 2014. Jul 4. doi:10.1111/febs.12905. PubMed PMID: 25040165. PubMed DOI PMC

Roczniak-Ferguson A, Petit CS, Froehlich F, et al. The transcription factor TFEB links mTORC1 signaling to transcriptional control of lysosome homeostasis. Sci Signal. 2012. Jun 12;5(228):ra42. doi:10.1126/scisignal.2002790. PubMed PMID: 22692423; PubMed Central PMCID: PMCPMC3437338. PubMed DOI PMC

Wang Z, Gong Y, Peng B, et al. MRE11 UFMylation promotes ATM activation. Nucleic Acids Res. 2019. May 7;47(8):4124–4135. doi:10.1093/nar/gkz110.PubMed PMID: 30783677; PubMed Central PMCID: PMCPMC6486557. PubMed DOI PMC

Kim YM, Jung CH, Seo M, et al. mTORC1 phosphorylates UVRAG to negatively regulate autophagosome and endosome maturation. Mol Cell. 2015. Jan 22;57(2):207–18. doi:10.1016/j.molcel.2014.11.013. PubMed PMID: 25533187; PubMed Central PMCID: PMC4304967. PubMed DOI PMC

Munson MJ, Allen GF, Toth R, et al. mTOR activates the VPS34-UVRAG complex to regulate autolysosomal tubulation and cell survival. EMBO J. 2015. Jul 2. doi:10.15252/embj.201590992. PubMed PMID: 26139536. PubMed DOI PMC

Lorente M, Garcia-Casas A, Salvador N, et al. Inhibiting SUMO1-mediated SUMOylation induces autophagy-mediated cancer cell death and reduces tumour cell invasion via RAC1. J Cell Sci. 2019. Oct 22;132(20). doi:10.1242/jcs.234120. PubMed PMID: 31578236; PubMed Central PMCID: PMCPMC6826015. PubMed DOI PMC

Chen Y, Azad MB, Gibson SB.. Superoxide is the major reactive oxygen species regulating autophagy. Cell Death Differ. 2009. Jul;16(7):1040–52. doi:10.1038/cdd.2009.49. PubMed PMID: 19407826. PubMed DOI

Lorin S, Borges A, Ribeiro Dos Santos L, et al. c-Jun NH2-terminal kinase activation is essential for DRAM-dependent induction of autophagy and apoptosis in 2-methoxyestradiol-treated Ewing sarcoma cells. Cancer Res. 2009. Sep 1;69(17):6924–31. doi: 10.1158/0008-5472.CAN-09-1270. PubMed PMID: 19706754. PubMed DOI

Xue L, Fletcher GC, Tolkovsky AM.. Autophagy is activated by apoptotic signalling in sympathetic neurons: an alternative mechanism of death execution. Mol Cell Neurosci. 1999. Sep;14(3):180–98. PubMed PMID: 10576889; eng. PubMed

Ge D, Han L, Huang S, et al. Identification of a novel MTOR activator and discovery of a competing endogenous RNA regulating autophagy in vascular endothelial cells. Autophagy. 2014. Jun;10(6):957–71. doi:10.4161/auto.28363. PubMed PMID: 24879147; PubMed Central PMCID: PMCPMC4091179. PubMed DOI PMC

Zhang N, Chen Y, Jiang R, et al.PARP and RIP 1 are required for autophagy induced by 11ʹ-deoxyverticillin A, which precedes caspase-dependent apoptosis. Autophagy. 2011. Jun;7(6):598–612. PubMed PMID: 21460625. PubMed

Radoshevich L, Murrow L, Chen N, et al. ATG12 conjugation to ATG3 regulates mitochondrial homeostasis and cell death. Cell. 2010. Aug 20;142(4):590–600. doi:10.1016/j.cell.2010.07.018. PubMed PMID: 20723759; PubMed Central PMCID: PMC2925044. PubMed DOI PMC

Leonardi M, Perna E, Tronnolone S, et al. Activated kinase screening identifies the IKBKE oncogene as a positive regulator of autophagy. Autophagy. 2019. Feb;15(2):312–326. doi:10.1080/15548627.2018.1517855. PubMed PMID: 30289335; PubMed Central PMCID: PMCPMC6333447. PubMed DOI PMC

Maiuri MC, Criollo A, Tasdemir E, et al. BH3-only proteins and BH3 mimetics induce autophagy by competitively disrupting the interaction between Beclin 1 and Bcl-2/Bcl-X(L). Autophagy. 2007. Jul-Aug;3(4):374–6. PubMed PMID: 17438366; eng. PubMed

Oltersdorf T, Elmore SW, Shoemaker AR, et al. An inhibitor of Bcl-2 family proteins induces regression of solid tumours. Nature. 2005. Jun 2;435(7042):677–81. doi:10.1038/nature03579. PubMed PMID: 15902208. PubMed DOI

Erazo T, Lorente M, Lopez-Plana A, et al. The New Antitumor Drug ABTL0812 Inhibits the Akt/mTORC1 Axis by Upregulating Tribbles-3 Pseudokinase. clin cancer res off j am assoc cancer res. 2016. May 15;22(10):2508–19. doi:10.1158/1078-0432.CCR-15-1808. PubMed PMID: 26671995. PubMed DOI

Felip I, Moiola CP, Megino-Luque C, et al. Therapeutic potential of the new TRIB3-mediated cell autophagy anticancer drug ABTL0812 in endometrial cancer. Gynecol Oncol. 2019. May;153(2):425–435. doi:10.1016/j.ygyno.2019.03.002. PubMed PMID: 30853360. PubMed DOI

Costello JL, Castro IG, Hacker C, et al. ACBD5 and VAPB mediate membrane associations between peroxisomes and the ER. J Cell Biol. 2017. Feb;216(2):331–342. doi:10.1083/jcb.201607055. PubMed PMID: 28108524; PubMed Central PMCID: PMCPMC5294785. PubMed DOI PMC

Nazarko TY. Atg37 regulates the assembly of the pexophagic receptor protein complex. Autophagy. 2014. Jul;10(7):1348–9. doi:10.4161/auto.29073. PubMed PMID: 24905344; PubMed Central PMCID: PMC4203562. PubMed DOI PMC

Kawaguchi K, Kikuma T, Higuchi Y, et al. Subcellular localization of acyl-CoA binding protein in Aspergillus oryzae is regulated by autophagy machinery. Biochem Biophys Res Commun. 2016. Nov 4;480(1):8–12. doi:10.1016/j.bbrc.2016.10.018. PubMed PMID: 27725156. PubMed DOI

Eisenberg T, Schroeder S, Andryushkova A, et al. Nucleocytosolic depletion of the energy metabolite acetyl-coenzyme a stimulates autophagy and prolongs lifespan. Cell Metab. 2014. Mar 4;19(3):431–44. doi:10.1016/j.cmet.2014.02.010. PubMed PMID: 24606900. PubMed DOI PMC

Marino G, Pietrocola F, Eisenberg T, et al. Regulation of autophagy by cytosolic acetyl-coenzyme a. Mol Cell. 2014. Mar 6;53(5):710–25. doi:10.1016/j.molcel.2014.01.016. PubMed PMID: 24560926. PubMed DOI

Nandi N, Tyra LK, Stenesen D, et al. Acinus integrates AKT1 and subapoptotic caspase activities to regulate basal autophagy. J Cell Biol. 2014. Oct 27;207(2):253–68. doi:10.1083/jcb.201404028. PubMed PMID: 25332163; PubMed Central PMCID: PMC4210446. PubMed DOI PMC

Nandi N, Tyra LK, Stenesen D, et al.Stress-induced Cdk5 activity enhances cytoprotective basal autophagy in Drosophila melanogaster by phosphorylating acinus at serine(437). eLife. 2017. Dec 11;6. doi:10.7554/eLife.30760. PubMed PMID: 29227247; PubMed Central PMCID: PMCPMC5760206. PubMed DOI PMC

Haberman AS, Akbar MA, Ray S, et al. Drosophila acinus encodes a novel regulator of endocytic and autophagic trafficking. Development. 2010. Jul;137(13):2157–66. doi:10.1242/dev.044230. PubMed PMID: 20504956; PubMed Central PMCID: PMC2882135. PubMed DOI PMC

Grevengoed TJ, Cooper DE, Young PA, et al. Loss of long-chain acyl-CoA synthetase isoform 1 impairs cardiac autophagy and mitochondrial structure through mechanistic target of rapamycin complex 1 activation. FASEB J. 2015. Nov;29(11):4641–53. doi:10.1096/fj.15-272732. PubMed PMID: 26220174; PubMed Central PMCID: PMCPMC4608904. PubMed DOI PMC

Yoshikawa Y, Ogawa M, Hain T, et al. Listeria monocytogenes ActA-mediated escape from autophagic recognition. Nat Cell Biol. 2009. Oct;11(10):1233–40. doi:10.1038/ncb1967. PubMed PMID: 19749745. PubMed DOI

Vekaria PH, Kumar A, Subramaniam D, et al. Functional cooperativity of p97 and histone deacetylase 6 in mediating DNA repair in mantle cell lymphoma cells. Leukemia. 2019. Jul;33(7):1675–1686. doi:10.1038/s41375-018-0355-y. PubMed PMID: 30664664; PubMed Central PMCID: PMCPMC6730676. PubMed DOI PMC

Till A, Lipinski S, Ellinghaus D, et al. Autophagy receptor CALCOCO2/NDP52 takes center stage in Crohn disease. Autophagy. 2013. Aug;9(8):1256–7. doi:10.4161/auto.25483. PubMed PMID: 23820297; PubMed Central PMCID: PMC3748200. PubMed DOI PMC

Chung SJ, Nagaraju GP, Nagalingam A, et al. ADIPOQ/adiponectin induces cytotoxic autophagy in breast cancer cells through STK11/LKB1-mediated activation of the AMPK-ULK1 axis. Autophagy. 2017. Aug 3;13(8):1386–1403. doi:10.1080/15548627.2017.1332565. PubMed PMID: 28696138; PubMed Central PMCID: PMCPMC5584870. PubMed DOI PMC

Braden CR, Neufeld TP.. Atg1-independent induction of autophagy by the Drosophila Ulk3 homolog, ADUK. FEBS J. 2016. Nov;283(21):3889–3897. doi:10.1111/febs.13906. PubMed PMID: 27717182; PubMed Central PMCID: PMCPMC5123689. PubMed DOI PMC

Eby KG, Rosenbluth JM, Mays DJ, et al. ISG20L1 is a p53 family target gene that modulates genotoxic stress-induced autophagy. Mol cancer 2010;9:95. doi: 1476-4598-9-95 [pii] doi:10.1186/1476-4598-9-95. PubMed PMID: 20429933; PubMed Central PMCID: PMC2873442. eng. PubMed DOI PMC

Kang R, Tang D, Livesey KM, et al. The Receptor for Advanced Glycation End-products (RAGE) protects pancreatic tumor cells against oxidative injury. Antioxid Redox Signal. 2011. Oct 15;15(8):2175–84. doi:10.1089/ars.2010.3378. PubMed PMID: 21126167; PubMed Central PMCID: PMC3166176. PubMed DOI PMC

Uchiki T, Weikel KA, Jiao W, et al. Glycation-altered proteolysis as a pathobiologic mechanism that links dietary glycemic index, aging, and age-related disease (in nondiabetics). Aging cell. 2012. Feb;11(1):1–13. doi:10.1111/j.1474-9726.2011.00752.x. PubMed PMID: 21967227; PubMed Central PMCID: PMCPMC3257376. PubMed DOI PMC

Johnston JA, Ward CL, Kopito RR.. Aggresomes: a cellular response to misfolded proteins. J Cell Biol. 1998. Dec 28;143(7):1883–98. PubMed PMID: 9864362; PubMed Central PMCID: PMC2175217. PubMed PMC

Kwon YT, Ciechanover A.. The ubiquitin code in the ubiquitin-proteasome system and autophagy. Trends Biochem Sci. 2017. Nov;42(11):873–886. doi:10.1016/j.tibs.2017.09.002. PubMed PMID: 28947091. PubMed DOI

Shen D, Coleman J, Chan E, et al. Novel cell- and tissue-based assays for detecting misfolded and aggregated protein accumulation within aggresomes and inclusion bodies. Cell Biochem Biophys. 2011. Jul;60(3):173–85. doi:10.1007/s12013-010-9138-4. PubMed PMID: 21132543; PubMed Central PMCID: PMCPMC3112480. PubMed DOI PMC

Viana R, Aguado C, Esteban I, et al. Role of AMP-activated protein kinase in autophagy and proteasome function. Biochem Biophys Res Commun. 2008. May 9;369(3):964–8. 10.1016/j.bbrc.2008.02.126. PubMed PMID: 18328803; eng. PubMed DOI

Pardossi-Piquard R, Petit A, Kawarai T, et al. Presenilin-dependent transcriptional control of the Abeta-degrading enzyme neprilysin by intracellular domains of betaAPP and APLP. Neuron. 2005. May 19;46(4):541–54. doi:10.1016/j.neuron.2005.04.008. PubMed PMID: 15944124. PubMed DOI

Goiran T, Duplan E, Chami M, et al. beta-amyloid precursor protein intracellular domain controls mitochondrial function by modulating phosphatase and tensin homolog-induced kinase 1 transcription in cells and in Alzheimer mice models. Biol Psychiatry. 2018. Mar 1;83(5):416–427. doi:10.1016/j.biopsych.2017.04.011. PubMed PMID: 28587718. PubMed DOI

Hadano S, Otomo A, Kunita R, et al. Loss of ALS2/Alsin exacerbates motor dysfunction in a SOD1-expressing mouse ALS model by disturbing endolysosomal trafficking. PLoS One. 2010;5(3):e9805. doi:10.1371/journal.pone.0009805. PubMed PMID: 20339559; PubMed Central PMCID: PMC2842444. PubMed DOI PMC

Otomo A, Kunita R, Suzuki-Utsunomiya K, et al. Defective relocalization of ALS2/alsin missense mutants to Rac1-induced macropinosomes accounts for loss of their cellular function and leads to disturbed amphisome formation. FEBS Lett. 2011. Mar 9;585(5):730–6. doi:10.1016/j.febslet.2011.01.045. PubMed PMID: 21300063. PubMed DOI

Antonioli M, Albiero F, Nazio F, et al. AMBRA1 interplay with cullin E3 ubiquitin ligases regulates autophagy dynamics. Dev Cell. 2014. Dec 22;31(6):734–46. doi:10.1016/j.devcel.2014.11.013. PubMed PMID: 25499913. PubMed DOI

Cianfanelli V, Fuoco C, Lorente M, et al. AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation. Nat Cell Biol. 2015. Jan;17(1):20–30. doi:10.1038/ncb3072. PubMed PMID: 25438055. PubMed DOI PMC

Fu M, St-Pierre P, Shankar J, et al. Regulation of mitophagy by the Gp78 E3 ubiquitin ligase. Mol Biol Cell. 2013. Apr;24(8):1153–62. doi:10.1091/mbc.E12-08-0607. PubMed PMID: 23427266; PubMed Central PMCID: PMC3623636. PubMed DOI PMC

Lee KY, Oh S, Choi YJ, et al. Activation of autophagy rescues amiodarone-induced apoptosis of lung epithelial cells and pulmonary toxicity in rats. Toxicol Sci. 2013. Nov;136(1):193–204. doi:10.1093/toxsci/kft168. PubMed PMID: 23912912. PubMed DOI

Mahavadi P, Knudsen L, Venkatesan S, et al. Regulation of macroautophagy in amiodarone-induced pulmonary fibrosis. J Pathol Clin Res. 2015. Oct;1(4):252–63. doi:10.1002/cjp2.20. PubMed PMID: 27499909; PubMed Central PMCID: PMCPMC4939895. PubMed DOI PMC

Lin CW, Chen YS, Lin CC, et al. Amiodarone as an autophagy promoter reduces liver injury and enhances liver regeneration and survival in mice after partial hepatectomy. Sci Rep. 2015. Oct 30;5:15807. doi:10.1038/srep15807. PubMed PMID: 26515640; PubMed Central PMCID: PMCPMC4626804. PubMed DOI PMC

Seglen PO, Berg TO, Blankson H, et al. Structural aspects of autophagy. Adv Exp Med Biol. 1996;389:103–11. PubMed PMID: 8860999; eng. PubMed

Meijer AJ, Codogno P.. AMP-activated protein kinase and autophagy. Autophagy. 2007. May-Jun;3(3):238–40. doi: 3710 [pii]. PubMed PMID: 17224623; eng. PubMed

Hutchins MU, Klionsky DJ.. Vacuolar localization of oligomeric alpha-mannosidase requires the cytoplasm to vacuole targeting and autophagy pathway components in Saccharomyces cerevisiae. J Biol Chem. 2001. Jun 8;276(23):20491–8. doi:10.1074/jbc.M101150200. PubMed PMID: 11264288; PubMed Central PMCID: PMCPMC2754691. PubMed DOI PMC

Katsiarimpa A, Anzenberger F, Schlager N, et al. The Arabidopsis deubiquitinating enzyme AMSH3 interacts with ESCRT-III subunits and regulates their localization. Plant Cell. 2011. Aug;23(8):3026–40. doi:10.1105/tpc.111.087254. PubMed PMID: 21810997; PubMed Central PMCID: PMC3180808. PubMed DOI PMC

Katsiarimpa A, Kalinowska K, Anzenberger F, et al. The deubiquitinating enzyme AMSH1 and the ESCRT-III subunit VPS2.1 are required for autophagic degradation in Arabidopsis. Plant Cell. 2013. Jun;25(6):2236–52. doi: 10.1105/tpc.113.113399. PubMed PMID: 23800962; PubMed Central PMCID: PMC3723623. PubMed DOI PMC

Freed EO, Gale M, Jr.. Antiviral innate immunity: editorial overview. J Mol Biol. 2014. Mar 20;426(6):1129–32. doi:10.1016/j.jmb.2014.01.005. PubMed PMID: 24462565; PubMed Central PMCID: PMCPMC6943832. PubMed DOI PMC

Ke PY, Chen SS.. Activation of the unfolded protein response and autophagy after hepatitis C virus infection suppresses innate antiviral immunity in vitro. J Clin Invest. 2011. Jan 4;121(1):37–56. doi:10.1172/JCI41474. PubMed PMID: 21135505; PubMed Central PMCID: PMC3007134. eng. PubMed DOI PMC

Shrivastava S, Raychoudhuri A, Steele R, et al. Knockdown of autophagy enhances the innate immune response in hepatitis C virus-infected hepatocytes. Hepatology. 2011. Feb;53(2):406–14. doi:10.1002/hep.24073. PubMed PMID: 21274862; eng. PubMed DOI PMC

Kononenko NL, Classen GA, Kuijpers M, et al. Retrograde transport of TrkB-containing auto-phagosomes via the adaptor AP-2 mediates neuronal complexity and prevents neurodegeneration. Nat Commun. 2017. Apr 7;8:14819. doi:10.1038/ncomms14819. PubMed PMID: 28387218; PubMed Central PMCID: PMCPMC5385568. PubMed DOI PMC

Verkerk AJ, Schot R, Dumee B, et al. Mutation in the AP4M1 gene provides a model for neuroaxonal injury in cerebral palsy. Am J Hum Genet. 2009. Jul;85(1):40–52. doi:10.1016/j.ajhg.2009.06.004. PubMed PMID: 19559397; PubMed Central PMCID: PMCPMC2706965. PubMed DOI PMC

Moreno-De-Luca A, Helmers SL, Mao H, et al. Adaptor protein complex-4 (AP-4) deficiency causes a novel autosomal recessive cerebral palsy syndrome with microcephaly and intellectual disability. J Med Genet. 2011. Feb;48(2):141–4. doi:10.1136/jmg.2010.082263. PubMed PMID: 20972249; PubMed Central PMCID: PMCPMC3150730. PubMed DOI PMC

Abou Jamra R, Philippe O, Raas-Rothschild A, et al. Adaptor protein complex 4 deficiency causes severe autosomal-recessive intellectual disability, progressive spastic paraplegia, shy character, and short stature. Am J Hum Genet. 2011. Jun 10;88(6):788–795. doi:10.1016/j.ajhg.2011.04.019. PubMed PMID: 21620353; PubMed Central PMCID: PMCPMC3113253. PubMed DOI PMC

Mattera R, Park SY, De Pace R, et al. AP-4 mediates export of ATG9A from the trans-Golgi network to promote autophagosome formation. Proc Natl Acad Sci U S A. 2017. Dec 12;114(50):E10697–E10706. doi:10.1073/pnas.1717327114. PubMed PMID: 29180427; PubMed Central PMCID: PMCPMC5740629. PubMed DOI PMC

Ivankovic D, Drew J, Lesept F, et al. Axonal autophagosome maturation defect through failure of ATG9A sorting underpins pathology in AP-4 deficiency syndrome. Autophagy. 2020. Mar;16(3):391–407. doi:10.1080/15548627.2019.1615302. PubMed PMID: 31142229. PubMed DOI PMC

Slabicki M, Theis M, Krastev DB, et al. A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. PLoS Biol. 2010. Jun 29;8(6):e1000408. doi:10.1371/journal.pbio.1000408. PubMed PMID: 20613862; PubMed Central PMCID: PMCPMC2893954. PubMed DOI PMC

Hirst J, Itzhak DN, Antrobus R, et al. Role of the AP-5 adaptor protein complex in late endosome-to-Golgi retrieval. PLoS Biol. 2018. Jan;16(1):e2004411. doi:10.1371/journal.pbio.2004411. PubMed PMID: 29381698; PubMed Central PMCID: PMCPMC5806898. PubMed DOI PMC

Khundadze M, Ribaudo F, Hussain A, et al. A mouse model for SPG48 reveals a block of autophagic flux upon disruption of adaptor protein complex five. Neurobiol Dis. 2019. Jul;127:419–431. doi:10.1016/j.nbd.2019.03.026. PubMed PMID: 30930081. PubMed DOI

Costa R, Morrison A, Wang J, et al. Activated protein C modulates cardiac metabolism and augments autophagy in the ischemic heart. J Thromb Haemost. 2012. Sep;10(9):1736–44. doi:10.1111/j.1538-7836.2012.04833.x. PubMed PMID: 22738025; PubMed Central PMCID: PMC3433592. PubMed DOI PMC

Yuga M, Gomi K, Klionsky DJ, et al. Aspartyl aminopeptidase is imported from the cytoplasm to the vacuole by selective autophagy in Saccharomyces cerevisiae. J Biol Chem. 2011. Apr 15;286(15):13704–13. doi:10.1074/jbc.M110.173906. PubMed PMID: 21343297; PubMed Central PMCID: PMC3075714. PubMed DOI PMC

Besteiro S. Autophagy in apicomplexan parasites. Curr Opin Microbiol. 2017. Dec;40:14–20. doi:10.1016/j.mib.2017.10.008. PubMed PMID: 29096193. PubMed DOI

Deretic V, Levine B.. Autophagy, immunity, and microbial adaptations. Cell Host Microbe. 2009. Jun 18;5(6):527–49. doi:10.1016/j.chom.2009.05.016. PubMed PMID: 19527881; PubMed Central PMCID: PMCPMC2720763. PubMed DOI PMC

Thekkinghat AA, Yadav KK, Rangarajan PN.. Apolipoprotein L9 interacts with LC3/GABARAP and is a microtubule-associated protein with a widespread subcellular distribution. Biol Open. 2019;8(9):bio045930. 10.1101/671065. PubMed PMID: 31515254; PubMed Central PMCID: PMCPMC6777357. PubMed DOI PMC

Rubinstein AD, Kimchi A.. Life in the balance - a mechanistic view of the crosstalk between autophagy and apoptosis. J Cell Sci. 2012. Nov 15;125(Pt 22):5259–68. doi:10.1242/jcs.115865. PubMed PMID: 23377657. PubMed DOI

Yang S, Rosenwald AG.. Autophagy in Saccharomyces cerevisiae requires the monomeric GTP-binding proteins, Arl1 and Ypt6. Autophagy. 2016. Oct 2;12(10):1721–1737. doi:10.1080/15548627.2016.1196316. PubMed PMID: 27462928; PubMed Central PMCID: PMCPMC5079543. PubMed DOI PMC

Wang P, Xu TY, Wei K, et al.ARRB1/beta-arrestin-1 mediates neuroprotection through coordination of BECN1-dependent autophagy in cerebral ischemia. Autophagy. 2014. Jun25;10(9):1535–48. PubMed PMID: 24988431. PubMed PMC

Villa E, Proics E, Rubio-Patino C, et al. Parkin-Independent Mitophagy Controls Chemotherapeutic Response in Cancer Cells. Cell Rep. 2017. Sep 19;20(12):2846–2859. doi:10.1016/j.celrep.2017.08.087. PubMed PMID: 28930681. PubMed DOI

Boda A, Lorincz P, Takats S, et al. Drosophila Arl8 is a general positive regulator of lysosomal fusion events. Biochim Biophys Acta Mol Cell Res. 2019. Apr;1866(4):533–544. doi:10.1016/j.bbamcr.2018.12.011. PubMed PMID: 30590083. PubMed DOI

Moosavi MA, Djavaheri-Mergny M.. Autophagy: New Insights into Mechanisms of Action and Resistance of Treatment in Acute Promyelocytic leukemia. Int J Mol Sci. 2019. Jul 20;20(14). doi:10.3390/ijms20143559. PubMed PMID: 31330838; PubMed Central PMCID: PMCPMC6678259. PubMed DOI PMC

Keller KE, Yang YF, Sun YY, et al. Ankyrin repeat and suppressor of cytokine signaling box containing protein-10 is associated with ubiquitin-mediated degradation pathways in trabecular meshwork cells. Mol Vis. 2013;19:1639–55. PubMed PMID: 23901248; PubMed Central PMCID: PMC3724959. PubMed PMC

Meyer N, Zielke S, Michaelis JB, et al. AT 101 induces early mitochondrial dysfunction and HMOX1 (heme oxygenase 1) to trigger mitophagic cell death in glioma cells. Autophagy. 2018;14(10):1693–1709. doi:10.1080/15548627.2018.1476812. PubMed PMID: 29938581; PubMed Central PMCID: PMCPMC6135628. PubMed DOI PMC

Warnsmann V, Meyer N, Hamann A, et al. A novel role of the mitochondrial permeability transition pore in (-)-gossypol-induced mitochondrial dysfunction. Mech Ageing Dev. 2018. Mar;170:45–58. doi:10.1016/j.mad.2017.06.004. PubMed PMID: 28684269. PubMed DOI

Wang P, Pleskot R, Zang J, et al. Plant AtEH/Pan1 proteins drive autophagosome formation at ER-PM contact sites with actin and endocytic machinery. Nat Commun. 2019. Nov 13;10(1):5132. doi:10.1038/s41467-019-12782-6. PubMed PMID: 31723129; PubMed Central PMCID: PMCPMC6853982. PubMed DOI PMC

Harding HP, Novoa I, Zhang Y, et al. Regulated translation initiation controls stress-induced gene expression in mammalian cells. Mol Cell. 2000. Nov;6(5):1099–108. doi:10.1016/s1097-2765(00)00108-8. PubMed PMID: 11106749. PubMed DOI

Gully JC, Sergeyev VG, Bhootada Y, et al. Up-regulation of activating transcription factor 4 induces severe loss of dopamine nigral neurons in a rat model of Parkinson’s disease. Neurosci Lett. 2016. Aug 3;627:36–41. doi:10.1016/j.neulet.2016.05.039. PubMed PMID: 27233218; PubMed Central PMCID: PMCPMC6052763. PubMed DOI PMC

Bhootada Y, Kotla P, Zolotukhin S, et al. Limited ATF4 expression in degenerating retinas with ongoing ER stress promotes photoreceptor survival in a mouse model of autosomal dominant retinitis pigmentosa. PLoS One. 2016;11(5):e0154779. doi:10.1371/journal.pone.0154779. PubMed PMID: 27144303; PubMed Central PMCID: PMCPMC4856272. PubMed DOI PMC

Rzymski T, Milani M, Pike L, et al. Regulation of autophagy by ATF4 in response to severe hypoxia. Oncogene. 2010. Aug 5;29(31):4424–35. doi:10.1038/onc.2010.191. PubMed PMID: 20514020. PubMed DOI

Sheng Z, Ma L, Sun JE, et al. BCR-ABL suppresses autophagy through ATF5-mediated regulation of mTOR transcription. Blood. 2011. Sep 8;118(10):2840–8. doi:10.1182/blood-2010-12-322537. PubMed PMID: 21715304; PubMed Central PMCID: PMC3172800. PubMed DOI PMC

Klionsky DJ, Cregg JM, Dunn WA, Jr., et al. A unified nomenclature for yeast autophagy-related genes. Dev cell 2003. Oct;5(4):539–45. PubMed PMID: 14536056. PubMed

Matsuura A, Tsukada M, Wada Y, et al. Apg1p, a novel protein kinase required for the autophagic process in Saccharomyces cerevisiae. Gene. 1997. Jun 19;192(2):245–50. doi:S0378-1119(97)00084-X [pii]. PubMed PMID: 9224897; eng. PubMed

Romanyuk D, Polak A, Maleszewska A, et al. Human hAtg2A protein expressed in yeast is recruited to preautophagosomal structure but does not complement autophagy defects of atg2Delta strain. Acta Biochim Pol. 2011;58(3):365–74. PubMed PMID: 21887408. PubMed

Kaminska J, Rzepnikowska W, Polak A, et al. Phosphatidylinositol-3-phosphate regulates response of cells to proteotoxic stress. Int J Biochem Cell Biol. 2016. Oct;79:494–504. doi:10.1016/j.biocel.2016.08.007. PubMed PMID: 27498190. PubMed DOI

Shintani T, Suzuki K, Kamada Y, et al.Apg2p functions in autophagosome formation on the perivacuolar structure. J Biol Chem. 2001. Aug 10;276(32):30452–60. doi:10.1074/jbc.M102346200M102346200 [pii].PubMed PMID: 11382761; eng. PubMed DOI

Gomez-Sanchez R, Rose J, Guimaraes R, et al. Atg9 establishes Atg2-dependent contact sites between the endoplasmic reticulum and phagophores. J Cell Biol. 2018. Aug 6;217(8):2743–2763. doi:10.1083/jcb.201710116. PubMed PMID: 29848619; PubMed Central PMCID: PMCPMC6080931. PubMed DOI PMC

Maeda S, Otomo C, Otomo T.. The autophagic membrane tether ATG2A transfers lipids between membranes. eLife. 2019. Jul 4;8. doi:10.7554/eLife.45777. PubMed PMID: 31271352; PubMed Central PMCID: PMCPMC6625793. PubMed DOI PMC

Osawa T, Kotani T, Kawaoka T, et al. Atg2 mediates direct lipid transfer between membranes for autophagosome formation. Nat Struct Mol Biol. 2019. Apr;26(4):281–288. doi:10.1038/s41594-019-0203-4. PubMed PMID: 30911189. PubMed DOI

Valverde DP, Yu S, Boggavarapu V, et al. ATG2 transports lipids to promote autophagosome biogenesis. J Cell Biol. 2019. Jun 3;218(6):1787–1798. doi:10.1083/jcb.201811139. PubMed PMID: 30952800; PubMed Central PMCID: PMCPMC6548141. PubMed DOI PMC

Kotani T, Kirisako H, Koizumi M, et al. The Atg2-Atg18 complex tethers pre-autophagosomal membranes to the endoplasmic reticulum for autophagosome formation. Proc Natl Acad Sci U S A. 2018. Oct 9;115(41):10363–10368. doi:10.1073/pnas.1806727115. PubMed PMID: 30254161; PubMed Central PMCID: PMCPMC6187169. PubMed DOI PMC

Ichimura Y, Kirisako T, Takao T, et al. A ubiquitin-like system mediates protein lipidation. Nature. 2000. Nov 23;408(6811):488–92. doi:10.1038/35044114. PubMed PMID: 11100732; eng. PubMed DOI

Schlumpberger M, Schaeffeler E, Straub M, et al. AUT1, a gene essential for autophagocytosis in the yeast Saccharomyces cerevisiae. J Bacteriol. 1997. Feb;179(4):1068–76. PubMed PMID: 9023185; PubMed Central PMCID: PMC178799. eng. PubMed PMC

Fernandez AF, Lopez-Otin C.. The functional and pathologic relevance of autophagy proteases. J Clin Invest. 2015. Jan;125(1):33–41. doi:10.1172/JCI73940. PubMed PMID: 25654548; PubMed Central PMCID: PMCPMC4382236. PubMed DOI PMC

Tanida I, Sou YS, Minematsu-Ikeguchi N, et al. Atg8L/Apg8L is the fourth mammalian modifier of mammalian Atg8 conjugation mediated by human Atg4B, Atg7 and Atg3. FEBS J. 2006. Jun;273(11):2553–62. doi:10.1111/j.1742-4658.2006.05260.x. PubMed PMID: 16704426; eng. PubMed DOI

Mizushima N, Noda T, Yoshimori T, et al. A protein conjugation system essential for autophagy. Nature. 1998. Sep 24;395(6700):395–8. doi:10.1038/26506. PubMed PMID: 9759731; eng. PubMed DOI

Kim J, Dalton VM, Eggerton KP, et al. Apg7p/Cvt2p is required for the cytoplasm-to-vacuole targeting, macroautophagy, and peroxisome degradation pathways. Mol Biol Cell. 1999. May;10(5):1337–51. PubMed PMID: 10233148; PubMed Central PMCID: PMC25275. eng. PubMed PMC

Tanida I, Mizushima N, Kiyooka M, et al. Apg7p/Cvt2p: A novel protein-activating enzyme essential for autophagy. Mol Biol Cell. 1999. May;10(5):1367–79. PubMed PMID: 10233150; PubMed Central PMCID: PMC25280. eng. PubMed PMC

Ogmundsdottir MH, Fock V, Sooman L, et al. A short isoform of ATG7 fails to lipidate LC3/GABARAP. Sci Rep. 2018. Sep 26;8(1):14391. doi:10.1038/s41598-018-32694-7. PubMed PMID: 30258106; PubMed Central PMCID: PMCPMC6158294. PubMed DOI PMC

Knorr RL, Nakatogawa H, Ohsumi Y, et al. Membrane morphology is actively transformed by covalent binding of the protein Atg8 to PE-lipids. PLoS One. 2014;9(12):e115357. doi:10.1371/journal.pone.0115357. PubMed PMID: 25522362; PubMed Central PMCID: PMCPMC4270758. PubMed DOI PMC

Noda T, Kim J, Huang W-P, et al. Apg9p/Cvt7p is an integral membrane protein required for transport vesicle formation in the Cvt and autophagy pathways. J Cell Biol. 2000. Feb 7;148(3):465–80. PubMed PMID: 10662773; PubMed Central PMCID: PMC2174799. eng. PubMed PMC

Saitoh T, Fujita N, Hayashi T, et al. Atg9a controls dsDNA-driven dynamic translocation of STING and the innate immune response. Proc Natl Acad Sci U S A. 2009. Dec 8;106(49):20842–6. doi:10.1073/pnas.0911267106. PubMed PMID: 19926846; PubMed Central PMCID: PMCPMC2791563. PubMed DOI PMC

Imagawa Y, Saitoh T, Tsujimoto Y.. Vital staining for cell death identifies Atg9a-dependent necrosis in developmental bone formation in mouse. Nat Commun. 2016. Nov 4;7:13391. doi:10.1038/ncomms13391. PubMed PMID: 27811852; PubMed Central PMCID: PMCPMC5097171. PubMed DOI PMC

Yamada T, Carson AR, Caniggia I, et al. Endothelial nitric-oxide synthase antisense (NOS3AS) gene encodes an autophagy-related protein (APG9-like2) highly expressed in trophoblast. J Biol Chem. 2005. May 6;280(18):18283–90. doi:10.1074/jbc.M413957200. PubMed PMID: 15755735; eng. PubMed DOI

Shintani T, Mizushima N, Ogawa Y, et al. Apg10p, a novel protein-conjugating enzyme essential for autophagy in yeast. EMBO J. 1999. Oct 1;18(19):5234–41. doi:10.1093/emboj/18.19.5234. PubMed PMID: 10508157; PubMed Central PMCID: PMC1171594. eng. PubMed DOI PMC

Zhao Q, Hu ZY, Zhang JP, et al. Dual Roles of Two Isoforms of Autophagy-related Gene ATG10 in HCV-Subgenomic replicon Mediated Autophagy Flux and Innate Immunity. Sci Rep. 2017. Sep 12;7(1):11250. doi:10.1038/s41598-017-11105-3. PubMed PMID: 28900156; PubMed Central PMCID: PMCPMC5595887. PubMed DOI PMC

Zhang MQ, Li JR, Peng ZG, et al. Differential effects of autophagy-related 10 protein on hcv replication and autophagy flux are mediated by its cysteine(44) and cysteine(135). Front Immunol. 2018;9:2176. doi:10.3389/fimmu.2018.02176. PubMed PMID: 30319633; PubMed Central PMCID: PMCPMC6165859. PubMed DOI PMC

Kim J, Kamada Y, Stromhaug PE, et al. Cvt9/Gsa9 functions in sequestering selective cytosolic cargo destined for the vacuole. J Cell Biol. 2001. Apr16;153(2):381–96. PubMed PMID: 11309418. PubMed PMC

Kamber RA, Shoemaker CJ, Denic V.. Receptor-bound targets of selective autophagy use a scaffold protein to activate the Atg1 kinase. Mol Cell. 2015. Aug 6;59(3):372–81. doi:10.1016/j.molcel.2015.06.009. PubMed PMID: 26166702. PubMed DOI PMC

Li F, Chung T, Vierstra RD.. AUTOPHAGY-RELATED11 plays a critical role in general autophagy- and senescence-induced mitophagy in Arabidopsis. Plant Cell. 2014. Feb;26(2):788–807. doi:10.1105/tpc.113.120014. PubMed PMID: 24563201; PubMed Central PMCID: PMCPMC3967041. PubMed DOI PMC

Turco E, Witt M, Abert C, et al. FIP200 claw domain binding to p62 promotes autophagosome formation at ubiquitin condensates. Mol Cell. 2019. Apr 18;74(2):330–346 e11. doi:10.1016/j.molcel.2019.01.035. PubMed PMID: 30853400; PubMed Central PMCID: PMCPMC6477179. PubMed DOI PMC

Lin L, Yang P, Huang X, et al. The scaffold protein EPG-7 links cargo-receptor complexes with the autophagic assembly machinery. J Cell Biol. 2013. Apr 1;201(1):113–29. doi:10.1083/jcb.201209098. PubMed PMID: 23530068; PubMed Central PMCID: PMC3613692. PubMed DOI PMC

Ochaba J, Lukacsovich T, Csikos G, et al. Potential function for the Huntingtin protein as a scaffold for selective autophagy. Proc Natl Acad Sci U S A. 2014. Nov 25;111(47):16889–94. doi:10.1073/pnas.1420103111. PubMed PMID: 25385587; PubMed Central PMCID: PMCPMC4250109. PubMed DOI PMC

Funakoshi T, Matsuura A, Noda T, et al. Analyses of APG13 gene involved in autophagy in yeast, Saccharomyces cerevisiae. Gene. 1997. Jun 19;192(2):207–13. doi:10.1016/s0378-1119(97)00031-0 [pii]. PubMed PMID: 9224892; eng. PubMed DOI

Kametaka S, Okano T, Ohsumi M, et al. Apg14p and Apg6/Vps30p form a protein complex essential for autophagy in the yeast, Saccharomyces cerevisiae. J Biol Chem 1998. Aug 28;273(35):22284–91. PubMed PMID: 9712845; eng. PubMed

Mukhopadhyay S, Schlaepfer IR, Bergman BC, et al. ATG14 facilitated lipophagy in cancer cells induce ER stress mediated mitoptosis through a ROS dependent pathway. Free Radical biol Med. 2017. Mar;104:199–213. doi:10.1016/j.freeradbiomed.2017.01.007. PubMed PMID: 28069524. PubMed DOI

Yang P, Zhang H.. The coiled-coil domain protein EPG-8 plays an essential role in the autophagy pathway in C. elegans. Autophagy. 2011. Feb;7(2):159–65. PubMed PMID: 21116129. PubMed

Epple UD, Suriapranata I, Eskelinen E-L, et al. Aut5/Cvt17p, a putative lipase essential for disintegration of autophagic bodies inside the vacuole. J Bacteriol. 2001. Oct;183(20):5942–55. doi:10.1128/JB.183.20.5942-5955.2001. PubMed PMID: 11566994; PubMed Central PMCID: PMC99673. eng. PubMed DOI PMC

Teter SA, Eggerton KP, Scott SV, et al. Degradation of lipid vesicles in the yeast vacuole requires function of Cvt17, a putative lipase. J Biol Chem. 2001. Jan 19;276(3):2083–7. doi:10.1074/jbc.C000739200C000739200 [pii]. PubMed PMID: 11085977; PubMed Central PMCID: PMC2749705. eng. PubMed DOI PMC

van Zutphen T, Todde V, de Boer R, et al. Lipid droplet autophagy in the yeast Saccharomyces cerevisiae. Mol Biol Cell. 2014. Jan;25(2):290–301. doi:10.1091/mbc.E13-08-0448. PubMed PMID: 24258026; PubMed Central PMCID: PMC3890349. PubMed DOI PMC

Mizushima N, Noda T, Ohsumi Y. Apg16p is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway. EMBO J. 1999. Jul 15;18(14):3888–96. doi:10.1093/emboj/18.14.3888. PubMed PMID: 10406794; PubMed Central PMCID: PMC1171465. eng. PubMed DOI PMC

Massey DC, Parkes M.. Genome-wide association scanning highlights two autophagy genes, ATG16L1 and IRGM, as being significantly associated with Crohn’s disease. Autophagy. 2007. Nov-Dec;3(6):649–51. doi: 5075 [pii]. PubMed PMID: 17921695; eng. PubMed

Yang SK, Hong M, Zhao W, et al. Genome-wide association study of Crohn’s disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations. Gut. 2014. Jan;63(1):80–7. doi:10.1136/gutjnl-2013-305193. PubMed PMID: 23850713. PubMed DOI

Chew LH, Setiaputra D, Klionsky DJ, et al. Structural characterization of the Saccharomyces cerevisiae autophagy regulatory complex Atg17-Atg31-Atg29. Autophagy. 2013. Oct;9(10):1467–74. doi:10.4161/auto.25687. PubMed PMID: 23939028. PubMed DOI PMC

Mao K, Chew LH, Inoue-Aono Y, et al. Atg29 phosphorylation regulates coordination of the Atg17-Atg31-Atg29 complex with the Atg11 scaffold during autophagy initiation. Proc Natl Acad Sci U S A. 2013. Jul 30;110(31):E2875–84. doi:10.1073/pnas.1300064110. PubMed PMID: 23858448; PubMed Central PMCID: PMC3732952. PubMed DOI PMC

Mao K, Chew LH, Yip CK, et al. The role of Atg29 phosphorylation in PAS assembly. Autophagy. 2013. Dec;9(12):2178–9. doi:10.4161/auto.26740. PubMed PMID: 24141181; PubMed Central PMCID: PMC4028347. PubMed DOI PMC

Leber R, Silles E, Sandoval IV, et al.Yol082p, a novel CVT protein involved in the selective targeting of aminopeptidase I to the yeast vacuole. J Biol Chem. 2001. Aug 3;276(31):29210–7. doi:10.1074/jbc.M101438200 M101438200 [pii]. PubMed PMID: 11382752; eng. PubMed DOI

Scott SV, Guan J, Hutchins MU, et al. Cvt19 is a receptor for the cytoplasm-to-vacuole targeting pathway. Mol Cell. 2001. Jun;7(6):1131–41. doi: S1097-2765(01)00263-5 [pii]. PubMed PMID: 11430817; PubMed Central PMCID: PMC2767243. eng. PubMed PMC

Nice DC, Sato TK, Stromhaug PE, et al. Cooperative binding of the cytoplasm to vacuole targeting pathway proteins, Cvt13 and Cvt20, to phosphatidylinositol 3-phosphate at the pre-autophagosomal structure is required for selective autophagy. J Biol Chem. 2002. Aug 16;277(33):30198–207. doi:10.1074/jbc.M204736200 M204736200 [pii]. PubMed PMID: 12048214; PubMed Central PMCID: PMC2754692. eng. PubMed DOI PMC

Popelka H, Damasio A, Hinshaw JE, et al. Structure and function of yeast Atg20, a sorting nexin that facilitates autophagy induction. Proc Natl Acad Sci U S A. 2017. Nov 21;114(47):E10112–E10121. doi:10.1073/pnas.1708367114. PubMed PMID: 29114050; PubMed Central PMCID: PMCPMC5703286. PubMed DOI PMC

Suriapranata I, Epple UD, Bernreuther D, et al. The breakdown of autophagic vesicles inside the vacuole depends on Aut4p. J Cell Sci. 2000. Nov;113:4025–33. PubMed PMID: 11058089; eng. PubMed

Yang Z, Huang J, Geng J, et al. Atg22 recycles amino acids to link the degradative and recycling functions of autophagy. Mol Biol Cell. 2006. Dec;17(12):5094–104. doi:E06-06-0479 [pii] doi:10.1091/mbc.E06-06-0479. PubMed PMID: 17021250; PubMed Central PMCID: PMC1679675. eng. PubMed DOI PMC

Legakis JE, Yen W-L, Klionsky DJ.. A cycling protein complex required for selective autophagy. Autophagy. 2007. Sep-Oct;3(5):422–32. doi: 4129 [pii]. PubMed PMID: 17426440; eng. PubMed

Tucker KA, Reggiori F, Dunn WA, Jr., et al. Atg23 is essential for the cytoplasm to vacuole targeting pathway and efficient autophagy but not pexophagy. J Biol Chem. 2003. Nov 28;278(48):48445–52. doi:10.1074/jbc.M309238200 M309238200 [pii]. PubMed PMID: 14504273; PubMed Central PMCID: PMC1705954. eng. PubMed DOI PMC

Yamamoto H, Kakuta S, Watanabe TM, et al. Atg9 vesicles are an important membrane source during early steps of autophagosome formation. J Cell Biol. 2012. Jul 23;198(2):219–33. doi:10.1083/jcb.201202061. PubMed PMID: 22826123; PubMed Central PMCID: PMCPMC3410421. PubMed DOI PMC

Backues SK, Orban DP, Bernard A, et al. Atg23 and Atg27 act at the early stages of Atg9 trafficking in S. cerevisiae. Traffic. 2015. Feb;16(2):172–90. doi:10.1111/tra.12240. PubMed PMID: 25385507; PubMed Central PMCID: PMCPMC4305007. PubMed DOI PMC

Monastyrska I, Kiel JAKW, Krikken AM, et al. The Hansenula polymorpha ATG25 gene encodes a novel coiled-coil protein that is required for macropexophagy. Autophagy. 2005. Jul;1(2):92–100. PubMed PMID: 16874036. PubMed

Cao Y, Klionsky DJ.. Atg26 is not involved in autophagy-related pathways in Saccharomyces cerevisiae. Autophagy. 2007. Jan 7;3(1):17–20. PubMed PMID: 17012830. PubMed

Yamashita S, Oku M, Wasada Y, et al.PI4P-signaling pathway for the synthesis of a nascent membrane structure in selective autophagy. J Cell Biol 2006. Jun5;173(5):709–17. PubMed PMID: 16754956. PubMed PMC

Yen W-L, Legakis JE, Nair U, et al. Atg27 is required for autophagy-dependent cycling of Atg9. Mol Biol Cell. 2007. Feb;18(2):581–93. doi:E06-07-0612[pii] 10.1091/mbc.E06-07-0612. PubMed PMID: 17135291; PubMed Central PMCID: PMC1783788. eng. PubMed DOI PMC

Stasyk OV, Stasyk OG, Mathewson RD, et al. Atg28, a novel coiled-coil protein involved in autophagic degradation of peroxisomes in the methylotrophic yeast Pichia pastoris. Autophagy. 2006. Jan-Mar;2(1):30–8. PubMed PMID: 16874081. PubMed

Kawamata T, Kamada Y, Suzuki K, et al. Characterization of a novel autophagy-specific gene, ATG29. Biochem Biophys Res Commun. 2005. Dec 30;338(4):1884–9. doi:S0006-291X(05)02441-1 [pii] doi:10.1016/j.bbrc.2005.10.163. PubMed PMID: 16289106; eng. PubMed DOI

Zientara-Rytter K, Ozeki K, Nazarko TY, et al. Pex3 and Atg37 compete to regulate the interaction between the pexophagy receptor, Atg30, and the Hrr25 kinase. Autophagy. 2018;14(3):368–384. doi:10.1080/15548627.2017.1413521. PubMed PMID: 29260977; PubMed Central PMCID: PMCPMC5915033. PubMed DOI PMC

Farre JC, Burkenroad A, Burnett SF, et al. Phosphorylation of mitophagy and pexophagy receptors coordinates their interaction with Atg8 and Atg11. EMBO Rep. 2013. May;14(5):441–9. doi:10.1038/embor.2013.40. PubMed PMID: 23559066; PubMed Central PMCID: PMCPMC3642380. PubMed DOI PMC

Kabeya Y, Kawamata T, Suzuki K, et al. Cis1/Atg31 is required for autophagosome formation in Saccharomyces cerevisiae. Biochem Biophys Res Commun. 2007. May 4;356(2):405–10. doi: S0006-291X(07)00437-8 [pii] doi:10.1016/j.bbrc.2007.02.150. PubMed PMID: 17362880; eng. PubMed DOI

Watanabe Y, Noda NN, Kumeta H, et al. Selective transport of alpha-mannosidase by autophagic pathways: structural basis for cargo recognition by Atg19 and Atg34. J Biol Chem. 2010. Sep 24;285(39):30026–33. doi:10.1074/jbc.M110.143545. PubMed PMID: 20659891; PubMed Central PMCID: PMC2943322. PubMed DOI PMC

Meijer WH, van der Klei IJ, Veenhuis M, et al. ATG genes involved in non-selective autophagy are conserved from yeast to man, but the selective Cvt and pexophagy pathways also require organism-specific genes. Autophagy. 2007;3:106–16. PubMed

Nazarko VY, Nazarko TY, Farre JC, et al. Atg35, a micropexophagy-specific protein that regulates micropexophagic apparatus formation in Pichia pastoris. Autophagy. 2011. Apr;7(4):375–85. doi:10.4161/auto.7.4.14369. PubMed PMID: 21169734; PubMed Central PMCID: PMCPMC3127218. PubMed DOI PMC

Motley AM, Nuttall JM, Hettema EH.. Pex3-anchored Atg36 tags peroxisomes for degradation in Saccharomyces cerevisiae. EMBO J. 2012. Jun 29;31(13):2852–68. doi:10.1038/emboj.2012.151. PubMed PMID: 22643220; PubMed Central PMCID: PMC3395097. PubMed DOI PMC

Araki Y, Ku WC, Akioka M, et al. Atg38 is required for autophagy-specific phosphatidylinositol 3-kinase complex integrity. J Cell Biol. 2013. Oct 28;203(2):299–313. doi:10.1083/jcb.201304123. PubMed PMID: 24165940; PubMed Central PMCID: PMC3812978. PubMed DOI PMC

Yao Z, Delorme-Axford E, Backues SK, et al. Atg41/Icy2 regulates autophagosome formation. Autophagy. 2015;11(12):2288–99. doi:10.1080/15548627.2015.1107692. PubMed PMID: 26565778; PubMed Central PMCID: PMCPMC4835205. PubMed DOI PMC

Parzych KR, Ariosa A, Mari M, et al. A newly characterized vacuolar serine carboxypeptidase, Atg42/Ybr139w, is required for normal vacuole function and the terminal steps of autophagy in the yeast Saccharomyces cerevisiae. Mol Biol Cell. 2018. May 1;29(9):1089–1099. doi:10.1091/mbc.E17-08-0516. PubMed PMID: 29514932; PubMed Central PMCID: PMCPMC5921575. PubMed DOI PMC

Hosokawa N, Sasaki T, Iemura S, et al. Atg101, a novel mammalian autophagy protein interacting with Atg13. Autophagy. 2009. Oct;5(7):973–9. doi: 9296 [pii]. PubMed PMID: 19597335; eng. PubMed

Mercer CA, Kaliappan A, Dennis PB.. A novel, human Atg13 binding protein, Atg101, interacts with ULK1 and is essential for macroautophagy. Autophagy. 2009. Jul;5(5):649–62. doi: 8249 [pii]. PubMed PMID: 19287211; eng. PubMed

Cerk IK, Salzburger B, Boeszoermenyi A, et al. A peptide derived from G0/G1 switch gene 2 acts as noncompetitive inhibitor of adipose triglyceride lipase. J Biol Chem. 2014. Nov 21;289(47):32559–70. doi:10.1074/jbc.M114.602599. PubMed PMID: 25258314; PubMed Central PMCID: PMCPMC4239610. PubMed DOI PMC

Honig A, Avin-Wittenberg T, Ufaz S, et al. A new type of compartment, defined by plant-specific Atg8-interacting proteins, is induced upon exposure of Arabidopsis plants to carbon starvation. Plant Cell. 2012. Jan;24(1):288–303. doi:10.1105/tpc.111.093112. PubMed PMID: 22253227; PubMed Central PMCID: PMC3289568. PubMed DOI PMC

Michaeli S, Clavel M, Lechner E, et al. The viral F-box protein P0 induces an ER-derived autophagy degradation pathway for the clearance of membrane-bound AGO1. Proc Natl Acad Sci U S A. 2019. Nov 5;116(45):22872–22883. doi:10.1073/pnas.1912222116. PubMed PMID: 31628252; PubMed Central PMCID: PMCPMC6842623. PubMed DOI PMC

Sjogaard IMZ, Bressendorff S, Prestel A, et al. The transmembrane autophagy cargo receptors ATI1 and ATI2 interact with ATG8 through intrinsically disordered regions with distinct biophysical properties. Biochem J. 2019. Feb 5;476(3):449–465. doi:10.1042/BCJ20180748. PubMed PMID: 30642888. PubMed DOI

Kastan MB, Bartek J.. Cell-cycle checkpoints and cancer. Nature. 2004. Nov 18;432(7015):316–23. doi:10.1038/nature03097. PubMed PMID: 15549093. PubMed DOI

Antonelli M, Strappazzon F, Arisi I, et al. ATM kinase sustains breast cancer stem-like cells by promoting ATG4C expression and autophagy. Oncotarget. 2017. Mar 28;8(13):21692–21709. doi:10.18632/oncotarget.15537. PubMed PMID: 28423511; PubMed Central PMCID: PMCPMC5400616. PubMed DOI PMC

Beauvarlet J, Bensadoun P, Darbo E, et al. Modulation of the ATM/autophagy pathway by a G-quadruplex ligand tips the balance between senescence and apoptosis in cancer cells. Nucleic Acids Res. 2019. Apr 8;47(6):2739–2756. doi:10.1093/nar/gkz095. PubMed PMID: 30759257; PubMed Central PMCID: PMCPMC6451122. PubMed DOI PMC

Zhao YG, Zhang H.. The ER-localized autophagy protein EPG-3/VMP1 regulates ER contacts with other organelles by modulating ATP2A/SERCA activity. Autophagy. 2018;14(2):362–363. doi:10.1080/15548627.2017.1415591. PubMed PMID: 29494262; PubMed Central PMCID: PMCPMC5902242. PubMed DOI PMC

Hsin IL, Sheu GT, Jan MS, et al. Inhibition of lysosome degradation on autophagosome formation and responses to GMI, an immunomodulatory protein from Ganoderma microsporum. Br J Pharmacol. 2012. Nov;167(6):1287–300. doi:10.1111/j.1476-5381.2012.02073.x. PubMed PMID: 22708544; PubMed Central PMCID: PMCPMC3504994. PubMed DOI PMC

Chang D, Nalls MA, Hallgrimsdottir IB, et al. A meta-analysis of genome-wide association studies identifies 17 new Parkinson’s disease risk loci. Nat Genet. 2017. Oct;49(10):1511–1516. doi:10.1038/ng.3955. PubMed PMID: 28892059; PubMed Central PMCID: PMCPMC5812477. PubMed DOI PMC

Dehay B, Ramirez A, Martinez-Vicente M, et al. Loss of P-type ATPase ATP13A2/PARK9 function induces general lysosomal deficiency and leads to Parkinson disease neurodegeneration. Proc Natl Acad Sci U S A. 2012. Jun 12;109(24):9611–6. doi:10.1073/pnas.1112368109. PubMed PMID: 22647602; PubMed Central PMCID: PMC3386132. PubMed DOI PMC

Gusdon AM, Zhu J, Van Houten B, et al. ATP13A2 regulates mitochondrial bioenergetics through macroautophagy. Neurobiol Dis. 2012. Mar;45(3):962–72. doi:10.1016/j.nbd.2011.12.015. PubMed PMID: 22198378; PubMed Central PMCID: PMC3291101. PubMed DOI PMC

Niu H, Rikihisa Y.. Ats-1: a novel bacterial molecule that links autophagy to bacterial nutrition. Autophagy. 2013. May;9(5):787–8. doi:10.4161/auto.23693. PubMed PMID: 23388398; PubMed Central PMCID: PMC3669189. PubMed DOI PMC

Niu H, Xiong Q, Yamamoto A, et al. Autophagosomes induced by a bacterial Beclin 1 binding protein facilitate obligatory intracellular infection. Proc Natl Acad Sci U S A. 2012. Dec 18;109(51):20800–7. doi:10.1073/pnas.1218674109. PubMed PMID: 23197835; PubMed Central PMCID: PMC3529060. PubMed DOI PMC

Isakson P, Bjoras M, Boe SO, et al. Autophagy contributes to therapy-induced degradation of the PML/RARA oncoprotein. Blood. 2010. Sep 30;116(13):2324–31. doi:10.1182/blood-2010-01-261040. PubMed PMID: 20574048. PubMed DOI

Orfali N, McKenna SL, Cahill MR, et al. Retinoid receptor signaling and autophagy in acute promyelocytic leukemia. Exp Cell Res. 2014. May 15;324(1):1–12. doi:10.1016/j.yexcr.2014.03.018. PubMed PMID: 24694321; PubMed Central PMCID: PMC4047711. PubMed DOI PMC

Li Z, Wang C, Wang Z, et al. Allele-selective lowering of mutant HTT protein by HTT-LC3 linker compounds. Nature. 2019. Nov;575(7781):203–209. doi:10.1038/s41586-019-1722-1. PubMed PMID: 31666698. PubMed DOI

Vanhee C, Zapotoczny G, Masquelier D, et al. The Arabidopsis multistress regulator TSPO is a heme binding membrane protein and a potential scavenger of porphyrins via an autophagy-dependent degradation mechanism. Plant Cell. 2011. Feb;23(2):785–805. doi:10.1105/tpc.110.081570. PubMed PMID: 21317376; PubMed Central PMCID: PMC3077796. PubMed DOI PMC

Herzog LK, Kevei E, Marchante R, et al. The Machado-Joseph disease deubiquitylase ataxin-3 interacts with LC3C/GABARAP and promotes autophagy. Aging cell. 2020. Jan;19(1):e13051. doi:10.1111/acel.13051. PubMed PMID: 31625269; PubMed Central PMCID: PMCPMC6974715. PubMed DOI PMC

Ashkenazi A, Bento CF, Ricketts T, et al. Polyglutamine tracts regulate autophagy. Autophagy. 2017. Sep 2;13(9):1613–1614. doi:10.1080/15548627.2017.1336278. PubMed PMID: 28722507; PubMed Central PMCID: PMCPMC5612341. PubMed DOI PMC

Sittler A, Muriel MP, Marinello M, et al. Deregulation of autophagy in postmortem brains of Machado-Joseph disease patients. Neuropathology. 2018. Apr;38(2):113–124. doi:10.1111/neup.12433. PubMed PMID: 29218765. PubMed DOI

Papp D, Kovacs T, Billes V, et al. AUTEN-67, an autophagy-enhancing drug candidate with potent antiaging and neuroprotective effects. Autophagy. 2016;12(2):273–86. doi:10.1080/15548627.2015.1082023. PubMed PMID: 26312549; PubMed Central PMCID: PMCPMC4835959. PubMed DOI PMC

Laraia L, Friese A, Corkery DP, et al. The cholesterol transfer protein GRAMD1A regulates autophagosome biogenesis. Nat Chem Biol. 2019. Jul;15(7):710–720. doi:10.1038/s41589-019-0307-5. PubMed PMID: 31222192. PubMed DOI

Wu YW, Waldmann H.. Toward the role of cholesterol and cholesterol transfer protein in autophagosome biogenesis. Autophagy. 2019. Dec;15(12):2167–2168. doi:10.1080/15548627.2019.1666595. PubMed PMID: 31512558; PubMed Central PMCID: PMCPMC6844521. PubMed DOI PMC

Dunn WA, Jr. Studies on the mechanisms of autophagy: formation of the autophagic vacuole. J Cell Biol. 1990. Jun;110(6):1923–33. PubMed PMID: 2351689; eng. PubMed PMC

Schulze RJ, Weller SG, Schroeder B, et al. Lipid droplet breakdown requires dynamin 2 for vesiculation of autolysosomal tubules in hepatocytes. J Cell Biol. 2013. Oct 28;203(2):315–26. doi:10.1083/jcb.201306140. PubMed PMID: 24145164; PubMed Central PMCID: PMC3812963. PubMed DOI PMC

Gundara JS, Robinson BG, Sidhu SB.. Evolution of the “autophagamiR”. Autophagy. 2011. Dec;7(12):1553–4. PubMed PMID: 22024754; PubMed Central PMCID: PMC3288028. PubMed PMC

Lenzi P, Lazzeri G, Biagioni F, et al. The autophagoproteasome a novel cell clearing organelle in baseline and stimulated conditions. Front Neuroanat. 2016;10:78. doi:10.3389/fnana.2016.00078. PubMed PMID: 27493626; PubMed Central PMCID: PMCPMC4955296. PubMed DOI PMC

Mijaljica D, Nazarko TY, Brumell JH, et al. Receptor protein complexes are in control of autophagy. Autophagy. 2012. Nov;8(11):1701–5. doi:10.4161/auto.21332. PubMed PMID: 22874568; PubMed Central PMCID: PMC3494607. PubMed DOI PMC

Farfel-Becker T, Roney JC, Cheng XT, et al. Neuronal soma-derived degradative lysosomes are continuously delivered to distal axons to maintain local degradation capacity. Cell Rep. 2019. Jul 2;28(1):51–64 e4. doi:10.1016/j.celrep.2019.06.013. PubMed PMID: 31269450; PubMed Central PMCID: PMCPMC6696943. PubMed DOI PMC

Farfel-Becker T, Roney JC, Cheng XT, et al. The secret life of degradative lysosomes in axons: delivery from the soma, enzymatic activity, and local autophagic clearance. Autophagy. 2020. Jan;16(1):167–168. doi:10.1080/15548627.2019.1669869. PubMed PMID: 31533518; PubMed Central PMCID: PMCPMC6984450. PubMed DOI PMC

Shpilka T, Welter E, Borovsky N, et al. Lipid droplets and their component triglycerides and steryl esters regulate autophagosome biogenesis. EMBO J. 2015. Aug 13;34(16):2117–31. doi:10.15252/embj.201490315. PubMed PMID: 26162625. PubMed DOI PMC

Renna M, Schaffner C, Brown K, et al. Azithromycin blocks autophagy and may predispose cystic fibrosis patients to mycobacterial infection. J Clin Invest. 2011. Sep;121(9):3554–63. doi:10.1172/JCI46095. PubMed PMID: 21804191; PubMed Central PMCID: PMCPMC3163956. PubMed DOI PMC

Saito T, Kuma A, Sugiura Y, et al. Autophagy regulates lipid metabolism through selective turnover of NCoR1. Nat Commun. 2019. Apr 5;10(1):1567. doi:10.1038/s41467-019-08829-3. PubMed PMID: 30952864; PubMed Central PMCID: PMCPMC6450892. PubMed DOI PMC

Heaton NS, Randall G.. Dengue virus-induced autophagy regulates lipid metabolism. Cell Host Microbe. 2010. Nov 18;8(5):422–32. doi:10.1016/j.chom.2010.10.006. PubMed PMID: 21075353; PubMed Central PMCID: PMC3026642. eng. PubMed DOI PMC

Florey O, Gammoh N, Kim SE, et al. V-ATPase and osmotic imbalances activate endolysosomal LC3 lipidation. Autophagy. 2015;11(1):88–99. doi:10.4161/15548627.2014.984277. PubMed PMID: 25484071; PubMed Central PMCID: PMCPMC4502810. PubMed DOI PMC

Sebti S, Prebois C, Perez-Gracia E, et al. BAT3 modulates p300-dependent acetylation of p53 and autophagy-related protein 7 (ATG7) during autophagy. Proc Natl Acad Sci U S A. 2014. Mar 18;111(11):4115–20. doi:10.1073/pnas.1313618111. PubMed PMID: 24591579; PubMed Central PMCID: PMC3964035. PubMed DOI PMC

Kowaltowski AJ, Smaili SS, Russell JT, et al. Elevation of resting mitochondrial membrane potential of neural cells by cyclosporin A, BAPTA-AM, and bcl-2. Am J Physiol Cell Physiol. 2000. Sep;279(3):C852–9. doi:10.1152/ajpcell.2000.279.3.C852. PubMed PMID: 10942734. PubMed DOI

Tang Q, Jin MW, Xiang JZ, et al. The membrane permeable calcium chelator BAPTA-AM directly blocks human ether a-go-go-related gene potassium channels stably expressed in HEK 293 cells. Biochem Pharmacol. 2007. Dec 3;74(11):1596–607. doi:10.1016/j.bcp.2007.07.042. PubMed PMID: 17826747. PubMed DOI

Chi Y, Li K, Yan Q, et al. Nonsteroidal anti-inflammatory drug flufenamic acid is a potent activator of AMP-activated protein kinase. J Pharmacol Exp Ther. 2011. Oct;339(1):257–66. doi:10.1124/jpet.111.183020. PubMed PMID: 21765041. PubMed DOI

Noda NN, Kobayashi T, Adachi W, et al. Structure of the novel C-terminal domain of vacuolar protein sorting 30/autophagy-related protein 6 and its specific role in autophagy. J Biol Chem. 2012. May 11;287(20):16256–66. doi:10.1074/jbc.M112.348250. PubMed PMID: 22437838; PubMed Central PMCID: PMC3351336. PubMed DOI PMC

Lindqvist LM, Heinlein M, Huang DC, et al. Prosurvival Bcl-2 family members affect autophagy only indirectly, by inhibiting Bax and Bak. Proc Natl Acad Sci U S A. 2014. Jun 10;111(23):8512–7. doi:10.1073/pnas.1406425111. PubMed PMID: 24912196; PubMed Central PMCID: PMC4060681. PubMed DOI PMC

Murakawa T, Yamaguchi O, Hashimoto A, et al. Bcl-2-like protein 13 is a mammalian Atg32 homologue that mediates mitophagy and mitochondrial fragmentation. Nat Commun. 2015;6:7527. doi:10.1038/ncomms8527. PubMed PMID: 26146385; PubMed Central PMCID: PMC4501433. PubMed DOI PMC

Paul S, Kashyap AK, Jia W, et al. Selective autophagy of the adaptor protein Bcl10 modulates T cell receptor activation of NF-kappaB. Immunity. 2012. Jun 29;36(6):947–58. doi:10.1016/j.immuni.2012.04.008. PubMed PMID: 22658522; PubMed Central PMCID: PMC3389288. PubMed DOI PMC

Baydyuk M, Xie Y, Tessarollo L, et al. Midbrain-derived neurotrophins support survival of immature striatal projection neurons. J Neurosci. 2013. Feb 20;33(8):3363–9. doi:10.1523/JNEUROSCI.3687-12.2013. PubMed PMID: 23426664; PubMed Central PMCID: PMCPMC3711532. PubMed DOI PMC

Ortega F, Perez-Sen R, Morente V, et al. P2X7, NMDA and BDNF receptors converge on GSK3 phosphorylation and cooperate to promote survival in cerebellar granule neurons. Cell Mol Life Sci. 2010. May;67(10):1723–33. doi:10.1007/s00018-010-0278-x. PubMed PMID: 20146080; PubMed Central PMCID: PMCPMC2858808. PubMed DOI PMC

Brito V, Puigdellivol M, Giralt A, et al. Imbalance of p75(NTR)/TrkB protein expression in Huntington’s disease: implication for neuroprotective therapies. Cell Death Dis. 2013. Apr 18;4:e595. doi:10.1038/cddis.2013.116. PubMed PMID: 23598407; PubMed Central PMCID: PMCPMC3641339. PubMed DOI PMC

Smith ED, Prieto GA, Tong L, et al. Rapamycin and interleukin-1beta impair brain-derived neurotrophic factor-dependent neuron survival by modulating autophagy. J Biol Chem. 2014. Jul 25;289(30):20615–29. doi:10.1074/jbc.M114.568659. PubMed PMID: 24917666; PubMed Central PMCID: PMCPMC4110274. PubMed DOI PMC

Liang X, Jackson S, Seaman M, Brown K, Kempkes B, Hibshoosh H, Levine B.. Induction of autophagy and inhibition of tumorigenesis by beclin 1. Nature. 1999;402:672–676. PubMed

Mei Y, Glover K, Su M, et al. Conformational flexibility of BECN1: Essential to its key role in autophagy and beyond. Protein Sci. 2016. Oct;25(10):1767–85. doi:10.1002/pro.2984. PubMed PMID: 27414988; PubMed Central PMCID: PMCPMC5029530. PubMed DOI PMC

Cheng B, Xu A, Qiao M, et al. BECN1s, a short splice variant of BECN1, functions in mitophagy. Autophagy. 2015;11:2048–2056. PubMed PMC

He C, Wei Y, Sun K, et al. Beclin 2 functions in autophagy, degradation of G protein-coupled receptors, and metabolism. Cell. 2013. Aug 29;154(5):1085–99. doi:10.1016/j.cell.2013.07.035. PubMed PMID: 23954414. PubMed DOI PMC

Dong X, Cheng A, Zou Z, et al. Endolysosomal trafficking of viral G protein-coupled receptor functions in innate immunity and control of viral oncogenesis. Proc Natl Acad Sci U S A. 2016. Mar 15;113(11):2994–9. doi:10.1073/pnas.1601860113. PubMed PMID: 26929373; PubMed Central PMCID: PMCPMC4801257. PubMed DOI PMC

Yang LJ, Chen Y, He J, et al. Betulinic acid inhibits autophagic flux and induces apoptosis in human multiple myeloma cells in vitro. Acta Pharmacol Sin. 2012. Dec;33(12):1542–8. doi:10.1038/aps.2012.102. PubMed PMID: 23064721; PubMed Central PMCID: PMC4001834. PubMed DOI PMC

Yin XM, Oltvai ZN, Korsmeyer SJ.. BH1 and BH2 domains of Bcl-2 are required for inhibition of apoptosis and heterodimerization with Bax. Nature. 1994. May 26;369(6478):321–3. doi:10.1038/369321a0. PubMed PMID: 8183370. PubMed DOI

Sinha S, Levine B.. The autophagy effector Beclin 1: a novel BH3-only protein. Oncogene. 2008. Dec;27Suppl 1:S137–48. doi:10.1038/onc.2009.51. PubMed PMID: 19641499; PubMed Central PMCID: PMCPMC2731580. PubMed DOI PMC

Minoia M, Boncoraglio A, Vinet J, et al. BAG3 induces the sequestration of proteasomal clients into cytoplasmic puncta: Implications for a proteasome-to-autophagy switch. Autophagy. 2014. Jul 10;10(9):1603–21. PubMed PMID: 25046115. PubMed PMC

Mukhopadhyay S, Naik PP, Panda PK, et al. Serum starvation induces anti-apoptotic cIAP1 to promote mitophagy through ubiquitination. Biochem Biophys Res Commun. 2016. Oct 28;479(4):940–946. doi:10.1016/j.bbrc.2016.09.143. PubMed PMID: 27693792. PubMed DOI

Humphry NJ, Wheatley SP.. Survivin inhibits excessive autophagy in cancer cells but does so independently of its interaction with LC3. Biol Open. 2018. Oct 22;7(10). doi:10.1242/bio.037374. PubMed PMID: 30348810; PubMed Central PMCID: PMCPMC6215416. PubMed DOI PMC

Ebner P, Poetsch I, Deszcz L, et al. The IAP family member BRUCE regulates autophagosome-lysosome fusion. Nat Commun. 2018. Feb 9;9(1):599. doi:10.1038/s41467-018-02823-x. PubMed PMID: 29426817; PubMed Central PMCID: PMCPMC5807552. PubMed DOI PMC

Kim Y, Kim YS, Kim DE, et al. BIX-01294 induces autophagy-associated cell death via EHMT2/G9a dysfunction and intracellular reactive oxygen species production. Autophagy. 2013. Dec;9(12):2126–39. doi:10.4161/auto.26308. PubMed PMID: 24322755. PubMed DOI

Artal-Martinez de Narvajas A, Gomez TS, Zhang JS, et al. Epigenetic regulation of autophagy by the methyltransferase G9a. Mol Cell Biol. 2013. Oct;33(20):3983–93. doi:10.1128/MCB.00813-13. PubMed PMID: 23918802; PubMed Central PMCID: PMCPMC3811684. PubMed DOI PMC

Li KC, Hua KT, Lin YS, et al. Inhibition of G9a induces DUSP4-dependent autophagic cell death in head and neck squamous cell carcinoma. Mol Cancer. 2014. Jul 15;13:172. doi:10.1186/1476-4598-13-172. PubMed PMID: 25027955; PubMed Central PMCID: PMCPMC4107555. PubMed DOI PMC

Ciechomska IA, Przanowski P, Jackl J, et al. BIX01294, an inhibitor of histone methyltransferase, induces autophagy-dependent differentiation of glioma stem-like cells. Sci Rep. 2016. Dec 9;6:38723. doi:10.1038/srep38723. PubMed PMID: 27934912; PubMed Central PMCID: PMCPMC5146656. PubMed DOI PMC

Webster BR, Scott I, Han K, et al. Restricted mitochondrial protein acetylation initiates mitochondrial autophagy. J Cell Sci. 2013. Nov 1;126(Pt 21):4843–9. doi:10.1242/jcs.131300. PubMed PMID: 24006259. PubMed DOI PMC

Boyd JM, Malstrom S, Subramanian T, et al. Adenovirus E1B 19 kDa and Bcl-2 proteins interact with a common set of cellular proteins. Cell. 1994. Oct21;79(2):341–51. PubMed PMID: 7954800. PubMed

Hanna RA, Quinsay MN, Orogo AM, et al. Microtubule-associated protein 1 light chain 3 (LC3) interacts with Bnip3 protein to selectively remove endoplasmic reticulum and mitochondria via autophagy. J Biol Chem. 2012. Jun 1;287(23):19094–104. doi:10.1074/jbc.M111.322933. PubMed PMID: 22505714; PubMed Central PMCID: PMC3365942. PubMed DOI PMC

Chourasia AH, Boland ML, Macleod KF.. Mitophagy and cancer. Cancer Metab. 2015;3:4. doi:10.1186/s40170-015-0130-8. PubMed PMID: 25810907; PubMed Central PMCID: PMC4373087. PubMed DOI PMC

Landes T, Emorine LJ, Courilleau D, et al. The BH3-only Bnip3 binds to the dynamin Opa1 to promote mitochondrial fragmentation and apoptosis by distinct mechanisms. EMBO Rep. 2010. Jun;11(6):459–65. doi:10.1038/embor.2010.50. PubMed PMID: 20436456; PubMed Central PMCID: PMC2892319. PubMed DOI PMC

Kasper LH, Boussouar F, Boyd K, et al. Two transactivation mechanisms cooperate for the bulk of HIF-1-responsive gene expression. EMBO J. 2005. Nov 16;24(22):3846–58. doi:10.1038/sj.emboj.7600846. PubMed PMID: 16237459; PubMed Central PMCID: PMC1283945. PubMed DOI PMC

Tracy K, Dibling BC, Spike BT, et al. BNIP3 is an RB/E2F target gene required for hypoxia-induced autophagy. Mol Cell Biol. 2007. Sep;27(17):6229–42. doi:10.1128/MCB.02246-06. PubMed PMID: 17576813; PubMed Central PMCID: PMC1952167. PubMed DOI PMC

Feng X, Liu X, Zhang W, et al. p53 directly suppresses BNIP3 expression to protect against hypoxia-induced cell death. EMBO J. 2011. Aug 17;30(16):3397–415. doi:10.1038/emboj.2011.248. PubMed PMID: 21792176; PubMed Central PMCID: PMC3160666. PubMed DOI PMC

Shaw J, Yurkova N, Zhang T, et al. Antagonism of E2F-1 regulated Bnip3 transcription by NF-kappaB is essential for basal cell survival. Proc Natl Acad Sci U S A. 2008. Dec 30;105(52):20734–9. doi:10.1073/pnas.0807735105. PubMed PMID: 19088195; PubMed Central PMCID: PMC2603431. PubMed DOI PMC

Diwan A, Krenz M, Syed FM, et al. Inhibition of ischemic cardiomyocyte apoptosis through targeted ablation of Bnip3 restrains postinfarction remodeling in mice. J Clin Invest. 2007. Oct;117(10):2825–33. doi:10.1172/JCI32490. PubMed PMID: 17909626; PubMed Central PMCID: PMC1994631. PubMed DOI PMC

Glick D, Zhang W, Beaton M, et al. BNip3 regulates mitochondrial function and lipid metabolism in the liver. Mol Cell Biol. 2012. Jul;32(13):2570–84. doi:10.1128/MCB.00167-12. PubMed PMID: 22547685; PubMed Central PMCID: PMC3434502. PubMed DOI PMC

Xiang G, Yang L, Long Q, et al. BNIP3L-dependent mitophagy accounts for mitochondrial clearance during 3 factors-induced somatic cell reprogramming. Autophagy. 2017. Sep 2;13(9):1543–1555. doi:10.1080/15548627.2017.1338545. PubMed PMID: 28722510; PubMed Central PMCID: PMCPMC5612220. PubMed DOI PMC

Melser S, Chatelain EH, Lavie J, et al. Rheb regulates mitophagy induced by mitochondrial energetic status. Cell Metab. 2013. May 7;17(5):719–30. doi:10.1016/j.cmet.2013.03.014. PubMed PMID: 23602449. PubMed DOI

Ding WX, Ni HM, Li M, et al. Nix is critical to two distinct phases of mitophagy, reactive oxygen species-mediated autophagy induction and Parkin-ubiquitin-p62-mediated mitochondrial priming. J Biol Chem. 2010. Sep 3;285(36):27879–90. doi:10.1074/jbc.M110.119537. PubMed PMID: 20573959; PubMed Central PMCID: PMCPMC2934655. PubMed DOI PMC

Farg MA, Sundaramoorthy V, Sultana JM, et al. C9ORF72, implicated in amytrophic lateral sclerosis and frontotemporal dementia, regulates endosomal trafficking. Hum Mol Genet. 2014. Jul 1;23(13):3579–95. doi:10.1093/hmg/ddu068. PubMed PMID: 24549040; PubMed Central PMCID: PMC4049310. PubMed DOI PMC

Sullivan PM, Zhou X, Robins AM, et al. The ALS/FTLD associated protein C9orf72 associates with SMCR8 and WDR41 to regulate the autophagy-lysosome pathway. Acta Neuropathol Commun. 2016. May 18;4(1):51. doi:10.1186/s40478-016-0324-5. PubMed PMID: 27193190; PubMed Central PMCID: PMCPMC4870812. PubMed DOI PMC

Webster CP, Smith EF, Bauer CS, et al. The C9orf72 protein interacts with Rab1a and the ULK1 complex to regulate initiation of autophagy. EMBO J. 2016. Aug 1;35(15):1656–76. doi:10.15252/embj.201694401. PubMed PMID: 27334615; PubMed Central PMCID: PMCPMC4969571. PubMed DOI PMC

Yang M, Liang C, Swaminathan K, et al. A C9ORF72/SMCR8-containing complex regulates ULK1 and plays a dual role in autophagy. Sci Adv. 2016. Sep;2(9):e1601167. doi:10.1126/sciadv.1601167. PubMed PMID: 27617292; PubMed Central PMCID: PMCPMC5010369. PubMed DOI PMC

Cali CP, Patino M, Tai YK, et al. C9orf72 intermediate repeats are associated with corticobasal degeneration, increased C9orf72 expression and disruption of autophagy. Acta Neuropathol. 2019. Nov;138(5):795–811. doi:10.1007/s00401-019-02045-5. PubMed PMID: 31327044; PubMed Central PMCID: PMCPMC6802287. PubMed DOI PMC

Zhao X, Su L, He X, et al. Long noncoding RNA CA7-4 promotes autophagy and apoptosis via sponging MIR877-3P and MIR5680 in high glucose-induced vascular endothelial cells. Autophagy. 2020. Jan;16(1):70–85. doi:10.1080/15548627.2019.1598750. PubMed PMID: 30957640; PubMed Central PMCID: PMCPMC6984615. PubMed DOI PMC

O’Farrell F, Wang S, Katheder N, et al. Two-tiered control of epithelial growth and autophagy by the insulin receptor and the ret-like receptor, stitcher. PLoS Biol. 2013. Jul;11(7):e1001612. doi:10.1371/journal.pbio.1001612. PubMed PMID: 23935447; PubMed Central PMCID: PMC3720245. PubMed DOI PMC

Mao K, Wang K, Liu X, et al. The scaffold protein Atg11 recruits fission machinery to drive selective mitochondria degradation by autophagy. Dev Cell. 2013. Jul 15;26(1):9–18. doi:10.1016/j.devcel.2013.05.024. PubMed PMID: 23810512; PubMed Central PMCID: PMC3720741. PubMed DOI PMC

Ikeda H, Hideshima T, Fulciniti M, et al. PI3K/p110delta is a novel therapeutic target in multiple myeloma. Blood. 2010. May 26;116:1460–8. doi: blood-2009-06-222943 [pii] doi:10.1182/blood-2009-06-222943. PubMed PMID: 20505158; Eng. PubMed DOI PMC

Verlhac P, Gregoire IP, Azocar O, et al. Autophagy receptor NDP52 regulates pathogen-containing autophagosome maturation. Cell Host Microbe. 2015. Apr 8;17(4):515–25. doi:10.1016/j.chom.2015.02.008. PubMed PMID: 25771791. PubMed DOI

Hu S, Guo Y, Wang Y, et al. Structure of Myosin VI/Tom1 complex reveals a cargo recognition mode of Myosin VI for tethering. Nat Commun. 2019. Aug 1;10(1):3459. doi:10.1038/s41467-019-11481-6. PubMed PMID: 31371777; PubMed Central PMCID: PMCPMC6673701. PubMed DOI PMC

Berchtold MW, Villalobo A.. The many faces of calmodulin in cell proliferation, programmed cell death, autophagy, and cancer. Biochim Biophys Acta. 2014. Feb;1843(2):398–435. doi:10.1016/j.bbamcr.2013.10.021. PubMed PMID: 24188867. PubMed DOI

Yagami T, Yamamoto Y, Koma H.. Pathophysiological roles of intracellular proteases in neuronal development and neurological diseases. Mol Neurobiol. 2019. May;56(5):3090–3112. doi:10.1007/s12035-018-1277-4. PubMed PMID: 30097848. PubMed DOI

Xia HG, Zhang L, Chen G, et al. Control of basal autophagy by calpain1 mediated cleavage of ATG5. Autophagy. 2010. Jan;6(1):61–6. doi:10.4161/auto.6.1.10326 [pii]. PubMed PMID: 19901552; PubMed Central PMCID: PMC2883879. eng. PubMed DOI PMC

Watchon M, Yuan KC, Mackovski N, et al. Calpain inhibition is protective in Machado-Joseph disease zebrafish due to induction of autophagy. J Neurosci. 2017. Aug 9;37(32):7782–7794. doi:10.1523/JNEUROSCI.1142-17.2017. PubMed PMID: 28687604; PubMed Central PMCID: PMCPMC6596655. PubMed DOI PMC

Zitvogel L, Kepp O, Senovilla L, et al. Immunogenic tumor cell death for optimal anticancer therapy: the calreticulin exposure pathway. Clin Cancer Res. 2010. Jun 15;16(12):3100–4. doi:10.1158/1078-0432.CCR-09-2891. PubMed PMID: 20421432. PubMed DOI

Obeid M, Tesniere A, Ghiringhelli F, et al. Calreticulin exposure dictates the immunogenicity of cancer cell death. Nat Med. 2007. Jan;13(1):54–61. doi:10.1038/nm1523. PubMed PMID: 17187072. PubMed DOI

Garg AD, Agostinis P.. ER stress, autophagy and immunogenic cell death in photodynamic therapy-induced anti-cancer immune responses. Photochem Photobiol Sci. 2014. Mar;13(3):474–87. doi:10.1039/c3pp50333j. PubMed PMID: 24493131. PubMed DOI

Hurley RL, Anderson KA, Franzone JM, et al. The Ca2+/calmodulin-dependent protein kinase kinases are AMP-activated protein kinase kinases. J Biol Chem. 2005. Aug 12;280(32):29060–6. doi:10.1074/jbc.M503824200. PubMed PMID: 15980064; eng. PubMed DOI

Shrivastava A, Kuzontkoski PM, Groopman JE, et al. Cannabidiol induces programmed cell death in breast cancer cells by coordinating the cross-talk between apoptosis and autophagy. Mol Cancer Ther. 2011. Jul;10(7):1161–72. doi:10.1158/1535-7163.MCT-10-1100. PubMed PMID: 21566064. PubMed DOI

Olivas-Aguirre M, Torres-Lopez L, Valle-Reyes JS, et al. Cannabidiol directly targets mitochondria and disturbs calcium homeostasis in acute lymphoblastic leukemia. Cell Death Dis. 2019. Oct 14;10(10):779. doi:10.1038/s41419-019-2024-0. PubMed PMID: 31611561; PubMed Central PMCID: PMCPMC6791884. PubMed DOI PMC

Codogno P, Mehrpour M, Proikas-Cezanne T.. Canonical and non-canonical autophagy: variations on a common theme of self-eating? Nat Rev Mol Cell Biol. 2011. Dec 14;13(1):7–12. doi:10.1038/nrm3249. PubMed PMID: 22166994. PubMed DOI

Demarchi F, Bertoli C, Copetti T, et al. Calpain is required for macroautophagy in mammalian cells. J Cell Biol. 2006. Nov 20;175(4):595–605. doi:jcb.200601024[pii] doi:10.1083/jcb.200601024. PubMed PMID: 17101693; PubMed Central PMCID: PMC2064596. eng. PubMed DOI PMC

Tsugawa H, Mori H, Matsuzaki J, et al. CAPZA1 determines the risk of gastric carcinogenesis by inhibiting Helicobacter pylori CagA-degraded autophagy. Autophagy. 2019. Feb;15(2):242–258. doi:10.1080/15548627.2018.1515530. PubMed PMID: 30176157; PubMed Central PMCID: PMCPMC6333452. PubMed DOI PMC

Du A, Huang S, Zhao X, et al. Suppression of CHRN endocytosis by carbonic anhydrase CAR3 in the pathogenesis of myasthenia gravis. Autophagy. 2017;13(11):1981–1994. doi:10.1080/15548627.2017.1375633. PubMed PMID: 28933591; PubMed Central PMCID: PMCPMC5788490. PubMed DOI PMC

Gamerdinger M, Carra S, Behl C.. Emerging roles of molecular chaperones and co-chaperones in selective autophagy: focus on BAG proteins. J Mol Med (Berl). 2011. Dec;89(12):1175–82. doi:10.1007/s00109-011-0795-6. PubMed PMID: 21818581. PubMed DOI

Kanki T, Kurihara Y, Jin X, et al. Casein kinase 2 is essential for mitophagy. EMBO Rep. 2013. Sep;14(9):788–94. doi:10.1038/embor.2013.114. PubMed PMID: 23897086; PubMed Central PMCID: PMCPMC3790056. PubMed DOI PMC

Tsapras P, Nezis IP.. Caspase involvement in autophagy. Cell Death Differ. 2017. Aug;24(8):1369–1379. doi:10.1038/cdd.2017.43. PubMed PMID: 28574508; PubMed Central PMCID: PMCPMC5520455. PubMed DOI PMC

Zhu Y, Zhao L, Liu L, et al. Beclin 1 cleavage by caspase-3 inactivates autophagy and promotes apoptosis. Protein Cell. 2010. May;1(5):468–77. doi:10.1007/s13238-010-0048-4. PubMed PMID: 21203962. PubMed DOI PMC

Li H, Wang P, Sun Q, et al. Following cytochrome c release, autophagy is inhibited during chemotherapy-induced apoptosis by caspase 8-mediated cleavage of Beclin 1. Cancer Res. 2011. May 15;71(10):3625–34. doi:10.1158/0008-5472.CAN-10-4475. PubMed PMID: 21444671; PubMed Central PMCID: PMC3096685. PubMed DOI PMC

Allavena G, Cuomo F, Baumgartner G, et al. Suppressed translation as a mechanism of initiation of CASP8 (caspase 8)-dependent apoptosis in autophagy-deficient NSCLC cells under nutrient limitation. Autophagy. 2018;14(2):252–268. doi:10.1080/15548627.2017.1405192. PubMed PMID: 29165042; PubMed Central PMCID: PMCPMC5902222. PubMed DOI PMC

Chi J, Wang L, Zhang X, et al. Activation of calcium-sensing receptor-mediated autophagy in angiotensinII-induced cardiac fibrosis in vitro. Biochem Biophys Res Commun. 2018. Mar 4;497(2):571–576. doi:10.1016/j.bbrc.2018.02.098. PubMed PMID: 29452090. PubMed DOI

Peng X, Wei C, Li HZ, et al. NPS2390, a selective calcium-sensing receptor antagonist controls the phenotypic modulation of hypoxic human pulmonary arterial smooth muscle cells by regulating autophagy. J Transl Int Med. 2019. Jun;7(2):59–68. doi:10.2478/jtim-2019-0013. PubMed PMID: 31380238; PubMed Central PMCID: PMCPMC6661874. PubMed DOI PMC

Liu L, Wang C, Lin Y, et al. Suppression of calcium sensing receptor ameliorates cardiac hypertrophy through inhibition of autophagy. Mol Med Rep. 2016. Jul;14(1):111–20. doi:10.3892/mmr.2016.5279. PubMed PMID: 27176663; PubMed Central PMCID: PMCPMC4918534. PubMed DOI PMC

Liu L, Wang C, Sun D, et al. Calhex(2)(3)(1) Ameliorates cardiac hypertrophy by inhibiting cellular autophagy in vivo and in vitro. Cell Physiol Biochem. 2015;36(4):1597–612. doi:10.1159/000430322. PubMed PMID: 26159880. PubMed DOI

Garcia-Marcos M, Ear J, Farquhar MG, et al. A GDI (AGS3) and a GEF (GIV) regulate autophagy by balancing G protein activity and growth factor signals. Mol Biol Cell. 2011. Mar;22(5):673–86. doi:10.1091/mbc.E10-08-0738. PubMed PMID: 21209316; PubMed Central PMCID: PMC3046063. eng. PubMed DOI PMC

Wild LWild F, Khan MM, Straka T, et al. Progress of endocytic CHRN to autophagic degradation is regulated by RAB5-GTPase and T145 phosphorylation of SH3GLB1 at mouse neuromuscular junctions in vivo. Autophagy. 2016. Dec;12(12):2300–2310. doi:10.1080/15548627.2016.1234564. PubMed PMID: 27715385; PubMed Central PMCID: PMCPMC5173261. PubMed DOI PMC

Wu SY, Lan SH, Liu HS.. Degradative autophagy selectively regulates CCND1 (cyclin D1) and MIR224, two oncogenic factors involved in hepatocellular carcinoma tumorigenesis. Autophagy. 2019. Apr;15(4):729–730. doi:10.1080/15548627.2019.1569918. PubMed PMID: 30646811; PubMed Central PMCID: PMCPMC6526824. PubMed DOI PMC

Sanjurjo L, Amezaga N, Aran G, et al. The human CD5L/AIM-CD36 axis: A novel autophagy inducer in macrophages that modulates inflammatory responses. Autophagy. 2015;11(3):487–502. doi:10.1080/15548627.2015.1017183. PubMed PMID: 25713983; PubMed Central PMCID: PMCPMC4502645. PubMed DOI PMC

Sanjurjo L, Aran G, Roher N, et al. AIM/CD5L: a key protein in the control of immune homeostasis and inflammatory disease. J Leukoc Biol. 2015. Aug;98(2):173–84. doi:10.1189/jlb.3RU0215-074R. PubMed PMID: 26048980. PubMed DOI

Sanjurjo L, Aran G, Tellez E, et al. CD5L Promotes M2 Macrophage Polarization through Autophagy-Mediated Upregulation of ID3. Front Immunol. 2018;9:480. doi:10.3389/fimmu.2018.00480. PubMed PMID: 29593730; PubMed Central PMCID: PMCPMC5858086. PubMed DOI PMC

Zhang Y, Xu M, Xia M, et al. Defective autophagosome trafficking contributes to impaired autophagic flux in coronary arterial myocytes lacking CD38 gene. Cardiovasc Res. 2014. Apr 1;102(1):68–78. doi:10.1093/cvr/cvu011. PubMed PMID: 24445604; PubMed Central PMCID: PMCPMC3958620. PubMed DOI PMC

Xiong J, Xia M, Xu M, et al. Autophagy maturation associated with CD38-mediated regulation of lysosome function in mouse glomerular podocytes. J Cell Mol Med. 2013. Dec;17(12):1598–607. doi:10.1111/jcmm.12173. PubMed PMID: 24238063; PubMed Central PMCID: PMCPMC3914646. PubMed DOI PMC

Latterich M, Frohlich KU, Schekman R.. Membrane fusion and the cell cycle: Cdc48p participates in the fusion of ER membranes. Cell. 1995. Sep 22;82(6):885–93. PubMed PMID: 7553849. PubMed

Krick R, Bremer S, Welter E, et al. Cdc48/p97 and Shp1/p47 regulate autophagosome biogenesis in concert with ubiquitin-like Atg8. J Cell Biol. 2010. Sep 20;190(6):965–73. doi:jcb.201002075[pii] doi:10.1083/jcb.201002075. PubMed PMID: 20855502; eng. PubMed DOI PMC

Joubert PE, Meiffren G, Gregoire IP, et al. Autophagy induction by the pathogen receptor CD46. Cell Host Microbe. 2009. Oct 22;6(4):354–66. doi: S1931-3128(09)00315-1 [pii] doi:10.1016/j.chom.2009.09.006. PubMed PMID: 19837375; eng. PubMed DOI

Celano SL, Yco LP, Kortus MG, et al. Identification of Kinases Responsible for p53-Dependent Autophagy. iScience. 2019. May 31;15:109–118. doi:10.1016/j.isci.2019.04.023. PubMed PMID: 31048145; PubMed Central PMCID: PMCPMC6495467. PubMed DOI PMC

Shukla AK, Spurrier J, Kuzina I, et al. Hyperactive Innate Immunity Causes Degeneration of Dopamine Neurons upon Altering Activity of Cdk5. Cell Rep. 2019. Jan 2;26(1):131–144 e4. doi:10.1016/j.celrep.2018.12.025. PubMed PMID: 30605670; PubMed Central PMCID: PMCPMC6442473. PubMed DOI PMC

Wong AS, Lee RH, Cheung AY, et al. Cdk5-mediated phosphorylation of endophilin B1 is required for induced autophagy in models of Parkinson’s disease. Nat Cell Biol. 2011. May;13(5):568–79. doi:10.1038/ncb2217. PubMed PMID: 21499257. PubMed DOI

Su LY, Li H, Lv L, et al. Melatonin attenuates MPTP-induced neurotoxicity via preventing CDK5-mediated autophagy and SNCA/alpha-synuclein aggregation. Autophagy. 2015;11(10):1745–59. doi:10.1080/15548627.2015.1082020. PubMed PMID: 26292069; PubMed Central PMCID: PMCPMC4824603. PubMed DOI PMC

Orlotti NI, Cimino-Reale G, Borghini E, et al. Autophagy acts as a safeguard mechanism against G-quadruplex ligand-mediated DNA damage. Autophagy. 2012. Aug;8(8):1185–96. doi:10.4161/auto.20519. PubMed PMID: 22627293. PubMed DOI

Liang J, Shao SH, Xu ZX, et al. The energy sensing LKB1-AMPK pathway regulates p27(kip1) phosphorylation mediating the decision to enter autophagy or apoptosis. Nat Cell Biol. 2007. Feb;9(2):218–24. doi: ncb1537 [pii] doi:10.1038/ncb1537. PubMed PMID: 17237771; eng. PubMed DOI

Budina-Kolomets A, Hontz RD, Pimkina J, et al. A conserved domain in exon 2 coding for the human and murine ARF tumor suppressor protein is required for autophagy induction. Autophagy. 2013. Oct;9(10):1553–65. doi:10.4161/auto.25831. PubMed PMID: 23939042. PubMed DOI PMC

Baechler BL, Bloemberg D, Quadrilatero J.. Mitophagy regulates mitochondrial network signaling, oxidative stress, and apoptosis during myoblast differentiation. Autophagy. 2019. Sep;15(9):1606–1619. doi:10.1080/15548627.2019.1591672. PubMed PMID: 30859901; PubMed Central PMCID: PMCPMC6693454. PubMed DOI PMC

Mishra SK, Gao YG, Deng Y, et al. CPTP: A sphingolipid transfer protein that regulates autophagy and inflammasome activation. Autophagy. 2018;14(5):862–879. doi:10.1080/15548627.2017.1393129. PubMed PMID: 29164996; PubMed Central PMCID: PMCPMC6070007. PubMed DOI PMC

Simanshu DK, Kamlekar RK, Wijesinghe DS, et al. Non-vesicular trafficking by a ceramide-1-phosphate transfer protein regulates eicosanoids. Nature. 2013. Aug 22;500(7463):463–7. doi:10.1038/nature12332. PubMed PMID: 23863933; PubMed Central PMCID: PMCPMC3951269. PubMed DOI PMC

Qi HY, Daniels MP, Liu Y, et al. A cytosolic phospholipase A2-initiated lipid mediator pathway induces autophagy in macrophages. J Iimmunol. 2011. Nov 15;187(10):5286–92. doi:10.4049/jimmunol.1004004. PubMed PMID: 22003202; PubMed Central PMCID: PMCPMC3208068. PubMed DOI PMC

Ward KE, Bhardwaj N, Vora M, et al. The molecular basis of ceramide-1-phosphate recognition by C2 domains. J Lipid Res. 2013. Mar;54(3):636–48. doi:10.1194/jlr.M031088. PubMed PMID: 23277511; PubMed Central PMCID: PMCPMC3617939. PubMed DOI PMC

He MX, He YW.. A role for c-FLIP(L) in the regulation of apoptosis, autophagy, and necroptosis in T lymphocytes. Cell Death Differ. 2013. Feb;20(2):188–97. doi:10.1038/cdd.2012.148. PubMed PMID: 23175183; PubMed Central PMCID: PMCPMC3554340. PubMed DOI PMC

Leidal AM, Cyr DP, Hill RJ, et al. Subversion of autophagy by Kaposi’s sarcoma-associated herpesvirus impairs oncogene-induced senescence. Cell Host Microbe. 2012. Feb 16;11(2):167–80. doi:10.1016/j.chom.2012.01.005. PubMed PMID: 22341465. PubMed DOI

Liang Q, Seo GJ, Choi YJ, et al. Crosstalk between the cGAS DNA sensor and beclin-1 autophagy protein shapes innate antimicrobial immune responses. Cell Host Microbe. 2014. Feb 12;15(2):228–38. doi:10.1016/j.chom.2014.01.009. PubMed PMID: 24528868; PubMed Central PMCID: PMC3950946. PubMed DOI PMC

Ohwada J, Ebiike H, Kawada H, et al. Discovery and biological activity of a novel class I PI3K inhibitor, CH5132799. Bioorg Med Chem Lett. 2011. Mar 15;21(6):1767–72. doi:10.1016/j.bmcl.2011.01.065. PubMed PMID: 21316229. PubMed DOI

Cuervo AM. Chaperone-mediated autophagy: selectivity pays off. Trends Endocrinol Metab 2010. Oct 24;21:142–50. doi: S1043-2760(09)00162-3 [pii] doi:10.1016/j.tem.2009.10.003. PubMed PMID: 19857975; Eng. PubMed DOI PMC

Dice J. Chaperone-mediated autophagy. Autophagy. 2007;3:295–9. PubMed

Agarraberes F, Terlecky S, Dice J.. An intralysosomal hsp70 is required for a selective pathway of lysosomal protein degradation. J Cell Biol. 1997;137:825–834. PubMed PMC

Liu EY, Xu N, O’Prey J, et al. Loss of autophagy causes a synthetic lethal deficiency in DNA repair. Proc Natl Acad Sci U S A. 2015. Jan 20;112(3):773–8. doi:10.1073/pnas.1409563112. PubMed PMID: 25568088; PubMed Central PMCID: PMCPMC4311830. PubMed DOI PMC

Mitsuhashi S, Hatakeyama H, Karahashi M, et al. Muscle choline kinase beta defect causes mitochondrial dysfunction and increased mitophagy. Hum Mol Genet. 2011. Oct 1;20(19):3841–51. doi:10.1093/hmg/ddr305. PubMed PMID: 21750112; PubMed Central PMCID: PMC3168292. PubMed DOI PMC

Fedorko M. Effect of chloroquine on morphology of cytoplasmic granules in maturing human leukocytes--an ultrastructural study. J Clin Invest. 1967. Dec;46(12):1932–42. doi:10.1172/JCI105683. PubMed PMID: 6073998; PubMed Central PMCID: PMC292946. eng. PubMed DOI PMC

Barbero-Camps E, Roca-Agujetas V, Bartolessis I, et al. Cholesterol impairs autophagy-mediated clearance of amyloid beta while promoting its secretion. Autophagy. 2018;14(7):1129–1154. doi:10.1080/15548627.2018.1438807. PubMed PMID: 29862881; PubMed Central PMCID: PMCPMC6103708. PubMed DOI PMC

Fraldi A, Annunziata F, Lombardi A, et al. Lysosomal fusion and SNARE function are impaired by cholesterol accumulation in lysosomal storage disorders. EMBO J. 2010. Nov 3;29(21):3607–20. doi:10.1038/emboj.2010.237. PubMed PMID: 20871593; PubMed Central PMCID: PMCPMC2982760. PubMed DOI PMC

Almacellas E, Pelletier J, Day C, et al. Lysosomal degradation ensures accurate chromosomal segregation to prevent chromosomal instability. Autophagy. 2020. Jun 23:1–18. doi:10.1080/15548627.2020.1764727. PubMed PMID: 32573315. PubMed DOI PMC

Lam HC, Cloonan SM, Bhashyam AR, et al. Histone deacetylase 6-mediated selective autophagy regulates COPD-associated cilia dysfunction. J Clin Invest. 2013. Dec;123(12):5212–30. doi:10.1172/JCI69636. PubMed PMID: 24200693; PubMed Central PMCID: PMCPMC3859407. PubMed DOI PMC

Lee J, Yi S, Kang YE, et al. Defective ciliogenesis in thyroid hurthle cell tumors is associated with increased autophagy. Oncotarget. 2016. Nov 29;7(48):79117–79130. doi:10.18632/oncotarget.12997. PubMed PMID: 27816963; PubMed Central PMCID: PMCPMC5346702. PubMed DOI PMC

Cloonan SM, Lam HC, Ryter SW, et al. “Ciliophagy”: The consumption of cilia components by autophagy. Autophagy. 2014. Mar;10(3):532–4. doi:10.4161/auto.27641. PubMed PMID: 24401596; PubMed Central PMCID: PMCPMC4077895. PubMed DOI PMC

Morleo M, Franco B.. The Autophagy-Cilia Axis: An Intricate Relationship. Cells. 2019. Aug 15;8(8). doi:10.3390/cells8080905. PubMed PMID: 31443299; PubMed Central PMCID: PMCPMC6721705. PubMed DOI PMC

Puustinen P, Rytter A, Mortensen M, et al. CIP2A oncoprotein controls cell growth and autophagy through mTORC1 activation. J Cell Biol. 2014. Mar 3;204(5):713–27. doi:10.1083/jcb.201304012. PubMed PMID: 24590173; PubMed Central PMCID: PMC3941044. PubMed DOI PMC

Du WW, Yang W, Li X, et al. A circular RNA circ-DNMT1 enhances breast cancer progression by activating autophagy. Oncogene. 2018. Nov;37(44):5829–5842. doi:10.1038/s41388-018-0369-y. PubMed PMID: 29973691. PubMed DOI

Liu F, Zhang J, Qin L, et al. Circular RNA EIF6 (Hsa_circ_0060060) sponges miR-144-3p to promote the cisplatin-resistance of human thyroid carcinoma cells by autophagy regulation. Aging (Albany NY). 2018. Dec 12;10(12):3806–3820. doi:10.18632/aging.101674. PubMed PMID: 30540564; PubMed Central PMCID: PMCPMC6326687. PubMed DOI PMC

Yu T, Ding Y, Zhang Y, et al. Circular RNA GATAD2A promotes H1N1 replication through inhibiting autophagy. Vet Microbiol. 2019. Apr;231:238–245. doi:10.1016/j.vetmic.2019.03.012. PubMed PMID: 30955816. PubMed DOI

Han B, Zhang Y, Zhang Y, et al. Novel insight into circular RNA HECTD1 in astrocyte activation via autophagy by targeting MIR142-TIPARP: implications for cerebral ischemic stroke. Autophagy. 2018;14(7):1164–1184. doi:10.1080/15548627.2018.1458173. PubMed PMID: 29938598; PubMed Central PMCID: PMCPMC6103660. PubMed DOI PMC

Yang L, Han B, Zhang Y, et al. Engagement of circular RNA HECW2 in the nonautophagic role of ATG5 implicated in the endothelial-mesenchymal transition. Autophagy. 2018;14(3):404–418. doi:10.1080/15548627.2017.1414755. PubMed PMID: 29260931; PubMed Central PMCID: PMCPMC5915020. PubMed DOI PMC

Huang R, Zhang Y, Han B, et al. Circular RNA HIPK2 regulates astrocyte activation via cooperation of autophagy and ER stress by targeting MIR124-2HG. Autophagy. 2017. Oct 3;13(10):1722–1741. doi:10.1080/15548627.2017.1356975. PubMed PMID: 28786753; PubMed Central PMCID: PMCPMC5640207. PubMed DOI PMC

Chen X, Mao R, Su W, et al. Circular RNA circHIPK3 modulates autophagy via MIR124-3p-STAT3-PRKAA/AMPKalpha signaling in STK11 mutant lung cancer. Autophagy. 2019. Jun 28:1–13. doi:10.1080/15548627.2019.1634945. PubMed PMID: 31232177. PubMed DOI PMC

Zhou ZB, Niu YL, Huang GX, et al. Silencing of circRNA.2837 plays a protective role in sciatic nerve injury by sponging the miR-34 family via regulating neuronal autophagy. Mol Ther Nucleic Acids. 2018. Sep 7;12:718–729. doi:10.1016/j.omtn.2018.07.011. PubMed PMID: 30098504; PubMed Central PMCID: PMCPMC6088565. PubMed DOI PMC

Zhou LY, Zhai M, Huang Y, et al. The circular RNA ACR attenuates myocardial ischemia/reperfusion injury by suppressing autophagy via modulation of the Pink1/ FAM65B pathway. Cell Death Differ. 2019. Jul;26(7):1299–1315. doi:10.1038/s41418-018-0206-4. PubMed PMID: 30349076; PubMed Central PMCID: PMCPMC6748144. PubMed DOI PMC

Kristensen LS, Andersen MS, Stagsted LVW, et al. The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet. 2019. Nov;20(11):675–691. doi:10.1038/s41576-019-0158-7. PubMed PMID: 31395983. PubMed DOI

Li X, Yang L, Chen LL.. The biogenesis, functions, and challenges of circular RNAs. Mol Cell. 2018. Aug 2;71(3):428–442. doi:10.1016/j.molcel.2018.06.034. PubMed PMID: 30057200. PubMed DOI

Zhang J, Wang P, Wan L, et al. The emergence of noncoding RNAs as Heracles in autophagy. Autophagy. 2017. Jun 3;13(6):1004–1024. doi:10.1080/15548627.2017.1312041. PubMed PMID: 28441084; PubMed Central PMCID: PMCPMC5486373. PubMed DOI PMC

Meng L, Liu S, Ding P, et al. Circular RNA ciRS-7 inhibits autophagy of ESCC cells by functioning as miR-1299 sponge to target EGFR signaling. J Cell Biochem. 2020. Feb;121(2):1039–1049. doi:10.1002/jcb.29339. PubMed PMID: 31490018. PubMed DOI

Chang NC, Nguyen M, Germain M, et al. Antagonism of Beclin 1-dependent autophagy by BCL-2 at the endoplasmic reticulum requires NAF-1. EMBO J. 2010. Feb 3;29(3):606–18. doi:10.1038/emboj.2009.369. PubMed PMID: 20010695; PubMed Central PMCID: PMC2830692. eng. PubMed DOI PMC

Chen YF, Kao CH, Chen YT, et al. Cisd2 deficiency drives premature aging and causes mitochondria-mediated defects in mice. Genes Dev. 2009. May 15;23(10):1183–94. doi:10.1101/gad.1779509. PubMed PMID: 19451219; PubMed Central PMCID: PMC2685531. eng. PubMed DOI PMC

Yang Z, Geng J, Yen W-L, et al. Positive or negative regulatory roles of different cyclin-dependent kinase Pho85-cyclin complexes orchestrate induction of autophagy in Saccharomyces cerevisiae Mol Cell. 2010;38:250–64. PubMed PMC

Cao Y, Espinola JA, Fossale E, et al. Autophagy is disrupted in a knock-in mouse model of juvenile neuronal ceroid lipofuscinosis. J Biol Chem. 2006. Jul 21;281(29):20483–93. doi:10.1074/jbc.M602180200. PubMed PMID: 16714284. PubMed DOI

Chandrachud U, Walker MW, Simas AM, et al. Unbiased cell-based screening in a neuronal cell model of batten disease highlights an interaction between Ca2+ homeostasis, autophagy, and CLN3 protein function. J Biol Chem. 2015. Jun 5;290(23):14361–80. doi:10.1074/jbc.M114.621706. PubMed PMID: 25878248; PubMed Central PMCID: PMC4505505. PubMed DOI PMC

Cortese A, Tucci A, Piccolo G, et al. Novel CLN3 mutation causing autophagic vacuolar myopathy. Neurology. 2014. Jun 10;82(23):2072–6. doi:10.1212/WNL.0000000000000490. PubMed PMID: 24827497; PubMed Central PMCID: PMC4118497. PubMed DOI PMC

Wang F, Wang H, Tuan HF, et al. Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements. Hum Genet. 2014. Mar;133(3):331–45. doi:10.1007/s00439-013-1381-5. PubMed PMID: 24154662; PubMed Central PMCID: PMC3945441. PubMed DOI PMC

Yen W-L, Shintani T, Nair U, et al. The conserved oligomeric Golgi complex is involved in double-membrane vesicle formation during autophagy. J Cell Biol. 2010. Jan 11;188(1):101–14. doi: jcb.200904075 [pii] doi:10.1083/jcb.200904075. PubMed PMID: 20065092; PubMed Central PMCID: PMC2812853. eng. PubMed DOI PMC

Sir D, Chen WL, Choi J, et al. Induction of incomplete autophagic response by hepatitis C virus via the unfolded protein response. Hepatology. 2008. Oct;48(4):1054–61. doi: 10.1002/hep.22464. PubMed PMID: 18688877; PubMed Central PMCID: PMCPMC2562598. PubMed DOI PMC

Shoji-Kawata S, Levine B.. Autophagy, antiviral immunity, and viral countermeasures. Biochim Biophys Acta. 2009. Sep;1793(9):1478–84. doi: 10.1016/j.bbamcr.2009.02.008. PubMed PMID: 19264100; PubMed Central PMCID: PMCPMC2739265. PubMed DOI PMC

Drose S, Bindseil KU, Bowman EJ, et al. Inhibitory effect of modified bafilomycins and concanamycins on P- and V-type adenosinetriphosphatases. Biochemistry. 1993. Apr 20;32(15):3902–6. doi: 10.1021/bi00066a008. PubMed PMID: 8385991. PubMed DOI

Marcelo A, Brito F, Carmo-Silva S, et al. Cordycepin activates autophagy through AMPK phosphorylation to reduce abnormalities in Machado-Joseph disease models. Hum Mol Genet. 2019. Jan 1;28(1):51–63. doi: 10.1093/hmg/ddy328. PubMed PMID: 30219871. PubMed DOI

Lancel S, Montaigne D, Marechal X, et al. Carbon monoxide improves cardiac function and mitochondrial population quality in a mouse model of metabolic syndrome. PLoS One. 2012;7(8):e41836. doi: 10.1371/journal.pone.0041836. PubMed PMID: 22870253; PubMed Central PMCID: PMC3411569. PubMed DOI PMC

Chen LL, Song JX, Lu JH, et al. Corynoxine, a natural autophagy enhancer, promotes the clearance of alpha-synuclein via Akt/mTOR pathway. J Neuroimmune Pharmacol. 2014. Feb 13:380–7. doi: 10.1007/s11481-014-9528-2. PubMed PMID: 24522518. PubMed DOI

Lu JH, Tan JQ, Durairajan SS, et al. Isorhynchophylline, a natural alkaloid, promotes the degradation of alpha-synuclein in neuronal cells via inducing autophagy. Autophagy. 2012. Jan;8(1):98–108 (see also the erratum in Autophagy 2012;8:864-6). doi:10.4161/auto.8.1.18313. PubMed PMID: 22113202. PubMed DOI

Casas C, Codogno P, Pinti M, et al. TRANSAUTOPHAGY: European network for multidisciplinary research and translation of autophagy knowledge. Autophagy. 2016;12(3):614–7. doi: 10.1080/15548627.2016.1140294. PubMed PMID: 27046256; PubMed Central PMCID: PMCPMC4836001. PubMed DOI PMC

Bao Y, Song WM, Wang P, et al. COST1 regulates autophagy to control plant drought tolerance. Proc Natl Acad Sci U S A. 2020. Mar 31;117(13):7482–7493. doi: 10.1073/pnas.1918539117. PubMed PMID: 32170020; PubMed Central PMCID: PMCPMC7132278. PubMed DOI PMC

Shi L, Wang J, Quan R, et al. CpATG8, a homolog of yeast autophagy protein ATG8, is required for pathogenesis and hypovirus accumulation in the chest blight fungus. Front Cell Infect Microbiol. 2019;9:222. doi: 10.3389/fcimb.2019.00222. PubMed PMID: 31355148; PubMed Central PMCID: PMCPMC6635641. PubMed DOI PMC

Mylka V, Deckers J, Ratman D, et al. The autophagy receptor SQSTM1/p62 mediates anti-inflammatory actions of the selective NR3C1/glucocorticoid receptor modulator compound A (CpdA) in macrophages. Autophagy. 2018;14(12):2049–2064. doi: 10.1080/15548627.2018.1495681. PubMed PMID: 30215534; PubMed Central PMCID: PMCPMC6984772. PubMed DOI PMC

Song H, Pu J, Wang L, et al. ATG16L1 phosphorylation is oppositely regulated by CSNK2/casein kinase 2 and PPP1/protein phosphatase 1 which determines the fate of cardiomyocytes during hypoxia/reoxygenation. Autophagy. 2015. Jun 17;11:1308–25. doi: 10.1080/15548627.2015.1060386. PubMed PMID: 26083323. PubMed DOI PMC

Cui L, Zhao H, Yin Y, et al. Function of Atg11 in non-selective autophagy and selective autophagy of Candida albicans. Biochem Biophys Res Commun. 2019. Sep 3;516(4):1152–1158. doi: 10.1016/j.bbrc.2019.06.148. PubMed PMID: 31284951. PubMed DOI

Festa BP, Chen Z, Berquez M, et al. Impaired autophagy bridges lysosomal storage disease and epithelial dysfunction in the kidney. Nat Commun. 2018. Jan 11;9(1):161. doi: 10.1038/s41467-017-02536-7. PubMed PMID: 29323117; PubMed Central PMCID: PMCPMC5765140. PubMed DOI PMC

Luciani A, Festa BP, Chen Z, et al. Defective autophagy degradation and abnormal tight junction-associated signaling drive epithelial dysfunction in cystinosis. Autophagy. 2018;14(7):1157–1159. doi: 10.1080/15548627.2018.1446625. PubMed PMID: 29806776; PubMed Central PMCID: PMCPMC6103718. PubMed DOI PMC

Zheng L, Shu WJ, Li YM, et al. The Paf1 complex transcriptionally regulates the mitochondrial-anchored protein Atg32 leading to activation of mitophagy. Autophagy. 2019. Sep 19:in press. doi: 10.1080/15548627.2019.1668228. PubMed PMID: 31525119. PubMed DOI PMC

Stoka V, Turk V, Turk B.. Lysosomal cathepsins and their regulation in aging and neurodegeneration. Ageing Res Rev. 2016. Dec;32:22–37. doi: 10.1016/j.arr.2016.04.010. PubMed PMID: 27125852. PubMed DOI

Campbell EM, Fares H.. Roles of CUP-5, the Caenorhabditis elegans orthologue of human TRPML1, in lysosome and gut granule biogenesis. BMC Cell Biol. 2010;11:40. doi: 10.1186/1471-2121-11-40. PubMed PMID: 20540742; PubMed Central PMCID: PMC2891664. PubMed DOI PMC

Fares H, Greenwald I.. Regulation of endocytosis by CUP-5, the Caenorhabditis elegans mucolipin-1 homolog. Nat Genet. 2001. May;28(1):64–8. doi: 10.1038/88281. PubMed PMID: 11326278. PubMed DOI

Hersh BM, Hartwieg E, Horvitz HR.. The Caenorhabditis elegans mucolipin-like gene cup-5 is essential for viability and regulates lysosomes in multiple cell types. Proc Natl Acad Sci U S A. 2002. Apr 2;99(7):4355–60. doi: 10.1073/pnas.062065399. PubMed PMID: 11904372; PubMed Central PMCID: PMC123652. PubMed DOI PMC

Sun T, Wang X, Lu Q, et al. CUP-5, the C. elegans ortholog of the mammalian lysosomal channel protein MLN1/TRPML1, is required for proteolytic degradation in autolysosomes. Autophagy. 2011. Nov;7(11):1308–15. doi: 10.4161/auto.7.11.17759. PubMed PMID: 21997367. PubMed DOI

Bruns C, McCaffery JM, Curwin AJ, et al. Biogenesis of a novel compartment for autophagosome-mediated unconventional protein secretion. J Cell Biol. 2011. Dec 12;195(6):979–92. doi: 10.1083/jcb.201106098. PubMed PMID: 22144692; PubMed Central PMCID: PMC3241719. PubMed DOI PMC

Yeung AWK, Horbanczuk M, Tzvetkov NT, et al. Curcumin: total-scale analysis of the scientific literature. Molecules. 2019. Apr 9;24(7). doi: 10.3390/molecules24071393. PubMed PMID: 30970601; PubMed Central PMCID: PMCPMC6480685. PubMed DOI PMC

Shakeri A, Cicero AFG, Panahi Y, et al. Curcumin: A naturally occurring autophagy modulator. J Cell Physiol. 2019. May;234(5):5643–5654. doi: 10.1002/jcp.27404. PubMed PMID: 30239005. PubMed DOI

Maiti P, Scott J, Sengupta D, et al. Curcumin and solid lipid curcumin particles induce autophagy, but inhibit mitophagy and the PI3K-Akt/mTOR Pathway in Cultured Glioblastoma Cells. Int J Mol Sci. 2019. Jan 18;20(2). doi: 10.3390/ijms20020399. PubMed PMID: 30669284; PubMed Central PMCID: PMCPMC6359162. PubMed DOI PMC

Wescott MP, Kufareva I, Paes C, et al. Signal transmission through the CXC chemokine receptor 4 (CXCR4) transmembrane helices. Proc Natl Acad Sci U S A. 2016. Aug 30;113(35):9928–33. doi: 10.1073/pnas.1601278113. PubMed PMID: 27543332; PubMed Central PMCID: PMCPMC5024644. PubMed DOI PMC

Nobrega C, Mendonca L, Marcelo A, et al. Restoring brain cholesterol turnover improves autophagy and has therapeutic potential in mouse models of spinocerebellar ataxia. Acta Neuropathol. 2019. Nov;138(5):837–858. doi: 10.1007/s00401-019-02019-7. PubMed PMID: 31197505. PubMed

Wang M, Tan W, Zhou J, et al. A small molecule inhibitor of isoprenylcysteine carboxymethyltransferase induces autophagic cell death in PC3 prostate cancer cells. J Biol Chem. 2008. Jul 4;283(27):18678–84. doi: M801855200 [pii] doi:10.1074/jbc.M801855200. PubMed PMID: 18434300; eng. PubMed DOI

Zou J, Chen Z, Wei X, et al. Cystatin C as a potential therapeutic mediator against Parkinson’s disease via VEGF-induced angiogenesis and enhanced neuronal autophagy in neurovascular units. Cell Death Dis. 2017. Jun 1;8(6):e2854. doi: 10.1038/cddis.2017.240. PubMed PMID: 28569795; PubMed Central PMCID: PMCPMC5520899. PubMed DOI PMC

Harding TM, Morano KA, Scott SV, et al. Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway. J Cell Biol. 1995. Nov;131(3):591–602. PubMed PMID: 7593182. PubMed PMC

Hansen M, Chandra A, Mitic LL, et al. A role for autophagy in the extension of lifespan by dietary restriction in C. elegans. PLoS Genet. 2008. Feb;4(2):e24. doi: 10.1371/journal.pgen.0040024. PubMed PMID: 18282106; PubMed Central PMCID: PMC2242811. PubMed DOI PMC

Lapierre LR, Gelino S, Melendez A, et al. Autophagy and lipid metabolism coordinately modulate life span in germline-less C. elegans. Curr Biol. 2011. Sep 27;21(18):1507–14. doi:10.1016/j.cub.2011.07.042. PubMed PMID: 21906946; PubMed Central PMCID: PMC3191188. eng. PubMed DOI PMC

Sandhof CA, Hoppe SO, Druffel-Augustin S, et al. Reducing INS-IGF1 signaling protects against non-cell autonomous vesicle rupture caused by SNCA spreading. Autophagy. 2019. Jul 29:1–22. doi: 10.1080/15548627.2019.1643657. PubMed PMID: 31354022. PubMed DOI PMC

Netea-Maier RT, Plantinga TS, Van De Veerdonk FL, et al. Modulation of inflammation by autophagy: consequences for human disease. Autophagy. 2016. Jul 29;12:245–60. doi: 10.1080/15548627.2015.1071759. PubMed PMID: 26222012. PubMed DOI PMC

Mills KH. TLR-dependent T cell activation in autoimmunity. Nat Rev Immunol. 2011. Nov 18;11(12):807–22. doi: 10.1038/nri3095. PubMed PMID: 22094985. PubMed DOI

Koren I, Reem E, Kimchi A.. DAP1, a novel substrate of mTOR, negatively regulates autophagy. Curr Biol. 2010. May 26;20:1093–8. doi: S0960-9822(10)00520-8 [pii] doi:10.1016/j.cub.2010.04.041. PubMed PMID: 20537536; Eng. PubMed DOI

Inbal B, Bialik S, Sabanay I, et al. DAP kinase and DRP-1 mediate membrane blebbing and the formation of autophagic vesicles during programmed cell death. J Cell Biol. 2002. Apr 29;157(3):455–68. doi: 10.1083/jcb.200109094 jcb.200109094 [pii]. PubMed PMID: 11980920; PubMed Central PMCID: PMC2173279. eng. PubMed DOI PMC

Yang Y, Willis TL, Button RW, et al. Cytoplasmic DAXX drives SQSTM1/p62 phase condensation to activate Nrf2-mediated stress response. Nat Commun. 2019. Aug 21;10(1):3759. doi: 10.1038/s41467-019-11671-2. PubMed PMID: 31434890; PubMed Central PMCID: PMCPMC6704147. PubMed DOI PMC

Chou TF, Brown SJ, Minond D, et al. Reversible inhibitor of p97, DBeQ, impairs both ubiquitin-dependent and autophagic protein clearance pathways. Proc Natl Acad Sci U S A. 2011. Mar 22;108(12):4834–9. doi: 10.1073/pnas.1015312108. PubMed PMID: 21383145; PubMed Central PMCID: PMCPMC3064330. PubMed DOI PMC

Bravo-San Pedro JM, Sica V, Martins I, et al. Acyl-CoA-binding protein is a lipogenic factor that triggers food intake and obesity. Cell Metab. 2019. Oct 1;30(4):754–767 e9. doi: 10.1016/j.cmet.2019.07.010. PubMed PMID: 31422903. PubMed DOI

Buraschi S, Neill T, Goyal A, et al. Decorin causes autophagy in endothelial cells via Peg3. Proc Natl Acad Sci U S A. 2013. Jul 9;110(28):E2582–91. doi: 10.1073/pnas.1305732110. PubMed PMID: 23798385; PubMed Central PMCID: PMC3710796. PubMed DOI PMC

Gubbiotti MA, Neill T, Frey H, et al. Decorin is an autophagy-inducible proteoglycan and is required for proper in vivo autophagy. Matrix Biol. 2015. Oct;48:14–25. doi: 10.1016/j.matbio.2015.09.001. PubMed PMID: 26344480; PubMed Central PMCID: PMCPMC4661125. PubMed DOI PMC

DeVorkin L, Go NE, Hou Y-CC, et al. The Drosophila effector caspase Dcp-1 regulates mitochondrial dynamics and autophagic flux via SesB. J Cell Biol. 2014. May 26;205(4):477–492. doi: 10.1083/jcb.201303144. PubMed PMID: 24862573; PubMed Central PMCID: PMC4033768. PubMed DOI PMC

Hu G, McQuiston T, Bernard A, et al. A conserved mechanism of TOR-dependent RCK-mediated mRNA degradation regulates autophagy. Nat Cell Biol. 2015. Jul;17(7):930–42. doi: 10.1038/ncb3189. PubMed PMID: 26098573; PubMed Central PMCID: PMC4528364. PubMed DOI PMC

Molitoris JK, McColl KS, Swerdlow S, et al. Glucocorticoid elevation of dexamethasone-induced gene 2 (Dig2/RTP801/REDD1) protein mediates autophagy in lymphocytes. J Biol Chem. 2011. Aug 26;286(34):30181–9. doi: 10.1074/jbc.M111.245423. PubMed PMID: 21733849; PubMed Central PMCID: PMC3191057. PubMed DOI PMC

Slavov N, Botstein D.. Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression. Mol Biol Cell. 2013. Jan;24(2):157–68. doi: 10.1091/mbc.E12-09-0670. PubMed PMID: 23135997; PubMed Central PMCID: PMC3541962. PubMed DOI PMC

Lv Q, Hua F, Hu ZW.. DEDD, a novel tumor repressor, reverses epithelial-mesenchymal transition by activating selective autophagy. Autophagy. 2012. Nov;8(11):1675–6. doi: 10.4161/auto.21438. PubMed PMID: 22874565; PubMed Central PMCID: PMCPMC3494596. PubMed DOI PMC

Lv Q, Wang W, Xue J, et al. DEDD interacts with PI3KC3 to activate autophagy and attenuate epithelial-mesenchymal transition in human breast cancer. Cancer Res. 2012. Jul 1;72(13):3238–50. doi: 10.1158/0008-5472.CAN-11-3832. PubMed PMID: 22719072. PubMed DOI

Mita M, Sankhala K, Abdel-Karim I, et al. Deforolimus (AP23573) a novel mTOR inhibitor in clinical development. Expert Opin Investig Drugs. 2008. Dec;17(12):1947–54. doi: 10.1517/13543780802556485. PubMed PMID: 19012509. PubMed DOI

Kohler K, Brunner E, Guan XL, et al. A combined proteomic and genetic analysis identifies a role for the lipid desaturase Desat1 in starvation-induced autophagy in Drosophila. Autophagy. 2009. Oct;5(7):980–90. PubMed PMID: 19587536. PubMed

Liu X, Yao Z, Jin M, et al. Dhh1 promotes autophagy-related protein translation during nitrogen starvation. PLoS Biol. 2019. Apr;17(4):e3000219. doi: 10.1371/journal.pbio.3000219. PubMed PMID: 30973873; PubMed Central PMCID: PMCPMC6459490. PubMed DOI PMC

Shahnazari S, Yen W-L, Birmingham CL, et al. A diacylglycerol-dependent signaling pathway contributes to regulation of antibacterial autophagy. Cell Host Microbe. 2010. Aug 19;8(2):137–46. doi: S1931-3128(10)00219-2 [pii] doi:10.1016/j.chom.2010.07.002. PubMed PMID: 20674539; eng. PubMed DOI PMC

Lu Z, Baquero MT, Yang H, et al. DIRAS3 regulates the autophagosome initiation complex in dormant ovarian cancer cells. Autophagy. 2014. Jun;10(6):1071–92. doi: 10.4161/auto.28577. PubMed PMID: 24879154; PubMed Central PMCID: PMC4091169. PubMed DOI PMC

Ejaz A, Mitterberger MC, Lu Z, et al. Weight loss upregulates the small GTPase DIRAS3 in human white adipose progenitor cells, which negatively regulates adipogenesis and activates autophagy via Akt-mTOR inhibition. EBioMedicine. 2016. Apr;6:149–161. doi: 10.1016/j.ebiom.2016.03.030. PubMed PMID: 27211557; PubMed Central PMCID: PMCPMC4856797. PubMed DOI PMC

Ejaz A, Mattesich M, Zwerschke W.. Silencing of the small GTPase DIRAS3 induces cellular senescence in human white adipose stromal/progenitor cells. Aging (Albany NY). 2017. Mar 17;9(3):860–879. doi: 10.18632/aging.101197. PubMed PMID: 28316325; PubMed Central PMCID: PMCPMC5391236. PubMed DOI PMC

Mao K, Liu X, Feng Y, et al. The progression of peroxisomal degradation through autophagy requires peroxisomal division. Autophagy. 2014. Apr;10(4):652–61. doi: 10.4161/auto.27852. PubMed PMID: 24451165; PubMed Central PMCID: PMC4091152. PubMed DOI PMC

Dagda RK, Gusdon AM, Pien I, et al. Mitochondrially localized PKA reverses mitochondrial pathology and dysfunction in a cellular model of Parkinson’s disease. Cell Death Differ. 2011. Dec;18(12):1914–23. doi: 10.1038/cdd.2011.74. PubMed PMID: 21637291; PubMed Central PMCID: PMC3177020. PubMed DOI PMC

Kwon MH, Callaway H, Zhong J, et al. A targeted genetic modifier screen links the SWI2/SNF2 protein domino to growth and autophagy genes in Drosophila melanogaster. G3 (Bethesda). 2013. May;3(5):815–25. doi: 10.1534/g3.112.005496. PubMed PMID: 23550128; PubMed Central PMCID: PMC3656729. PubMed DOI PMC

Gomez-Santos C, Ferrer I, Santidrian AF, et al. Dopamine induces autophagic cell death and alpha-synuclein increase in human neuroblastoma SH-SY5Y cells. J Neurosci Res. 2003. Aug 1;73(3):341–50. doi:10.1002/jnr.10663. PubMed PMID: 12868068. PubMed DOI

Leng ZG, Lin SJ, Wu ZR, et al. Activation of DRD5 (dopamine receptor D5) inhibits tumor growth by autophagic cell death. Autophagy. 2017. Aug 3;13(8):1404–1419. doi: 10.1080/15548627.2017.1328347. PubMed PMID: 28613975; PubMed Central PMCID: PMCPMC5584849. PubMed DOI PMC

Dolma S, Selvadurai HJ, Lan X, et al. Inhibition of Dopamine Receptor D4 Impedes Autophagic Flux, Proliferation, and Survival of Glioblastoma Stem Cells. Cancer cell. 2016. Jun 13;29(6):859–873. doi: 10.1016/j.ccell.2016.05.002. PubMed PMID: 27300435; PubMed Central PMCID: PMCPMC5968455. PubMed DOI PMC

Barroso-Chinea P, Luis-Ravelo D, Fumagallo-Reading F, et al. DRD3 (dopamine receptor D3) but not DRD2 activates autophagy through MTORC1 inhibition preserving protein synthesis. Autophagy. 2019. Oct 2:1–17. doi: 10.1080/15548627.2019.1668606. PubMed PMID: 31538542. PubMed DOI PMC

Valbuena A, Castro-Obregon S, Lazo PA.. Downregulation of VRK1 by p53 in response to DNA damage is mediated by the autophagic pathway. PLoS One. 2011;6(2):e17320. doi: 10.1371/journal.pone.0017320. PubMed PMID: 21386980; PubMed Central PMCID: PMC3046209. eng. PubMed DOI PMC

Guan JJ, Zhang XD, Sun W, et al. DRAM1 regulates apoptosis through increasing protein levels and lysosomal localization of BAX. Cell Death Dis. 2015. Jan 29;6:e1624. doi: 10.1038/cddis.2014.546. PubMed PMID: 25633293; PubMed Central PMCID: PMCPMC4669745. PubMed DOI PMC

Crighton D, Wilkinson S, O’Prey J, et al. DRAM, a p53-induced modulator of autophagy, is critical for apoptosis. Cell. 2006. Jul 14;126(1):121–34. doi: 10.1016/j.cell.2006.05.034. PubMed PMID: 16839881; eng. PubMed DOI

O’Prey J, Skommer J, Wilkinson S, et al. Analysis of DRAM-related proteins reveals evolutionarily conserved and divergent roles in the control of autophagy. Cell cycle. 2009. Jul 15;8(14):2260–5. doi: 10.4161/cc.8.14.9050. PubMed PMID: 19556885. PubMed DOI

Yoon JH, Her S, Kim M, et al. The expression of damage-regulated autophagy modulator 2 (DRAM2) contributes to autophagy induction. Mol Biol Rep. 2012. Feb;39(2):1087–93. doi: 10.1007/s11033-011-0835-x. PubMed PMID: 21584698. PubMed DOI

Kim JK, Lee HM, Park KS, et al. MIR144* inhibits antimicrobial responses against Mycobacterium tuberculosis in human monocytes and macrophages by targeting the autophagy protein DRAM2. Autophagy. 2017. Feb;13(2):423–441. doi: 10.1080/15548627.2016.1241922. PubMed PMID: 27764573; PubMed Central PMCID: PMCPMC5324854. PubMed DOI PMC

McPhee CK, Logan MA, Freeman MR, et al. Activation of autophagy during cell death requires the engulfment receptor Draper. Nature. 2010. Jun 24;465(7301):1093–U159. doi: Doi 10.1038/Nature09127. PubMed PMID: ISI:000279056900056; English. PubMed DOI PMC

Nolan TM, Brennan B, Yang M, et al. Selective autophagy of BES1 mediated by DSK2 balances plant growth and survival. Dev Cell. 2017. Apr 10;41(1):33–46 e7. doi: 10.1016/j.devcel.2017.03.013. PubMed PMID: 28399398; PubMed Central PMCID: PMCPMC5720862. PubMed DOI PMC

Chen TH, Chen MR, Chen TY, et al. Cardiac fibrosis in mouse expressing DsRed tetramers involves chronic autophagy and proteasome degradation insufficiency. Oncotarget. 2016. Aug 23;7(34):54274–54289. doi: 10.18632/oncotarget.11026. PubMed PMID: 27494843; PubMed Central PMCID: PMCPMC5342341. PubMed DOI PMC

Choi JC, Wu W, Muchir A, et al. Dual specificity phosphatase 4 mediates cardiomyopathy caused by lamin A/C (LMNA) gene mutation. J Biol Chem. 2012. Nov 23;287(48):40513–24. doi: 10.1074/jbc.M112.404541. PubMed PMID: 23048029; PubMed Central PMCID: PMCPMC3504766. PubMed DOI PMC

Ragusa MJ, Stanley RE, Hurley JH.. Architecture of the Atg17 complex as a scaffold for autophagosome biogenesis. Cell. 2012. Dec 21;151(7):1501–12. doi: 10.1016/j.cell.2012.11.028. PubMed PMID: 23219485; PubMed Central PMCID: PMC3806636. PubMed DOI PMC

Jia K, Levine B.. Autophagy is required for dietary restriction-mediated life span extension in C. elegans. Autophagy. 2007. Nov-Dec;3(6):597–9. PubMed PMID: 17912023. PubMed

Toth ML, Sigmond T, Borsos E, et al. Longevity pathways converge on autophagy genes to regulate life span in Caenorhabditis elegans. Autophagy. 2008. Apr;4(3):330–8. PubMed PMID: 18219227. PubMed

Bandyopadhyay U, Sridhar S, Kaushik S, et al. Identification of regulators of chaperone-mediated autophagy. Mol Cell. 2010. Aug 27;39(4):535–47. doi: 10.1016/j.molcel.2010.08.004. PubMed PMID: 20797626; PubMed Central PMCID: PMC2945256. PubMed DOI PMC

Nicastro R, Sardu A, Panchaud N, et al. The Architecture of the Rag GTPase Signaling Network. Biomolecules. 2017. Jun 30;7(3). doi: 10.3390/biom7030048. PubMed PMID: 28788436; PubMed Central PMCID: PMCPMC5618229. PubMed DOI PMC

Zhang T, Peli-Gulli MP, Zhang Z, et al. Structural insights into the EGO-TC-mediated membrane tethering of the TORC1-regulatory Rag GTPases. Sci Adv. 2019. Sep;5(9):eaax8164. doi: 10.1126/sciadv.aax8164. PubMed PMID: 31579828; PubMed Central PMCID: PMCPMC6760929. PubMed DOI PMC

Talloczy Z, Jiang W, HWt Virgin, et al. Regulation of starvation- and virus-induced autophagy by the eIF2alpha kinase signaling pathway. Proc Natl Acad Sci U S A. 2002. Jan 8;99(1):190–5. doi:10.1073/pnas.012485299. PubMed PMID: 11756670; PubMed Central PMCID: PMC117537. eng. PubMed DOI PMC

Chng SC, Ho L, Tian J, et al. ELABELA: a hormone essential for heart development signals via the apelin receptor. Dev Cell. 2013. Dec 23;27(6):672–80. doi: 10.1016/j.devcel.2013.11.002. PubMed PMID: 24316148. PubMed DOI

Pauli A, Norris ML, Valen E, et al. Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science. 2014. Feb 14;343(6172):1248636. doi: 10.1126/science.1248636. PubMed PMID: 24407481; PubMed Central PMCID: PMCPMC4107353. PubMed DOI PMC

Chen H, Wang L, Wang W, et al. ELABELA and an ELABELA Fragment Protect against AKI. J Am Soc Nephrol. 2017. Sep;28(9):2694–2707. doi: 10.1681/ASN.2016111210. PubMed PMID: 28583915; PubMed Central PMCID: PMCPMC5576937. PubMed DOI PMC

Zhao X, Fang Y, Yang Y, et al. Elaiophylin, a novel autophagy inhibitor, exerts antitumor activity as a single agent in ovarian cancer cells. Autophagy. 2015. Apr 20;11:1849–63. doi: 10.1080/15548627.2015.1017185. PubMed PMID: 25893854. PubMed DOI PMC

Kim S, Naylor SA, DiAntonio A.. Drosophila Golgi membrane protein Ema promotes autophagosomal growth and function. Proc Natl Acad Sci U S A. 2012. May 1;109(18):E1072–81. doi: 10.1073/pnas.1120320109. PubMed PMID: 22493244; PubMed Central PMCID: PMC3344964. PubMed DOI PMC

Berge T, Leikfoss IS, Harbo HF.. From identification to characterization of the multiple sclerosis susceptibility gene CLEC16A. Int J Mol Sci. 2013;14(3):4476–97. doi: 10.3390/ijms14034476. PubMed PMID: 23439554; PubMed Central PMCID: PMC3634488. PubMed DOI PMC

Soleimanpour SA, Gupta A, Bakay M, et al. The diabetes susceptibility gene Clec16a regulates mitophagy. Cell. 2014. Jun 19;157(7):1577–90. doi: 10.1016/j.cell.2014.05.016. PubMed PMID: 24949970. PubMed DOI PMC

Li Y, Zhao Y, Hu J, et al. A novel ER-localized transmembrane protein, EMC6, interacts with RAB5A and regulates cell autophagy. Autophagy. 2013. Feb 1;9(2):150–63. doi: 10.4161/auto.22742. PubMed PMID: 23182941; PubMed Central PMCID: PMC3552880. PubMed DOI PMC

Soukup SF, Kuenen S, Vanhauwaert R, et al. A LRRK2-Dependent EndophilinA Phosphoswitch Is Critical for Macroautophagy at Presynaptic Terminals. Neuron. 2016. Nov 23;92(4):829–844. doi: 10.1016/j.neuron.2016.09.037. PubMed PMID: 27720484. PubMed DOI

Murdoch JD, Rostosky CM, Gowrisankaran S, et al. Endophilin-A Deficiency Induces the Foxo3a-Fbxo32 Network in the Brain and Causes Dysregulation of Autophagy and the Ubiquitin-Proteasome System. Cell Rep. 2016. Oct 18;17(4):1071–1086. doi: 10.1016/j.celrep.2016.09.058. PubMed PMID: 27720640; PubMed Central PMCID: PMCPMC5080600. PubMed DOI PMC

Poluzzi C, Casulli J, Goyal A, et al. Endorepellin evokes autophagy in endothelial cells. J Biol Chem. 2014. Jun 6;289(23):16114–28. doi: 10.1074/jbc.M114.556530. PubMed PMID: 24737315; PubMed Central PMCID: PMC4047384. PubMed DOI PMC

Neill T, Andreuzzi E, Wang ZX, et al. Endorepellin remodels the endothelial transcriptome toward a pro-autophagic and pro-mitophagic gene signature. J Biol Chem. 2018. Aug 3;293(31):12137–12148. doi: 10.1074/jbc.RA118.002934. PubMed PMID: 29921586; PubMed Central PMCID: PMCPMC6078466. PubMed DOI PMC

Dewi FRP, Jiapaer S, Kobayashi A, et al. Nucleoporin TPR (translocated promoter region, nuclear basket protein) upregulation alters MTOR-HSF1 trails and suppresses autophagy induction in ependymoma. Autophagy. 2020. Mar 24:in press. doi: 10.1080/15548627.2020.1741318. PubMed PMID: 32207633. PubMed DOI PMC

Tian E, Wang F, Han J, et al. epg-1 functions in autophagy-regulated processes and may encode a highly divergent Atg13 homolog in C. elegans. Autophagy. 2009. Jul;5(5):608–15. doi: 8624 [pii]. PubMed PMID: 19377305; eng. PubMed

Devkota S, Jeong H, Kim Y, et al. Functional characterization of EI24-induced autophagy in the degradation of RING-domain E3 ligases. Autophagy. 2016. Nov;12(11):2038–2053. doi: 10.1080/15548627.2016.1217371. PubMed PMID: 27541728; PubMed Central PMCID: PMCPMC5103340. PubMed DOI PMC

Nam T, Han JH, Devkota S, et al. Emerging paradigm of crosstalk between autophagy and the ubiquitin-proteasome system. Mol Cells. 2017. Dec 31;40(12):897–905. doi: 10.14348/molcells.2017.0226. PubMed PMID: 29237114; PubMed Central PMCID: PMCPMC5750708. PubMed DOI PMC

Cullup T, Kho AL, Dionisi-Vici C, et al. Recessive mutations in EPG5 cause Vici syndrome, a multisystem disorder with defective autophagy. Nat Genet. 2013. Jan;45(1):83–7. doi: 10.1038/ng.2497. PubMed PMID: 23222957; PubMed Central PMCID: PMC4012842. PubMed DOI PMC

Liang Q, Yang P, Tian E, et al. The C. elegans ATG101 homolog EPG-9 directly interacts with EPG-1/Atg13 and is essential for autophagy. Autophagy. 2012. Oct;8(10):1426–33. doi: 10.4161/auto.21163. PubMed PMID: 22885670. PubMed DOI

Li S, Yang P, Tian E, et al. Arginine methylation modulates autophagic degradation of PGL granules in C. elegans. Mol Cell. 2013. Nov 7;52(3):421–33. doi: 10.1016/j.molcel.2013.09.014. PubMed PMID: 24140420. PubMed DOI

Aguado C, Sarkar S, Korolchuk VI, et al. Laforin, the most common protein mutated in Lafora disease, regulates autophagy. Hum Mol Genet. 2010. Jul 15;19(14):2867–76. doi: ddq190 [pii] doi:10.1093/hmg/ddq190. PubMed PMID: 20453062; eng. PubMed DOI PMC

Ganesh S, Agarwala KL, Amano K, et al. Regional and developmental expression of Epm2a gene and its evolutionary conservation. Biochem Biophys Res Commun. 2001. May 25;283(5):1046–53. doi: 10.1006/bbrc.2001.4914. PubMed PMID: 11355878. PubMed DOI

Jain N, Mishra R, Ganesh S.. FoxO3a-mediated autophagy is down-regulated in the laforin deficient mice, an animal model for Lafora progressive myoclonus epilepsy. Biochem Biophys Res Commun. 2016. May 27;474(2):321–327. doi: 10.1016/j.bbrc.2016.04.094. PubMed PMID: 27107699. PubMed DOI

Brodsky JL. Cleaning up: ER-associated degradation to the rescue. Cell. 2012. Dec 7;151(6):1163–7. doi: 10.1016/j.cell.2012.11.012. PubMed PMID: 23217703; PubMed Central PMCID: PMCPMC3521611. PubMed DOI PMC

Roperto S, Russo V, De Falco F, et al. FUNDC1-mediated mitophagy in bovine papillomavirus-infected urothelial cells. Vet Microbiol. 2019. Jul;234:51–60. doi: 10.1016/j.vetmic.2019.05.017. PubMed PMID: 31213272. PubMed DOI

Budnik A, Stephens DJ.. ER exit sites--localization and control of COPII vesicle formation. FEBS Lett. 2009. Dec 3;583(23):3796–803. doi: 10.1016/j.febslet.2009.10.038. PubMed PMID: 19850039. PubMed DOI

Raote I, Malhotra V.. Protein transport by vesicles and tunnels. J Cell Biol. 2019. Mar 4;218(3):737–739. doi: 10.1083/jcb.201811073. PubMed PMID: 30718263; PubMed Central PMCID: PMCPMC6400553. PubMed DOI PMC

Kurokawa K, Nakano A.. The ER exit sites are specialized ER zones for the transport of cargo proteins from the ER to the Golgi apparatus. J Biochem. 2019. Feb 1;165(2):109–114. doi: 10.1093/jb/mvy080. PubMed PMID: 30304445. PubMed DOI

Bockler S, Westermann B.. Mitochondrial ER contacts are crucial for mitophagy in yeast. Dev Cell. 2014. Feb 24;28(4):450–8. doi: 10.1016/j.devcel.2014.01.012. PubMed PMID: 24530295. PubMed DOI

Belgareh-Touze N, Cavellini L, Cohen MM.. Ubiquitination of ERMES components by the E3 ligase Rsp5 is involved in mitophagy. Autophagy. 2017. Jan 2;13(1):114–132. doi: 10.1080/15548627.2016.1252889. PubMed PMID: 27846375; PubMed Central PMCID: PMCPMC5240830. PubMed DOI PMC

Kaufman DR, Papillon J, Larose L, et al. Deletion of inositol-requiring enzyme-1alpha in podocytes disrupts glomerular capillary integrity and autophagy. Mol Biol Cell. 2017. Jun 15;28(12):1636–1651. doi: 10.1091/mbc.E16-12-0828. PubMed PMID: 28428258; PubMed Central PMCID: PMCPMC5469607. PubMed DOI PMC

Lin M, Liu H, Xiong Q, et al. Ehrlichia secretes Etf-1 to induce autophagy and capture nutrients for its growth through RAB5 and class III phosphatidylinositol 3-kinase. Autophagy. 2016. Nov;12(11):2145–2166. doi: 10.1080/15548627.2016.1217369. PubMed PMID: 27541856; PubMed Central PMCID: PMCPMC5103349. PubMed DOI PMC

Rikihisa Y. Role and function of the type IV secretion system in Anaplasma and Ehrlichia species. Curr Top Microbiol Immunol. 2017;413:297–321. doi: 10.1007/978-3-319-75241-9_12. PubMed PMID: 29536364. PubMed DOI

Rikihisa Y. Subversion of RAB5-regulated autophagy by the intracellular pathogen Ehrlichia chaffeensis. Small GTPases. 2019. Sep;10(5):343–349. doi: 10.1080/21541248.2017.1332506. PubMed PMID: 28650718; PubMed Central PMCID: PMCPMC6748376. PubMed DOI PMC

Sinha S, Roy S, Reddy BS, et al. A lipid-modified estrogen derivative that treats breast cancer independent of estrogen receptor expression through simultaneous induction of autophagy and apoptosis. Mol Cancer Res. 2011. Mar;9(3):364–74. doi: 10.1158/1541-7786.MCR-10-0526. PubMed PMID: 21289296. PubMed DOI PMC

Zhou F, Wu Z, Zhao M, et al. Rab5-dependent autophagosome closure by ESCRT. J Cell Biol. 2019. Jun 3;218(6):1908–1927. doi: 10.1083/jcb.201811173. PubMed PMID: 31010855; PubMed Central PMCID: PMCPMC6548130. PubMed DOI PMC

Wang L, Yu C, Lu Y, et al. TMEM166, a novel transmembrane protein, regulates cell autophagy and apoptosis. Apoptosis. 2007. Aug;12(8):1489–502. doi: 10.1007/s10495-007-0073-9. PubMed PMID: 17492404; eng. PubMed DOI

Yu C, Wang L, Lv B, et al. TMEM74, a lysosome and autophagosome protein, regulates autophagy. Biochem Biophys Res Commun. 2008. May 2;369(2):622–9. doi: S0006-291X(08)00324-0 [pii] doi:10.1016/j.bbrc.2008.02.055. PubMed PMID: 18294959; eng. PubMed DOI

Bodemann BO, Orvedahl A, Cheng T, et al. RalB and the exocyst mediate the cellular starvation response by direct activation of autophagosome assembly. Cell. 2011. Jan 21;144(2):253–67. doi: S0092-8674(10)01436-4 [pii] doi:10.1016/j.cell.2010.12.018. PubMed PMID: 21241894; eng. PubMed DOI PMC

Singh S, Kumari R, Chinchwadkar S, et al. Exocyst Subcomplex Functions in Autophagosome Biogenesis by Regulating Atg9 Trafficking. J Mol Biol. 2019. Jul 12;431(15):2821–2834. doi: 10.1016/j.jmb.2019.04.048. PubMed PMID: 31103773; PubMed Central PMCID: PMCPMC6698439. PubMed DOI PMC

Abrahamsen H, Stenmark H.. Protein secretion: unconventional exit by exophagy. Curr Biol. 2010. May 11;20(9):R415–8. doi: S0960-9822(10)00292-7 [pii] doi:10.1016/j.cub.2010.03.011. PubMed PMID: 20462486; eng. PubMed DOI

Clucas J, Valderrama F.. ERM proteins in cancer progression. J Cell Sci. 2015. Mar 15;128(6):1253. doi: 10.1242/jcs.170027. PubMed PMID: 25774052. PubMed DOI

Qureshi-Baig K, Kuhn D, Viry E, et al. Hypoxia-induced autophagy drives colorectal cancer initiation and progression by activating the PRKC/PKC-EZR (ezrin) pathway. Autophagy. 2019. Nov 27:1–17. doi:10.1080/15548627.2019.1687213. PubMed PMID: 31775562. PubMed DOI PMC

Pi H, Liu M, Xi Y, et al. Long-term exercise prevents hepatic steatosis: a novel role of FABP1 in regulation of autophagy-lysosomal machinery. FASEB J. 2019. Nov;33(11):11870–11883. doi: 10.1096/fj.201900812R. PubMed PMID: 31366243; PubMed Central PMCID: PMCPMC6902714. PubMed DOI PMC

He L, Ren Y, Zheng Q, et al. Fas-associated protein with death domain (FADD) regulates autophagy through promoting the expression of Ras homolog enriched in brain (Rheb) in human breast adenocarcinoma cells. Oncotarget. 2016. Apr 26;7(17):24572–84. doi: 10.18632/oncotarget.8249. PubMed PMID: 27013580; PubMed Central PMCID: PMCPMC5029724. PubMed DOI PMC

Bell BD, Leverrier S, Weist BM, et al. FADD and caspase-8 control the outcome of autophagic signaling in proliferating T cells. Proc Natl Acad Sci U S A. 2008. Oct 28;105(43):16677–82. doi: 10.1073/pnas.0808597105. PubMed PMID: 18946037; PubMed Central PMCID: PMCPMC2575479. PubMed DOI PMC

Kohno S, Shiozaki Y, Keenan AL, et al. An N-terminal-truncated isoform of FAM134B (FAM134B-2) regulates starvation-induced hepatic selective ER-phagy. Life Sci Alliance. 2019. Jun;2(3). doi: 10.26508/lsa.201900340. PubMed PMID: 31101736; PubMed Central PMCID: PMCPMC6526285. PubMed DOI PMC

Iorio F, Bosotti R, Scacheri E, et al. Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc Natl Acad Sci U S A. 2010. Aug 17;107(33):14621–6. doi: 1000138107 [pii] doi:10.1073/pnas.1000138107. PubMed PMID: 20679242; eng. PubMed DOI PMC

Lisa-Santamaria P, Jimenez A, Revuelta JL.. The protein factor-arrest 11 (Far11) is essential for the toxicity of human caspase-10 in yeast and participates in the regulation of autophagy and the DNA damage signaling. J Biol Chem. 2012. Aug 24;287(35):29636–47. doi: 10.1074/jbc.M112.344192. PubMed PMID: 22782902; PubMed Central PMCID: PMC3436162. PubMed DOI PMC

Furukawa K, Fukuda T, Yamashita SI, et al. The PP2A-like protein phosphatase Ppg1 and the far complex cooperatively counteract CK2-mediated phosphorylation of Atg32 to inhibit mitophagy. Cell Rep. 2018. Jun 19;23(12):3579–3590. doi: 10.1016/j.celrep.2018.05.064. PubMed PMID: 29925000. PubMed DOI

Meng N, Mu X, Lv X, et al. Autophagy represses fascaplysin-induced apoptosis and angiogenesis inhibition via ROS and p8 in vascular endothelia cells. Biomed Pharmacother. 2019. Jun;114:108866. doi: 10.1016/j.biopha.2019.108866. PubMed PMID: 30999113. PubMed DOI

Xu Y, Tian C, Sun J, et al. FBXW7-induced MTOR degradation forces autophagy to counteract persistent prion infection. Mol Neurobiol. 2016. Jan;53(1):706–719. doi: 10.1007/s12035-014-9028-7. PubMed PMID: 25579381. PubMed DOI

Wakatsuki S, Tokunaga S, Shibata M, et al. GSK3B-mediated phosphorylation of MCL1 regulates axonal autophagy to promote Wallerian degeneration. J Cell Biol. 2017. Feb;216(2):477–493. doi: 10.1083/jcb.201606020. PubMed PMID: 28053206; PubMed Central PMCID: PMCPMC5294778. PubMed DOI PMC

McKnight NC, Jefferies HB, Alemu EA, et al. Genome-wide siRNA screen reveals amino acid starvation-induced autophagy requires SCOC and WAC. EMBO J. 2012. Apr 18;31(8):1931–46. doi: 10.1038/emboj.2012.36. PubMed PMID: 22354037; PubMed Central PMCID: PMC3343327. PubMed DOI PMC

Palumbo P, Petracca A, Maggi R, et al. A novel dominant-negative FGFR1 variant causes Hartsfield syndrome by deregulating RAS/ERK1/2 pathway. Eur J Hum Genet. 2019. Jul;27(7):1113–1120. doi: 10.1038/s41431-019-0350-4. PubMed PMID: 30787447; PubMed Central PMCID: PMCPMC6777633. PubMed DOI PMC

Vaccari I, Carbone A, Previtali SC, et al. Loss of Fig4 in both Schwann cells and motor neurons contributes to CMT4J neuropathy. Hum Mol Genet. 2015. Jan 15;24(2):383–96. doi: 10.1093/hmg/ddu451. PubMed PMID: 25187576; PubMed Central PMCID: PMC4275070. PubMed DOI PMC

Jinn TR, Wu CM, Tu WC, et al. Functional expression of FIP-gts, a fungal immunomodulatory protein from Ganoderma tsugae in Sf21 insect cells. Biosci Biotechnol Biochem. 2006. Nov;70(11):2627–34. doi: 10.1271/bbb.60232. PubMed PMID: 17090952. PubMed DOI

Meduri G, Guillemeau K, Dounane O, et al. Caspase-cleaved Tau-D(421) is colocalized with the immunophilin FKBP52 in the autophagy-endolysosomal system of Alzheimer’s disease neurons. Neurobiol Aging. 2016. Oct;46:124–37. doi: 10.1016/j.neurobiolaging.2016.06.017. PubMed PMID: 27479154. PubMed DOI

Romano S, D’Angelillo A, Pacelli R, et al. Role of FK506-binding protein 51 in the control of apoptosis of irradiated melanoma cells. Cell Death Differ. 2010. Jan;17(1):145–57. doi: cdd2009115 [pii] doi:10.1038/cdd.2009.115. PubMed PMID: 19696786; eng. PubMed DOI

Gassen NC, Hartmann J, Zschocke J, et al. Association of FKBP51 with priming of autophagy pathways and mediation of antidepressant treatment response: evidence in cells, mice, and humans. PLoS Med. 2014. Nov;11(11):e1001755. doi: 10.1371/journal.pmed.1001755. PubMed PMID: 25386878; PubMed Central PMCID: PMC4227651. PubMed DOI PMC

Bai X, Ma D, Liu A, et al. Rheb activates mTOR by antagonizing its endogenous inhibitor, FKBP38. Science. 2007. Nov 9;318(5852):977–80. doi: 10.1126/science.1147379. PubMed PMID: 17991864. PubMed DOI

Nickerson ML, Warren MB, Toro JR, et al. Mutations in a novel gene lead to kidney tumors, lung wall defects, and benign tumors of the hair follicle in patients with the Birt-Hogg-Dube syndrome. Cancer cell. 2002. Aug;2(2):157–64. PubMed PMID: 12204536. PubMed

Petit CS, Roczniak-Ferguson A, Ferguson SM.. Recruitment of folliculin to lysosomes supports the amino acid-dependent activation of Rag GTPases. J Cell Biol. 2013. Sep 30;202(7):1107–22. doi: 10.1083/jcb.201307084. PubMed PMID: 24081491; PubMed Central PMCID: PMC3787382. PubMed DOI PMC

Tsun ZY, Bar-Peled L, Chantranupong L, et al. The folliculin tumor suppressor is a GAP for the RagC/D GTPases that signal amino acid levels to mTORC1. Mol Cell. 2013. Nov 21;52(4):495–505. doi: 10.1016/j.molcel.2013.09.016. PubMed PMID: 24095279; PubMed Central PMCID: PMC3867817. PubMed DOI PMC

Huett A, Ng A, Cao Z, et al. A novel hybrid yeast-human network analysis reveals an essential role for FNBP1L in antibacterial autophagy. J Iimmunol. 2009. Apr 15;182(8):4917–30. doi: 182/8/4917 [pii] doi:10.4049/jimmunol.0803050. PubMed PMID: 19342671; PubMed Central PMCID: PMC2752416. eng. PubMed DOI PMC

Zhao Y, Yang J, Liao W, et al. Cytosolic FoxO1 is essential for the induction of autophagy and tumour suppressor activity. Nat Cell Biol. 2010. Jul;12(7):665–75. doi: ncb2069 [pii] doi:10.1038/ncb2069. PubMed PMID: 20543840; eng. PubMed DOI

Hariharan N, Maejima Y, Nakae J, et al. Deacetylation of FoxO by Sirt1 plays an essential role in mediating starvation-induced autophagy in cardiac myocytes. Circ Res. 2010. Dec 10;107(12):1470–82. doi:10.1161/CIRCRESAHA.110.227371. PubMed PMID: 20947830; PubMed Central PMCID: PMC3011986. eng. PubMed DOI PMC

Attaix D, Bechet D.. FoxO3 controls dangerous proteolytic liaisons. Cell Metab. 2007. Dec;6(6):425–7. doi: S1550-4131(07)00340-3 [pii] PubMed

Sun LL, Li M, Suo F, et al. Global analysis of fission yeast mating genes reveals new autophagy factors. PLoS Genet. 2013;9(8):e1003715. doi: 10.1371/journal.pgen.1003715. PubMed PMID: 23950735; PubMed Central PMCID: PMC3738441. PubMed DOI PMC

Zhang Q, Yang W, Man N, et al. Autophagy-mediated chemosensitization in cancer cells by fullerene C60 nanocrystal. Autophagy. 2009. Nov;5(8):1107–17. doi: 10.4161/auto.5.8.9842. PubMed PMID: 19786831. PubMed DOI

Xu J, Wang H, Hu Y, et al. Inhibition of CaMKIIalpha Activity Enhances Antitumor Effect of Fullerene C60 Nanocrystals by Suppression of Autophagic Degradation. Adv Sci (Weinh). 2019. Apr 17;6(8):1801233. doi: 10.1002/advs.201801233. PubMed PMID: 31016106; PubMed Central PMCID: PMCPMC6468974. PubMed DOI PMC

Lim Y, Rubio-Pena K, Sobraske PJ, et al. Fndc-1 contributes to paternal mitochondria elimination in C. elegans. Dev Biol. 2019. Oct 1;454(1):15–20. doi: 10.1016/j.ydbio.2019.06.016. PubMed PMID: 31233739; PubMed Central PMCID: PMCPMC6717525. PubMed DOI PMC

Pankiv S, Alemu EA, Brech A, et al. FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end-directed vesicle transport [Research Support, Non-U.S. Gov’t]. J Cell Biol. 2010. Jan 25;188(2):253–69. doi: 10.1083/jcb.200907015. PubMed PMID: 20100911; PubMed Central PMCID: PMC2812517. eng. PubMed DOI PMC

Lakhani R, Vogel KR, Till A, et al. Defects in GABA metabolism affect selective autophagy pathways and are alleviated by mTOR inhibition. EMBO Mol Med. 2014. Apr;6(4):551–66. doi: 10.1002/emmm.201303356. PubMed PMID: 24578415; PubMed Central PMCID: PMC3992080. PubMed DOI PMC

Tanida I, Tanida-Miyake E, Ueno T, et al. The human homolog of Saccharomyces cerevisiae Apg7p is a Protein-activating enzyme for multiple substrates including human Apg12p, GATE-16, GABARAP, and MAP-LC3. J Biol Chem. 2001. Jan 19;276(3):1701–6. doi: 10.1074/jbc.C000752200 C000752200 [pii]. PubMed PMID: 11096062; eng. PubMed DOI

Saez JC, Berthoud VM, Branes MC, et al. Plasma membrane channels formed by connexins: their regulation and functions. Physiol Rev. 2003. Oct;83(4):1359–400. doi: 10.1152/physrev.00007.2003. PubMed PMID: 14506308. PubMed DOI

Bejarano E, Yuste A, Patel B, et al. Connexins modulate autophagosome biogenesis. Nat Cell Biol. 2014. May;16(5):401–14. doi: 10.1038/ncb2934. PubMed PMID: 24705551; PubMed Central PMCID: PMCPMC4008708. PubMed DOI PMC

Iyyathurai J, Decuypere JP, Leybaert L, et al. Connexins: substrates and regulators of autophagy. BMC Cell Biol. 2016. May 24;17Suppl 1:20. doi: 10.1186/s12860-016-0093-9. PubMed PMID: 27229147; PubMed Central PMCID: PMCPMC4896244. PubMed DOI PMC

Lichtenstein A, Minogue PJ, Beyer EC, et al. Autophagy: a pathway that contributes to connexin degradation. J Cell Sci. 2011. Mar 15;124(Pt 6):910–20. doi: 10.1242/jcs.073072. PubMed PMID: 21378309; PubMed Central PMCID: PMCPMC3048889. PubMed DOI PMC

Gu J, Wang Y, Wang X, et al. Effect of the LncRNA GAS5-MiR-23a-ATG3 axis in regulating autophagy in patients with breast cancer. Cell Physiol Biochem. 2018;48(1):194–207. doi: 10.1159/000491718. PubMed PMID: 30007957. PubMed DOI

Zhang N, Yang GQ, Shao XM, et al. GAS5 modulated autophagy is a mechanism modulating cisplatin sensitivity in NSCLC cells. Eur Rev Med Pharmacol Sci. 2016. Jun;20(11):2271–7. PubMed PMID: 27338051. PubMed

Li L, Huang C, He Y, et al. Knockdown of Long Non-Coding RNA GAS5 Increases miR-23a by Targeting ATG3 Involved in Autophagy and Cell Viability. Cell Physiol Biochem. 2018;48(4):1723–1734. doi: 10.1159/000492300. PubMed PMID: 30078013. PubMed DOI

Mata IF, Samii A, Schneer SH, et al. Glucocerebrosidase gene mutations: a risk factor for Lewy body disorders. Arch Neurol. 2008. Mar;65(3):379–82. doi: 10.1001/archneurol.2007.68. PubMed PMID: 18332251; PubMed Central PMCID: PMC2826203. PubMed DOI PMC

Mitsui J, Mizuta I, Toyoda A, et al. Mutations for Gaucher disease confer high susceptibility to Parkinson disease. Arch Neurol. 2009. May;66(5):571–6. doi: 10.1001/archneurol.2009.72. PubMed PMID: 19433656. PubMed DOI

Sidransky E, Nalls MA, Aasly JO, et al. Multicenter analysis of glucocerebrosidase mutations in Parkinson’s disease. N Engl J Med. 2009. Oct 22;361(17):1651–61. doi: 10.1056/NEJMoa0901281. PubMed PMID: 19846850; PubMed Central PMCID: PMC2856322. PubMed DOI PMC

Osellame LD, Rahim AA, Hargreaves IP, et al. Mitochondria and quality control defects in a mouse model of Gaucher disease--links to Parkinson’s disease. Cell Metab. 2013. Jun 4;17(6):941–53. doi: 10.1016/j.cmet.2013.04.014. PubMed PMID: 23707074; PubMed Central PMCID: PMC3678026. PubMed DOI PMC

Moreau K, Rubinsztein DC.. The plasma membrane as a control center for autophagy. Autophagy. 2012. May 1;8(5):861–3. doi: 10.4161/auto.20060. PubMed PMID: 22617437; PubMed Central PMCID: PMC3378426. PubMed DOI PMC

Todd LR, Damin MN, Gomathinayagam R, et al. Growth factor erv1-like modulates Drp1 to preserve mitochondrial dynamics and function in mouse embryonic stem cells [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Mol Biol Cell. 2010. Apr 1;21(7):1225–36. doi:10.1091/mbc.E09-11-0937. PubMed PMID: 20147447; PubMed Central PMCID: PMC2847526. eng. PubMed DOI PMC

Ferreira-Marques M, Aveleira CA, Carmo-Silva S, et al. Caloric restriction stimulates autophagy in rat cortical neurons through neuropeptide Y and ghrelin receptors activation. Aging (Albany NY). 2016. Jul;8(7):1470–84. doi: 10.18632/aging.100996. PubMed PMID: 27441412; PubMed Central PMCID: PMCPMC4993343. PubMed DOI PMC

Cecarini V, Bonfili L, Cuccioloni M, et al. Effects of Ghrelin on the Proteolytic Pathways of Alzheimer’s Disease Neuronal Cells. Mol Neurobiol. 2016. Jul;53(5):3168–3178. doi: 10.1007/s12035-015-9227-x. PubMed PMID: 26033219. PubMed

Santt O, Pfirrmann T, Braun B, et al. The yeast GID complex, a novel ubiquitin ligase (E3) involved in the regulation of carbohydrate metabolism [Research Support, Non-U.S. Gov’t]. Mol Biol Cell. 2008. Aug;19(8):3323–33. doi: 10.1091/mbc.E08-03-0328. PubMed PMID: 18508925; PubMed Central PMCID: PMC2488282. eng. PubMed DOI PMC

Liu H, Pfirrmann T.. The Gid-complex: an emerging player in the ubiquitin ligase league. Biol Chem. 2019. Oct 25;400(11):1429–1441. doi: 10.1515/hsz-2019-0139. PubMed PMID: 30893051. PubMed DOI

Braun B, Pfirrmann T, Menssen R, et al. Gid9, a second RING finger protein contributes to the ubiquitin ligase activity of the Gid complex required for catabolite degradation. FEBS Lett. 2011. Dec 15;585(24):3856–61. doi: 10.1016/j.febslet.2011.10.038. PubMed PMID: 22044534. PubMed DOI

Chen SJ, Wu X, Wadas B, et al. An N-end rule pathway that recognizes proline and destroys gluconeogenic enzymes. Science. 2017. Jan 27;355(6323). doi: 10.1126/science.aal3655. PubMed PMID: 28126757; PubMed Central PMCID: PMCPMC5457285. PubMed DOI PMC

Menssen R, Schweiggert J, Schreiner J, et al. Exploring the topology of the Gid complex, the E3 ubiquitin ligase involved in catabolite-induced degradation of gluconeogenic enzymes. J Biol Chem. 2012. Jul 20;287(30):25602–14. doi: 10.1074/jbc.M112.363762. PubMed PMID: 22645139; PubMed Central PMCID: PMCPMC3408164. PubMed DOI PMC

Texier Y, Toedt G, Gorza M, et al. Elution profile analysis of SDS-induced subcomplexes by quantitative mass spectrometry. Mol Cell Proteomics. 2014. May;13(5):1382–91. doi: 10.1074/mcp.O113.033233. PubMed PMID: 24563533; PubMed Central PMCID: PMCPMC4014293. PubMed DOI PMC

Pfirrmann T, Villavicencio-Lorini P, Subudhi AK, et al. RMND5 from Xenopus laevis is an E3 ubiquitin-ligase and functions in early embryonic forebrain development. PLoS One. 2015;10(3):e0120342. doi: 10.1371/journal.pone.0120342. PubMed PMID: 25793641; PubMed Central PMCID: PMCPMC4368662. PubMed DOI PMC

Lampert F, Stafa D, Goga A, et al. The multi-subunit GID/CTLH E3 ubiquitin ligase promotes cell proliferation and targets the transcription factor Hbp1 for degradation. eLife. 2018. Jun 18;7. doi: 10.7554/eLife.35528. PubMed PMID: 29911972; PubMed Central PMCID: PMCPMC6037477. PubMed DOI PMC

Liu H, Ding J, Kohnlein K, et al. The GID ubiquitin ligase complex is a regulator of AMPK activity and organismal lifespan. Autophagy. 2019. Dec 3:1–17. doi: 10.1080/15548627.2019.1695399. PubMed PMID: 31795790. PubMed DOI PMC

Villar VH, Duran RV.. Glutamoptosis: A new cell death mechanism inhibited by autophagy during nutritional imbalance. Autophagy. 2017. Jun 3;13(6):1078–1079. doi: 10.1080/15548627.2017.1299315. PubMed PMID: 28296535; PubMed Central PMCID: PMCPMC5486366. PubMed DOI PMC

Villar VH, Nguyen TL, Delcroix V, et al. mTORC1 inhibition in cancer cells protects from glutaminolysis-mediated apoptosis during nutrient limitation. Nat Commun. 2017. Jan 23;8:14124. doi: 10.1038/ncomms14124. PubMed PMID: 28112156; PubMed Central PMCID: PMCPMC5264013. PubMed DOI PMC

Kalamidas SA, Kotoulas OB.. Glycogen autophagy in newborn rat hepatocytes. Histol Histopathol. 2000. Oct;15(4):1011–8. PubMed PMID: 11005224. PubMed

Mellor KM, Varma U, Stapleton DI, et al. Cardiomyocyte glycophagy is regulated by insulin and exposure to high extracellular glucose. Am J Physiol Heart Circ Physiol. 2014. Apr 15;306(8):H1240–5. doi: 10.1152/ajpheart.00059.2014. PubMed PMID: 24561860. PubMed DOI

Delbridge LMD, Mellor KM, Taylor DJ, et al. Myocardial stress and autophagy: mechanisms and potential therapies. Nat Rev Cardiol. 2017. Jul;14(7):412–425. doi: 10.1038/nrcardio.2017.35. PubMed PMID: 28361977; PubMed Central PMCID: PMCPMC6245608. PubMed DOI PMC

Li CH, Ko JL, Ou CC, et al. The protective role of GMI, an immunomodulatory protein from ganoderma microsporum, on 5-fluorouracil-induced oral and intestinal mucositis. Integr Cancer Ther. 2019. Jan-Dec;18:1534735419833795. doi: 10.1177/1534735419833795. PubMed PMID: 30879354; PubMed Central PMCID: PMCPMC6423674. PubMed DOI PMC

Ogier-Denis E, Couvineau A, Maoret JJ, et al. A heterotrimeric Gi3-protein controls autophagic sequestration in the human colon cancer cell line HT-29. J Biol Chem. 1995. Jan 6;270(1):13–6. PubMed PMID: 7814364; eng. PubMed

Ogier-Denis E, Houri JJ, Bauvy C, et al. Guanine nucleotide exchange on heterotrimeric Gi3 protein controls autophagic sequestration in HT-29 cells. J Biol Chem. 1996. Nov 8;271(45):28593–600. PubMed PMID: 8910489; eng. PubMed

Yamaguchi H, Arakawa S, Kanaseki T, et al. Golgi membrane-associated degradation pathway in yeast and mammals. EMBO J. 2016. Sep 15;35(18):1991–2007. doi: 10.15252/embj.201593191. PubMed PMID: 27511903; PubMed Central PMCID: PMCPMC5282831. PubMed DOI PMC

Xiang Y, Wang Y.. GRASP55 and GRASP65 play complementary and essential roles in Golgi cisternal stacking. J Cell Biol. 2010. Jan 25;188(2):237–51. doi: 10.1083/jcb.200907132. PubMed PMID: 20083603; PubMed Central PMCID: PMCPMC2812519. PubMed DOI PMC

Zhang X, Wang L, Ireland SC, et al. GORASP2/GRASP55 collaborates with the PtdIns3K UVRAG complex to facilitate autophagosome-lysosome fusion. Autophagy. 2019. Oct;15(10):1787–1800. doi: 10.1080/15548627.2019.1596480. PubMed PMID: 30894053; PubMed Central PMCID: PMCPMC6735621. PubMed DOI PMC

Zhang X, Wang L, Lak B, et al. GRASP55 senses glucose deprivation through O-GlcNAcylation to promote autophagosome-lysosome fusion. Dev Cell. 2018. Apr 23;45(2):245–261 e6. doi: 10.1016/j.devcel.2018.03.023. PubMed PMID: 29689198. PubMed DOI PMC

Taylor JP. Multisystem proteinopathy: intersecting genetics in muscle, bone, and brain degeneration. Neurology. 2015. Aug 25;85(8):658–60. doi: 10.1212/WNL.0000000000001862. PubMed PMID: 26208960. PubMed DOI

Alberti S, Carra S.. Quality Control of Membraneless Organelles. J Mol Biol. 2018. Nov 2;430(23):4711–4729. doi: 10.1016/j.jmb.2018.05.013. PubMed PMID: 29758260. PubMed DOI

Alberti S, Mateju D, Mediani L, et al. Granulostasis: protein quality control of RNP granules. Front Mol Neurosci. 2017;10:84. doi: 10.3389/fnmol.2017.00084. PubMed PMID: 28396624; PubMed Central PMCID: PMCPMC5367262. PubMed DOI PMC

Baksi S, Bagh S, Sarkar S, et al. Systemic study of a natural feedback loop in Huntington’s disease at the onset of neurodegeneration. Biosystems. 2016. Dec;150:46–51. doi: 10.1016/j.biosystems.2016.08.012. PubMed PMID: 27587340. PubMed DOI

Baksi S, Jana NR, Bhattacharyya NP, et al. Grb2 is regulated by foxd3 and has roles in preventing accumulation and aggregation of mutant huntingtin. PLoS One. 2013;8(10):e76792. doi: 10.1371/journal.pone.0076792. PubMed PMID: 24116161; PubMed Central PMCID: PMCPMC3792889. PubMed DOI PMC

Holler CJ, Taylor G, Deng Q, et al. Intracellular proteolysis of progranulin generates stable, lysosomal granulins that are haploinsufficient in patients with frontotemporal dementia caused by GRN mutations. eNeuro. 2017. Jul-Aug;4(4). doi: 10.1523/ENEURO.0100-17.2017. PubMed PMID: 28828399; PubMed Central PMCID: PMCPMC5562298. PubMed DOI PMC

Chang MC, Srinivasan K, Friedman BA, et al. Progranulin deficiency causes impairment of autophagy and TDP-43 accumulation. J Exp Med. 2017. Sep 4;214(9):2611–2628. doi: 10.1084/jem.20160999. PubMed PMID: 28778989; PubMed Central PMCID: PMCPMC5584112. PubMed DOI PMC

Ward ME, Chen R, Huang HY, et al. Individuals with progranulin haploinsufficiency exhibit features of neuronal ceroid lipofuscinosis. Sci Transl Med. 2017. Apr 12;9(385). doi: 10.1126/scitranslmed.aah5642. PubMed PMID: 28404863; PubMed Central PMCID: PMCPMC5526610. PubMed DOI PMC

Lin SY, Li TY, Liu Q, et al. GSK3-TIP60-ULK1 signaling pathway links growth factor deprivation to autophagy. Science. 2012. Apr 27;336(6080):477–81. doi: 10.1126/science.1217032. PubMed PMID: 22539723. PubMed DOI

Parr C, Carzaniga R, Gentleman SM, et al. Glycogen synthase kinase 3 inhibition promotes lysosomal biogenesis and autophagic degradation of the amyloid-beta precursor protein. Mol Cell Biol. 2012. Nov;32(21):4410–8. doi: 10.1128/MCB.00930-12. PubMed PMID: 22927642; PubMed Central PMCID: PMCPMC3486153. PubMed DOI PMC

Marchand B, Arsenault D, Raymond-Fleury A, et al. Glycogen synthase kinase-3 (GSK3) inhibition induces prosurvival autophagic signals in human pancreatic cancer cells. J Biol Chem. 2015. Feb 27;290(9):5592–605. doi: 10.1074/jbc.M114.616714. PubMed PMID: 25561726; PubMed Central PMCID: PMCPMC4342473. PubMed DOI PMC

Wang W, Wang Q, Wan D, et al. Histone HIST1H1C/H1.2 regulates autophagy in the development of diabetic retinopathy. Autophagy. 2017. May 4;13(5):941–954. doi: 10.1080/15548627.2017.1293768. PubMed PMID: 28409999; PubMed Central PMCID: PMCPMC5446066. PubMed DOI PMC

Bonner WM, Redon CE, Dickey JS, et al. GammaH2AX and cancer. Nat Rev Cancer. 2008. Dec;8(12):957–67. doi: 10.1038/nrc2523. PubMed PMID: 19005492; PubMed Central PMCID: PMCPMC3094856. PubMed DOI PMC

Cerezo M, Lehraiki A, Millet A, et al. Compounds Triggering ER Stress Exert Anti-Melanoma Effects and Overcome BRAF Inhibitor Resistance. Cancer cell. 2016. Jun 13;29(6):805–819. doi: 10.1016/j.ccell.2016.04.013. PubMed PMID: 27238082. PubMed DOI

Cerezo M, Rocchi S.. New anti-cancer molecules targeting HSPA5/BIP to induce endoplasmic reticulum stress, autophagy and apoptosis. Autophagy. 2017. Jan 2;13(1):216–217. doi: 10.1080/15548627.2016.1246107. PubMed PMID: 27791469; PubMed Central PMCID: PMCPMC5240825. PubMed DOI PMC

Yue F, Li W, Zou J, et al. Blocking the association of HDAC4 with MAP1S accelerates autophagy clearance of mutant Huntingtin. Aging (Albany NY). 2015. Oct;7(10):839–53. doi: 10.18632/aging.100818. PubMed PMID: 26540094; PubMed Central PMCID: PMCPMC4637209. PubMed DOI PMC

Lee JY, Koga H, Kawaguchi Y, et al. HDAC6 controls autophagosome maturation essential for ubiquitin-selective quality-control autophagy. EMBO J. 2010. Mar 3;29(5):969–80. doi: 10.1038/emboj.2009.405. PubMed PMID: 20075865; PubMed Central PMCID: PMC2837169. eng. PubMed DOI PMC

Cecarini V, Bonfili L, Cuccioloni M, et al. Crosstalk between the ubiquitin-proteasome system and autophagy in a human cellular model of Alzheimer’s disease. Biochim Biophys Acta. 2012. Nov;1822(11):1741–51. doi: 10.1016/j.bbadis.2012.07.015. PubMed PMID: 22867901. PubMed DOI

Ridinger J, Koeneke E, Kolbinger FR, et al. Dual role of HDAC10 in lysosomal exocytosis and DNA repair promotes neuroblastoma chemoresistance. Sci Rep. 2018. Jul 3;8(1):10039. doi: 10.1038/s41598-018-28265-5. PubMed PMID: 29968769; PubMed Central PMCID: PMCPMC6030077. PubMed DOI PMC

Oehme I, Linke JP, Bock BC, et al. Histone deacetylase 10 promotes autophagy-mediated cell survival. Proc Natl Acad Sci U S A. 2013. Jul 9;110(28):E2592–601. doi: 10.1073/pnas.1300113110. PubMed PMID: 23801752; PubMed Central PMCID: PMCPMC3710791. PubMed DOI PMC

Masson GR, Burke JE, Ahn NG, et al. Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods. 2019. Jul;16(7):595–602. doi: 10.1038/s41592-019-0459-y. PubMed PMID: 31249422; PubMed Central PMCID: PMCPMC6614034. PubMed DOI PMC

Liu XM, Yamasaki A, Du XM, et al. Lipidation-independent vacuolar functions of Atg8 rely on its noncanonical interaction with a vacuole membrane protein. eLife. 2018. Nov 19;7. doi: 10.7554/eLife.41237. PubMed PMID: 30451685; PubMed Central PMCID: PMCPMC6279349. PubMed DOI PMC

Dehne N, Brune B.. HIF-1 in the inflammatory microenvironment. Exp Cell Res. 2009. Jul 1;315(11):1791–7. doi: 10.1016/j.yexcr.2009.03.019. PubMed PMID: 19332053. PubMed DOI

Neubert P, Weichselbaum A, Reitinger C, et al. HIF1A and NFAT5 coordinate Na(+)-boosted antibacterial defense via enhanced autophagy and autolysosomal targeting. Autophagy. 2019. Nov;15(11):1899–1916. doi: 10.1080/15548627.2019.1596483. PubMed PMID: 30982460; PubMed Central PMCID: PMCPMC6844503. PubMed DOI PMC

Bohensky J, Shapiro IM, Leshinsky S, et al. HIF-1 regulation of chondrocyte apoptosis: induction of the autophagic pathway. Autophagy. 2007. May-Jun;3(3):207–14. doi: 3708 [pii]. PubMed PMID: 17224629; eng. PubMed

Mellor HR, Harris AL.. The role of the hypoxia-inducible BH3-only proteins BNIP3 and BNIP3L in cancer. Cancer Metastasis Rev. 2007. Dec; 26 (3–4): 553–66. doi: 10.1007/s10555-007-9080-0. PubMed PMID: 17805942; eng. PubMed DOI

Mimouna S, Bazin M, Mograbi B, et al. HIF1A regulates xenophagic degradation of adherent and invasive Escherichia coli (AIEC). Autophagy. 2014;10(12):2333–45. doi: 10.4161/15548627.2014.984275. PubMed PMID: 25484075; PubMed Central PMCID: PMC4502747. PubMed DOI PMC

Yuan J, Pu M, Zhang Z, et al. Histone H3-K56 acetylation is important for genomic stability in mammals. Cell cycle. 2009. Jun 1;8(11):1747–53. doi: 10.4161/cc.8.11.8620. PubMed PMID: 19411844; PubMed Central PMCID: PMCPMC2776713. PubMed DOI PMC

Roberts DJ, Miyamoto S.. Hexokinase II integrates energy metabolism and cellular protection: Akting on mitochondria and TORCing to autophagy. Cell Death Differ. 2015. Feb;22(2):248–57. doi: 10.1038/cdd.2014.173. PubMed PMID: 25323588; PubMed Central PMCID: PMC4291497. PubMed DOI PMC

Liau SS, Jazag A, Ito K, et al. Overexpression of HMGA1 promotes anoikis resistance and constitutive Akt activation in pancreatic adenocarcinoma cells. Br J Cancer. 2007. Mar 26;96(6):993–1000. doi: 10.1038/sj.bjc.6603654. PubMed PMID: 17342093; PubMed Central PMCID: PMCPMC2360112. PubMed DOI PMC

Tang D, Kang R, Cheh CW, et al. HMGB1 release and redox regulates autophagy and apoptosis in cancer cells. Oncogene. 2010. Sep 23;29(38):5299–310. doi: 10.1038/onc.2010.261. PubMed PMID: 20622903; PubMed Central PMCID: PMC2945431. eng. PubMed DOI PMC

Thorburn J, Horita H, Redzic J, et al. Autophagy regulates selective HMGB1 release in tumor cells that are destined to die [Research Support, N.I.H., Extramural]. Cell Death Differ. 2009. Jan;16(1):175–83. doi: 10.1038/cdd.2008.143. PubMed PMID: 18846108; PubMed Central PMCID: PMC2605182. eng. PubMed DOI PMC

Khambu B, Huda N, Chen X, et al. HMGB1 promotes ductular reaction and tumorigenesis in autophagy-deficient livers. J Clin Invest. 2018. Jun 1;128(6):2419–2435. doi: 10.1172/JCI91814. PubMed PMID: 29558368; PubMed Central PMCID: PMCPMC5983330. PubMed DOI PMC

Suliman HB, Keenan JE, Piantadosi CA.. Mitochondrial quality-control dysregulation in conditional HO-1(-/-) mice. JCI Insight. 2017. Feb 9;2(3):e89676. doi: 10.1172/jci.insight.89676. PubMed PMID: 28194437; PubMed Central PMCID: PMCPMC5291731. PubMed DOI PMC

Wang CW, Stromhaug PE, Kauffman EJ, et al. Yeast homotypic vacuole fusion requires the Ccz1-Mon1 complex during the tethering/docking stage. J Cell Biol. 2003. Dec 8;163(5):973–85. doi: 10.1083/jcb.200308071. PubMed PMID: 14662743; PubMed Central PMCID: PMCPMC1705953. PubMed DOI PMC

Takats S, Pircs K, Nagy P, et al. Interaction of the HOPS complex with Syntaxin 17 mediates autophagosome clearance in Drosophila. Mol Biol Cell. 2014. Apr;25(8):1338–54. doi: 10.1091/mbc.E13-08-0449. PubMed PMID: 24554766; PubMed Central PMCID: PMCPMC3982998. PubMed DOI PMC

Jiang P, Nishimura T, Sakamaki Y, et al. The HOPS complex mediates autophagosome-lysosome fusion through interaction with syntaxin 17. Mol Biol Cell. 2014. Apr;25(8):1327–37. doi: 10.1091/mbc.E13-08-0447. PubMed PMID: 24554770; PubMed Central PMCID: PMCPMC3982997. PubMed DOI PMC

Chen ZH, Wang WT, Huang W, et al. The lncRNA HOTAIRM1 regulates the degradation of PML-RARA oncoprotein and myeloid cell differentiation by enhancing the autophagy pathway. Cell Death Differ. 2017. Feb;24(2):212–224. doi: 10.1038/cdd.2016.111. PubMed PMID: 27740626; PubMed Central PMCID: PMCPMC5299705. PubMed DOI PMC

Velentzas PD, Zhang L, Das G, et al. The proton-coupled monocarboxylate transporter hermes is necessary for autophagy during cell death. Dev Cell. 2018. Nov 5;47(3):281–293 e4. doi: 10.1016/j.devcel.2018.09.015. PubMed PMID: 30318245; PubMed Central PMCID: PMCPMC6219939. PubMed DOI PMC

Pfaffenwimmer T, Reiter W, Brach T, et al. Hrr25 kinase promotes selective autophagy by phosphorylating the cargo receptor Atg19. EMBO Rep. 2014. Aug;15(8):862–70. doi: 10.15252/embr.201438932. PubMed PMID: 24968893. PubMed DOI PMC

Tanaka C, Tan LJ, Mochida K, et al. Hrr25 triggers selective autophagy-related pathways by phosphorylating receptor proteins. J Cell Biol. 2014. Oct 13;207(1):91–105. doi: 10.1083/jcb.201402128. PubMed PMID: 25287303; PubMed Central PMCID: PMC4195827. PubMed DOI PMC

Mochida K, Ohsumi Y, Nakatogawa H.. Hrr25 phosphorylates the autophagic receptor Atg34 to promote vacuolar transport of alpha-mannosidase under nitrogen starvation conditions. FEBS Lett. 2014. Nov 3;588(21):3862–9. doi: 10.1016/j.febslet.2014.09.032. PubMed PMID: 25281559. PubMed DOI

Holland P, Knaevelsrud H, Soreng K, et al. HS1BP3 negatively regulates autophagy by modulation of phosphatidic acid levels. Nat Commun. 2016. Dec 22;7:13889. doi: 10.1038/ncomms13889. PubMed PMID: 28004827; PubMed Central PMCID: PMCPMC5412012. PubMed DOI PMC

Choutka C, DeVorkin L, Go NE, et al. Hsp83 loss suppresses proteasomal activity resulting in an upregulation of caspase-dependent compensatory autophagy.. Autophagy. 2017. Sep 2;13(9):1573–1589. doi: 10.1080/15548627.2017.1339004. PubMed PMID: 28806103; PubMed Central PMCID: PMCPMC5612217. PubMed DOI PMC

Leu JI, Pimkina J, Frank A, et al. A small molecule inhibitor of inducible heat shock protein 70. Mol Cell. 2009. Oct 9;36(1):15–27. doi: 10.1016/j.molcel.2009.09.023. PubMed PMID: 19818706; PubMed Central PMCID: PMC2771108. PubMed DOI PMC

Li J, Ni M, Lee B, et al. The unfolded protein response regulator GRP78/BiP is required for endoplasmic reticulum integrity and stress-induced autophagy in mammalian cells. Cell Death Differ. 2008. Sep;15(9):1460–71. doi: 10.1038/cdd.2008.81. PubMed PMID: 18551133; PubMed Central PMCID: PMC2758056. PubMed DOI PMC

Cha-Molstad H, Sung KS, Hwang J, et al. Amino-terminal arginylation targets endoplasmic reticulum chaperone BiP for autophagy through p62 binding. Nat Cell Biol. 2015. Jul;17(7):917–29. doi: 10.1038/ncb3177. PubMed PMID: 26075355; PubMed Central PMCID: PMCPMC4490096. PubMed DOI PMC

Kwon DH, Park OH, Kim L, et al. Insights into degradation mechanism of N-end rule substrates by p62/SQSTM1 autophagy adapter. Nat Commun. 2018. Aug 17;9(1):3291. doi: 10.1038/s41467-018-05825-x. PubMed PMID: 30120248; PubMed Central PMCID: PMCPMC6098011. PubMed PMC

Chiang HL, Terlecky SR, Plant CP, et al. A role for a 70-kilodalton heat shock protein in lysosomal degradation of intracellular proteins [Research Support, U.S. Gov’t, P.H.S.]. Science. 1989. Oct 20;246(4928):382–5. PubMed PMID: 2799391; eng. PubMed

Kaushik S, Massey AC, Cuervo AM.. Lysosome membrane lipid microdomains: novel regulators of chaperone-mediated autophagy. EMBO J. 2006. Aug 17;25:3921–3933. PubMed PMID: 16917501. PubMed PMC

Garcia-Mata R, Gao YS, Sztul E.. Hassles with taking out the garbage: aggravating aggresomes. Traffic. 2002. Jun;3(6):388–96. PubMed PMID: 12010457. PubMed

Thirumalaikumar VP, Wagner M, Balazadeh S, et al. Autophagy is responsible for the accumulation of proteogenic dipeptides in response to heat stress in Arabidopsis thaliana. FEBS J. 2020. Apr 17. doi: 10.1111/febs.15336. PubMed PMID: 32301545. PubMed DOI

Xu C, Liu J, Hsu LC, et al. Functional interaction of heat shock protein 90 and Beclin 1 modulates Toll-like receptor-mediated autophagy. FASEB J. 2011. Aug;25(8):2700–10. doi: 10.1096/fj.10-167676. PubMed PMID: 21543763; PubMed Central PMCID: PMC3136344. PubMed DOI PMC

Bandhyopadhyay U, Kaushik S, Vartikovsky L, et al. Dynamic organization of the receptor for chaperone-mediated autophagy at the lysosomal membrane. Mol Cell Biol. 2008;28:5747–63. PubMed PMC

Haidar M, Asselbergh B, Adriaenssens E, et al. Neuropathy-causing mutations in HSPB1 impair autophagy by disturbing the formation of SQSTM1/p62 bodies.. Autophagy. 2019. Jun;15(6):1051–1068. doi: 10.1080/15548627.2019.1569930. PubMed PMID: 30669930; PubMed Central PMCID: PMCPMC6526868. PubMed DOI PMC

Cicardi ME, Cristofani R, Rusmini P, et al. Tdp-25 routing to autophagy and proteasome ameliorates its aggregation in amyotrophic lateral sclerosis target cells. Sci Rep. 2018. Aug 17;8(1):12390. doi: 10.1038/s41598-018-29658-2. PubMed PMID: 30120266; PubMed Central PMCID: PMCPMC6098007. PubMed DOI PMC

Crippa V, Sau D, Rusmini P, et al. The small heat shock protein B8 (HspB8) promotes autophagic removal of misfolded proteins involved in amyotrophic lateral sclerosis (ALS). Hum Mol Genet. 2010. Sep 1;19(17):3440–56. doi: 10.1093/hmg/ddq257. PubMed PMID: 20570967. PubMed DOI

Li B, Hu Q, Wang H, et al. Omi/HtrA2 is a positive regulator of autophagy that facilitates the degradation of mutant proteins involved in neurodegenerative diseases. Cell Death Differ. 2010. May 14;17:1773–84. doi: cdd201055 [pii] doi10.1038/cdd.2010.55. PubMed PMID: 20467442; Eng. PubMed DOI

Cilenti L, Ambivero CT, Ward N, et al. Inactivation of Omi/HtrA2 protease leads to the deregulation of mitochondrial Mulan E3 ubiquitin ligase and increased mitophagy. Biochim Biophys Acta. 2014. Jul;1843(7):1295–307. doi: 10.1016/j.bbamcr.2014.03.027. PubMed PMID: 24709290. PubMed DOI

Kang S, Fernandes-Alnemri T, Alnemri ES.. A novel role for the mitochondrial HTRA2/OMI protease in aging. Autophagy. 2013. Mar;9(3):420–1. doi: 10.4161/auto.22920. PubMed PMID: 23242108; PubMed Central PMCID: PMC3590264. PubMed DOI PMC

Kang S, Louboutin JP, Datta P, et al. Loss of HtrA2/Omi activity in non-neuronal tissues of adult mice causes premature aging. Cell Death Differ. 2013. Feb;20(2):259–69. doi: 10.1038/cdd.2012.117. PubMed PMID: 22976834; PubMed Central PMCID: PMC3554338. PubMed DOI PMC

Ravikumar B, Duden R, Rubinsztein DC.. Aggregate-prone proteins with polyglutamine and polyalanine expansions are degraded by autophagy. Hum Mol Genet. 2002. May 1;11(9):1107–17. doi: 10.1093/hmg/11.9.1107. PubMed PMID: 11978769. PubMed DOI

Franich NR, Basso M, Andre EA, et al. Striatal mutant huntingtin protein levels decline with age in homozygous huntington’s disease knock-in mouse models. J Huntingtons Dis. 2018;7(2):137–150. doi: 10.3233/JHD-170274. PubMed PMID: 29843246; PubMed Central PMCID: PMCPMC6002862. PubMed DOI PMC

Yamamoto A, Cremona ML, Rothman JE.. Autophagy-mediated clearance of huntingtin aggregates triggered by the insulin-signaling pathway. J Cell Biol. 2006. Feb 27;172(5):719–31. doi: 10.1083/jcb.200510065. PubMed PMID: 16505167; PubMed Central PMCID: PMCPMC2063704. PubMed DOI PMC

Jeong H, Then F, Melia TJ, Jr., et al. Acetylation targets mutant huntingtin to auto-phagosomes for degradation. Cell. 2009. Apr 3;137(1):60–72. doi: 10.1016/j.cell.2009.03.018. PubMed PMID: 19345187; PubMed Central PMCID: PMCPMC2940108. PubMed DOI PMC

Filimonenko M, Isakson P, Finley KD, et al. The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. Mol Cell. 2010. Apr 23;38(2):265–79. doi:10.1016/j.molcel.2010.04.007. PubMed PMID: 20417604; PubMed Central PMCID: PMC2867245. eng. PubMed DOI PMC

Thompson LM, Aiken CT, Kaltenbach LS, et al. IKK phosphorylates Huntingtin and targets it for degradation by the proteasome and lysosome. J Cell Biol. 2009. Dec 28;187(7):1083–99. doi: 10.1083/jcb.200909067. PubMed PMID: 20026656; PubMed Central PMCID: PMCPMC2806289. PubMed DOI PMC

Ochaba J, Fote G, Kachemov M, et al. IKKbeta slows Huntington’s disease progression in R6/1 mice. Proc Natl Acad Sci U S A. 2019. May 28;116(22):10952–10961. doi: 10.1073/pnas.1814246116. PubMed PMID: 31088970; PubMed Central PMCID: PMCPMC6561205. PubMed DOI PMC

Al-Ramahi I, Giridharan SSP, Chen YC, et al. Inhibition of PIP4Kgamma ameliorates the pathological effects of mutant huntingtin protein. eLife. 2017. Dec 26;6. doi: 10.7554/eLife.29123. PubMed PMID: 29256861; PubMed Central PMCID: PMCPMC5743427. PubMed DOI PMC

Tsunemi T, Ashe TD, Morrison BE, et al. PGC-1alpha rescues Huntington’s disease proteotoxicity by preventing oxidative stress and promoting TFEB function. Sci Transl Med. 2012. Jul 11;4(142):142ra97. doi: 10.1126/scitranslmed.3003799. PubMed PMID: 22786682; PubMed Central PMCID: PMCPMC4096245. PubMed DOI PMC

Wong YC, Holzbaur EL.. The regulation of autophagosome dynamics by huntingtin and HAP1 is disrupted by expression of mutant huntingtin, leading to defective cargo degradation. J Neurosci. 2014. Jan 22;34(4):1293–305. doi: 10.1523/JNEUROSCI.1870-13.2014. PubMed PMID: 24453320; PubMed Central PMCID: PMCPMC3898289. PubMed DOI PMC

Caviston JP, Ross JL, Antony SM, et al. Huntingtin facilitates dynein/dynactin-mediated vesicle transport. Proc Natl Acad Sci U S A. 2007. Jun 12;104(24):10045–50. doi: 10.1073/pnas.0610628104. PubMed PMID: 17548833; PubMed Central PMCID: PMCPMC1891230. PubMed DOI PMC

Rui YN, Xu Z, Patel B, et al. Huntingtin functions as a scaffold for selective macroautophagy. Nat Cell Biol. 2015. Mar;17(3):262–75. doi: 10.1038/ncb3101. PubMed PMID: 25686248; PubMed Central PMCID: PMCPMC4344873. PubMed DOI PMC

Coll NS, Smidler A, Puigvert M, et al. The plant metacaspase AtMC1 in pathogen-triggered programmed cell death and aging: functional linkage with autophagy. Cell Death Differ. 2014. Sep;21(9):1399–408. doi: 10.1038/cdd.2014.50. PubMed PMID: 24786830; PubMed Central PMCID: PMC4131171. PubMed DOI PMC

Choudhury KR, Bucha S, Baksi S, et al. Chaperone-like protein HYPK and its interacting partners augment autophagy. Eur J Cell Biol. 2016. Jun-Jul; 95 (6–7): 182–94. doi: 10.1016/j.ejcb.2016.03.003. PubMed PMID: 27067261. PubMed DOI

Kim J, Cheon H, Jeong YT, et al. Amyloidogenic peptide oligomer accumulation in autophagy-deficient beta cells induces diabetes. J Clin Invest. 2014. Aug;124(8):3311–24. doi: 10.1172/JCI69625. PubMed PMID: 25036705; PubMed Central PMCID: PMC4109549. PubMed DOI PMC

Rivera JF, Costes S, Gurlo T, et al. Autophagy defends pancreatic beta cells from human islet amyloid polypeptide-induced toxicity. J Clin Invest. 2014. Aug;124(8):3489–500. doi: 10.1172/JCI71981. PubMed PMID: 25036708; PubMed Central PMCID: PMC4109537. PubMed DOI PMC

Shigihara N, Fukunaka A, Hara A, et al. Human IAPP-induced pancreatic beta cell toxicity and its regulation by autophagy. J Clin Invest. 2014. Aug;124(8):3634–44. doi: 10.1172/JCI69866. PubMed PMID: 25036706; PubMed Central PMCID: PMC4109539. PubMed DOI PMC

Lotze MT, Buchser WJ, Liang X.. Blocking the interleukin 2 (IL2)-induced systemic autophagic syndrome promotes profound antitumor effects and limits toxicity. Autophagy. 2012. Aug;8(8):1264–6. doi: 10.4161/auto.20752. PubMed PMID: 22660171. PubMed DOI

Campbell-Valois FX, Sachse M, Sansonetti PJ, et al. Escape of actively secreting shigella flexneri from ATG8/LC3-positive vacuoles formed during cell-to-cell spread is facilitated by IcsB and VirA. mBio. 2015. May 26;6(3):e02567–14. doi: 10.1128/mBio.02567-14. PubMed PMID: 26015503; PubMed Central PMCID: PMCPMC4447254. PubMed DOI PMC

Liu W, Zhou Y, Peng T, et al. N(epsilon)-fatty acylation of multiple membrane-associated proteins by Shigella IcsB effector to modulate host function. Nat Microbiol. 2018. Sep;3(9):996–1009. doi: 10.1038/s41564-018-0215-6. PubMed PMID: 30061757; PubMed Central PMCID: PMCPMC6466622. PubMed DOI PMC

Dunker AK, Lawson JD, Brown CJ, et al. Intrinsically disordered protein. J Mol Graph Model. 2001;19(1):26–59. PubMed PMID: 11381529. PubMed

Tompa P. Intrinsically unstructured proteins. Trends Biochem Sci. 2002. Oct;27(10):527–33. PubMed PMID: 12368089. PubMed

Uversky VN, Gillespie JR, Fink AL.. Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins. 2000. Nov 15;41(3):415–27. PubMed PMID: 11025552. PubMed

Peng Z, Yan J, Fan X, et al. Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life. Cell Mol Life Sci. 2015. Jan;72(1):137–51. doi: 10.1007/s00018-014-1661-9. PubMed PMID: 24939692. PubMed DOI PMC

De Guzman RN, Wojciak JM, Martinez-Yamout MA, et al. CBP/p300 TAZ1 domain forms a structured scaffold for ligand binding. Biochemistry. 2005. Jan 18;44(2):490–7. doi: 10.1021/bi048161t. PubMed PMID: 15641773. PubMed DOI

Dunker AK, Brown CJ, Lawson JD, et al. Intrinsic disorder and protein function. Biochemistry. 2002. May 28;41(21):6573–82. PubMed PMID: 12022860. PubMed

Dunker AK, Silman I, Uversky VN, et al. Function and structure of inherently disordered proteins. Curr Opin Struct Biol. 2008. Dec;18(6):756–64. doi: 10.1016/j.sbi.2008.10.002. PubMed PMID: 18952168. PubMed DOI

Tompa P. The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett. 2005. Jun 13;579(15):3346–54. doi: 10.1016/j.febslet.2005.03.072. PubMed PMID: 15943980. PubMed DOI

Peng Z, Xue B, Kurgan L, et al. Resilience of death: intrinsic disorder in proteins involved in the programmed cell death. Cell Death Differ. 2013. Sep;20(9):1257–67. doi: 10.1038/cdd.2013.65. PubMed PMID: 23764774; PubMed Central PMCID: PMC3741502. PubMed DOI PMC

Popelka H, Uversky VN, Klionsky DJ.. Identification of Atg3 as an intrinsically disordered polypeptide yields insights into the molecular dynamics of autophagy-related proteins in yeast.. Autophagy. 2014. Jun;10(6):1093–104. doi: 10.4161/auto.28616. PubMed PMID: 24879155; PubMed Central PMCID: PMC4091170. PubMed DOI PMC

van der Lee R, Buljan M, Lang B, et al. Classification of intrinsically disordered regions and proteins. Chem Rev. 2014. Jul 9;114(13):6589–631. doi: 10.1021/cr400525m. PubMed PMID: 24773235; PubMed Central PMCID: PMC4095912. PubMed DOI PMC

Uversky VN. Intrinsic disorder-based protein interactions and their modulators. Curr Pharm Des. 2013;19(23):4191–213. PubMed PMID: 23170892. PubMed

Pejaver V, Hsu WL, Xin F, et al. The structural and functional signatures of proteins that undergo multiple events of post-translational modification. Protein Sci. 2014. Aug;23(8):1077–93. doi: 10.1002/pro.2494. PubMed PMID: 24888500; PubMed Central PMCID: PMC4116656. PubMed DOI PMC

Chiang HS, Maric M.. Lysosomal thiol reductase negatively regulates autophagy by altering glutathione synthesis and oxidation. Free Radic Biol Med. 2011. Aug 1;51(3):688–99. doi: 10.1016/j.freeradbiomed.2011.05.015. PubMed PMID: 21640818. PubMed DOI

Pampliega O, Orhon I, Patel B, et al. Functional interaction between autophagy and ciliogenesis. Nature. 2013. Oct 10;502(7470):194–200. doi: 10.1038/nature12639. PubMed PMID: 24089209; PubMed Central PMCID: PMCPMC3896125. PubMed DOI PMC

Finetti F, Cassioli C, Cianfanelli V, et al. The intraflagellar transport protein IFT20 controls lysosome biogenesis by regulating the post-Golgi transport of acid hydrolases. Cell Death Differ. 2020. Jan;27(1):310–328. doi: 10.1038/s41418-019-0357-y. PubMed PMID: 31142807. PubMed DOI PMC

Criollo A, Senovilla L, Authier H, et al. The IKK complex contributes to the induction of autophagy. EMBO J. 2010. Feb 3;29(3):619–31. doi: emboj2009364 [pii] doi:10.1038/emboj.2009.364. PubMed PMID: 19959994; eng. PubMed DOI PMC

Pang M, Wang H, Rao P, et al. Autophagy links beta-catenin and Smad signaling to promote epithelial-mesenchymal transition via upregulation of integrin linked kinase. Int J Biochem Cell Biol. 2016. Jul;76:123–34. doi: 10.1016/j.biocel.2016.05.010. PubMed PMID: 27177845. PubMed DOI

Wu X, Tu BP.. Selective regulation of autophagy by the Iml1-Npr2-Npr3 complex in the absence of nitrogen starvation. Mol Biol Cell. 2011. Nov;22(21):4124–33. doi: 10.1091/mbc.E11-06-0525. PubMed PMID: 21900499; PubMed Central PMCID: PMC3204073. PubMed DOI PMC

Blanchet FP, Moris A, Nikolic DS, et al. Human immunodeficiency virus-1 inhibition of immunoamphisomes in dendritic cells impairs early innate and adaptive immune responses. Immunity. 2010. May 28;32(5):654–69. doi: S1074-7613(10)00160-3 [pii] doi:10.1016/j.immuni.2010.04.011. PubMed PMID: 20451412; eng. PubMed DOI PMC

Deretic V. Autophagy in innate and adaptive immunity. Trends Immunol. 2005. Oct;26(10):523–8. doi: S1471-4906(05)00206-1 [pii] doi:10.1016/j.it.2005.08.003. PubMed PMID: 16099218; eng. PubMed DOI

Piippo N, Korhonen E, Hytti M, et al. Hsp90 inhibition as a means to inhibit activation of the NLRP3 inflammasome. Sci Rep. 2018. Apr 30;8(1):6720. doi: 10.1038/s41598-018-25123-2. PubMed PMID: 29712950; PubMed Central PMCID: PMCPMC5928092. PubMed DOI PMC

Piippo N, Korkmaz A, Hytti M, et al. Decline in cellular clearance systems induces inflammasome signaling in human ARPE-19 cells. Biochim Biophys Acta. 2014. Dec;1843(12):3038–46. doi: 10.1016/j.bbamcr.2014.09.015. PubMed PMID: 25268952. PubMed DOI

Yuan X, Bhat OM, Meng N, et al. Protective role of autophagy in Nlrp3 inflammasome activation and medial thickening of mouse coronary arteries. Am J Pathol. 2018. Dec;188(12):2948–2959. doi: 10.1016/j.ajpath.2018.08.014. PubMed PMID: 30273598; PubMed Central PMCID: PMCPMC6334256. PubMed DOI PMC

Seveau S, Turner J, Gavrilin MA, et al. Checks and balances between autophagy and inflammasomes during infection. J Mol Biol. 2018. Jan 19;430(2):174–192. doi: 10.1016/j.jmb.2017.11.006. PubMed PMID: 29162504; PubMed Central PMCID: PMCPMC5766433. PubMed DOI PMC

Dennis EA, Norris PC.. Eicosanoid storm in infection and inflammation. Nat Rev Immunol. 2015. Aug;15(8):511–23. doi: 10.1038/nri3859. PubMed PMID: 26139350; PubMed Central PMCID: PMCPMC4606863. PubMed DOI PMC

Nathan C, Ding A.. Nonresolving inflammation. Cell. 2010. Mar 19;140(6):871–82. doi: 10.1016/j.cell.2010.02.029. PubMed PMID: 20303877. PubMed DOI

Chiurchiu V, Leuti A, Maccarrone M.. Bioactive lipids and chronic inflammation: managing the fire within. Front Immunol. 2018;9:38. doi: 10.3389/fimmu.2018.00038. PubMed PMID: 29434586; PubMed Central PMCID: PMCPMC5797284. PubMed DOI PMC

Matsuzawa-Ishimoto Y, Hwang S, Cadwell K.. Autophagy and Inflammation. Annu Rev Immunol. 2018. Apr 26;36:73–101. doi: 10.1146/annurev-immunol-042617-053253. PubMed PMID: 29144836. PubMed DOI

Dortet L, Mostowy S, Samba-Louaka A, et al. Recruitment of the major vault protein by InlK: a Listeria monocytogenes strategy to avoid autophagy. PLoS Pathog. 2011. Aug;7(8):e1002168. doi: 10.1371/journal.ppat.1002168. PubMed PMID: 21829365; PubMed Central PMCID: PMC3150275. PubMed DOI PMC

Raj K, Tissue-specific Sarkar S.. upregulation of Drosophila insulin receptor (InR) mitigates poly(q)-mediated neurotoxicity by restoration of cellular transcription machinery. Mol Neurobiol. 2019. Feb;56(2):1310–1329. doi: 10.1007/s12035-018-1160-3. PubMed PMID: 29881950. PubMed DOI

Ravikumar B, Sarkar S, Davies JE, et al. Regulation of mammalian autophagy in physiology and pathophysiology. Physiol Rev. 2010;90(4):1383–1435. doi: 10.1152/physrev.00030.2009. PubMed DOI

Nelson C, Ambros V, Baehrecke EH.. miR-14 regulates autophagy during developmental cell death by targeting ip3-kinase 2. Mol Cell. 2014. Nov 6;56(3):376–88. doi: 10.1016/j.molcel.2014.09.011. PubMed PMID: 25306920; PubMed Central PMCID: PMCPMC4252298. PubMed DOI PMC

Singh SB, Davis AS, Taylor GA, et al. Human IRGM induces autophagy to eliminate intracellular mycobacteria. Science. 2006. Sep 8;313(5792):1438–41. PubMed PMID: 16888103; eng PubMed

Chauhan S, Mandell MA, Deretic V.. IRGM governs the core autophagy machinery to conduct antimicrobial defense. Mol Cell. 2015. May 7;58(3):507–21. doi: 10.1016/j.molcel.2015.03.020. PubMed PMID: 25891078; PubMed Central PMCID: PMCPMC4427528. PubMed DOI PMC

Mehto S, Jena KK, Nath P, et al. The Crohn’s disease risk factor IRGM limits NLRP3 inflammasome activation by impeding its assembly and by mediating its selective autophagy. Mol Cell. 2019. Feb 7;73(3):429–445 e7. doi: 10.1016/j.molcel.2018.11.018. PubMed PMID: 30612879; PubMed Central PMCID: PMCPMC6372082. PubMed DOI PMC

Gregoire IP, Richetta C, Meyniel-Schicklin L, et al. IRGM is a common target of RNA viruses that subvert the autophagy network. PLoS Pathog. 2011. Dec;7(12):e1002422. doi: 10.1371/journal.ppat.1002422. PubMed PMID: 22174682; PubMed Central PMCID: PMCPMC3234227. PubMed DOI PMC

Bugnicourt A, Mari M, Reggiori F, et al. Irs4p and Tax4p: two redundant EH domain proteins involved in autophagy. Traffic. 2008. May;9(5):755–69. doi: 10.1111/j.1600-0854.2008.00715.x. PubMed PMID: 18298591. PubMed DOI

Namkoong S, Lee KI, Lee JI, et al. The integral membrane protein ITM2A, a transcriptional target of PKA-CREB, regulates autophagic flux via interaction with the vacuolar ATPase. Autophagy. 2015;11(5):756–68. doi: 10.1080/15548627.2015.1034412. PubMed PMID: 25951193; PubMed Central PMCID: PMC4502675. PubMed DOI PMC

Ivanova H, Vervliet T, Monaco G, et al. Bcl-2-protein family as modulators of IP3 receptors and other organellar Ca(2+) channels. Cold Spring Harb Perspect Biol. 2020; 12(4):a035089. doi: 10.1101/cshperspect.a035089. PubMed PMID: 31501195; PubMed Central PMCID: PMC7111250. PubMed DOI PMC

Bittremieux M, Parys JB, Pinton P, et al. ER functions of oncogenes and tumor suppressors: Modulators of intracellular Ca(2+) signaling. Biochim Biophys Acta. 2016. Jun;1863(6 Pt B):1364–78. doi: 10.1016/j.bbamcr.2016.01.002. PubMed PMID: 26772784. PubMed DOI

Filadi R, Leal NS, Schreiner B, et al. TOM70 sustains cell bioenergetics by promoting IP3R3-mediated ER to mitochondria Ca(2+) transfer. Curr Biol. 2018. Feb 5;28(3):369–382 e6. doi: 10.1016/j.cub.2017.12.047. PubMed PMID: 29395920. PubMed DOI

Yogev O, Goldberg R, Anzi S, et al. Jun proteins are starvation-regulated inhibitors of autophagy. Cancer Res. 2010. Mar 15;70(6):2318–27. doi: 10.1158/0008-5472.CAN-09-3408. PubMed PMID: 20197466. PubMed DOI

Taylor R, Jr., Chen PH, Chou CC, et al. KCS1 deletion in Saccharomyces cerevisiae leads to a defect in translocation of autophagic proteins and reduces autophagosome formation. Autophagy. 2012. Sep;8(9):1300–11. doi: 10.4161/auto.20681. PubMed PMID: 22889849; PubMed Central PMCID: PMC3442877. PubMed DOI PMC

Ambrosio S, Sacca CD, Amente S, et al. Lysine-specific demethylase LSD1 regulates autophagy in neuroblastoma through SESN2-dependent pathway. Oncogene. 2017. Nov 30;36(48):6701–6711. doi: 10.1038/onc.2017.267. PubMed PMID: 28783174; PubMed Central PMCID: PMCPMC5717079. PubMed DOI PMC

Abdel-Aziz AK, Pallavicini I, Ceccacci E, et al. Tuning mTORC1 activity dictates the response of acute myeloid leukemia to LSD1 inhibition. Haematologica. 2019. Sep 19. doi: 10.3324/haematol.2019.224501. PubMed PMID: 31537694. PubMed DOI PMC

Chao A, Lin CY, Chao AN, et al. Lysine-specific demethylase 1 (LSD1) destabilizes p62 and inhibits autophagy in gynecologic malignancies. Oncotarget. 2017. Sep 26;8(43):74434–74450. doi: 10.18632/oncotarget.20158. PubMed PMID: 29088798; PubMed Central PMCID: PMCPMC5650353. PubMed DOI PMC

Zhao E, Tang C, Jiang X, et al. Inhibition of cell proliferation and induction of autophagy by KDM2B/FBXL10 knockdown in gastric cancer cells. Cell Signal. 2017. Aug;36:222–229. doi: 10.1016/j.cellsig.2017.05.011. PubMed PMID: 28506929. PubMed DOI

Lee DF, Kuo HP, Liu M, et al. KEAP1 E3 ligase-mediated downregulation of NF-kappaB signaling by targeting IKKbeta. Mol Cell. 2009. Oct 9;36(1):131–40. doi: 10.1016/j.molcel.2009.07.025. PubMed PMID: 19818716; PubMed Central PMCID: PMC2770835. PubMed DOI PMC

Stepkowski TM, Kruszewski MK.. Molecular cross-talk between the NRF2/KEAP1 signaling pathway, autophagy, and apoptosis. Free Radic Biol Med. 2011. May 1;50(9):1186–95. doi: 10.1016/j.freeradbiomed.2011.01.033. PubMed PMID: 21295136. PubMed DOI

Orenstein SJ, Cuervo AM.. Chaperone-mediated autophagy: molecular mechanisms and physiological relevance. Semin Cell Dev Biol. 2010. Sep;21(7):719–26. doi: 10.1016/j.semcdb.2010.02.005. PubMed PMID: 20176123; PubMed Central PMCID: PMCPMC2914824. PubMed DOI PMC

Bejarano E, Murray JW, Wang X, et al. Defective recruitment of motor proteins to autophagic compartments contributes to autophagic failure in aging. Aging cell. 2018. Aug;17(4):e12777. doi: 10.1111/acel.12777. PubMed PMID: 29845728; PubMed Central PMCID: PMCPMC6052466. PubMed DOI PMC

Mytych J, Solek P, Tabecka-Lonczynska A, et al. Klotho-mediated changes in shelterin complex promote cytotoxic autophagy and apoptosis in amitriptyline-treated hippocampal neuronal cells. Mol Neurobiol. 2019. Oct;56(10):6952–6963. doi: 10.1007/s12035-019-1575-5. PubMed PMID: 30945158. PubMed DOI

Mytych J, Solek P, Koziorowski M.. Klotho modulates ER-mediated signaling crosstalk between prosurvival autophagy and apoptotic cell death during LPS challenge. Apoptosis. 2019. Feb;24(1–2):95–107. doi: 10.1007/s10495-018-1496-1. PubMed PMID: 30357572. PubMed DOI

Mauvezin C, Neisch AL, Ayala CI, et al. Coordination of autophagosome-lysosome fusion and transport by a Klp98A-Rab14 complex in Drosophila. J Cell Sci. 2016. Mar 1;129(5):971–82. doi: 10.1242/jcs.175224. PubMed PMID: 26763909; PubMed Central PMCID: PMCPMC4813314. PubMed DOI PMC

Zhang K, Wang M, Tamayo AT, et al. Novel selective inhibitors of nuclear export CRM1 antagonists for therapy in mantle cell lymphoma. Exp Hematol. 2013. Jan;41(1):67–78 e4. doi: 10.1016/j.exphem.2012.09.002. PubMed PMID: 22986101. PubMed DOI

Bryant KL, Stalnecker CA, Zeitouni D, et al. Combination of ERK and autophagy inhibition as a treatment approach for pancreatic cancer. Nat Med. 2019. Apr;25(4):628–640. doi: 10.1038/s41591-019-0368-8. PubMed PMID: 30833752; PubMed Central PMCID: PMCPMC6484853. PubMed DOI PMC

Feng MM, Baryla J, Liu H, et al. Cytoprotective effect of lacritin on human corneal epithelial cells exposed to benzalkonium chloride in vitro. Curr Eye Res. 2014. Jun;39(6):604–10. doi: 10.3109/02713683.2013.859275. PubMed PMID: 24401093; PubMed Central PMCID: PMC4371594. PubMed DOI PMC

Ma P, Beck SL, Raab RW, et al. Heparanase deglycanation of syndecan-1 is required for binding of the epithelial-restricted prosecretory mitogen lacritin. J Cell Biol. 2006. Sep 25;174(7):1097–106. doi: 10.1083/jcb.200511134. PubMed PMID: 16982797; PubMed Central PMCID: PMC1666580. PubMed DOI PMC

Wang N, Zimmerman K, Raab RW, et al. Lacritin rescues stressed epithelia via rapid forkhead box O3 (FOXO3)-associated autophagy that restores metabolism. J Biol Chem. 2013. Jun 21;288(25):18146–61. doi: 10.1074/jbc.M112.436584. PubMed PMID: 23640897; PubMed Central PMCID: PMC3689958. PubMed DOI PMC

Tuohetahuntila M, Molenaar MR, Spee B, et al. Lysosome-mediated degradation of a distinct pool of lipid droplets during hepatic stellate cell activation. J Biol Chem. 2017. Jul 28;292(30):12436–12448. doi: 10.1074/jbc.M117.778472. PubMed PMID: 28615446; PubMed Central PMCID: PMCPMC5535019. PubMed DOI PMC

Wiersma VI, van Ziel AM, Vazquez-Sanchez S, et al. Granulovacuolar degeneration bodies are neuron-selective lysosomal structures induced by intracellular tau pathology. Acta Neuropathol. 2019. Dec;138(6):943–970. doi: 10.1007/s00401-019-02046-4. PubMed PMID: 31456031; PubMed Central PMCID: PMCPMC6851499. PubMed DOI PMC

Li C, Wang X, Li X, et al. Proteasome inhibition activates autophagy-lysosome pathway associated with TFEB dephosphorylation and nuclear translocation. Front Cell Dev Biol 2019;7:170. doi: 10.3389/fcell.2019.00170. PubMed PMID: 31508418; PubMed Central PMCID: PMCPMC6713995. PubMed DOI PMC

Tanaka Y, Guhde G, Suter A, et al. Accumulation of autophagic vacuoles and cardiomyopathy in Lamp-2-deficient mice. Nature. 2000;406:902–906. PubMed

Nishino I, Fu J, Tanji K, et al. Primary LAMP-2 deficiency causes X-linked vacuolar cardiomyopathy and myopathy (Danon disease). Nature. 2000. Aug 24;406(6798):906–10. doi: 10.1038/35022604. PubMed PMID: 10972294. PubMed DOI

Wang WT, Han C, Sun YM, et al. Activation of the lysosome-associated membrane protein LAMP5 by DOT1L serves as a bodyguard for MLL fusion oncoproteins to evade degradation in leukemia. clin cancer res off j am assoc cancer res. 2019. May 1;25(9):2795–2808. doi: 10.1158/1078-0432.CCR-18-1474. PubMed PMID: 30651276. PubMed DOI

Hayashi K, Taura M, Iwasaki A.. The interaction between IKKalpha and LC3 promotes type I interferon production through the TLR9-containing LAPosome. Sci Signal. 2018. May 1;11(528). doi: 10.1126/scisignal.aan4144. PubMed PMID: 29717061; PubMed Central PMCID: PMCPMC6462218. PubMed DOI PMC

Ma J, Becker C, Lowell CA, et al. Dectin-1-triggered recruitment of light chain 3 protein to phagosomes facilitates major histocompatibility complex class II presentation of fungal-derived antigens. J Biol Chem. 2012. Oct 5;287(41):34149–56. doi: 10.1074/jbc.M112.382812. PubMed PMID: 22902620; PubMed Central PMCID: PMCPMC3464523. PubMed DOI PMC

Ma J, Becker C, Reyes C, et al. Cutting edge: FYCO1 recruitment to dectin-1 phagosomes is accelerated by light chain 3 protein and regulates phagosome maturation and reactive oxygen production. J Iimmunol. 2014. Feb 15;192(4):1356–60. doi: 10.4049/jimmunol.1302835. PubMed PMID: 24442442; PubMed Central PMCID: PMCPMC3966112. PubMed DOI PMC

Tam JM, Mansour MK, Khan NS, et al. Dectin-1-dependent LC3 recruitment to phagosomes enhances fungicidal activity in macrophages. J Infect Dis. 2014. Dec 1;210(11):1844–54. doi: 10.1093/infdis/jiu290. PubMed PMID: 24842831; PubMed Central PMCID: PMCPMC4271056. PubMed DOI PMC

Lamprinaki D, Beasy G, Zhekova A, et al. LC3-associated phagocytosis is required for dendritic cell inflammatory cytokine response to gut commensal yeast Saccharomyces cerevisiae. Front Immunol. 2017;8:1397. doi: 10.3389/fimmu.2017.01397. PubMed PMID: 29118762; PubMed Central PMCID: PMCPMC5661120. PubMed DOI PMC

Huang J, Canadien V, Lam GY, et al. Activation of antibacterial autophagy by NADPH oxidases [Research Support, Non-U.S. Gov’t]. Proc Natl Acad Sci U S A. 2009. Apr 14;106(15):6226–31. doi: 10.1073/pnas.0811045106. PubMed PMID: 19339495; PubMed Central PMCID: PMC2664152. eng. PubMed DOI PMC

Monisha J, Roy NK, Padmavathi G, et al. NGAL is downregulated in oral squamous cell carcinoma and leads to increased survival, proliferation, migration and chemoresistance. Cancers (Basel). 2018. Jul 10;10(7). doi: 10.3390/cancers10070228. PubMed PMID: 29996471; PubMed Central PMCID: PMCPMC6071146. PubMed DOI PMC

Aits S, Kricker J, Liu B, et al. Sensitive detection of lysosomal membrane permeabilization by lysosomal galectin puncta assay. Autophagy. 2015;11(8):1408–24. doi: 10.1080/15548627.2015.1063871. PubMed PMID: 26114578; PubMed Central PMCID: PMCPMC4590643. PubMed DOI PMC

Chauhan S, Kumar S, Jain A, et al. TRIMs and galectins globally cooperate and TRIM16 and galectin-3 co-direct autophagy in endomembrane damage homeostasis. Dev Cell. 2016. Oct 10;39(1):13–27. doi: 10.1016/j.devcel.2016.08.003. PubMed PMID: 27693506; PubMed Central PMCID: PMCPMC5104201. PubMed DOI PMC

Kim BW, Hong SB, Kim JH, et al. Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8. Nat Commun. 2013;4:1613. doi: 10.1038/ncomms2606. PubMed PMID: 23511477. PubMed DOI

Tsai JP, Lee CH, Ying TH, et al. Licochalcone A induces autophagy through PI3K/Akt/mTOR inactivation and autophagy suppression enhances Licochalcone A-induced apoptosis of human cervical cancer cells. Oncotarget. 2015. Oct 6;6(30):28851–66. doi: 10.18632/oncotarget.4767. PubMed PMID: 26311737; PubMed Central PMCID: PMCPMC4745696. PubMed DOI PMC

Esterbauer H. Estimation of peroxidative damage. A critical review. Pathol Biol. 1996. Jan;44(1):25–8. PubMed PMID: 8734296. PubMed

Dodson M, Wani WY, Redmann M, et al. Regulation of autophagy, mitochondrial dynamics, and cellular bioenergetics by 4-hydroxynonenal in primary neurons. Autophagy. 2017;13(11):1828–1840. doi: 10.1080/15548627.2017.1356948. PubMed PMID: 28837411; PubMed Central PMCID: PMCPMC5788494. PubMed DOI PMC

Zhang Y, Li X, Carpinteiro A, et al. Acid sphingomyelinase amplifies redox signaling in Pseudomonas aeruginosa-induced macrophage apoptosis. J Iimmunol. 2008. Sep 15;181(6):4247–54. doi: 10.4049/jimmunol.181.6.4247. PubMed PMID: 18768882. PubMed DOI

Osawa T, Noda NN.. Atg2: A novel phospholipid transfer protein that mediates de novo autophagosome biogenesis. Protein Sci. 2019. Jun;28(6):1005–1012. doi: 10.1002/pro.3623. PubMed PMID: 30993752; PubMed Central PMCID: PMCPMC6511744. PubMed DOI PMC

Lee AJ, Roylance R, Sander J, et al. CERT depletion predicts chemotherapy benefit and mediates cytotoxic and polyploid-specific cancer cell death through autophagy induction. J Pathol. 2012. Feb;226(3):482–94. doi: 10.1002/path.2998. PubMed PMID: 21953249. PubMed DOI

Mao D, Lin G, Tepe B, et al. VAMP associated proteins are required for autophagic and lysosomal degradation by promoting a PtdIns4P-mediated endosomal pathway. Autophagy. 2019. Jul;15(7):1214–1233. doi: 10.1080/15548627.2019.1580103. PubMed PMID: 30741620; PubMed Central PMCID: PMCPMC6613884. PubMed DOI PMC

Arlia-Ciommo A, Leonov A, Beach A, et al. Caloric restriction delays yeast chronological aging by remodeling carbohydrate and lipid metabolism, altering peroxisomal and mitochondrial functionalities, and postponing the onsets of apoptotic and liponecrotic modes of regulated cell death. Oncotarget. 2018. Mar 23;9(22):16163–16184. doi: 10.18632/oncotarget.24604. PubMed PMID: 29662634; PubMed Central PMCID: PMCPMC5882325. PubMed DOI PMC

Arlia-Ciommo A, Leonov A, Mohammad K, et al. Mechanisms through which lithocholic acid delays yeast chronological aging under caloric restriction conditions. Oncotarget. 2018. Oct 9;9(79):34945–34971. doi: 10.18632/oncotarget.26188. PubMed PMID: 30405886; PubMed Central PMCID: PMCPMC6201858. PubMed DOI PMC

Lam T, Harmancey R, Vasquez H, et al. Reversal of intramyocellular lipid accumulation by lipophagy and a p62-mediated pathway. Cell Death Discov 2016;2:16061. doi: 10.1038/cddiscovery.2016.61. PubMed PMID: 27625792; PubMed Central PMCID: PMCPMC4993124. PubMed DOI PMC

Popelka H, Klionsky DJ.. Analysis of the native conformation of the LIR/AIM motif in the Atg8/LC3/GABARAP-binding proteins. Autophagy. 2015;11(12):2153–9. doi: 10.1080/15548627.2015.1111503. PubMed PMID: 26565669; PubMed Central PMCID: PMCPMC4835208. PubMed DOI PMC

Bertolo C, Roa S, Sagardoy A, et al. LITAF, a BCL6 target gene, regulates autophagy in mature B-cell lymphomas. Br J Haematol. 2013. Sep;162(5):621–30. doi: 10.1111/bjh.12440. PubMed PMID: 23795761; PubMed Central PMCID: PMC4111142. PubMed DOI PMC

Boya P. Lysosomal function and dysfunction: mechanism and disease. Antioxid Redox Signal. 2012. Sep 1;17(5):766–74. doi: 10.1089/ars.2011.4405. PubMed PMID: 22098160. PubMed DOI

Gabande-Rodriguez E, Boya P, Labrador V, et al. High sphingomyelin levels induce lysosomal damage and autophagy dysfunction in Niemann Pick disease type A. Cell Death Differ. 2014. Jun;21(6):864–75. doi: 10.1038/cdd.2014.4. PubMed PMID: 24488099; PubMed Central PMCID: PMC4013520. PubMed DOI PMC

Kagan JC. Lipopolysaccharide Detection across the Kingdoms of Life. Trends Immunol. 2017. Oct;38(10):696–704. doi: 10.1016/j.it.2017.05.001. PubMed PMID: 28551077; PubMed Central PMCID: PMCPMC5624813. PubMed DOI PMC

Chen M, Liu J, Yang W, et al. Lipopolysaccharide mediates hepatic stellate cell activation by regulating autophagy and retinoic acid signaling. Autophagy. 2017;13(11):1813–1827. doi: 10.1080/15548627.2017.1356550. PubMed PMID: 29160747; PubMed Central PMCID: PMCPMC5788469. PubMed DOI PMC

Doyle A, Zhang G, Abdel Fattah EA, et al. Toll-like receptor 4 mediates lipopolysaccharide-induced muscle catabolism via coordinate activation of ubiquitin-proteasome and autophagy-lysosome pathways. FASEB J. 2011. Jan;25(1):99–110. doi: 10.1096/fj.10-164152. PubMed PMID: 20826541; PubMed Central PMCID: PMCPMC3005430. PubMed DOI PMC

Carew JS, Espitia CM, Esquivel JA, II, et al. Lucanthone is a novel inhibitor of autophagy that induces cathepsin D-mediated apoptosis [Research Support, Non-U.S. Gov’t]. J Biol Chem. 2011. Feb 25;286(8):6602–13. doi: 10.1074/jbc.M110.151324. PubMed PMID: 21148553; PubMed Central PMCID: PMC3057822. eng. PubMed DOI PMC

Martinez Jaramillo C, Trujillo-Vargas CM.. LRBA in the endomembrane system. Colomb Med (Cali). 2018. Sep 30;49(3):236–243. doi: 10.25100/cm.v49i2.3802. PubMed PMID: 30410199; PubMed Central PMCID: PMCPMC6220489. PubMed DOI PMC

Joyce S, Nour AM.. Blocking transmembrane219 protein signaling inhibits autophagy and restores normal cell death. PLoS One 2019;14(6):e0218091. doi: 10.1371/journal.pone.0218091. PubMed PMID: 31220095; PubMed Central PMCID: PMCPMC6586287. PubMed DOI PMC

Zou J, Yue F, Jiang X, et al. Mitochondrion-associated protein LRPPRC suppresses the initiation of basal levels of autophagy via enhancing Bcl-2 stability. Biochem J. 2013. Sep 15;454(3):447–57. doi: 10.1042/BJ20130306. PubMed PMID: 23822101; PubMed Central PMCID: PMC3778712. PubMed DOI PMC

Zou J, Yue F, Li W, et al. Autophagy inhibitor LRPPRC suppresses mitophagy through interaction with mitophagy initiator Parkin. PLoS One. 2014;9(4):e94903. doi: 10.1371/journal.pone.0094903. PubMed PMID: 24722279; PubMed Central PMCID: PMC3983268. PubMed DOI PMC

Alegre-Abarrategui J, Christian H, Lufino MM, et al. LRRK2 regulates autophagic activity and localizes to specific membrane microdomains in a novel human genomic reporter cellular model. Hum Mol Genet. 2009. Nov 1;18(21):4022–34. doi: 10.1093/hmg/ddp346. PubMed PMID: 19640926; PubMed Central PMCID: PMC2758136. eng. PubMed DOI PMC

Verma M, Callio J, Otero PA, et al. Mitochondrial Calcium Dysregulation Contributes to Dendrite Degeneration Mediated by PD/LBD-Associated LRRK2 Mutants. J Neurosci. 2017. Nov 15;37(46):11151–11165. doi: 10.1523/JNEUROSCI.3791-16.2017. PubMed PMID: 29038245; PubMed Central PMCID: PMCPMC5688524. PubMed DOI PMC

Steger M, Tonelli F, Ito G, et al. Phosphoproteomics reveals that Parkinson’s disease kinase LRRK2 regulates a subset of Rab GTPases. eLife. 2016. Jan 29;5. doi: 10.7554/eLife.12813. PubMed PMID: 26824392; PubMed Central PMCID: PMCPMC4769169. PubMed DOI PMC

Eguchi T, Kuwahara T, Sakurai M, et al. LRRK2 and its substrate Rab GTPases are sequentially targeted onto stressed lysosomes and maintain their homeostasis. Proc Natl Acad Sci U S A. 2018. Sep 25;115(39):E9115–E9124. doi: 10.1073/pnas.1812196115. PubMed PMID: 30209220; PubMed Central PMCID: PMCPMC6166828. PubMed DOI PMC

Ng ACY, Eisenberg JM, Heath RJW, et al. Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity. Proc Natl Acad Sci USA 2011. Jun 29;108:4631–4638. PubMed PMID: 20616063; Eng. PubMed PMC

Blommaart EF, Krause U, Schellens JP, et al. The phosphatidylinositol 3-kinase inhibitors wortmannin and LY294002 inhibit autophagy in isolated rat hepatocytes. Eur J Biochem FEBS 1997. Jan 15;243(1–2):240–6. PubMed PMID: 9030745. PubMed

McAfee Q, Zhang Z, Samanta A, et al. Autophagy inhibitor Lys05 has single-agent antitumor activity and reproduces the phenotype of a genetic autophagy deficiency. Proc Natl Acad Sci U S A. 2012. May 22;109(21):8253–8. doi: 10.1073/pnas.1118193109. PubMed PMID: 22566612; PubMed Central PMCID: PMC3361415. PubMed DOI PMC

Amaravadi RK, Winkler JD.. Lys05: a new lysosomal autophagy inhibitor. Autophagy. 2012. Sep;8(9):1383–4. doi: 10.4161/auto.20958. PubMed PMID: 22878685; PubMed Central PMCID: PMC3442884. PubMed DOI PMC

Villamil Giraldo AM, Appelqvist H, Ederth T, et al. Lysosomotropic agents: impact on lysosomal membrane permeabilization and cell death. Biochem Soc Trans. 2014. Oct;42(5):1460–4. doi: 10.1042/BST20140145. PubMed PMID: 25233432. PubMed DOI

Pineda CT, Ramanathan S, Fon Tacer K, et al. Degradation of AMPK by a Cancer-Specific Ubiquitin Ligase. Cell. 2015. Feb 12;160(4):715–28. doi: 10.1016/j.cell.2015.01.034. PubMed PMID: 25679763. PubMed DOI PMC

Bai H, Inoue J, Kawano T, et al. A transcriptional variant of the LC3A gene is involved in autophagy and frequently inactivated in human cancers. Oncogene. 2012. Oct 4;31(40):4397–408. doi: 10.1038/onc.2011.613. PubMed PMID: 22249245. PubMed DOI

Nassar M, Samaha H, Ghabriel M, et al. LC3A silencing hinders aggresome vimentin cage clearance in primary choroid plexus carcinoma. Sci Rep. 2017. Aug 14;7(1):8022. doi: 10.1038/s41598-017-07403-5. PubMed PMID: 28808307; PubMed Central PMCID: PMCPMC5556083. PubMed DOI PMC

Mann SS, Hammarback JA.. Molecular characterization of light chain 3. A microtubule binding subunit of MAP1A and MAP1B. J Biol Chem. 1994. Apr 15;269(15):11492–7. PubMed PMID: 7908909. PubMed

Xie R, Nguyen S, McKeehan K, et al. Microtubule-associated protein 1S (MAP1S) bridges autophagic components with microtubules and mitochondria to affect autophagosomal biogenesis and degradation. J Biol Chem. 2011. Mar 25;286(12):10367–77. doi: 10.1074/jbc.M110.206532. PubMed PMID: 21262964; PubMed Central PMCID: PMC3060490. PubMed DOI PMC

Liu W, Jiang Y, Sun J, et al. Activation of TGF-beta-activated kinase 1 (TAK1) restricts Salmonella Typhimurium growth by inducing AMPK activation and autophagy. Cell Death Dis. 2018. May 1;9(5):570. doi: 10.1038/s41419-018-0612-z. PubMed PMID: 29752434; PubMed Central PMCID: PMCPMC5948208. PubMed DOI PMC

Sheng T, Sun Y, Sun J, et al. Role of TGF-beta-activated kinase 1 (TAK1) activation in H5N1 influenza A virus-induced c-Jun terminal kinase activation and virus replication. Virology. 2019. Nov;537:263–271. doi: 10.1016/j.virol.2019.09.004. PubMed PMID: 31539775. PubMed DOI

Liu W, Zhuang J, Jiang Y, et al. Toll-like receptor signalling cross-activates the autophagic pathway to restrict Salmonella Typhimurium growth in macrophages. Cell Microbiol. 2019. Dec;21(12):e13095. doi: 10.1111/cmi.13095. PubMed PMID: 31392811. PubMed DOI

Herrero-Martin G, Hoyer-Hansen M, Garcia-Garcia C, et al. TAK1 activates AMPK-dependent cytoprotective autophagy in TRAIL-treated epithelial cells. EMBO J. 2009. Mar 18;28(6):677–85. doi: 10.1038/emboj.2009.8. PubMed PMID: 19197243; PubMed Central PMCID: PMC2666037. eng. PubMed DOI PMC

Hashimoto K, Simmons AN, Kajino-Sakamoto R, et al. TAK1 regulates the Nrf2 antioxidant system through modulating p62/SQSTM1. Antioxid Redox Signal. 2016. Dec 10;25(17):953–964. doi: 10.1089/ars.2016.6663. PubMed PMID: 27245349; PubMed Central PMCID: PMCPMC5144887. PubMed DOI PMC

Kehl SR, Soos BA, Saha B, et al. TAK1 converts Sequestosome 1/p62 from an autophagy receptor to a signaling platform. EMBO Rep. 2019. Sep;20(9):e46238. doi: 10.15252/embr.201846238. PubMed PMID: 31347268; PubMed Central PMCID: PMCPMC6726904. PubMed DOI PMC

Hsu CL, Lee EX, Gordon KL, et al. MAP4K3 mediates amino acid-dependent regulation of autophagy via phosphorylation of TFEB. Nat Commun. 2018. Mar 5;9(1):942. doi: 10.1038/s41467-018-03340-7. PubMed PMID: 29507340; PubMed Central PMCID: PMCPMC5838220. PubMed DOI PMC

Ogier-Denis E, Pattingre S, El Benna J, et al. Erk1/2-dependent phosphorylation of Galpha-interacting protein stimulates its GTPase accelerating activity and autophagy in human colon cancer cells. J Biol Chem. 2000. Dec 15;275(50):39090–5. doi: 10.1074/jbc.M006198200M006198200[pii]. PubMed PMID: 10993892; eng. PubMed DOI

Fu MM, Nirschl JJ, Holzbaur EL.. LC3 binding to the scaffolding protein JIP1 regulates processive dynein-driven transport of auto-phagosomes. Dev Cell. 2014. Jun 9;29(5):577–90. doi: 10.1016/j.devcel.2014.04.015. PubMed PMID: 24914561. PubMed DOI PMC

Raciti M, Lotti LV, Valia S, et al. JNK2 is activated during ER stress and promotes cell survival. Cell Death Dis. 2012;3:e429. doi: 10.1038/cddis.2012.167. PubMed PMID: 23171849; PubMed Central PMCID: PMC3542603. PubMed DOI PMC

Keil E, Hocker R, Schuster M, et al. Phosphorylation of Atg5 by the Gadd45beta-MEKK4-p38 pathway inhibits autophagy. Cell Death Differ. 2013. Feb;20(2):321–32. doi: 10.1038/cdd.2012.129. PubMed PMID: 23059785; PubMed Central PMCID: PMC3554344. PubMed DOI PMC

Menon MB, Dhamija S, Kotlyarov A, et al. The problem of pyridinyl imidazole class inhibitors of MAPK14/p38alpha and MAPK11/p38beta in autophagy research. Autophagy. 2015. Aug 3;11(8):1425–7. doi: 10.1080/15548627.2015.1059562. PubMed PMID: 26061537. PubMed DOI PMC

Menon MB, Kotlyarov A, Gaestel M.. SB202190-induced cell type-specific vacuole formation and defective autophagy do not depend on p38 MAP kinase inhibition. PLoS One. 2011;6(8):e23054. doi: 10.1371/journal.pone.0023054. PubMed PMID: 21853067; PubMed Central PMCID: PMC3154272. PubMed DOI PMC

Colecchia D, Dapporto F, Tronnolone S, et al. MAPK15 is part of the ULK complex and controls its activity to regulate early phases of the autophagic process. J Biol Chem. 2018. Oct 12;293(41):15962–15976. doi: 10.1074/jbc.RA118.002527. PubMed PMID: 30131341; PubMed Central PMCID: PMCPMC6187625. PubMed DOI PMC

Wang Z, Zhang J, Wang Y, et al. Matrine, a novel autophagy inhibitor, blocks trafficking and the proteolytic activation of lysosomal proteases. Carcinogenesis. 2013. Jan;34(1):128–38. doi: 10.1093/carcin/bgs295. PubMed PMID: 23002236. PubMed DOI

Elgendy M, Ciro M, Abdel-Aziz AK, et al. Beclin 1 restrains tumorigenesis through Mcl-1 destabilization in an autophagy-independent reciprocal manner. Nat Commun. 2014. Dec 4;5:5637. doi: 10.1038/ncomms6637. PubMed PMID: 25472497. PubMed DOI

Elgendy M, Minucci S.. A novel autophagy-independent, oncosuppressive function of BECN1: Degradation of MCL1. Autophagy. 2015;11(3):581–2. doi: 10.1080/15548627.2015.1029836. PubMed PMID: 25837021; PubMed Central PMCID: PMCPMC4502650. PubMed DOI PMC

Fliniaux I, Germain E, Farfariello V, et al. TRPs and Ca(2+) in cell death and survival. Cell Calcium. 2018. Jan;69:4–18. doi: 10.1016/j.ceca.2017.07.002. PubMed PMID: 28760561. PubMed DOI

Di Paola S, Scotto-Rosato A, Medina DL.. TRPML1: The Ca((2+))retaker of the lysosome. Cell Calcium. 2018. Jan;69:112–121. doi: 10.1016/j.ceca.2017.06.006. PubMed PMID: 28689729. PubMed DOI

Scotto Rosato A, Montefusco S, Soldati C, et al. TRPML1 links lysosomal calcium to autophagosome biogenesis through the activation of the CaMKKbeta/VPS34 pathway. Nat Commun. 2019. Dec 10;10(1):5630. doi: 10.1038/s41467-019-13572-w. PubMed PMID: 31822666; PubMed Central PMCID: PMCPMC6904751. PubMed DOI PMC

Li RJ, Xu J, Fu C, et al. Regulation of mTORC1 by lysosomal calcium and calmodulin. eLife. 2016. Oct 27;5. 10.7554/eLife.19360 PubMed PMID: 27787197; PubMed Central PMCID: PMCPMC5106211. PubMed DOI PMC

Venkatachalam K, Wong CO, Zhu MX.. The role of TRPMLs in endolysosomal trafficking and function. Cell Calcium. 2015. Jul;58(1):48–56. doi: 10.1016/j.ceca.2014.10.008. PubMed PMID: 25465891; PubMed Central PMCID: PMCPMC4412768. PubMed DOI PMC

Lorente M, Torres S, Salazar M, et al. Stimulation of ALK by the growth factor midkine renders glioma cells resistant to autophagy-mediated cell death. Autophagy. 2011. Sep;7(9):1071–3. PubMed PMID: 21593591. PubMed

Lorente M, Torres S, Salazar M, et al. Stimulation of the midkine/ALK axis renders glioma cells resistant to cannabinoid antitumoral action. Cell Death Differ. 2011. Jun;18(6):959–73. doi: 10.1038/cdd.2010.170. PubMed PMID: 21233844; PubMed Central PMCID: PMC3131933. PubMed DOI PMC

Kimura T, Jain A, Choi SW, et al. TRIM-mediated precision autophagy targets cytoplasmic regulators of innate immunity. J Cell Biol. 2015. Sep 14;210(6):973–89. doi: 10.1083/jcb.201503023. PubMed PMID: 26347139; PubMed Central PMCID: PMCPMC4576868. PubMed DOI PMC

van Doorn WG, Woltering EJ.. Many ways to exit? Cell death categories in plants. Trends Plant Sci. 2005. Mar;10(3):117–22. doi: 10.1016/j.tplants.2005.01.006. PubMed PMID: 15749469. PubMed DOI

Bagniewska-Zadworna A, Byczyk J, Eissenstat DM, et al. Avoiding transport bottlenecks in an expanding root system: xylem vessel development in fibrous and pioneer roots under field conditions. Am J Bot. 2012. Sep;99(9):1417–26. doi: 10.3732/ajb.1100552. PubMed PMID: 22917946. PubMed DOI

Eastwood MD, Cheung SW, Lee KY, et al. Developmentally programmed nuclear destruction during yeast gametogenesis. Dev Cell. 2012. Jul 17;23(1):35–44. doi: 10.1016/j.devcel.2012.05.005. PubMed PMID: 22727375. PubMed DOI

Lin L, Rodrigues F, Kary C, et al. Complement-Related Regulates Autophagy in Neighboring Cells. Cell. 2017. Jun 29;170(1):158–171e8. 10.1016/j.cell.2017.06.018. PubMed PMID: 28666117; PubMed Central PMCID: PMCPMC5533186. PubMed DOI PMC

Kourelis TV, Siegel RD.. Metformin and cancer: new applications for an old drug. Med Oncol. 2012. Jun;29(2):1314–27. doi: 10.1007/s12032-011-9846-7. PubMed PMID: 21301998. PubMed DOI

Chen Y, Dorn GW, PINK1-phosphorylated mitofusin 2 is a Parkin receptor for culling damaged mitochondria. Science. 2013. Apr 26;340(6131):471–5. doi: 10.1126/science.1231031. PubMed PMID: 23620051; PubMed Central PMCID: PMCPMC3774525. PubMed DOI PMC

Gong G, Song M, Csordas G, et al. Parkin-mediated mitophagy directs perinatal cardiac metabolic maturation in mice. Science. 2015. Dec 4;350(6265):aad2459. doi: 10.1126/science.aad2459. PubMed PMID: 26785495; PubMed Central PMCID: PMCPMC4747105. PubMed DOI PMC

Zhao T, Huang X, Han L, et al. Central role of mitofusin 2 in autophagosome-lysosome fusion in cardiomyocytes. J Biol Chem. 2012. Jul 6;287(28):23615–25. doi: 10.1074/jbc.M112.379164. PubMed PMID: 22619176; PubMed Central PMCID: PMCPMC3390636. PubMed DOI PMC

Fedeli C, Filadi R, Rossi A, et al. PSEN2 (presenilin 2) mutants linked to familial Alzheimer disease impair autophagy by altering Ca(2+) homeostasis. Autophagy. 2019. Dec;15(12):2044–2062. doi: 10.1080/15548627.2019.1596489. PubMed PMID: 30892128; PubMed Central PMCID: PMCPMC6844518. PubMed DOI PMC

Kousi M, Siintola E, Dvorakova L, et al. Mutations in CLN7/MFSD8 are a common cause of variant late-infantile neuronal ceroid lipofuscinosis. Brain. 2009. Mar;132\(Pt 3):810–9. doi: 10.1093/brain/awn366. PubMed PMID: 19201763. PubMed DOI

Brandenstein L, Schweizer M, Sedlacik J, et al. Lysosomal dysfunction and impaired autophagy in a novel mouse model deficient for the lysosomal membrane protein Cln7. Hum Mol Genet. 2016. Feb 15;25(4):777–91. doi: 10.1093/hmg/ddv615. PubMed PMID: 26681805. PubMed DOI

Oku M, Warnecke D, Noda T, et al. Peroxisome degradation requires catalytically active sterol glucosyltransferase with a GRAM domain. EMBO J 2003. Jul 1;22(13):3231–41. PubMed PMID: 12839986. PubMed PMC

Gu R, Liu N, Luo S, et al. MicroRNA-9 regulates the development of knee osteoarthritis through the NF-kappaB1 pathway in chondrocytes. Medicine (Baltimore). 2016. Sep;95(36):e4315. doi: 10.1097/MD.0000000000004315. PubMed PMID: 27603333; PubMed Central PMCID: PMCPMC5023855. PubMed DOI PMC

Cai J, Zhang H, Zhang YF, et al. MicroRNA-29 enhances autophagy and cleanses exogenous mutant alphaB-crystallin in retinal pigment epithelial cells. Exp Cell Res. 2019. Jan 1;374(1):231–248. doi: 10.1016/j.yexcr.2018.11.028. PubMed PMID: 30513336. PubMed DOI

Seca H, Lima RT, Lopes-Rodrigues V, et al. Targeting miR-21 induces autophagy and chemosensitivity of leukemia cells. Curr Drug Targets 2013. Sep;14(10):1135–43. PubMed PMID: 23834154. PubMed

D’Adamo S, Alvarez-Garcia O, Muramatsu Y, et al. MicroRNA-155 suppresses autophagy in chondrocytes by modulating expression of autophagy proteins. Osteoarthritis Cartilage. 2016. Jun;24(6):1082–91. doi: 10.1016/j.joca.2016.01.005. PubMed PMID: 26805019; PubMed Central PMCID: PMCPMC4875787. PubMed DOI PMC

Pennati M, Lopergolo A, Profumo V, et al. miR-205 impairs the autophagic flux and enhances cisplatin cytotoxicity in castration-resistant prostate cancer cells. Biochem Pharmacol. 2014. Feb 15;87(4):579–97. doi: 10.1016/j.bcp.2013.12.009. PubMed PMID: 24370341. PubMed DOI

Lan SH, Wu SY, Zuchini R, et al. Autophagy suppresses tumorigenesis of hepatitis B virus-associated hepatocellular carcinoma through degradation of microRNA-224. Hepatology. 2014. Feb;59(2):505–17. doi: 10.1002/hep.26659. PubMed PMID: 23913306. PubMed DOI PMC

Lan SH, Wu SY, Zuchini R, et al. Autophagy-preferential degradation of MIR224 participates in hepatocellular carcinoma tumorigenesis. Autophagy. 2014. Sep;10(9):1687–9. doi: 10.4161/auto.29959. PubMed PMID: 25068270; PubMed Central PMCID: PMCPMC4206546. PubMed DOI PMC

Tao Z, Feng C, Mao C, et al. MiR-4465 directly targets PTEN to inhibit AKT/mTOR pathway-mediated autophagy. Cell Stress Chaperones. 2019. Jan;24(1):105–113. doi: 10.1007/s12192-018-0946-6. PubMed PMID: 30421325; PubMed Central PMCID: PMCPMC6363616. PubMed DOI PMC

Dubinsky AN, Dastidar SG, Hsu CL, et al. Let-7 coordinately suppresses components of the amino acid sensing pathway to repress mTORC1 and induce autophagy. Cell Metab. 2014. Oct 7;20(4):626–38. 10.1016/j.cmet.2014.09.001 PubMed PMID: 25295787; PubMed Central PMCID: PMCPMC4245205. PubMed DOI PMC

Petri R, Pircs K, Jonsson ME, et al. let-7 regulates radial migration of new-born neurons through positive regulation of autophagy. EMBO J. 2017. May 15;36(10):1379–1391. doi: 10.15252/embj.201695235. PubMed PMID: 28336683; PubMed Central PMCID: PMCPMC5430214. PubMed DOI PMC

Gu H, Li L, Cui C, et al. Overexpression of let-7a increases neurotoxicity in a PC12 cell model of Alzheimer’s disease via regulating autophagy. Exp Ther Med. 2017. Oct;14(4):3688–3698. doi: 10.3892/etm.2017.4977. PubMed PMID: 29042965; PubMed Central PMCID: PMCPMC5639351. PubMed DOI PMC

Shamsuzzama, Kumar L, Nazir A.. Modulation of Alpha-synuclein Expression and Associated Effects by MicroRNA Let-7 in Transgenic C. elegans. Front Mol Neurosci. 2017;10:328. doi: 10.3389/fnmol.2017.00328. PubMed PMID: 29081733; PubMed Central PMCID: PMCPMC5645510. PubMed DOI PMC

Ding Z, Wang X, Schnackenberg L, et al. Regulation of autophagy and apoptosis in response to ox-LDL in vascular smooth muscle cells, and the modulatory effects of the microRNA hsa-let-7 g. Int J Cardiol. 2013. Sep 30;168(2):1378–85. doi: 10.1016/j.ijcard.2012.12.045. PubMed PMID: 23305858. PubMed DOI

Martina JA, Diab HI, Lishu L, et al. The nutrient-responsive transcription factor TFE3 promotes autophagy, lysosomal biogenesis, and clearance of cellular debris. Sci Signal. 2014. Jan 21;7(309):ra9. doi: 10.1126/scisignal.2004754. PubMed PMID: 24448649. PubMed DOI PMC

Eid N, Ito Y, Otsuki Y.. Triggering of Parkin Mitochondrial Translocation in Mitophagy: Implications for Liver Diseases. Front Pharmacol. 2016;7:100. doi: 10.3389/fphar.2016.00100. PubMed PMID: 27199746; PubMed Central PMCID: PMCPMC4850158. PubMed DOI PMC

Eid N, Ito Y, Horibe A, et al.Ethanol-Induced Mitochondrial Damage in Sertoli Cells is Associated with Parkin Overexpression and Activation of Mitophagy. Cells. 2019. Mar 25;8(3). doi: 10.3390/cells8030283. PubMed PMID: 30934625; PubMed Central PMCID: PMCPMC6468925. PubMed DOI PMC

Lemasters JJ. Selective mitochondrial autophagy, or mitophagy, as a targeted defense against oxidative stress, mitochondrial dysfunction, and aging. Rejuvenation Res. 2005. Spring;8(1):3–5. PubMed PMID: 15798367. PubMed

Chazotte B. Labeling mitochondria with MitoTracker dyes. Cold Spring Harb Protoc. 2011. Aug 1;2011(8):990–2. doi: 10.1101/pdb.prot5648. PubMed PMID: 21807856. PubMed DOI

Kou Y, He Y, Qiu J, et al. Mitochondrial dynamics and mitophagy are necessary for proper invasive growth in rice blast. Mol Plant Pathol 2019. Aug;20(8):1147–1162. doi: 10.1111/mpp.12822. PubMed PMID: 31218796; PubMed Central PMCID: PMCPMC6640187. PubMed DOI PMC

Nordmann M, Cabrera M, Perz A, et al. The Mon1-Ccz1 complex is the GEF of the late endosomal Rab7 homolog Ypt7. Curr Biol. 2010. Sep 28;20(18):1654–9. doi: 10.1016/j.cub.2010.08.002. PubMed PMID: 20797862. PubMed DOI

Hegedus K, Takats S, Boda A, et al. The Ccz1-Mon1-Rab7 module and Rab5 control distinct steps of autophagy. Mol Biol Cell. 2016. Oct 15;27(20):3132–3142. 10.1091/mbc.E16-03-0205. PubMed PMID: 27559127; PubMed Central PMCID: PMCPMC5063620. PubMed DOI PMC

Gerondopoulos A, Langemeyer L, Liang JR, et al. BLOC-3 mutated in Hermansky-Pudlak syndrome is a Rab32/38 guanine nucleotide exchange factor. Curr Biol. 2012. Nov 20;22(22):2135–9. 10.1016/j.cub.2012.09.020. PubMed PMID: 23084991; PubMed Central PMCID: PMCPMC3502862. PubMed DOI PMC

Gao J, Langemeyer L, Kummel D, et al. Molecular mechanism to target the endosomal Mon1-Ccz1 GEF complex to the pre-autophagosomal structure. eLife. 2018. Feb 15;7. 10.7554/eLife.31145. PubMed PMID: 29446751; PubMed Central PMCID: PMCPMC5841931. PubMed DOI PMC

Choi HS, Jeong EH, Lee TG, et al. Autophagy inhibition with monensin enhances cell cycle arrest and apoptosis induced by mTOR or epidermal growth factor receptor inhibitors in lung cancer cells. Tuberc Respir Dis (Seoul) 2013. Jul;75(1):9–17. doi: 10.4046/trd.2013.75.1.9. PubMed PMID: 23946753; PubMed Central PMCID: PMCPMC3741474. PubMed DOI PMC

Oldfield CJ, Cheng Y, Cortese MS, et al. Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry. 2005. Sep 20;44(37):12454–70. doi: 10.1021/bi050736e. PubMed PMID: 16156658. PubMed DOI

Mohan A, Oldfield CJ, Radivojac P, et al. Analysis of molecular recognition features (MoRFs). J Mol Biol. 2006. Oct 6;362(5):1043–59. doi: 10.1016/j.jmb.2006.07.087. PubMed PMID: 16935303. PubMed DOI

Cheng Y, Oldfield CJ, Meng J, et al. Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry. 2007. Nov 27;46(47):13468–77. 10.1021/bi7012273 PubMed PMID: 17973494; PubMed Central PMCID: PMCPMC2570644. PubMed DOI PMC

Yan J, Dunker AK, Uversky VN, et al. Molecular recognition features (MoRFs) in three domains of life. Mol Biosyst. 2016. Mar;12(3):697–710. 10.1039/c5mb00640f. PubMed PMID: 26651072. PubMed DOI

Choi YJ, Hwang KC, Park JY, et al. Identification and characterization of a novel mouse and human MOPT gene containing MORN-motif protein in testis. Theriogenology. 2010. Feb;73(3):273–81. doi: 10.1016/j.theriogenology.2009.09.010. PubMed PMID: 19913896. PubMed DOI

Lee SK, Shanmughapriya S, Mok MCY, et al. Structural insights into mitochondrial calcium uniporter regulation by divalent cations. Cell Chem Biol. 2016. Sep 22;23(9):1157–1169. doi: 10.1016/j.chembiol.2016.07.012 PubMed PMID: 27569754; PubMed Central PMCID: PMCPMC5035232. PubMed DOI PMC

Tomar D, Dong Z, Shanmughapriya S, et al. MCUR1 is a scaffold factor for the MCU complex function and promotes mitochondrial bioenergetics. Cell Rep. 2016. May 24;15(8):1673–85. doi: 10.1016/j.celrep.2016.04.050. PubMed PMID: 27184846; PubMed Central PMCID: PMCPMC4880542. PubMed DOI PMC

Frost LS, Lopes VS, Bragin A, et al. The contribution of melanoregulin to microtubule-associated protein 1 light chain 3 (LC3) associated phagocytosis in retinal pigment epithelium. Mol Neurobiol. 2015. Oct 10;52:1135–1151. 10.1007/s12035-014-8920-5. PubMed PMID: 25301234. PubMed DOI PMC

Petherick KJ, Conway OJ, Mpamhanga C, et al. Pharmacological inhibition of ULK1 kinase blocks mammalian target of rapamycin (mTOR)-dependent autophagy. J Biol Chem. 2015. May 1;290(18):11376–83. doi: 10.1074/jbc.C114.627778. PubMed PMID: 25833948; PubMed Central PMCID: PMC4416842. PubMed DOI PMC

Bhutia SK, Kegelman TP, Das SK, et al. Astrocyte elevated gene-1 induces protective autophagy. Proc Natl Acad Sci USA 2010. Dec 2;107:22243–8. doi: 10.1073/pnas.1009479107. PubMed PMID: 21127263; Eng. PubMed DOI PMC

Wu Y, Cheng S, Zhao H, et al. PI3P phosphatase activity is required for autophagosome maturation and autolysosome formation. EMBO Rep. 2014. Sep;15(9):973–81. 10.15252/embr.201438618. PubMed PMID: 25124690. PubMed DOI PMC

Al-Qusairi L, Prokic I, Amoasii L, et al. Lack of myotubularin (MTM1) leads to muscle hypotrophy through unbalanced regulation of the autophagy and ubiquitin-proteasome pathways. FASEB J. 2013. Aug;27(8):3384–94. 10.1096/fj.12-220947. PubMed PMID: 23695157. PubMed DOI

Taguchi-Atarashi N, Hamasaki M, Matsunaga K, et al. Modulation of local PtdIns3P levels by the PI phosphatase MTMR3 regulates constitutive autophagy. Traffic. 2010. Jan 6;11:468–78. doi: TRA1034 [pii] doi:10.1111/j.1600-0854.2010.01034.x. PubMed PMID: 20059746; Eng. PubMed DOI

Vergne I, Roberts E, Elmaoued RA, et al. Control of autophagy initiation by phosphoinositide 3-phosphatase Jumpy. EMBO J. 2009. Aug 5;28(15):2244–58. emboj2009159 [pii] doi:10.1038/emboj.2009.159. PubMed PMID: 19590496; PubMed Central PMCID: PMC2726690. eng. PubMed DOI PMC

Zou J, Zhang C, Marjanovic J, et al. Myotubularin-related protein (MTMR) 9 determines the enzymatic activity, substrate specificity, and role in autophagy of MTMR8. Proc Natl Acad Sci U S A. 2012. Jun 12;109(24):9539–44. 10.1073/pnas.1207021109. PubMed PMID: 22647598; PubMed Central PMCID: PMC3386095. PubMed DOI PMC

Hnia K, Kretz C, Amoasii L, et al. Primary T-tubule and autophagy defects in the phosphoinositide phosphatase Jumpy/MTMR14 knockout mice muscle. Adv Biol Regul. 2012. Jan;52(1):98–107. doi: 10.1016/j.advenzreg.2011.09.007. PubMed PMID: 21930146. PubMed DOI

Yun J, Puri R, Yang H, et al. MUL1 acts in parallel to the PINK1/parkin pathway in regulating mitofusin and compensates for loss of PINK1/parkin. eLife. 2014. Jun 4;3:e01958. doi: 10.7554/eLife.01958. PubMed PMID: 24898855; PubMed Central PMCID: PMCPMC4044952. PubMed DOI PMC

Puri R, Cheng XT, Lin MY, et al. Mul1 restrains Parkin-mediated mitophagy in mature neurons by maintaining ER-mitochondrial contacts. Nat Commun. 2019. Aug 13;10(1):3645. doi: 10.1038/s41467-019-11636-5. PubMed PMID: 31409786; PubMed Central PMCID: PMCPMC6692330. PubMed DOI PMC

Rusten TE, Vaccari T, Lindmo K, et al. ESCRTs and Fab1 regulate distinct steps of autophagy. Curr Biol. 2007. Oct 23;17(20):1817–25. doi: 10.1016/j.cub.2007.09.032. PubMed PMID: 17935992. PubMed DOI

Yotsu RR, Suzuki K, Simmonds RE, et al. Buruli Ulcer: a Review of the Current Knowledge. Curr Trop Med Rep. 2018;5(4):247–256. doi: 10.1007/s40475-018-0166-2. PubMed PMID: 30460172; PubMed Central PMCID: PMCPMC6223704. PubMed DOI PMC

Brandstaetter H, Kishi-Itakura C, Tumbarello DA, et al. Loss of functional MYO1C/myosin 1c, a motor protein involved in lipid raft trafficking, disrupts autophagosome-lysosome fusion. Autophagy. 2014;10(12):2310–23. doi: 10.4161/15548627.2014.984272. PubMed PMID: 25551774; PubMed Central PMCID: PMC4502697. PubMed DOI PMC

Tumbarello DA, Waxse BJ, Arden SD, et al. Autophagy receptors link myosin VI to auto-phagosomes to mediate Tom1-dependent autophagosome maturation and fusion with the lysosome. Nat Cell Biol. 2012. Oct;14(10):1024–35. doi: 10.1038/ncb2589. PubMed PMID: 23023224; PubMed Central PMCID: PMC3472162. PubMed DOI PMC

Hong H, Koon AC, Chen ZS, et al. AQAMAN, a bisamidine-based inhibitor of toxic protein inclusions in neurons, ameliorates cytotoxicity in polyglutamine disease models. J Biol Chem. 2019. Feb 22;294(8):2757–2770. 10.1074/jbc.RA118.006307. PubMed PMID: 30593503; PubMed Central PMCID: PMCPMC6393596. PubMed DOI PMC

Kuo HP, Lee DF, Chen CT, et al. ARD1 stabilization of TSC2 suppresses tumorigenesis through the mTOR signaling pathway. Sci Signaling 2010;3(108):ra9. doi: 3/108/ra9 [pii] doi:10.1126/scisignal.2000590. PubMed PMID: 20145209; PubMed Central PMCID: PMC2874891. eng.10.1126/scisignal. 2000590.PubMed PMID: 20145209; PubMed Central PMCID: PMC2874891. eng. PubMed DOI PMC

Zhang Y, Cheng Y, Ren X, et al. NAC1 modulates sensitivity of ovarian cancer cells to cisplatin by altering the HMGB1-mediated autophagic response. Oncogene. 2012. Feb 23;31(8):1055–64. 10.1038/onc.2011.290. PubMed PMID: 21743489; PubMed Central PMCID: PMC3275651. PubMed DOI PMC

Fang EF, Scheibye-Knudsen M, Brace LE, et al. Defective mitophagy in XPA via PARP-1 hyperactivation and NAD(+)/SIRT1 reduction. Cell. 2014. May 8;157(4):882–896. 10.1016/j.cell.2014.03.026. PubMed PMID: 24813611; PubMed Central PMCID: PMCPMC4625837. PubMed DOI PMC

Fang EF. Mitophagy and NAD(+) inhibit Alzheimer disease. Autophagy. 2019. Jun;15(6):1112–1114. doi: 10.1080/15548627.2019.1596497. PubMed PMID: 30922179; PubMed Central PMCID: PMCPMC6526831. PubMed DOI PMC

Wang P, Guan YF, Du H, et al. Induction of autophagy contributes to the neuroprotection of nicotinamide phosphoribosyltransferase in cerebral ischemia. Autophagy. 2012. Jan;8(1):77–87. doi: 10.4161/auto.8.1.18274. PubMed PMID: 22113203. PubMed DOI

Jin R, Liu L, Zhu W, et al. Iron oxide nanoparticles promote macrophage autophagy and inflammatory response through activation of toll-like Receptor-4 signaling. Biomaterials. 2019. May;203:23–30. 10.1016/j.biomaterials.2019.02.026 PubMed PMID: 30851490. PubMed DOI

Wan HY, Chen JL, Zhu X, et al. Titania-coated gold nano-bipyramids for blocking autophagy flux and sensitizing cancer cells to proteasome inhibitor-induced death. Adv Sci (Weinh). 2018. Mar;5(3):1700585. 10.1002/advs.201700585 PubMed PMID: 29593960; PubMed Central PMCID: PMCPMC5867123. PubMed DOI PMC

Lin YX, Wang Y, Wang H.. Recent advances in nanotechnology for autophagy detection. Small. 2017. Sep;13(33). 10.1002/smll.201700996 PubMed PMID: 28677891. PubMed DOI

Zhang C, Ren J, He J, et al. Long-term monitoring of tumor-related autophagy in vivo by Fe3O4NO. nanoparticles Biomaterials. 2018. Oct;179:186–198. doi: 10.1016/j.biomaterials.2018.07.004. PubMed PMID: 30037455. PubMed DOI

Shi Z, Chen X, Zhang L, et al. FA-PEG decorated MOF nanoparticles as a targeted drug delivery system for controlled release of an autophagy inhibitor. Biomater Sci. 2018. Sep 25;6(10):2582–2590. 10.1039/c8bm00625c. PubMed PMID: 30151542. PubMed DOI

Gong C, Hu C, Gu F, et al. Co-delivery of autophagy inhibitor ATG7 siRNA and docetaxel for breast cancer treatment. J Control Release. 2017. Nov 28;266:272–286. doi: 10.1016/j.jconrel.2017.09.042. PubMed PMID: 28987884. PubMed DOI

Naydenov NG, Harris G, Morales V, et al. Loss of a membrane trafficking protein alphaSNAP induces non-canonical autophagy in human epithelia. Cell cycle. 2012. Dec 15;11(24):4613–25. 10.4161/cc.22885. PubMed PMID: 23187805; PubMed Central PMCID: PMC3562306. PubMed DOI PMC

Hafren A, Macia JL, Love AJ, et al. Selective autophagy limits cauliflower mosaic virus infection by NBR1-mediated targeting of viral capsid protein and particles. Proc Natl Acad Sci U S A. 2017. Mar 7;114(10):E2026–E2035. doi: 10.1073/pnas.1610687114 PubMed PMID: 28223514; PubMed Central PMCID: PMCPMC5347569. PubMed DOI PMC

Wang P, Richardson C, Hawes C, et al. Arabidopsis NAP1 regulates the formation of auto-phagosomes. Curr Biol. 2016. Aug 8;26(15):2060–2069. 10.1016/j.cub.2016.06.008 PubMed PMID: 27451899. PubMed DOI

Hohfeld J. Autophagy: press and push for destruction. Curr Biol. 2016. Aug 8;26(15):R703–R705. 10.1016/j.cub.2016.06.017. PubMed PMID: 27505239. PubMed DOI

Hitomi J, Christofferson DE, Ng A, et al. Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway. Cell. 2008. Dec 26;135(7):1311–23. doi: 10.1016/j.cell.2008.10.044. PubMed PMID: 19109899; PubMed Central PMCID: PMC2621059. eng. PubMed DOI PMC

Bonapace L, Bornhauser BC, Schmitz M, et al. Induction of autophagy-dependent necroptosis is required for childhood acute lymphoblastic leukemia cells to overcome glucocorticoid resistance [Research Support, Non-U.S. Gov’t]. J Clin Invest. 2010. Apr 1;120(4):1310–23. doi: 10.1172/JCI39987. PubMed PMID: 20200450; PubMed Central PMCID: PMC2846044. eng. PubMed DOI PMC

Ogasawara M, Yano T, Tanno M, et al. Suppression of autophagic flux contributes to cardiomyocyte death by activation of necroptotic pathways. J Mol Cell Cardiol. 2017. Jul;108:203–213. doi: 10.1016/j.yjmcc.2017.06.008. PubMed PMID: 28647341. PubMed DOI

Pei G, Buijze H, Liu H, et al. The E3 ubiquitin ligase NEDD4 enhances killing of membrane-perturbing intracellular bacteria by promoting autophagy. Autophagy. 2017;13(12):2041–2055. doi: 10.1080/15548627.2017.1376160. PubMed PMID: 29251248; PubMed Central PMCID: PMCPMC5788543. PubMed DOI PMC

Aramburu J, Drews-Elger K, Estrada-Gelonch A, et al. Regulation of the hypertonic stress response and other cellular functions by the Rel-like transcription factor NFAT5 Biochem Pharm. 2006. Nov 30;72(11):1597–604. doi: 10.1016/j.bcp.2006.07.002. PubMed PMID: 16904650. PubMed DOI

Halterman JA, Kwon HM, Wamhoff BR.. Tonicity-independent regulation of the osmosensitive transcription factor TonEBP (NFAT5). Am J Physiol Cell Physiol. 2012. Jan 1;302(1):C1–8. 10.1152/ajpcell.00327.2011 PubMed PMID: 21998140; PubMed Central PMCID: PMCPMC3328893. PubMed DOI PMC

Aramburu J, Lopez-Rodriguez C.. Regulation of Inflammatory Functions of Macrophages and T Lymphocytes by NFAT5. Front Immunol. 2019;10:535. 10.3389/fimmu.2019.00535 PubMed PMID: 30949179; PubMed Central PMCID: PMCPMC6435587. PubMed DOI PMC

Liu C, Choi H, Johnson ZI, et al. Lack of evidence for involvement of TonEBP and hyperosmotic stimulus in induction of autophagy in the nucleus pulposus. Sci Rep. 2017. Jul 3;7(1):4543. doi: 10.1038/s41598-017-04876-2. PubMed PMID: 28674405; PubMed Central PMCID: PMCPMC5495809. PubMed DOI PMC

Valdor R, Mocholi E, Botbol Y, et al. Chaperone-mediated autophagy regulates T cell responses through targeted degradation of negative regulators of T cell activation. Nat Immunol. 2014. Nov;15(11):1046–54. doi: 10.1038/ni.3003.. PubMed PMID: 25263126; PubMed Central PMCID: PMCPMC4208273. PubMed DOI PMC

Bae SH, Sung SH, Oh SY, et al. Sestrins activate Nrf2 by promoting p62-dependent autophagic degradation of Keap1 and prevent oxidative liver damage. Cell Metab. 2013. Jan 8;17(1):73–84. doi: 10.1016/j.cmet.2012.12.002. PubMed PMID: 23274085. PubMed DOI

Djavaheri-Mergny M, Amelotti M, Mathieu J, et al. Regulation of autophagy by NFkappaB transcription factor and reactives oxygen species. Autophagy. 2007. Jul-Aug;3(4):390–2. PubMed PMID: 17471012; eng. PubMed

Copetti T, Demarchi F, Schneider C.. p65/RelA binds and activates the beclin 1 promoter. Autophagy. 2009. Aug;5(6):858–9. 10.4161/auto.8822 PubMed PMID: 19458474. PubMed DOI

Wattin M, Gaweda L, Muller P, et al.Modulation of protein quality control and proteasome to autophagy switch in immortalized myoblasts from duchenne muscular dystrophy patients. Int J Mol Sci. 2018. Jan 7;19(1). 10.3390/ijms19010178 PubMed PMID: 29316663; PubMed Central PMCID: PMCPMC5796127. PubMed DOI PMC

Criado O, Aguado C, Gayarre J, et al. Lafora bodies and neurological defects in malin-deficient mice correlate with impaired autophagy. Hum Mol Genet. 2012. Apr 1;21(7):1521–33. 10.1093/hmg/ddr590 PubMed PMID: 22186026. PubMed DOI

Nozima BH, Mendes TB, Pereira G, et al. FAM129A regulates autophagy in thyroid carcinomas in an oncogene-dependent manner. Endocr Relat Cancer. 2019. Jan 1;26(1):227–238. 10.1530/ERC-17-0530 PubMed PMID: 30400008. PubMed DOI

Princely Abudu Y, Pankiv S, Mathai BJ, et al. NIPSNAP1 and NIPSNAP2 Act as “Eat Me” Signals for Mitophagy. Dev Cell. 2019. May 20;49(4):509–525e12. 10.1016/j.devcel.2019.03.013 PubMed PMID: 30982665. PubMed DOI

Cervia D, Perrotta C, Moscheni C, et al. Nitric oxide and sphingolipids control apoptosis and autophagy with a significant impact on Alzheimer’s disease. J Biol Regulator Hom Agents 2013. Apr-Jun;27(2 Suppl):11–22. PubMed PMID: 24813312. PubMed

Rabkin SW. Nitric oxide-induced cell death in the heart: the role of autophagy. Autophagy. 2007. Jul-Aug;3(4):347–9. PubMed PMID: 17438363. PubMed

Zang L, He H, Ye Y, et al. Nitric oxide augments oridonin-induced efferocytosis by human histocytic lymphoma U937 cells via autophagy and the NF-kappaB-COX-2-IL-1beta pathway. Free Radic Res. 2012. Oct;46(10):1207–19. doi: 10.3109/10715762.2012.700515. PubMed PMID: 22670565. PubMed DOI

Lei Y, Wen H, Yu Y, et al. The mitochondrial proteins NLRX1 and TUFM form a complex that regulates type I interferon and autophagy. Immunity. 2012. Jun 29;36(6):933–46. doi: 10.1016/j.immuni.2012.03.025. PubMed PMID: 22749352; PubMed Central PMCID: PMCPMC3397828. PubMed DOI PMC

Lei Y, Kansy BA, Li J, et al. EGFR-targeted mAb therapy modulates autophagy in head and neck squamous cell carcinoma through NLRX1-TUFM protein complex. Oncogene. 2016. Sep 8;35(36):4698–707. doi: 10.1038/onc.2016.11. PubMed PMID: 26876213; PubMed Central PMCID: PMCPMC5257174. PubMed DOI PMC

Zhang Y, Yao Y, Qiu X, et al. Listeria hijacks host mitophagy through a novel mitophagy receptor to evade killing. Nat Immunol. 2019. Apr;20(4):433–446. doi: 10.1038/s41590-019-0324-2. PubMed PMID: 30804553. PubMed DOI

Wang K, Ma H, Liu H, et al. The Glycoprotein and Nucleocapsid Protein of Hantaviruses Manipulate Autophagy Flux to Restrain Host Innate Immune Responses. Cell Rep. 2019. May 14;27(7):2075–2091 e5. doi: 10.1016/j.celrep.2019.04.061. PubMed PMID: 31091447. PubMed DOI

Schlattner U, Tokarska-Schlattner M, Epand RM, et al. Mitochondrial NM23-H4/NDPK-D: a bifunctional nanoswitch for bioenergetics and lipid signaling. Naunyn Schmiedebergs Arch Pharmacol. 2015. Feb;388(2):271–8. doi: 10.1007/s00210-014-1047-4. PubMed PMID: 25231795. PubMed DOI

Schlattner U, Tokarska-Schlattner M, Epand RM, et al. NME4/nucleoside diphosphate kinase D in cardiolipin signaling and mitophagy. Lab Invest. 2018. Feb;98(2):228–232. doi: 10.1038/labinvest.2017.113. PubMed PMID: 29035377. PubMed DOI

Panchaud N, Peli-Gulli MP, De Virgilio C.. Amino acid deprivation inhibits TORC1 through a GTPase-activating protein complex for the Rag family GTPase Gtr1. Sci Signal. 2013. May 28;6(277):ra42. doi: 10.1126/scisignal.2004112. PubMed PMID: 23716719. PubMed DOI

Panchaud N, Peli-Gulli MP, De Virgilio C.. SEACing the GAP that nEGOCiates TORC1 activation: evolutionary conservation of Rag GTPase regulation. Cell cycle. 2013. Sep 15;12(18):2948–52. doi: 10.4161/cc.26000. PubMed PMID: 23974112; PubMed Central PMCID: PMCPMC3875668. PubMed DOI PMC

Sarkar S, Carroll B, Buganim Y, et al. Impaired autophagy in the lipid-storage disorder Niemann-Pick type C1 disease. Cell Rep. 2013. Dec 12;5(5):1302–15. doi: 10.1016/j.celrep.2013.10.042. PubMed PMID: 24290752; PubMed Central PMCID: PMCPMC3957429. PubMed DOI PMC

Maetzel D, Sarkar S, Wang H, et al. Genetic and chemical correction of cholesterol accumulation and impaired autophagy in hepatic and neural cells derived from Niemann-Pick Type C patient-specific iPS cells. Stem Cell Reports. 2014. Jun 3;2(6):866–80. doi: 10.1016/j.stemcr.2014.03.014. PubMed PMID: 24936472; PubMed Central PMCID: PMCPMC4050353. PubMed DOI PMC

Schwerd T, Pandey S, Yang HT, et al. Impaired antibacterial autophagy links granulomatous intestinal inflammation in Niemann-Pick disease type C1 and XIAP deficiency with NOD2 variants in Crohn’s disease. Gut. 2017. Jun;66(6):1060–1073. doi: 10.1136/gutjnl-2015-310382. PubMed PMID: 26953272; PubMed Central PMCID: PMCPMC5532464. PubMed DOI PMC

Aveleira CA, Botelho M, Carmo-Silva S, et al. Neuropeptide Y stimulates autophagy in hypothalamic neurons. Proc Natl Acad Sci U S A. 2015. Mar 31;112(13):E1642–51. doi: 10.1073/pnas.1416609112. PubMed PMID: 25775546; PubMed Central PMCID: PMC4386327. PubMed DOI PMC

Catalani E, De Palma C, Perrotta C, et al.Current evidence for a role of neuropeptides in the regulation of autophagy. Biomed Res Int. 2017;2017:5856071. doi: 10.1155/2017/5856071. PubMed PMID: 28593174; PubMed Central PMCID: PMCPMC5448050. PubMed DOI PMC

Cervia D, Catalani E, Casini G.. Neuroprotective peptides in retinal disease. J Clin Med. 2019. Aug 1;8(8). doi: 10.3390/jcm8081146. PubMed PMID: 31374938; PubMed Central PMCID: PMCPMC6722704. PubMed DOI PMC

Cao Y, Wang Y, Abi Saab WF, et al. NRBF2 regulates macroautophagy as a component of Vps34 Complex I. Biochem J. 2014. Jul 15;461(2):315–22. doi: 10.1042/BJ20140515. PubMed PMID: 24785657; PubMed Central PMCID: PMC4180102. PubMed DOI PMC

Lu J, He L, Behrends C, et al. NRBF2 regulates autophagy and prevents liver injury by modulating Atg14L-linked phosphatidylinositol-3 kinase III activity. Nat Commun. 2014;5:3920. doi: 10.1038/ncomms4920. PubMed PMID: 24849286. PubMed DOI PMC

Judith D, Mostowy S, Bourai M, et al. Species-specific impact of the autophagy machinery on Chikungunya virus infection. EMBO Rep. 2013. Jun;14(6):534–44. doi: 10.1038/embor.2013.51. PubMed PMID: 23619093; PubMed Central PMCID: PMC3674439. PubMed DOI PMC

El-Ami T, Moll L, Carvalhal Marques F, et al. A novel inhibitor of the insulin/IGF signaling pathway protects from age-onset, neurodegeneration-linked proteotoxicity. Aging cell. 2014. Feb;13(1):165–74. doi: 10.1111/acel.12171. PubMed PMID: 24261972; PubMed Central PMCID: PMCPMC4326862. PubMed DOI PMC

Moll L, Ben-Gedalya T, Reuveni H, et al. The inhibition of IGF-1 signaling promotes proteostasis by enhancing protein aggregation and deposition. FASEB J. 2016. Apr;30(4):1656–69. doi: 10.1096/fj.15-281675. PubMed PMID: 26722006. PubMed DOI

Ji CH, Kim HY, Heo AJ, et al. The N-degron pathway mediates ER-phagy. Mol Cell. 2019. Sep 5;75(5):1058–1072 e9. doi: 10.1016/j.molcel.2019.06.028. PubMed PMID: 31375263. PubMed DOI

Franco ML, Melero C, Sarasola E, et al. Mutations in TrkA causing congenital insensitivity to pain with anhidrosis (CIPA) induce misfolding, aggregation, and mutation-dependent neurodegeneration by dysfunction of the autophagic flux. J Biol Chem. 2016. Oct 7;291(41):21363–21374. doi: 10.1074/jbc.M116.722587. PubMed PMID: 27551041; PubMed Central PMCID: PMCPMC5076807. PubMed DOI PMC

Funasaka T, Tsuka E, Wong RW.. Regulation of autophagy by nucleoporin Tpr. Sci Rep. 2012;2:878. doi: 10.1038/srep00878. PubMed PMID: 23170199; PubMed Central PMCID: PMC3501823. PubMed DOI PMC

Fullgrabe J, Klionsky DJ, Joseph B.. The return of the nucleus: transcriptional and epigenetic control of autophagy. Nat Rev Mol Cell Biol. 2014. Jan;15(1):65–74. doi: 10.1038/nrm3716. PubMed PMID: 24326622. PubMed DOI

Wyant GA, Abu-Remaileh M, Frenkel EM, et al. NUFIP1 is a ribosome receptor for starvation-induced ribophagy. Science. 2018. May 18;360(6390):751–758. doi: 10.1126/science.aar2663. PubMed PMID: 29700228; PubMed Central PMCID: PMCPMC6020066. PubMed DOI PMC

Lee CW, Wilfling F, Ronchi P, et al. Selective autophagy degrades nuclear pore complexes. Nat Cell Biol. 2020. Feb22(2):159–166. doi: 10.1038/s41556-019-0459-2. PubMed PMID: 32029894. PubMed DOI

Kong DK, Georgescu SP, Cano C, et al. Deficiency of the transcriptional regulator p8 results in increased autophagy and apoptosis, and causes impaired heart function. Mol Biol Cell. 2010. Apr;21(8):1335–49. doi: 10.1091/mbc.E09-09-0818. PubMed PMID: 20181828; PubMed Central PMCID: PMC2854092. eng. PubMed DOI PMC

Chang KY, Tsai SY, Wu CM, et al. Novel phosphoinositide 3-kinase/mTOR dual inhibitor, NVP-BGT226, displays potent growth-inhibitory activity against human head and neck cancer cells in vitro and in vivo. clin cancer res off j am assoc cancer res. 2011. Nov 15;17(22):7116–26. doi: 10.1158/1078-0432.CCR-11-0796. PubMed PMID: 21976531. PubMed DOI

De Leo MG, Staiano L, Vicinanza M, et al. Autophagosome-lysosome fusion triggers a lysosomal response mediated by TLR9 and controlled by OCRL. Nat Cell Biol. 2016. Aug;18(8):839–850. doi: 10.1038/ncb3386. PubMed PMID: 27398910; PubMed Central PMCID: PMCPMC5040511. PubMed DOI PMC

Wang P, Lazarus BD, Forsythe ME, et al. O-GlcNAc cycling mutants modulate proteotoxicity in Caenorhabditis elegans models of human neurodegenerative diseases. Proc Natl Acad Sci U S A. 2012. Oct 23;109(43):17669–74. doi: 10.1073/pnas.1205748109. PubMed PMID: 22988095; PubMed Central PMCID: PMC3491483. PubMed DOI PMC

Yang X, Qian K.. Protein O-GlcNAcylation: emerging mechanisms and functions. Nat Rev Mol Cell Biol. 2017. Jul;18(7):452–465. 10.1038/nrm.2017.22. PubMed PMID: 28488703; PubMed Central PMCID: PMCPMC5667541. PubMed DOI PMC

Guo B, Liang Q, Li L, et al. O-GlcNAc-modification of SNAP-29 regulates autophagosome maturation. Nat Cell Biol. 2014. Dec;16(12):1215–26. 10.1038/ncb3066. PubMed PMID: 25419848. PubMed DOI

Gundara JS, Zhao J, Robinson BG, et al. Oncophagy: harnessing regulation of autophagy in cancer therapy. Endocr Relat Cancer. 2012. Dec;19(6):R281–95. doi: 10.1530/ERC-12-0325. PubMed PMID: 23082009. PubMed DOI

Wong YC, Holzbaur EL.. Optineurin is an autophagy receptor for damaged mitochondria in parkin-mediated mitophagy that is disrupted by an ALS-linked mutation. Proc Natl Acad Sci U S A. 2014. Oct 21;111(42):E4439–48. doi: 10.1073/pnas.1405752111. PubMed PMID: 25294927; PubMed Central PMCID: PMCPMC4210283. PubMed DOI PMC

Wong YC, Holzbaur EL.. Temporal dynamics of PARK2/parkin and OPTN/optineurin recruitment during the mitophagy of damaged mitochondria. Autophagy. 2015;11(2):422–4. doi: 10.1080/15548627.2015.1009792. PubMed PMID: 25801386; PubMed Central PMCID: PMCPMC4502688. PubMed DOI PMC

Richter B, Sliter DA, Herhaus L, et al. Phosphorylation of OPTN by TBK1 enhances its binding to Ub chains and promotes selective autophagy of damaged mitochondria. Proc Natl Acad Sci U S A. 2016. Apr 12;113(15):4039–44. doi: 10.1073/pnas.1523926113. PubMed PMID: 27035970; PubMed Central PMCID: PMCPMC4839414. PubMed DOI PMC

Korac J, Schaeffer V, Kovacevic I, et al. Ubiquitin-independent function of optineurin in autophagic clearance of protein aggregates. J Cell Sci. 2013. Jan15;126\(Pt 2):580–92. 10.1242/jcs.114926. PubMed PMID: 23178947; PubMed Central PMCID: PMCPMC3654196. PubMed DOI PMC

Li F, Xie X, Wang Y, et al. Structural insights into the interaction and disease mechanism of neurodegenerative disease-associated optineurin and TBK1 proteins. Nat Commun. 2016. Sep 13;7:12708. 10.1038/ncomms12708. PubMed PMID: 27620379; PubMed Central PMCID: PMCPMC5027247. PubMed DOI PMC

Li F, Xu D, Wang Y, et al. Structural insights into the ubiquitin recognition by OPTN (optineurin) and its regulation by TBK1-mediated phosphorylation. Autophagy. 2018;14(1):66–79. 10.1080/15548627.2017.1391970. PubMed PMID: 29394115; PubMed Central PMCID: PMCPMC5846504. PubMed DOI PMC

Maruyama H, Morino H, Ito H, et al. Mutations of optineurin in amyotrophic lateral sclerosis. Nature. 2010. May 13;465(7295):223–6. 10.1038/nature08971. PubMed PMID: 20428114. PubMed DOI

Mijaljica D. Autophagy in 2020 and beyond: eating our way into a healthy future. Autophagy. 2010. Jan6(1):194–6. PubMed PMID: 20110773. PubMed

Zhang CF, Gruber F, Ni C, et al. Suppression of autophagy dysregulates the antioxidant response and causes premature senescence of melanocytes. J Invest Dermatol. 2015. May;135(5):1348–57. 10.1038/jid.2014.439. PubMed PMID: 25290687. PubMed DOI

Zhao Y, Zhang CF, Rossiter H, et al. Autophagy is induced by UVA and promotes removal of oxidized phospholipids and protein aggregates in epidermal keratinocytes. J Invest Dermatol. 2013. Jun;133(6):1629–37. 10.1038/jid.2013.26. PubMed PMID: 23340736. PubMed DOI

Veldhoen RA, Banman SL, Hemmerling DR, et al. The chemotherapeutic agent paclitaxel inhibits autophagy through two distinct mechanisms that regulate apoptosis. Oncogene. 2013. Feb 7;32(6):736–46. 10.1038/onc.2012.92. PubMed PMID: 22430212. PubMed DOI

Ren H, Fu K, Mu C, et al. DJ-1, a cancer and Parkinson’s disease associated protein, regulates autophagy through JNK pathway in cancer cells. Cancer Lett 2010. May 24;297:101–8. doi:10.1016/j.canlet.2010.05.001. PubMed PMID: 20510502; Eng. PubMed DOI

Meissner C, Lorenz H, Hehn B, et al. Intramembrane protease PARL defines a negative regulator of PINK1- and PARK2/Parkin-dependent mitophagy. Autophagy. 2015. Jun 23;11:1484–98. 10.1080/15548627.2015.1063763. PubMed PMID: 26101826. PubMed DOI PMC

Jin SM, Lazarou M, Wang C, et al. Mitochondrial membrane potential regulates PINK1 import and proteolytic destabilization by PARL. J Cell Biol. 2010. Nov 29;191(5):933–42. 10.1083/jcb.201008084. PubMed PMID: 21115803; PubMed Central PMCID: PMC2995166. PubMed DOI PMC

Meissner C, Lorenz H, Weihofen A, et al. The mitochondrial intramembrane protease PARL cleaves human Pink1 to regulate Pink1 trafficking. J Neurochem. 2011. Jun;117(5):856–67. doi: 10.1111/j.1471-4159.2011.07253.x. PubMed PMID: 21426348. PubMed DOI

Shi G, Lee JR, Grimes DA, et al. Functional alteration of PARL contributes to mitochondrial dysregulation in Parkinson’s disease. Hum Mol Genet. 2011. May 15;20(10):1966–74. 10.1093/hmg/ddr077. PubMed PMID: 21355049. PubMed DOI

Munoz-Gamez JA, Rodriguez-Vargas JM, Quiles-Perez R, et al. PARP-1 is involved in autophagy induced by DNA damage. Autophagy. 2009. Jan 1;5(1):61–74. PubMed PMID: 19001878; eng. PubMed

Huang Q, Shen HM.. To die or to live: the dual role of poly(ADP-ribose) polymerase-1 in autophagy and necrosis under oxidative stress and DNA damage. Autophagy. 2009. Feb;5(2):273–6. PubMed PMID: 19139632. PubMed

Wang LJ, Chen PR, Hsu LP, et al. Concomitant induction of apoptosis and autophagy by prostate apoptosis response-4 in hypopharyngeal carcinoma cells. Am J Pathol. 2014. Feb;184(2):418–30. doi: 10.1016/j.ajpath.2013.10.012. PubMed PMID: 24418097. PubMed DOI

Thayyullathil F, Rahman A, Pallichankandy S, et al. ROS-dependent prostate apoptosis response-4 (Par-4) up-regulation and ceramide generation are the prime signaling events associated with curcumin-induced autophagic cell death in human malignant glioma. FEBS Open Bio 2014;4:763–76. 10.1016/j.fob.2014.08.005. PubMed PMID: 25349781; PubMed Central PMCID: PMC4208092. PubMed DOI PMC

Silvente-Poirot S, Poirot M.. Cholesterol metabolism and cancer: the good, the bad and the ugly. Curr Opin Pharmacol. 2012. Dec;12(6):673–6. 10.1016/j.coph.2012.10.004. PubMed PMID: 23103112. PubMed DOI

Andrejeva G, Gowan S, Lin G, et al. De novo phosphatidylcholine synthesis is required for autophagosome membrane formation and maintenance during autophagy. Autophagy. 2019. Sep 13:1–17. 10.1080/15548627.2019.1659608. PubMed PMID: 31517566. PubMed DOI PMC

Li X, Rydzewski N, Hider A, et al. A molecular mechanism to regulate lysosome motility for lysosome positioning and tubulation. Nat Cell Biol. 2016. Apr;18(4):404–17. 10.1038/ncb3324. PubMed PMID: 26950892; PubMed Central PMCID: PMCPMC4871318. PubMed DOI PMC

Murrow L, Malhotra R, Debnath J.. ATG12-ATG3 interacts with Alix to promote basal autophagic flux and late endosome function. Nat Cell Biol. 2015. Mar;17(3):300–10. 10.1038/ncb3112. PubMed PMID: 25686249; PubMed Central PMCID: PMC4344874. PubMed DOI PMC

Bock BC, Tagscherer KE, Fassl A, et al. The PEA-15 protein regulates autophagy via activation of JNK. J Biol Chem. 2010. Jul 9;285(28):21644–54. 10.1074/jbc.M109.096628. PubMed PMID: 20452983; eng. PubMed DOI PMC

Noh HS, Hah YS, Zada S, et al. PEBP1, a RAF kinase inhibitory protein, negatively regulates starvation-induced autophagy by direct interaction with LC3. Autophagy. 2016. Nov;12(11):2183–2196. doi: 10.1080/15548627.2016.1219013. PubMed PMID: 27540684; PubMed Central PMCID: PMCPMC5103343. PubMed DOI PMC

Ahmed M, Lai TH, Zada S, et al. Functional linkage of RKIP to the epithelial to mesenchymal transition and autophagy during the development of prostate cancer. Cancers (Basel). 2018. Aug 16;10(8). doi: 10.3390/cancers10080273. PubMed PMID: 30115852; PubMed Central PMCID: PMCPMC6115972. PubMed DOI PMC

Torres A, Gubbiotti MA, Iozzo RV.. Decorin-inducible Peg3 Evokes Beclin 1-mediated autophagy and thrombospondin 1-mediated angiostasis. J Biol Chem. 2017. Mar 24;292(12):5055–5069. 10.1074/jbc.M116.753632. PubMed PMID: 28174297; PubMed Central PMCID: PMCPMC5377817. PubMed DOI PMC

Neill T, Sharpe C, Owens RT, et al. Decorin-evoked paternally expressed gene 3 (PEG3) is an upstream regulator of the transcription factor EB (TFEB) in endothelial cell autophagy. J Biol Chem. 2017. Sep 29;292(39):16211–16220. doi: 10.1074/jbc.M116.769950. PubMed PMID: 28798237; PubMed Central PMCID: PMCPMC5625051. PubMed DOI PMC

Rami A, Fekadu J, Rawashdeh O.. The Hippocampal Autophagic Machinery is Depressed in the Absence of the Circadian Clock Protein PER1 that may Lead to Vulnerability During Cerebral Ischemia. Curr Neurovasc Res. 2017;14(3):207–214. doi: 10.2174/1567202614666170619083239. PubMed PMID: 28625127. PubMed DOI

Lee MY, Sumpter R, Jr., Zou Z, et al. Peroxisomal protein PEX13 functions in selective autophagy. EMBO Rep. 2017. Jan;18(1):48–60. doi: 10.15252/embr.201642443. PubMed PMID: 27827795; PubMed Central PMCID: PMCPMC5210156. PubMed DOI PMC

Ano Y, Hattori T, Oku M, et al. A sorting nexin PpAtg24 regulates vacuolar membrane dynamics during pexophagy via binding to phosphatidylinositol-3-phosphate. ?Mol Biol Cell 2005. Feb;16(2):446–57. PubMed PMID: 15563611. PubMed PMC

Klarer AC, O’Neal J, Imbert-Fernandez Y, et al. Inhibition of 6-phosphofructo-2-kinase (PFKFB3) induces autophagy as a survival mechanism. Cancer Metab. 2014. Jan 23;2(1):2. doi: 10.1186/2049-3002-2-2. PubMed PMID: 24451478; PubMed Central PMCID: PMCPMC3913946. PubMed DOI PMC

Yano T, Mita S, Ohmori H, et al. Autophagic control of listeria through intracellular innate immune recognition in drosophila. Nat Immunol. 2008. Aug;9(8):908–16. doi: 10.1038/ni.1634. PubMed PMID: 18604211; PubMed Central PMCID: PMC2562576. eng. PubMed DOI PMC

Seglen PO, Gordon PB, Holen I.. Non-selective autophagy. Semin Cell Biol. 1990. Dec;1(6):441–8. PubMed PMID: 2103895; eng. PubMed

He C, Klionsky DJ.. Atg9 trafficking in autophagy-related pathways. Autophagy. 2007. May-Jun;3(3):271–4. PubMed PMID: 17329962; eng. PubMed

Zhou F, Zou S, Chen Y, et al. A Rab5 GTPase module is important for autophagosome closure. PLoS Genet. 2017. Sep;13(9):e1007020. doi: 10.1371/journal.pgen.1007020. PubMed PMID: 28934205; PubMed Central PMCID: PMCPMC5626503. PubMed DOI PMC

Amer AO, Swanson MS.. Autophagy is an immediate macrophage response to Legionella pneumophila. Cell Microbiol 2005. Jun;7(6):765–78. PubMed PMID: 15888080; eng. PubMed PMC

Yan C, Gong L, Chen L, et al. PHB2 (prohibitin 2) promotes PINK1-PRKN/Parkin-dependent mitophagy by the PARL-PGAM5-PINK1 axis. Autophagy. 2020. Mar;16(3):419–434. 10.1080/15548627.2019.1628520. PubMed PMID: 31177901; PubMed Central PMCID: PMCPMC6999623. PubMed DOI PMC

Huang H, Kawamata T, Horie T, et al. Bulk RNA degradation by nitrogen starvation-induced autophagy in yeast. EMBO J. 2015. Jan 14;34(2):154–68. doi: 10.15252/embj.201489083. PubMed PMID: 25468960. PubMed DOI PMC

Meijer AJ, Klionsky DJ.. Vps34 is a phosphatidylinositol 3-kinase, not a phosphoinositide 3-kinase. Autophagy. 2011. Jun;7(6):563–4. PubMed PMID: 21278489; PubMed Central PMCID: PMC3625115. PubMed PMC

Devereaux K, Dall’Armi C, Alcazar-Roman A, et al. Regulation of mammalian autophagy by class II and III PI 3-kinases through PI3P synthesis. PLoS One. 2013;8(10):e76405. doi: 10.1371/journal.pone.0076405. PubMed PMID: 24098492; PubMed Central PMCID: PMC3789715. PubMed DOI PMC

Stjepanovic G, Baskaran S, Lin MG, et al.Vps34 kinase domain dynamics regulate the autophagic PI 3-kinase complex. Mol Cell. 2017. Aug 3;67(3):528–534 e3. doi: 10.1016/j.molcel.2017.07.003 PubMed PMID: 28757208; PubMed Central PMCID: PMCPMC5573195. PubMed DOI PMC

Ma M, Liu JJ, Li Y, et al.Cryo-EM structure and biochemical analysis reveal the basis of the functional difference between human PI3KC3-C1 and -C2. Cell Res. 2017. Aug27(8):989–1001. doi: 10.1038/cr.2017.94 PubMed PMID: 28731030; PubMed Central PMCID: PMCPMC5539356. PubMed DOI PMC

Baskaran S, Carlson LA, Stjepanovic G, et al.Architecture and dynamics of the autophagic phosphatidylinositol 3-kinase complex. eLife. 2014. Dec 9;3. doi: 10.7554/eLife.05115 PubMed PMID: 25490155; PubMed Central PMCID: PMCPMC4281882. PubMed DOI PMC

Byfield MP, Murray JT, Backer JM.. hVps34 is a nutrient-regulated lipid kinase required for activation of p70 S6 kinase. J Biol Chem. 2005. Sep 23;280(38):33076–82. doi: 10.1074/jbc.M507201200. PubMed PMID: 16049009. PubMed DOI

Roppenser B, Grinstein S, Brumell JH.. Modulation of host phosphoinositide metabolism during Salmonella invasion by the type III secreted effector SopB. Methods Cell Biol. 2012;108:173–86. doi: 10.1016/B978-0-12-386487-1.00009-2. PubMed PMID: 22325603. PubMed DOI

Cuesta-Geijo MA, Galindo I, Hernaez B, et al. Endosomal maturation, Rab7 GTPase and phosphoinositides in African swine fever virus entry. PLoS One. 2012;7(11):e48853. doi: 10.1371/journal.pone.0048853. PubMed PMID: 23133661; PubMed Central PMCID: PMC3486801. PubMed DOI PMC

Jin N, Mao K, Jin Y, et al. Roles for PI(3,5)P2 in nutrient sensing through TORC1. Mol Biol Cell. 2014. Jan 29;25:1171–85. doi: 10.1091/mbc.E14-01-0021. PubMed PMID: 24478451. PubMed DOI PMC

Sharma G, Guardia CM, Roy A, et al. A family of PIKFYVE inhibitors with therapeutic potential against autophagy-dependent cancer cells disrupt multiple events in lysosome homeostasis. Autophagy. 2019. Oct;15(10):1694–1718. doi: 10.1080/15548627.2019.1586257. PubMed PMID: 30806145; PubMed Central PMCID: PMCPMC6735543. PubMed DOI PMC

Tan X, Thapa N, Choi S, et al. Emerging roles of PtdIns(4,5)P2–beyond the plasma membrane. J Cell Sci. 2015. Nov 15;128(22):4047–56. doi: 10.1242/jcs.175208. PubMed PMID: 26574506; PubMed Central PMCID: PMCPMC4712784. PubMed DOI PMC

Tan X, Thapa N, Liao Y, et al. PtdIns(4,5)P2 signaling regulates ATG14 and autophagy. Proc Natl Acad Sci U S A. 2016. Sep 27;113(39):10896–901. doi: 10.1073/pnas.1523145113. PubMed PMID: 27621469; PubMed Central PMCID: PMCPMC5047215. PubMed DOI PMC

Wakatsuki S, Araki T.. Specific phospholipid scramblases are involved in exposure of phosphatidylserine, an “eat-me” signal for phagocytes, on degenerating axons. Commun Integr Biol. 2017;10(2):e1296615. doi: 10.1080/19420889.2017.1296615. PubMed PMID: 28451058; PubMed Central PMCID: PMCPMC5398206. PubMed DOI PMC

Jenzer C, Simionato E, Largeau C, et al. Autophagy mediates phosphatidylserine exposure and phagosome degradation during apoptosis through specific functions of GABARAP/LGG-1 and LC3/LGG-2. Autophagy. 2019. Feb;15(2):228–241. doi: 10.1080/15548627.2018.1512452. PubMed PMID: 30160610; PubMed Central PMCID: PMCPMC6333449. PubMed DOI PMC

Lundquist MR, Goncalves MD, Loughran RM, et al. Phosphatidylinositol-5-phosphate 4-kinases regulate cellular lipid metabolism by facilitating autophagy. Mol Cells. 2018. May 3;70(3):531–544 e9. doi: 10.1016/j.molcel.2018.03.037. PubMed PMID: 29727621; PubMed Central PMCID: PMCPMC5991623. PubMed DOI PMC

Liao G, Gao B, Gao Y, et al. Phycocyanin inhibits tumorigenic potential of pancreatic cancer cells: role of apoptosis and autophagy. Sci Rep. 2016. Oct 3;6:34564. doi: 10.1038/srep34564. PubMed PMID: 27694919; PubMed Central PMCID: PMCPMC5046139. PubMed DOI PMC

Wang H, Sun HQ, Zhu X, et al. GABARAPs regulate PI4P-dependent autophagosome:lysosome fusion. Proc Natl Acad Sci U S A. 2015. Jun 2;112(22):7015–20. doi: 10.1073/pnas.1507263112. PubMed PMID: 26038556; PubMed Central PMCID: PMC4460452. PubMed DOI PMC

Marat AL, Wallroth A, Lo WT, et al. mTORC1 activity repression by late endosomal phosphatidylinositol 3,4-bisphosphate. Science. 2017. Jun 2;356(6341):968–972. doi: 10.1126/science.aaf8310. PubMed PMID: 28572395. PubMed DOI

Dou Z, Chattopadhyay M, Pan JA, et al. The class IA phosphatidylinositol 3-kinase p110-beta subunit is a positive regulator of autophagy. J Cell Biol. 2010. Nov 15;191(4):827–43. doi: 10.1083/jcb.201006056. PubMed PMID: 21059846; PubMed Central PMCID: PMC2983054. eng. PubMed DOI PMC

Lindmo K, Brech A, Finley KD, et al. The PI 3-kinase regulator Vps15 is required for autophagic clearance of protein aggregates. Autophagy. 2008. May;4(4):500–6. PubMed PMID: 18326940. PubMed

Murray JT, Panaretou C, Stenmark H, et al. Role of Rab5 in the recruitment of hVps34/p150 to the early endosome. Traffic. 2002. Jun;3(6):416–27. PubMed PMID: 12010460. PubMed

Bertolin G, Ferrando-Miguel R, Jacoupy M, et al. The TOMM machinery is a molecular switch in PINK1 and PARK2/PARKIN-dependent mitochondrial clearance. Autophagy. 2013. Nov 1;9(11):1801–17. doi: 10.4161/auto.25884. PubMed PMID: 24149440. PubMed DOI

Greene AW, Grenier K, Aguileta MA, et al. Mitochondrial processing peptidase regulates PINK1 processing, import and Parkin recruitment. EMBO Rep. 2012. Apr;13(4):378–85. doi: 10.1038/embor.2012.14. PubMed PMID: 22354088; PubMed Central PMCID: PMC3321149. PubMed DOI PMC

Jin SM, Youle RJ.. The accumulation of misfolded proteins in the mitochondrial matrix is sensed by PINK1 to induce PARK2/Parkin-mediated mitophagy of polarized mitochondria. Autophagy. 2013. Nov 1;9(11):1750–7. doi: 10.4161/auto.26122. PubMed PMID: 24149988; PubMed Central PMCID: PMC4028334. PubMed DOI PMC

Vives-Bauza C, Zhou C, Huang Y, et al. PINK1-dependent recruitment of Parkin to mitochondria in mitophagy. Proc Natl Acad Sci U S A. 2010. Jan 5;107(1):378–83. doi: 10.1073/pnas.0911187107. PubMed PMID: 19966284; PubMed Central PMCID: PMC2806779. eng. PubMed DOI PMC

Budovskaya YV, Stephan JS, Reggiori F, et al. The Ras/cAMP-dependent protein kinase signaling pathway regulates an early step of the autophagy process in Saccharomyces cerevisiae. J Biol Chem. 2004. May 14;279(20):20663–71. doi: 10.1074/jbc.M400272200 PubMed PMID: 15016820; PubMed Central PMCID: PMC1705971. eng PubMed DOI PMC

Shahab S, Namolovan A, Mogridge J, et al. Bacterial toxins can inhibit host cell autophagy through cAMP generation. Autophagy. 2011;7:957–65. PubMed

Palorini R, De Rasmo D, Gaviraghi M, et al. Oncogenic K-ras expression is associated with derangement of the cAMP/PKA pathway and forskolin-reversible alterations of mitochondrial dynamics and respiration. Oncogene. 2013. Jan 17;32(3):352–62. doi:10.1038/onc.2012.50. PubMed PMID: 22410778. PubMed DOI

Palorini R, Votta G, Pirola Y, et al. Protein kinase A activation promotes cancer cell resistance to glucose starvation and anoikis. PLoS Genet. 2016. Mar;12(3):e1005931. doi:10.1371/journal.pgen.1005931. PubMed PMID: 26978032; PubMed Central PMCID: PMCPMC4792400. PubMed DOI PMC

Agop-Nersesian C, Niklaus L, Wacker R, et al. Host cell cytosolic immune response during Plasmodium liver stage development. FEMS Microbiol Rev 2018. May 1;42(3):324–334. doi:10.1093/femsre/fuy007. PubMed PMID: 29529207; PubMed Central PMCID: PMCPMC5995216. PubMed DOI PMC

Niklaus L, Agop-Nersesian C, Schmuckli-Maurer J, et al. Deciphering host lysosome-mediated elimination of Plasmodium berghei liver stage parasites. Sci Rep. 2019. May 28;9(1):7967. doi:10.1038/s41598-019-44449-z. PubMed PMID: 31138850; PubMed Central PMCID: PMCPMC6538699. PubMed DOI PMC

Jenkins GM, Frohman MA.. Phospholipase D: a lipid centric review. Cell Mol Life Sci. 2005. Oct;62(19–20):2305–16. doi:10.1007/s00018-005-5195-z. PubMed PMID: 16143829. PubMed DOI PMC

Dall’Armi C, Hurtado-Lorenzo A, Tian H, et al. The phospholipase D1 pathway modulates macroautophagy. Nat Commun. 2010;1:142. doi:10.1038/ncomms1144. PubMed PMID: 21266992; PubMed Central PMCID: PMCPMC3328354. PubMed DOI PMC

Yoon MS. Vps34 and PLD1 take center stage in nutrient signaling: their dual roles in regulating autophagy. Cell Commun Signal. 2015. Nov 21;13:44. doi:10.1186/s12964-015-0122-x. PubMed PMID: 26589724; PubMed Central PMCID: PMCPMC4654845. PubMed DOI PMC

Luningschror P, Binotti B, Dombert B, et al. Plekhg5-regulated autophagy of synaptic vesicles reveals a pathogenic mechanism in motoneuron disease. Nat Commun. 2017. Oct 30;8(1):678. doi:10.1038/s41467-017-00689-z. PubMed PMID: 29084947; PubMed Central PMCID: PMCPMC5662736. PubMed DOI PMC

McEwan DG, Popovic D, Gubas A, et al. PLEKHM1 regulates autophagosome-lysosome fusion through HOPS complex and LC3/GABARAP proteins. Mol Cell. 2015. Jan 8;57(1):39–54. doi:10.1016/j.molcel.2014.11.006. PubMed PMID: 25498145. PubMed DOI

Ruf S, Heberle AM, Langelaar-Makkinje M, et al. PLK1 (polo like kinase 1) inhibits MTOR complex 1 and promotes autophagy. Autophagy. 2017. Mar 4;13(3):486–505. doi:10.1080/15548627.2016.1263781. PubMed PMID: 28102733; PubMed Central PMCID: PMCPMC5361591. PubMed DOI PMC

Broadley K, Larsen L, Herst PM, et al. The novel phloroglucinol PMT7 kills glycolytic cancer cells by blocking autophagy and sensitizing to nutrient stress [Research Support, Non-U.S. Gov’t]. J Cell Biochem. 2011. Jul;112(7):1869–79. doi:10.1002/jcb.23107. PubMed PMID: 21433059; eng. PubMed DOI

Martinez-Lopez N, Garcia-Macia M, Sahu S, et al. Autophagy in the CNS and periphery coordinate lipophagy and lipolysis in the brown adipose tissue and liver. Cell Metab. 2016. Jan 12;23(1):113–27. doi:10.1016/j.cmet.2015.10.008. PubMed PMID: 26698918; PubMed Central PMCID: PMCPMC4715637. PubMed DOI PMC

Dupont N, Chauhan S, Arko-Mensah J, et al. Neutral lipid stores and lipase PNPLA5 contribute to autophagosome biogenesis. Curr Biol. 2014. Mar 17;24(6):609–20. doi:10.1016/j.cub.2014.02.008. PubMed PMID: 24613307; PubMed Central PMCID: PMC4016984. PubMed DOI PMC

Elimam H, Papillon J, Kaufman DR, et al. Genetic ablation of calcium-independent phospholipase A2gamma induces glomerular injury in mice. J Biol Chem. 2016. Jul 8;291(28):14468–82. doi:10.1074/jbc.M115.696781. PubMed PMID: 27226532; PubMed Central PMCID: PMCPMC4938171. PubMed DOI PMC

Bhullar KS, Rupasinghe HP.. Polyphenols: multipotent therapeutic agents in neurodegenerative diseases. Oxid Med Cell Longev. 2013;2013:891748. doi:10.1155/2013/891748. PubMed PMID: 23840922; PubMed Central PMCID: PMC3690243. PubMed DOI PMC

Macedo D, Tavares L, McDougall GJ, et al. (Poly)phenols protect from alpha-synuclein toxicity by reducing oxidative stress and promoting autophagy. Hum Mol Genet. 2015. Mar 15;24(6):1717–32. doi:10.1093/hmg/ddu585. PubMed PMID: 25432533. PubMed DOI

Hasima N, Ozpolat B.. Regulation of autophagy by polyphenolic compounds as a potential therapeutic strategy for cancer. Cell Death Dis. 2014;5:e1509. doi:10.1038/cddis.2014.467. PubMed PMID: 25375374; PubMed Central PMCID: PMC4260725. PubMed DOI PMC

Song WH, Yi YJ, Sutovsky M, et al. Autophagy and ubiquitin-proteasome system contribute to sperm mitophagy after mammalian fertilization. Proc Natl Acad Sci U S A. 2016. Sep 6;113(36):E5261–70. doi:10.1073/pnas.1605844113. PubMed PMID: 27551072; PubMed Central PMCID: PMCPMC5018771. PubMed DOI PMC

Cai S, Geng S, Jin F, et al. POU5F1/Oct-4 expression in breast cancer tissue is significantly associated with non-sentinel lymph node metastasis. BMC Cancer. 2016. Mar 1;16:175. doi:10.1186/s12885-015-1966-6. PubMed PMID: 26931354; PubMed Central PMCID: PMCPMC4774000. PubMed DOI PMC

Sharif T, Martell E, Dai C, et al. Autophagic homeostasis is required for the pluripotency of cancer stem cells. Autophagy. 2017. Feb;13(2):264–284. doi:10.1080/15548627.2016.1260808. PubMed PMID: 27929731; PubMed Central PMCID: PMCPMC5324853. PubMed DOI PMC

Pfister AS, Keil M, Kuhl M.. The Wnt target protein Peter Pan defines a novel p53-independent nucleolar stress-response pathway. J Biol Chem. 2015. Apr 24;290(17):10905–18. doi:10.1074/jbc.M114.634246. PubMed PMID: 25759387; PubMed Central PMCID: PMCPMC4409253. PubMed DOI PMC

Laplante M, Sabatini DM.. Regulation of mTORC1 and its impact on gene expression at a glance. J Cell Sci. 2013. Apr 15;126(Pt 8):1713–9. doi:10.1242/jcs.125773. PubMed PMID: 23641065; PubMed Central PMCID: PMC3678406. PubMed DOI PMC

Palomer X, Capdevila-Busquets E, Botteri G, et al. PPARbeta/delta attenuates palmitate-induced endoplasmic reticulum stress and induces autophagic markers in human cardiac cells. Int J Cardiol. 2014. Jun 1;174(1):110–8. doi:10.1016/j.ijcard.2014.03.176. PubMed PMID: 24767130. PubMed DOI

Pawson T, Nash P.. Protein-protein interactions define specificity in signal transduction. Genes dev 2000. May 1;14(9):1027–47. PubMed PMID: 10809663. PubMed

Phizicky EM, Fields S.. Protein-protein interactions: methods for detection and analysis. Microbiol Rev 1995. Mar;59(1):94–123. PubMed PMID: 7708014; PubMed Central PMCID: PMC239356. PubMed PMC

Safari-Alighiarloo N, Taghizadeh M, Rezaei-Tavirani M, et al. Protein-protein interaction networks (PPI) and complex diseases. Gastroenterol Hepatol Bed Bench. 2014. Mar;7(1):17–31. PubMed PMID: 25436094; PubMed Central PMCID: PMC4017556. PubMed PMC

Le Guezennec X, Brichkina A, Huang YF, et al. Wip1-dependent regulation of autophagy, obesity, and atherosclerosis. Cell Metab. 2012. Jul 3;16(1):68–80. doi:10.1016/j.cmet.2012.06.003. PubMed PMID: 22768840. PubMed DOI

Chikh A, Sanza P, Raimondi C, et al. iASPP is a novel autophagy inhibitor in keratinocytes. J Cell Sci. 2014. Jul 15;127\(Pt 14):3079–93. doi:10.1242/jcs.144816. PubMed PMID: 24777476. PubMed DOI

Uddin MN, Ito S, Nishio N, et al. Gadd34 induces autophagy through the suppression of the mTOR pathway during starvation. Biochem Biophys Res Commun. 2011. Mar 22;407:692–8. doi:10.1016/j.bbrc.2011.03.077. PubMed PMID: 21439266; Eng. PubMed DOI

Fujiwara N, Usui T, Ohama T, et al. Regulation of beclin 1 protein phosphorylation and autophagy by protein phosphatase 2A (PP2A) and death-associated protein kinase 3 (DAPK3). J Biol Chem. 2016. May 13;291(20):10858–66. doi:10.1074/jbc.M115.704908. PubMed PMID: 26994142; PubMed Central PMCID: PMCPMC4865930. PubMed DOI PMC

Pala R, Alomari N, Nauli SM.. Primary cilium-dependent signaling mechanisms. Int J Mol Sci. 2017. Oct 28;18(11). doi:10.3390/ijms18112272. PubMed PMID: 29143784; PubMed Central PMCID: PMCPMC5713242. PubMed DOI PMC

Reiter JF, Leroux MR.. Genes and molecular pathways underpinning ciliopathies. Nat Rev Mol Cell Biol. 2017. Sep;18(9):533–547. doi:10.1038/nrm.2017.60. PubMed PMID: 28698599; PubMed Central PMCID: PMCPMC5851292. PubMed DOI PMC

Hasegawa J, Iwamoto R, Otomo T, et al. Autophagosome-lysosome fusion in neurons requires INPP5E, a protein associated with Joubert syndrome. EMBO J. 2016. Sep 1;35(17):1853–67. doi:10.15252/embj.201593148. PubMed PMID: 27340123; PubMed Central PMCID: PMCPMC5007553. PubMed DOI PMC

Struchtrup A, Wiegering A, Stork B, et al. The ciliary protein RPGRIP1L governs autophagy independently of its proteasome-regulating function at the ciliary base in mouse embryonic fibroblasts. Autophagy. 2018;14(4):567–583. doi:10.1080/15548627.2018.1429874. PubMed PMID: 29372668; PubMed Central PMCID: PMCPMC5959336. PubMed DOI PMC

Orhon I, Dupont N, Zaidan M, et al. Primary-cilium-dependent autophagy controls epithelial cell volume in response to fluid flow. Nat Cell Biol. 2016. Jun;18(6):657–67. doi:10.1038/ncb3360. PubMed PMID: 27214279. PubMed DOI

Jang J, Wang Y, Lalli MA, et al. Primary cilium-autophagy-Nrf2 (PAN) axis activation commits human embryonic stem cells to a neuroectoderm fate. Cell. 2016. Apr 7;165(2):410–20. doi:10.1016/j.cell.2016.02.014. PubMed PMID: 27020754. PubMed DOI

Tang Z, Lin MG, Stowe TR, et al. Autophagy promotes primary ciliogenesis by removing OFD1 from centriolar satellites. Nature. 2013. Oct 10;502(7470):254–7. doi:10.1038/nature12606. PubMed PMID: 24089205; PubMed Central PMCID: PMCPMC4075283. PubMed DOI PMC

Wang S, Livingston MJ, Su Y, et al. Reciprocal regulation of cilia and autophagy via the MTOR and proteasome pathways. Autophagy. 2015. Apr 3;11(4):607–16. doi:10.1080/15548627.2015.1023983. PubMed PMID: 25906314; PubMed Central PMCID: PMCPMC4502771. PubMed DOI PMC

Liu ZQ, Lee JN, Son M, et al. Ciliogenesis is reciprocally regulated by PPARA and NR1H4/FXR through controlling autophagy in vitro and in vivo. Autophagy. 2018;14(6):1011–1027. doi:10.1080/15548627.2018.1448326. PubMed PMID: 29771182; PubMed Central PMCID: PMCPMC6103415. PubMed DOI PMC

Eisenberg-Lerner A, Kimchi A.. PKD is a kinase of Vps34 that mediates ROS-induced autophagy downstream of DAPk. Cell Death Differ. 2012. May;19(5):788–97. doi:10.1038/cdd.2011.149. PubMed PMID: 22095288; PubMed Central PMCID: PMC3321617. PubMed DOI PMC

Durcan TM, Tang MY, Perusse JR, et al. USP8 regulates mitophagy by removing K6-linked ubiquitin conjugates from parkin. EMBO J. 2014. Sep 12;ww:2473–91. doi:10.15252/embj.201489729. PubMed PMID: 25216678. PubMed DOI PMC

Moravcevic K, Oxley CL, Lemmon MA.. Conditional peripheral membrane proteins: facing up to limited specificity. Structure. 2012. Jan 11;20(1):15–27. doi:10.1016/j.str.2011.11.012. PubMed PMID: 22193136; PubMed Central PMCID: PMC3265387. PubMed DOI PMC

Baskaran S, Ragusa MJ, Boura E, et al. Two-site recognition of phosphatidylinositol 3-phosphate by PROPPINs in autophagy. Mol Cell. 2012. Aug 10;47(3):339–48. doi:10.1016/j.molcel.2012.05.027. PubMed PMID: 22704557; PubMed Central PMCID: PMC3595537. PubMed DOI PMC

Krick R, Busse RA, Scacioc A, et al. Structural and functional characterization of the two phosphoinositide binding sites of PROPPINs, a beta-propeller protein family. Proc Natl Acad Sci U S A. 2012. Jul 24;109(30):E2042–9. doi:10.1073/pnas.1205128109. PubMed PMID: 22753491; PubMed Central PMCID: PMC3409749. PubMed DOI PMC

Watanabe Y, Kobayashi T, Yamamoto H, et al. Structure-based analyses reveal distinct binding sites for Atg2 and phosphoinositides in Atg18. J Biol Chem. 2012. Sep 14;287(38):31681–90. doi:10.1074/jbc.M112.397570. PubMed PMID: 22851171; PubMed Central PMCID: PMC3442503. PubMed DOI PMC

Finley D, Prado MA.. The Proteasome and Its Network: Engineering for Adaptability. Cold Spring Harb Perspect Biol. 2020. Jan 2;12(1). doi:10.1101/cshperspect.a033985. PubMed PMID: 30833452; PubMed Central PMCID: PMCPMC6829053. PubMed DOI PMC

Allavena G, Boyd C, Oo KS, et al. Suppressed translation and ULK1 degradation as potential mechanisms of autophagy limitation under prolonged starvation. Autophagy. 2016. Nov;12(11):2085–2097. doi:10.1080/15548627.2016.1226733. PubMed PMID: 27629431; PubMed Central PMCID: PMCPMC5103336. PubMed DOI PMC

Dong Z, Cui H.. The autophagy-lysosomal pathways and their emerging roles in modulating proteostasis in tumors. Cells. 2018. Dec 20;8(1). doi:10.3390/cells8010004. PubMed PMID: 30577555; PubMed Central PMCID: PMCPMC6356230. PubMed DOI PMC

Starokadomskyy P, Dmytruk KV.. A bird’s-eye view of autophagy. Autophagy. 2013. Jul;9(7):1121–6. doi:10.4161/auto.24544. PubMed PMID: 23615436; PubMed Central PMCID: PMC3722328. PubMed DOI PMC

Neely KM, Green KN, Laferla FM.. Presenilin is necessary for efficient proteolysis through the autophagy-lysosome system in a gamma-secretase-independent manner. J Neurosci. 2011. Feb 23;31(8):2781–91. doi:10.1523/JNEUROSCI.5156-10.2010. PubMed PMID: 21414900; PubMed Central PMCID: PMC3064964. eng. PubMed DOI PMC

Yin Z, Liu X, Ariosa A, et al. Psp2, a novel regulator of autophagy that promotes autophagy-related protein translation. Cell Res. 2019. Dec;29(12):994–1008. doi:10.1038/s41422-019-0246-4. PubMed PMID: 31666677; PubMed Central PMCID: PMCPMC6951345. PubMed DOI PMC

Miller S, Tavshanjian B, Oleksy A, et al. Shaping development of autophagy inhibitors with the structure of the lipid kinase Vps34. Science. 2010. Mar 26;327(5973):1638–42. doi:10.1126/science.1184429. PubMed PMID: 20339072; PubMed Central PMCID: PMCPMC2860105. PubMed DOI PMC

Memisoglu G, Eapen VV, Yang Y, et al. PP2C phosphatases promote autophagy by dephosphorylation of the Atg1 complex. Proc Natl Acad Sci U S A. 2019. Jan 29;116(5):1613–1620. doi:10.1073/pnas.1817078116. PubMed PMID: 30655342; PubMed Central PMCID: PMCPMC6358665. PubMed DOI PMC

Conte A, Kisslinger A, Procaccini C, et al. Convergent Effects of Resveratrol and PYK2 on Prostate Cells. Int J Mol Sci. 2016. Sep 13;17(9). doi:10.3390/ijms17091542. PubMed PMID: 27649143; PubMed Central PMCID: PMCPMC5037816. PubMed DOI PMC

Ueda H, Abbi S, Zheng C, et al. Suppression of Pyk2 kinase and cellular activities by FIP200. J Cell Biol. 2000. Apr 17;149(2):423–30. doi:10.1083/jcb.149.2.423. PubMed PMID: 10769033; PubMed Central PMCID: PMCPMC2175150. PubMed DOI PMC

Walsh CT, Garneau-Tsodikova S, Gatto GJ, Jr.. Protein posttranslational modifications: the chemistry of proteome diversifications. Angew Chem Int Ed Engl 2005. Dec 1;44(45):7342–72. doi:10.1002/anie.200501023. PubMed PMID: 16267872. PubMed DOI

Witze ES, Old WM, Resing KA, et al. Mapping protein post-translational modifications with mass spectrometry. Nat Methods. 2007. Oct;4(10):798–806. doi:10.1038/nmeth1100. PubMed PMID: 17901869. PubMed DOI

Popelka H, Klionsky DJ.. Posttranslationally-modified structures in the autophagy machinery: an integrative perspective. FEBS J. 2015. Jun 23;282:3474–88. doi:10.1111/febs.13356. PubMed PMID: 26108642. PubMed DOI PMC

Huang YH, Al-Aidaroos AQ, Yuen HF, et al. A role of autophagy in PTP4A3-driven cancer progression. Autophagy. 2014. Oct 1;10(10):1787–800. doi:10.4161/auto.29989. PubMed PMID: 25136802; PubMed Central PMCID: PMC4198363. PubMed DOI PMC

Martin KR, Xu Y, Looyenga BD, et al. Identification of PTPsigma as an autophagic phosphatase. J Cell Sci. 2011. Mar 1;124(Pt 5):812–9. doi:10.1242/jcs.080341. PubMed PMID: 21303930; PubMed Central PMCID: PMC3039021. eng. PubMed DOI PMC

Mandell MA, Jain A, Arko-Mensah J, et al. TRIM proteins regulate autophagy and can target autophagic substrates by direct recognition. Dev Cell. 2014. Aug 25;30(4):394–409. doi:10.1016/j.devcel.2014.06.013. PubMed PMID: 25127057; PubMed Central PMCID: PMC4146662. PubMed DOI PMC

Andres S, Pevny S, Ziegenhagen R, et al. Safety aspects of the use of quercetin as a dietary supplement. Mol Nutr Food Res 2018. Jan;62(1). doi:10.1002/mnfr.201700447. PubMed PMID: 29127724. PubMed DOI

Russo M, Russo GL.. Autophagy inducers in cancer. Biochem Pharmacol. 2018. Jul;153:51–61. doi:10.1016/j.bcp.2018.02.007. PubMed PMID: 29438677. PubMed DOI

Zhu Y, Tchkonia T, Pirtskhalava T, et al. The Achilles’ heel of senescent cells: from transcriptome to senolytic drugs. Aging cell. 2015. Aug;14(4):644–58. doi:10.1111/acel.12344. PubMed PMID: 25754370; PubMed Central PMCID: PMCPMC4531078. PubMed DOI PMC

Kang C, Elledge SJ.. How autophagy both activates and inhibits cellular senescence. Autophagy. 2016. May 3;12(5):898–9. doi:10.1080/15548627.2015.1121361. PubMed PMID: 27129029; PubMed Central PMCID: PMCPMC4854549. PubMed DOI PMC

Fujita N, Huang W, Lin TH, et al. Genetic screen in Drosophila muscle identifies autophagy-mediated T-tubule remodeling and a Rab2 role in autophagy. eLife. 2017. Jan 7;6. doi:10.7554/eLife.23367. PubMed PMID: 28063257; PubMed Central PMCID: PMCPMC5249261. PubMed DOI PMC

Lorincz P, Toth S, Benko P, et al. Rab2 promotes autophagic and endocytic lysosomal degradation. J Cell Biol. 2017. Jul 3;216(7):1937–1947. doi:10.1083/jcb.201611027. PubMed PMID: 28483915; PubMed Central PMCID: PMCPMC5496615. PubMed DOI PMC

Ding X, Jiang X, Tian R, et al. RAB2 regulates the formation of autophagosome and autolysosome in mammalian cells. Autophagy. 2019. Oct;15(10):1774–1786. doi:10.1080/15548627.2019.1596478. PubMed PMID: 30957628; PubMed Central PMCID: PMCPMC6735470. PubMed DOI PMC

Nagy G, Ward J, Mosser DD, et al. Regulation of CD4 expression via recycling by HRES-1/RAB4 controls susceptibility to HIV infection. J Biol Chem. 2006. Nov 10;281(45):34574–91. doi:10.1074/jbc.M606301200. PubMed PMID: 16935861. PubMed DOI

Fernandez DR, Telarico T, Bonilla E, et al. Activation of mammalian target of rapamycin controls the loss of TCRzeta in lupus T cells through HRES-1/Rab4-regulated lysosomal degradation. J Iimmunol. 2009. Feb 15;182(4):2063–73. doi:10.4049/jimmunol.0803600. PubMed PMID: 19201859; PubMed Central PMCID: PMC2676112. PubMed DOI PMC

Caza TN, Fernandez DR, Talaber G, et al. HRES-1/Rab4-mediated depletion of Drp1 impairs mitochondrial homeostasis and represents a target for treatment in SLE. Ann Rheum Dis. 2014. Oct;73(10):1888–97. doi:10.1136/annrheumdis-2013-203794. PubMed PMID: 23897774; PubMed Central PMCID: PMC4047212. PubMed DOI PMC

Talaber G, Miklossy G, Oaks Z, et al. HRES-1/Rab4 promotes the formation of LC3(+) auto-phagosomes and the accumulation of mitochondria during autophagy. PLoS One. 2014;9(1):e84392. doi:10.1371/journal.pone.0084392. PubMed PMID: 24404161; PubMed Central PMCID: PMC3880286. PubMed DOI PMC

Weidberg H, Shvets E, Elazar Z.. Biogenesis and cargo selectivity of auto-phagosomes. Annual Rev Biochem. 2011;80:125–156. PubMed PMID: 21548784. PubMed

Hammerling BC, Najor RH, Cortez MQ, et al. A Rab5 endosomal pathway mediates Parkin-dependent mitochondrial clearance. Nat Commun. 2017. Jan 30;8:14050. doi: 10.1038/ncomms14050. PubMed PMID: 28134239; PubMed Central PMCID: PMCPMC5290275. PubMed DOI PMC

Ayala CI, Kim J, Neufeld TP.. Rab6 promotes insulin receptor and cathepsin trafficking to regulate autophagy induction and activity in Drosophila. J Cell Sci. 2018. Sep 7;131(17). doi: 10.1242/jcs.216127. PubMed PMID: 30111579; PubMed Central PMCID: PMCPMC6140324. PubMed DOI PMC

Stenmark H. Rab GTPases as coordinators of vesicle traffic. Nat Rev Mol Cell Biol. 2009. Aug;10(8):513–525. PubMed PMID: 19603039; eng. PubMed

Kuchitsu Y, Homma Y, Fujita N, et al. Rab7 knockout unveils regulated autolysosome maturation induced by glutamine starvation. J Cell Sci. 2018. Apr 6;131(7). doi: 10.1242/jcs.215442. PubMed PMID: 29514857. PubMed DOI

Keeling E, DS Chatelet, DA Johnston, et al. Oxidative stress and dysfunctional intracellular traffic linked to an unhealthy diet results in impaired cargo transport in the retinal pigment epithelium (RPE). Mol Nutr Food Res. 2019. Aug;63(15):e1800951. doi: 10.1002/mnfr.201800951. PubMed PMID: 30835933. PubMed DOI

Rink J, Ghigo E, Kalaidzidis Y, et al. Rab conversion as a mechanism of progression from early to late endosomes. Cell. 2005. Sep 9;122(5):735–749. doi: 10.1016/j.cell.2005.06.043. PubMed PMID: 16143105; eng. PubMed DOI

Pilli M, Arko-Mensah J, Ponpuak M, et al. TBK-1 promotes autophagy-mediated antimicrobial defense by controlling autophagosome maturation. Immunity. 2012. Aug 24;37(2):223–234. PubMed PMID: 22921120; PubMed Central PMCID: PMC3428731. PubMed PMC

Honda S, Arakawa S, Nishida Y, et al. Ulk1-mediated Atg5-independent macroautophagy mediates elimination of mitochondria from embryonic reticulocytes. Nat Commun. 2014. Jun 4;5:4004. PubMed PMID: 24895007. PubMed

Saito T, Nah J, Oka SI, et al. An alternative mitophagy pathway mediated by Rab9 protects the heart against ischemia. J Clin Invest. 2019. Feb 1;129(2):802–819. doi: 10.1172/JCI122035. PubMed PMID: 30511961; PubMed Central PMCID: PMCPMC6355232. PubMed DOI PMC

Nozawa T, Aikawa C, Goda A, et al. The small GTPases Rab9A and Rab23 function at distinct steps in autophagy during Group A Streptococcus infection. Cell Microbiol. 2012. Aug;14(8):1149–1165. doi: 10.1111/j.1462-5822.2012.01792.x. PubMed PMID: 22452336. PubMed DOI

Wauters F, Cornelissen T, Imberechts D, et al. LRRK2 mutations impair depolarization-induced mitophagy through inhibition of mitochondrial accumulation of RAB10. Autophagy. 2020. Feb;16(2):203–222. doi: 10.1080/15548627.2019.1603548. PubMed PMID: 30945962; PubMed Central PMCID: PMCPMC6984591. PubMed DOI PMC

Kelly EE, Horgan CP, McCaffrey MW.. Rab11 proteins in health and disease. Biochem Soc Trans. 2012. Dec 1;40(6):1360–1367. PubMed PMID: 23176481. PubMed

Longatti A, Lamb CA, Razi M, et al. TBC1D14 regulates autophagosome formation via Rab11- and ULK1-positive recycling endosomes. J Cell Biol. 2012. May 28;197(5):659–675. doi: 10.1083/jcb.201111079. PubMed PMID: 22613832; PubMed Central PMCID: PMC3365497. PubMed DOI PMC

Fader CM, Sanchez D, Furlan M, et al. Induction of autophagy promotes fusion of multivesicular bodies with autophagic vacuoles in k562 cells. Traffic. 2008. Feb;9(2):230–250. doi: 10.1111/j.1600-0854.2007.00677.x. PubMed PMID: 17999726; eng. PubMed DOI

Szatmari Z, Kis V, Lippai M, et al. Rab11 facilitates cross-talk between autophagy and endosomal pathway through regulation of Hook localization. Molecular Biol Cell. 2014. Feb;25(4):522–531. doi: 10.1091/mbc.E13-10-0574. PubMed PMID: 24356450; PubMed Central PMCID: PMCPMC3923643. PubMed DOI PMC

Matsui T, Fukuda M. Rab12 regulates mTORC1 activity and autophagy through controlling the degradation of amino-acid transporter PAT4. EMBO Rep. 2013. May;14(5):450–457. PubMed PMID: 23478338; PubMed Central PMCID: PMC3642374. PubMed PMC

Zhang L, Dai F, Cui L, et al. Up-regulation of the active form of small GTPase Rab13 promotes macroautophagy in vascular endothelial cells. Biochim Biophys Acta Mol Cell Res. 2017. Apr;1864(4):613–624. doi: 10.1016/j.bbamcr.2017.01.003. PubMed PMID: 28087344. PubMed DOI

Jean S, Cox S, Nassari S, et al. Starvation-induced MTMR13 and RAB21 activity regulates VAMP8 to promote autophagosome-lysosome fusion. EMBO Rep. 2015. Mar;16(3):297–311. PubMed PMID: 25648148; PubMed Central PMCID: PMC4364869. PubMed PMC

Munafo DB, Colombo MI.. Induction of autophagy causes dramatic changes in the subcellular distribution of GFP-Rab24. Traffic. 2002. Jul;3(7):472–482. PubMed PMID: 12047555; eng. PubMed

Yla-Anttila P, Mikkonen E, Otteby KE, et al. RAB24 facilitates clearance of autophagic compartments during basal conditions. Autophagy. 2015. Sep 1;11:1833–1848. doi: 10.1080/15548627.2015.1086522. PubMed PMID: 26325487. PubMed DOI PMC

Binotti B, Pavlos NJ, Riedel D, et al. The GTPase Rab26 links synaptic vesicles to the autophagy pathway. eLife. 2015. Feb 2;4:e05597. doi: 10.7554/eLife.05597. PubMed PMID: 25643395; PubMed Central PMCID: PMCPMC4337689. PubMed DOI PMC

Hirota Y, Tanaka Y.. A small GTPase, human Rab32, is required for the formation of autophagic vacuoles under basal conditions [Research Support, Non-U.S. Gov’t]. Cell Mol Life Sci. 2009. Sep;66(17):2913–2932. PubMed PMID: 19593531; eng. PubMed PMC

Itoh T, Fujita N, Kanno E, et al. Golgi-resident small GTPase Rab33B interacts with Atg16L and modulates autophagosome formation. Mol Biol Cell. 2008. Jul;19(7):2916–2925. PubMed PMID: 18448665; PubMed Central PMCID: PMC2441679. eng. PubMed PMC

Itoh T, Kanno E, Uemura T, et al. OATL1, a novel autophagosome-resident Rab33B-GAP, regulates autophagosomal maturation [Research Support, Non-U.S. Gov’t]. J Cell Biol. 2011. Mar 7;192(5):839–853. doi: 10.1083/jcb.201008107. PubMed PMID: 21383079; PubMed Central PMCID: PMC3051816. eng. PubMed DOI PMC

Song Y, Shang D, Cheng H, et al. The small GTPase RAB37 functions as an organizer for autophagosome biogenesis. Autophagy. 2018;14(4):727–729. doi: 10.1080/15548627.2018.1434374. PubMed PMID: 29388490; PubMed Central PMCID: PMCPMC5959331. PubMed DOI PMC

Sheng Y, Song Y, Li Z, et al. RAB37 interacts directly with ATG5 and promotes autophagosome formation via regulating ATG5-12-16 complex assembly. Cell Death Differ. 2018. May;25(5):918–934. doi: 10.1038/s41418-017-0023-1. PubMed PMID: 29229996; PubMed Central PMCID: PMCPMC5943352. PubMed DOI PMC

Ye X, Zhou XJ, Zhang H.. Exploring the role of autophagy-related gene 5 (ATG5) yields important insights into autophagy in autoimmune/autoinflammatory diseases. Front Immunol. 2018;9:2334. PubMed PMID: 30386331; PubMed Central PMCID: PMCPMC6199349. PubMed PMC

Chen XW, Leto D, Xiong T, et al. A Ral GAP complex links PI 3-kinase/Akt signaling to RalA activation in insulin action. Mol Biol Cell. 2011. Jan 1;22(1):141–152. PubMed PMID: 21148297; PubMed Central PMCID: PMC3016972. PubMed PMC

Gentry LR, Martin TD, Reiner DJ, et al. Ral small GTPase signaling and oncogenesis: more than just 15minutes of fame. Biochim Biophys Acta. 2014. Dec;1843(12):2976–2988. PubMed PMID: 25219551; PubMed Central PMCID: PMC4201770. PubMed PMC

Martin TD, Chen XW, Kaplan RE, et al. Ral and Rheb GTPase activating proteins integrate mTOR and GTPase signaling in aging, autophagy, and tumor cell invasion. Mol Cell. 2014. Jan 23;53(2):209–220. PubMed PMID: 24389102; PubMed Central PMCID: PMC3955741. PubMed PMC

Geng J, Nair U, Yasumura-Yorimitsu K, et al. Post-Golgi Sec proteins are required for autophagy in Saccharomyces cerevisiae. Mol Biol Cell. 2010. Jul 1;21(13):2257–2269. doi: 10.1091/mbc.E09-11-0969. PubMed PMID: 20444978; PubMed Central PMCID: PMC2893989. eng. PubMed DOI PMC

Shirakawa R, Fukai S, Kawato M, et al. Tuberous sclerosis tumor suppressor complex-like complexes act as GTPase-activating proteins for Ral GTPases. J Biol Chem. 2009. Aug 7;284(32):21580–21588. doi: 10.1074/jbc.M109.012112. PubMed PMID: 19520869; PubMed Central PMCID: PMC2755882. PubMed DOI PMC

Oeckinghaus A, Postler TS, Rao P, et al. kappaB-Ras proteins regulate both NF-kappaB-dependent inflammation and Ral-dependent proliferation. Cell Rep. 2014. Sep 25;8(6):1793–1807. PubMed PMID: 25220458; PubMed Central PMCID: PMC4177457. PubMed PMC

Mestre MB, Colombo MI.. cAMP and EPAC are key players in the regulation of the signal transduction pathway involved in the alpha-hemolysin autophagic response. PLoS Pathog. 2012;8(5):e1002664. PubMed PMID: 22654658; PubMed Central PMCID: PMCPMC3359991. PubMed PMC

Mestre MB, Colombo MI.. Staphylococcus aureus promotes autophagy by decreasing intracellular cAMP levels. Autophagy. 2012. Dec;8(12):1865–1867. doi: 10.4161/auto.22161. PubMed PMID: 23047465; PubMed Central PMCID: PMCPMC3541307. PubMed DOI PMC

Laurent AC, Bisserier M, Lucas A, et al. Exchange protein directly activated by cAMP 1 promotes autophagy during cardiomyocyte hypertrophy. Cardiovasc Res. 2015. Jan 1;105(1):55–64. doi: 10.1093/cvr/cvu242. PubMed PMID: 25411381. PubMed DOI

Chu KY, O’Reilly L, Mellet N, et al. Oleate disrupts cAMP signaling, contributing to potent stimulation of pancreatic beta-cell autophagy. J Biol Chem. 2019. Jan 25;294(4):1218–1229. doi: 10.1074/jbc.RA118.004833. PubMed PMID: 30518550; PubMed Central PMCID: PMCPMC6349129. PubMed DOI PMC

Li W, Yue F, Dai Y, et al. Suppressor of hepatocellular carcinoma RASSF1A activates autophagy initiation and maturation. Cell Death Differ. 2019. Aug;26(8):1379–1395. doi: 10.1038/s41418-018-0211-7. PubMed PMID: 30315205; PubMed Central PMCID: PMCPMC6748129. PubMed DOI PMC

Thakur A, Mikkelsen H, Jungersen G.. Intracellular Pathogens: host Immunity and Microbial Persistence Strategies. J Immunol Res. 2019;2019:1356540. doi: 10.1155/2019/1356540. PubMed PMID: 31111075; PubMed Central PMCID: PMCPMC6487120. PubMed DOI PMC

Horenkamp FA, Kauffman KJ, Kohler LJ, et al. The legionella anti-autophagy effector RavZ targets the autophagosome via PI3P- and curvature-sensing motifs. Dev Cell. 2015. Sep 14;34(5):569–576. doi: 10.1016/j.devcel.2015.08.010. PubMed PMID: 26343456; PubMed Central PMCID: PMCPMC4594837. PubMed DOI PMC

Vargas JNS, Wang C, Bunker E, et al. Spatiotemporal Control of ULK1 Activation by NDP52 and TBK1 during Selective Autophagy. Mol Cell. 2019. Apr 18;74(2):347–362e6. doi: 10.1016/j.molcel.2019.02.010. PubMed PMID: 30853401; PubMed Central PMCID: PMCPMC6642318. PubMed DOI PMC

Ravenhill BJ, Boyle KB, von Muhlinen N, et al. The cargo receptor NDP52 initiates selective autophagy by recruiting the ULK complex to cytosol-invading bacteria. Mol Cell. 2019. Apr 18;74(2):320–329e6. doi: 10.1016/j.molcel.2019.01.041. PubMed PMID: 30853402; PubMed Central PMCID: PMCPMC6477152. PubMed DOI PMC

Punnonen EL, Reunanen H, Hirsimaki P, et al. Filipin labelling and intramembrane particles on the membranes of early and later autophagic vacuoles in Ehrlich ascites cells. Virchows Archiv B Cell Pathol Mol Pathol. 1988;54(5):317–326. PubMed PMID: 2451345; eng. PubMed

Huang XC, Inoue-Aono Y, Moriyasu Y, et al. Plant cell wall-penetrable, redox-responsive silica nanoprobe for the imaging of starvation-induced vesicle trafficking. Anal Chem. 2016. Oct 18;88(20):10231–10236. doi: 10.1021/acs.analchem.6b02920. PubMed PMID: 27673337. PubMed DOI

Opipari AJ, Tan L, Boitano AE, Sorenson DR, Aurora A, Liu JR.. Resveratrol-induced autophagocytosis in ovarian cancer cells. Cancer Res. 2004;15:696–703. PubMed

Klionsky DJ, Cuervo AM, Dunn WA, Jr., et al. How shall I eat thee?. Autophagy. 2007. Sep-Oct;3(5):413–416. PubMed PMID: 17568180; eng. PubMed

Ogier-Denis E, Petiot A, Bauvy C, et al. Control of the expression and activity of the Galpha-interacting protein (GAIP) in human intestinal cells. J Biol Chem. 1997. Sep 26;272(39):24599–24603. PubMed PMID: 9305927; eng. PubMed

Fransson S, Ruusala A, Aspenstrom P.. The atypical Rho GTPases Miro-1 and Miro-2 have essential roles in mitochondrial trafficking. Biochem Biophys Res Commun. 2006. Jun 2;344(2):500–510. doi: 10.1016/j.bbrc.2006.03.163. PubMed PMID: 16630562. PubMed DOI

Lopez-Domenech G, Covill-Cooke C, Ivankovic D, et al. Miro proteins coordinate microtubule- and actin-dependent mitochondrial transport and distribution. Embo J. 2018. Feb 1;37(3):321–336. PubMed PMID: 29311115; PubMed Central PMCID: PMCPMC5793800. PubMed PMC

Wang X, Winter D, Ashrafi G, et al. PINK1 and Parkin target Miro for phosphorylation and degradation to arrest mitochondrial motility. Cell. 2011. Nov 11;147(4):893–906. doi: 10.1016/j.cell.2011.10.018. PubMed PMID: 22078885; PubMed Central PMCID: PMCPMC3261796. PubMed DOI PMC

Birsa N, Norkett R, Wauer T, et al. Lysine 27 ubiquitination of the mitochondrial transport protein Miro is dependent on serine 65 of the Parkin ubiquitin ligase. J Biol Chem. 2014. May 23;289(21):14569–14582. doi: 10.1074/jbc.M114.563031. PubMed PMID: 24671417; PubMed Central PMCID: PMCPMC4031514. PubMed DOI PMC

Safiulina D, Kuum M, Choubey V, et al. Miro proteins prime mitochondria for Parkin translocation and mitophagy. Embo J. 2019. Jan 15;38(2). doi: 10.15252/embj.201899384. PubMed PMID: 30504269; PubMed Central PMCID: PMCPMC6331716. PubMed DOI PMC

Khobrekar NV, Quintremil S, Dantas TJ, et al. The dynein adaptor RILP controls neuronal autophagosome biogenesis, transport, and clearance. Dev Cell. 2020. Apr 20;53(2):141–153e4. doi: 10.1016/j.devcel.2020.03.011. PubMed PMID: 32275887. PubMed DOI PMC

Yorimitsu T, Zaman S, Broach JR, et al. Protein kinase A and Sch9 cooperatively regulate induction of autophagy in Saccharomyces cerevisiae. Mol Biol Cell. 2007. Oct;18(10):4180–4189. Doi:10.1091/mbc.E07-05-0485. PubMed PMID: 17699586; PubMed Central PMCID: PMC1995722. eng. PubMed DOI PMC

Yonekawa T, Gamez G, Kim J, et al. RIP1 negatively regulates basal autophagic flux through TFEB to control sensitivity to apoptosis. EMBO Rep. 2015. Jun;16(6):700–708. PubMed PMID: 25908842; PubMed Central PMCID: PMC4467854. PubMed PMC

Hillwig MS, Contento AL, Meyer A, et al. RNS2, a conserved member of the RNase T2 family, is necessary for ribosomal RNA decay in plants. Proc Natl Acad Sci U S A. 2011. Jan 18;108(3):1093–1098. PubMed PMID: 21199950; PubMed Central PMCID: PMC3024651. eng. PubMed PMC

Haud N, Kara F, Diekmann S, et al. rnaset2 mutant zebrafish model familial cystic leukoencephalopathy and reveal a role for RNase T2 in degrading ribosomal RNA. Proc Natl Acad Sci U S A. 2011. Jan 18;108(3):1099–1103. doi: 10.1073/pnas.1009811107. PubMed PMID: 21199949; PubMed Central PMCID: PMC3024650. PubMed DOI PMC

Liu Y, Zou W, Yang P, et al. Autophagy-dependent ribosomal RNA degradation is essential for maintaining nucleotide homeostasis during C. elegans development. eLife. 2018. Aug 13;7. doi: 10.7554/eLife.36588. PubMed PMID: 30102152; PubMed Central PMCID: PMCPMC6101943. PubMed DOI PMC

Floyd BE, Mugume Y, Morriss SC, et al. Localization of RNS2 ribonuclease to the vacuole is required for its role in cellular homeostasis. Planta. 2017. Apr;245(4):779–792. doi: 10.1007/s00425-016-2644-x. PubMed PMID: 28025674. PubMed DOI

Xu C, Feng K, Zhao X, et al. Regulation of autophagy by E3 ubiquitin ligase RNF216 through BECN1 ubiquitination. Autophagy. 2014. Nov 11;10:2239–2250. PubMed PMID: 25484083. PubMed PMC

Gurkar AU, Chu K, Raj L, et al. Identification of ROCK1 kinase as a critical regulator of Beclin1-mediated autophagy during metabolic stress. Nat Commun. 2013;4:2189. doi: 10.1038/ncomms3189. PubMed PMID: 23877263; PubMed Central PMCID: PMCPMC3740589. PubMed DOI PMC

Shi J, Surma M, Yang Y, et al. Disruption of both ROCK1 and ROCK2 genes in cardiomyocytes promotes autophagy and reduces cardiac fibrosis during aging. Faseb J. 2019. Jun;33(6):7348–7362. PubMed PMID: 30848941; PubMed Central PMCID: PMCPMC6529334. PubMed PMC

Shi J, Surma M, Wei L.. Disruption of ROCK1 gene restores autophagic flux and mitigates doxorubicin-induced cardiotoxicity. Oncotarget. 2018. Feb 27;9(16):12995–13008. PubMed PMID: 29560126; PubMed Central PMCID: PMCPMC5849190. PubMed PMC

Hac A, Domachowska A, Narajczyk M, et al. S6K1 controls autophagosome maturation in autophagy induced by sulforaphane or serum deprivation. Eur J Cell Biol. 2015. Oct;94(10):470–481. doi: 10.1016/j.ejcb.2015.05.001. PubMed PMID: 26054233. PubMed DOI

Xu X, Sun J, Song R, et al. Inhibition of p70 S6 kinase (S6K1) activity by A77 1726, the active metabolite of leflunomide, induces autophagy through TAK1-mediated AMPK and JNK activation. Oncotarget. 2017. May 2;8(18):30438–30454. doi: 10.18632/oncotarget.16737. PubMed PMID: 28389629; PubMed Central PMCID: PMCPMC5444754. PubMed DOI PMC

Sun J, Mu Y, Jiang Y, et al. Inhibition of p70 S6 kinase activity by A77 1726 induces autophagy and enhances the degradation of superoxide dismutase 1 (SOD1) protein aggregates. Cell Death Dis. 2018. Mar 14;9(3):407. PubMed PMID: 29540819; PubMed Central PMCID: PMCPMC5851998. PubMed PMC

Selman C, Tullet JM, Wieser D, et al. Ribosomal protein S6 kinase 1 signaling regulates mammalian life span. Science. 2009. Oct 2;326(5949):140–144. doi: 10.1126/science.1177221. PubMed PMID: 19797661; PubMed Central PMCID: PMCPMC4954603. PubMed DOI PMC

Aguilar V, Alliouachene S, Sotiropoulos A, et al. S6 kinase deletion suppresses muscle growth adaptations to nutrient availability by activating AMP kinase. Cell Metab. 2007. Jun;5(6):476–487. doi: 10.1016/j.cmet.2007.05.006. PubMed PMID: 17550782. PubMed DOI

Kim E, Goraksha-Hicks P, Li L, et al. Regulation of TORC1 by Rag GTPases in nutrient response. Nat Cell Biol. 2008. Aug;10(8):935–945. PubMed PMID: 18604198; PubMed Central PMCID: PMC2711503. Eng. PubMed PMC

White E. Exploiting the bad eating habits of Ras-driven cancers. Genes Dev. 2013. Oct 1;27(19):2065–2071. doi: 10.1101/gad.228122.113. PubMed PMID: 24115766; PubMed Central PMCID: PMC3850091. PubMed DOI PMC

Cheng X, Ma X, Zhu Q, et al. Pacer is a mediator of mTORC1 and GSK3-TIP60 signaling in regulation of autophagosome maturation and lipid metabolism. Mol Cell. 2019. Feb 21;73(4):788–802e7. PubMed PMID: 30704899. PubMed

Beltran S, Nassif M, Vicencio E, et al. Network approach identifies Pacer as an autophagy protein involved in ALS pathogenesis. Mol Neurodegener. 2019. Mar 27;14(1):14. doi: 10.1186/s13024-019-0313-9. PubMed PMID: 30917850; PubMed Central PMCID: PMCPMC6437924. PubMed DOI PMC

Tandon M, Othman AH, Ashok V, et al. The role of Runx2 in facilitating autophagy in metastatic breast cancer cells. J Cell Physiol. 2018. Jan;233(1):559–571. PubMed PMID: 28345763. PubMed

Vervliet T, Pintelon I, Welkenhuyzen K, et al. Basal ryanodine receptor activity suppresses autophagic flux. Biochem Pharmacol. 2017. May 15;132:133–142. doi: 10.1016/j.bcp.2017.03.011. PubMed PMID: 28322744. PubMed DOI

Shao Y, Gao Z, Marks PA, et al. Apoptotic and autophagic cell death induced by histone deacetylase inhibitors. Proc Natl Acad Sci U S A. 2004. Dec 28;101(52):18030–18035. PubMed PMID: 15596714; PubMed Central PMCID: PMC539807. PubMed PMC

Stankov MV, El Khatib M, Kumar Thakur B, et al. Histone deacetylase inhibitors induce apoptosis in myeloid leukemia by suppressing autophagy. Leukemia. 2014. Mar;28(3):577–588. PubMed PMID: 24080946; PubMed Central PMCID: PMC3947652. PubMed PMC

Frohlich LF, Mrakovcic M, Smole C, et al. Molecular mechanism leading to SAHA-induced autophagy in tumor cells: evidence for a p53-dependent pathway. Cancer Cell Int. 2016;16(1):68. doi: 10.1186/s12935-016-0343-0. PubMed PMID: 27601937; PubMed Central PMCID: PMCPMC5011867. PubMed DOI PMC

Galadari S, Rahman A, Pallichankandy S, et al. Molecular targets and anticancer potential of sanguinarine-a benzophenanthridine alkaloid. Phytomedicine. 2017. Oct 15;34:143–153. PubMed PMID: 28899497. PubMed

Pallichankandy S, Rahman A, Thayyullathil F, et al. ROS-dependent activation of autophagy is a critical mechanism for the induction of anti-glioma effect of sanguinarine. Free Radic Biol Med. 2015. Dec;89:708–720. PubMed PMID: 26472194. PubMed

Ni C, Narzt MS, Nagelreiter IM, et al. Autophagy deficient melanocytes display a senescence associated secretory phenotype that includes oxidized lipid mediators. Int J Biochem Cell Biol. 2016. Dec;81(Pt B):375–382. PubMed PMID: 27732890. PubMed

Dokudovskaya S, Waharte F, Schlessinger A, et al. A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics. 2011. Jun;10(6):M110006478. doi: 10.1074/mcp.M110.006478. PubMed PMID: 21454883; PubMed Central PMCID: PMC3108837. eng. PubMed DOI PMC

Tabecka-Lonczynska A, Mytych J, Solek P, et al. Autophagy as a consequence of seasonal functions of testis and epididymis in adult male European bison (Bison bonasus, Linnaeus 1758). Cell Tissue Res. 2020. Mar;379(3):613–624. doi: 10.1007/s00441-019-03111-w. PubMed PMID: 31705214. PubMed DOI

Nair U, Jotwani A, Geng J, et al. SNARE proteins are required for macroautophagy. Cell. 2011. Jul 22;146(2):290–302. doi: 10.1016/j.cell.2011.06.022. PubMed PMID: 21784249; PubMed Central PMCID: PMC3143362. eng. PubMed DOI PMC

Ishihara N, Hamasaki M, Yokota S, et al. Autophagosome requires specific early Sec proteins for its formation and NSF/SNARE for vacuolar fusion. Mol Biol Cell. 2001. Nov;12(11):3690–3702. PubMed PMID: 11694599; eng. PubMed PMC

Loi M, Raimondi A, Morone D, et al. ESCRT-III-driven piecemeal micro-ER-phagy remodels the ER during recovery from ER stress. Nat Commun. 2019. Nov 7;10(1):5058. doi: 10.1038/s41467-019-12991-z. PubMed PMID: 31699981; PubMed Central PMCID: PMCPMC6838186. PubMed DOI PMC

Jiang S, Dupont N, Castillo EF, et al. Secretory versus degradative autophagy: unconventional secretion of inflammatory mediators. J Innate Immun. 2013;5(5):471–479. PubMed PMID: 23445716; PubMed Central PMCID: PMC3723810. PubMed PMC

Marino G, Fernandez AF, Cabrera S, et al. Autophagy is essential for mouse sense of balance [Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t]. J Clin Invest. 2010. Jul 1;120(7):2331–2344. PubMed PMID: 20577052; PubMed Central PMCID: PMC2898610. eng. PubMed PMC

Cabrera S, Fernandez AF, Marino G, et al. ATG4B/autophagin-1 regulates intestinal homeostasis and protects mice from experimental colitis. Autophagy. 2013. Aug;9(8):1188–1200. doi: 10.4161/auto.24797. PubMed PMID: 23782979; PubMed Central PMCID: PMCPMC3748191. PubMed DOI PMC

Cabrera S, Marino G, Fernandez AF, et al. Autophagy, proteases and the sense of balance. Autophagy. 2010. Oct;6(7):961–963. doi: 10.4161/auto.6.7.13065. PubMed PMID: 20724821; eng. PubMed DOI

Bel S, Hooper LV.. Secretory autophagy of lysozyme in Paneth cells. Autophagy. 2018;14(4):719–721. doi: 10.1080/15548627.2018.1430462. PubMed PMID: 29388875; PubMed Central PMCID: PMCPMC5959324. PubMed DOI PMC

Bel S, Pendse M, Wang Y, et al. Paneth cells secrete lysozyme via secretory autophagy during bacterial infection of the intestine. Science. 2017. Sep 8;357(6355):1047–1052. doi: 10.1126/science.aal4677. PubMed PMID: 28751470; PubMed Central PMCID: PMCPMC5702267. PubMed DOI PMC

Li J, Qi W, Chen G, et al. Mitochondrial outer-membrane E3 ligase MUL1 ubiquitinates ULK1 and regulates selenite-induced mitophagy. Autophagy. 2015;11(8):1216–1229. doi: 10.1080/15548627.2015.1017180. PubMed PMID: 26018823; PubMed Central PMCID: PMCPMC4590677. PubMed DOI PMC

Gewirtz DA. Autophagy, senescence and tumor dormancy in cancer therapy. Autophagy. 2009. Nov;5(8):1232–1234. doi: 10.4161/auto.5.8.9896. PubMed PMID: 19770583. PubMed DOI

Liu K, Guo C, Lao Y, et al. A fine-tuning mechanism underlying self-control for autophagy: deSUMOylation of BECN1 by SENP3. Autophagy. 2019. Aug 2:1–16. doi: 10.1080/15548627.2019.1647944. PubMed PMID: 31373534. PubMed DOI PMC

Mostowy S, Bonazzi M, Hamon MA, et al. Entrapment of intracytosolic bacteria by septin cage-like structures. Cell Host Microbe. 2010. Nov 18;8(5):433–444. PubMed PMID: 21075354; eng. PubMed

Barve G, Sanyal P, Manjithaya R.. Septin localization and function during autophagy. Curr Genet. 2018. Oct;64(5):1037–1041. doi: 10.1007/s00294-018-0834-8. PubMed PMID: 29651536. PubMed DOI

Hidvegi T, Ewing M, Hale P, et al. An autophagy-enhancing drug promotes degradation of mutant alpha1-antitrypsin Z and reduces hepatic fibrosis. Science. 2010. Jul 9;329(5988):229–232. PubMed PMID: 20522742. PubMed

Lee JH, Budanov AV, Karin M.. Sestrins orchestrate cellular metabolism to attenuate aging. Cell Metab. 2013. Dec 3;18(6):792–801. doi: 10.1016/j.cmet.2013.08.018. PubMed PMID: 24055102; PubMed Central PMCID: PMC3858445. PubMed DOI PMC

Ho A, Cho CS, Namkoong S, et al. Biochemical basis of sestrin physiological activities. Trends Biochem Sci. 2016. Jul;41(7):621–632. doi: 10.1016/j.tibs.2016.04.005. PubMed PMID: 27174209; PubMed Central PMCID: PMCPMC4930368. PubMed DOI PMC

Kumar A, Shaha C.. SESN2 facilitates mitophagy by helping Parkin translocation through ULK1 mediated Beclin1 phosphorylation. Sci Rep. 2018. Jan 12;8(1):615. doi: 10.1038/s41598-017-19102-2. PubMed PMID: 29330382; PubMed Central PMCID: PMCPMC5766514. PubMed DOI PMC

Kim MJ, Bae SH, Ryu JC, et al. SESN2/sestrin2 suppresses sepsis by inducing mitophagy and inhibiting NLRP3 activation in macrophages. Autophagy. 2016. Aug 2;12(8):1272–91. doi: 10.1080/15548627.2016.1183081. PubMed PMID: 27337507; PubMed Central PMCID: PMCPMC4968237. PubMed DOI PMC

Budanov AV, Karin M.. p53 target genes sestrin1 and sestrin2 connect genotoxic stress and mTOR signaling. Cell. 2008. Aug 8;134(3):451–60. doi: 10.1016/j.cell.2008.06.028. PubMed PMID: 18692468; PubMed Central PMCID: PMC2758522. PubMed DOI PMC

Park HW, Park H, Ro SH, et al. Hepatoprotective role of Sestrin2 against chronic ER stress. Nat Commun. 2014;5:4233. doi: 10.1038/ncomms5233. PubMed PMID: 24947615; PubMed Central PMCID: PMC4074707. PubMed DOI PMC

Wolfson RL, Chantranupong L, Saxton RA, et al. Sestrin2 is a leucine sensor for the mTORC1 pathway. Science. 2016. Jan 1;351(6268):43–8. doi: 10.1126/science.aab2674. PubMed PMID: 26449471; PubMed Central PMCID: PMCPMC4698017. PubMed DOI PMC

Ben-Sahra I, Dirat B, Laurent K, et al. Sestrin2 integrates Akt and mTOR signaling to protect cells against energetic stress-induced death. Cell Death Differ. 2013. Apr;20(4):611–9. doi: 10.1038/cdd.2012.157. PubMed PMID: 23238567; PubMed Central PMCID: PMC3595485. PubMed DOI PMC

Ouchida AT, Uyemura VT, Queiroz AL, et al. SET protein accumulation prevents cell death in head and neck squamous cell carcinoma through regulation of redox state and autophagy. Biochim Biophys Acta Mol Cell Res. 2019. Apr;1866(4):623–637. doi: 10.1016/j.bbamcr.2019.01.005. PubMed PMID: 30658075. PubMed DOI

Wang Y, Zheng X, Yu B, et al. Disruption of microtubules in plants suppresses macroautophagy and triggers starch excess-associated chloroplast autophagy. Autophagy. 2015;11(12):2259–74. doi: 10.1080/15548627.2015.1113365. PubMed PMID: 26566764; PubMed Central PMCID: PMCPMC4835195. PubMed DOI PMC

Kim YM, Stone M, Hwang TH, et al. SH3BP4 is a negative regulator of amino acid-Rag GTPase-mTORC1 signaling. Mol Cell. 2012. Jun 29;46(6):833–46. doi: 10.1016/j.molcel.2012.04.007. PubMed PMID: 22575674; PubMed Central PMCID: PMCPMC3389276. PubMed DOI PMC

Antas P, Novellasdemunt L, Kucharska A, et al. SH3BP4 regulates intestinal stem cells and tumorigenesis by modulating beta-catenin nuclear localization. Cell Rep. 2019. Feb 26;26(9):2266–2273 e4. doi: 10.1016/j.celrep.2019.01.110. PubMed PMID: 30811977; PubMed Central PMCID: PMCPMC6391711. PubMed DOI PMC

Takahashi Y, Coppola D, Matsushita N, et al. Bif-1 interacts with Beclin 1 through UVRAG and regulates autophagy and tumorigenesis. Nat Cell Biol. 2007. Oct;9(10):1142–51. doi: 10.1038/ncb1634. PubMed PMID: 17891140; PubMed Central PMCID: PMC2254521. eng. PubMed DOI PMC

Zhang C, Li A, Zhang X, et al. A novel TIP30 protein complex regulates EGF receptor signaling and endocytic degradation. J Biol Chem. 2011. Mar 18;286(11):9373–81. doi: 10.1074/jbc.M110.207720. PubMed PMID: 21252234; PubMed Central PMCID: PMC3058969. PubMed DOI PMC

Khan MM, Strack S, Wild F, et al. Role of autophagy, SQSTM1, SH3GLB1, and TRIM63 in the turnover of nicotinic acetylcholine receptors. Autophagy. 2014. Jan;10(1):123–36. doi: 10.4161/auto.26841. PubMed PMID: 24220501. PubMed DOI PMC

Zhang P, Holowatyj AN, Ulrich CM, et al. Tumor suppressive autophagy in intestinal stem cells controls gut homeostasis. Autophagy. 2019. Sep;15(9):1668–1670. doi: 10.1080/15548627.2019.1633863. PubMed PMID: 31213134; PubMed Central PMCID: PMCPMC6693466. PubMed DOI PMC

Onnis A, Cianfanelli V, Cassioli C, et al. The pro-oxidant adaptor p66SHC promotes B cell mitophagy by disrupting mitochondrial integrity and recruiting LC3-II. Autophagy. 2018;14(12):2117–2138. doi: 10.1080/15548627.2018.1505153. PubMed PMID: 30109811; PubMed Central PMCID: PMCPMC6984773. PubMed DOI PMC

Vion AC, Kheloufi M, Hammoutene A, et al. Autophagy is required for endothelial cell alignment and atheroprotection under physiological blood flow. Proc Natl Acad Sci U S A. 2017. Oct 10;114(41):E8675–E8684. doi: 10.1073/pnas.1702223114. PubMed PMID: 28973855; PubMed Central PMCID: PMCPMC5642679. PubMed DOI PMC

Belaid A, Ndiaye PD, Klionsky DJ, et al. Signalphagy: Scheduled signal termination by macroautophagy. Autophagy. 2013. Aug 13;9(10):1629–30. PubMed PMID: 24004837. PubMed PMC

Lee IH, Cao L, Mostoslavsky R, et al. A role for the NAD-dependent deacetylase Sirt1 in the regulation of autophagy. Proc Natl Acad Sci U S A. 2008. Mar 4;105(9):3374–9. doi: 10.1073/pnas.0712145105. PubMed PMID: 18296641; PubMed Central PMCID: PMC2265142. eng. PubMed DOI PMC

Webster BR, Scott I, Traba J, et al. Regulation of autophagy and mitophagy by nutrient availability and acetylation. Biochim Biophys Acta. 2014. Apr 4;1841(4):525–34. doi: 10.1016/j.bbalip.2014.02.001. PubMed PMID: 24525425; PubMed Central PMCID: PMC3969632. PubMed DOI PMC

Pi H, Xu S, Reiter RJ, et al. SIRT3-SOD2-mROS-dependent autophagy in cadmium-induced hepatotoxicity and salvage by melatonin. Autophagy. 2015. Jul 3;11(7):1037–51. doi: 10.1080/15548627.2015.1052208. PubMed PMID: 26120888. PubMed DOI PMC

Polletta L, Vernucci E, Carnevale I, et al. SIRT5 regulation of ammonia-induced autophagy and mitophagy. Autophagy. 2015;11(2):253–70. doi: 10.1080/15548627.2015.1009778. PubMed PMID: 25700560; PubMed Central PMCID: PMC4502726. PubMed DOI PMC

Takasaka N, Araya J, Hara H, et al. Autophagy induction by SIRT6 through attenuation of insulin-like growth factor signaling is involved in the regulation of human bronchial epithelial cell senescence. J Iimmunol. 2014. Feb 1;192(3):958–68. doi: 10.4049/jimmunol.1302341. PubMed PMID: 24367027. PubMed DOI

Birmingham CL, Canadien V, Kaniuk NA, et al. Listeriolysin O allows Listeria monocytogenes replication in macrophage vacuoles [Research Support, Non-U.S. Gov’t]. Nature. 2008. Jan 17;451(7176):350–4. doi: 10.1038/nature06479. PubMed PMID: 18202661; eng. PubMed DOI

Bhardwaj V, Kanagawa O, Swanson PE, et al. Chronic Listeria infection in SCID mice: requirements for the carrier state and the dual role of T cells in transferring protection or suppression [Research Support, U.S. Gov’t, P.H.S.]. J Iimmunol. 1998. Jan 1;160(1):376–84. PubMed PMID: 9551994; eng. PubMed

Digomann D, Kurth I, Tyutyunnykova A, et al. The CD98 heavy chain is a marker and regulator of head and neck squamous cell carcinoma radiosensitivity. clin cancer res off j am assoc cancer res. 2019. May 15;25(10):3152–3163. doi: 10.1158/1078-0432.CCR-18-2951. PubMed PMID: 30670494. PubMed DOI

Liu H, Ma Y, He HW, et al. SLC9A3R1 stimulates autophagy via BECN1 stabilization in breast cancer cells. Autophagy. 2015. Jul 28;11:2323–34. doi: 10.1080/15548627.2015.1074372. PubMed PMID: 26218645. PubMed DOI PMC

Catalina-Rodriguez O, Kolukula VK, Tomita Y, et al. The mitochondrial citrate transporter, CIC, is essential for mitochondrial homeostasis. Oncotarget. 2012. Oct;3(10):1220–35. PubMed PMID: 23100451; PubMed Central PMCID: PMC3717962. PubMed PMC

Rebsamen M, Pochini L, Stasyk T, et al. SLC38A9 is a component of the lysosomal amino acid sensing machinery that controls mTORC1. Nature. 2015. Mar 26;519(7544):477–81. doi: 10.1038/nature14107. PubMed PMID: 25561175; PubMed Central PMCID: PMC4376665. PubMed DOI PMC

Deretic V, Saitoh T, Akira S.. Autophagy in infection, inflammation and immunity. Nat Rev Immunol. 2013. Oct;13(10):722–37. doi:10.1038/nri3532. PubMed PMID: 24064518. PubMed DOI PMC

Reef S, Zalckvar E, Shifman O, et al. A short mitochondrial form of p19ARF induces autophagy and caspase-independent cell death. Mol Cell. 2006. May 19;22(4):463–75. doi:10.1016/j.molcel.2006.04.014. PubMed PMID: 16713577; eng. PubMed DOI

Mohamud Y, Shi J, Qu J, et al. Enteroviral infection inhibits autophagic flux via disruption of the SNARE complex to enhance viral replication. Cell Rep. 2018. Mar 20;22(12):3292–3303. doi:10.1016/j.celrep.2018.02.090. PubMed PMID: 29562184. PubMed DOI

Corona AK, Saulsbery HM, Corona Velazquez AF, et al. Enteroviruses remodel autophagic trafficking through regulation of host SNARE proteins to promote virus replication and cell exit. Cell Rep. 2018. Mar 20;22(12):3304–3314. doi:10.1016/j.celrep.2018.03.003. PubMed PMID: 29562185; PubMed Central PMCID: PMCPMC5894509. PubMed DOI PMC

Batelli S, Peverelli E, Rodilossi S, et al. Macroautophagy and the proteasome are differently involved in the degradation of alpha-synuclein wild type and mutated A30P in an in vitro inducible model (PC12/TetOn). Neuroscience. 2011. Nov 10;195:128–37. doi:10.1016/j.neuroscience.2011.08.030. PubMed PMID: 21906659; PubMed Central PMCID: PMC3188703. PubMed DOI PMC

Song JX, Lu JH, Liu LF, et al. HMGB1 is involved in autophagy inhibition caused by SNCA/alpha-synuclein overexpression: a process modulated by the natural autophagy inducer corynoxine B. Autophagy. 2014. Jan;10(1):144–54. doi:10.4161/auto.26751. PubMed PMID: 24178442. PubMed DOI PMC

Baksi S, Singh N.. alpha-Synuclein impairs ferritinophagy in the retinal pigment epithelium: Implications for retinal iron dyshomeostasis in Parkinson’s disease. Sci Rep. 2017. Oct 9;7(1):12843. doi:10.1038/s41598-017-12862-x. PubMed PMID: 28993630; PubMed Central PMCID: PMCPMC5634503. PubMed DOI PMC

Freeman D, Cedillos R, Choyke S, et al. Alpha-synuclein induces lysosomal rupture and cathepsin dependent reactive oxygen species following endocytosis. PLoS One. 2013;8(4):e62143. doi:10.1371/journal.pone.0062143. PubMed PMID: 23634225; PubMed Central PMCID: PMCPMC3636263. PubMed DOI PMC

Flavin WP, Bousset L, Green ZC, et al. Endocytic vesicle rupture is a conserved mechanism of cellular invasion by amyloid proteins. Acta Neuropathol. 2017. Oct;134(4):629–653. doi:10.1007/s00401-017-1722-x. PubMed PMID: 28527044. PubMed DOI

Haft CR, de la Luz Sierra M, Barr VA, et al. Identification of a family of sorting nexin molecules and characterization of their association with receptors. Mol Cell Biol. 1998. Dec;18(12):7278–87. doi:10.1128/mcb.18.12.7278. PubMed PMID: 9819414; PubMed Central PMCID: PMCPMC109309. PubMed DOI PMC

Traer CJ, Rutherford AC, Palmer KJ, et al. SNX4 coordinates endosomal sorting of TfnR with dynein-mediated transport into the endocytic recycling compartment. Nat Cell Biol. 2007. Dec;9(12):1370–80. doi:10.1038/ncb1656. PubMed PMID: 17994011. PubMed DOI

Ma M, Burd CG, Chi RJ.. Distinct complexes of yeast Snx4 family SNX-BARs mediate retrograde trafficking of Snc1 and Atg27. Traffic. 2017. Feb;18(2):134–144. doi:10.1111/tra.12462. PubMed PMID: 28026081; PubMed Central PMCID: PMCPMC5262529. PubMed DOI PMC

Knaevelsrud H, Soreng K, Raiborg C, et al. Membrane remodeling by the PX-BAR protein SNX18 promotes autophagosome formation. J Cell Biol. 2013. Jul 22;202(2):331–49. doi:10.1083/jcb.201205129. PubMed PMID: 23878278; PubMed Central PMCID: PMC3718966. PubMed DOI PMC

Canuel M, Korkidakis A, Konnyu K, et al. Sortilin mediates the lysosomal targeting of cathepsins D and H. Biochem Biophys Res Commun. 2008. Aug 22;373(2):292–7. doi:10.1016/j.bbrc.2008.06.021. PubMed PMID: 18559255. PubMed DOI

Tan YS, Sansanaphongpricha K, Xie Y, et al. Mitigating SOX2-potentiated immune escape of head and neck squamous cell carcinoma with a STING-inducing nanosatellite vaccine. clin cancer res off j am assoc cancer res. 2018. Sep 1;24(17):4242–4255. doi:10.1158/1078-0432.CCR-17-2807. PubMed PMID: 29769207; PubMed Central PMCID: PMCPMC6125216. PubMed DOI PMC

Barnett TC, Liebl D, Seymour LM, et al. The globally disseminated M1T1 clone of group A Streptococcus evades autophagy for intracellular replication. Cell Host Microbe. 2013. Dec 11;14(6):675–82. doi:10.1016/j.chom.2013.11.003. PubMed PMID: 24331465; PubMed Central PMCID: PMC3918495. PubMed DOI PMC

Hirst J, Borner GH, Edgar J, et al. Interaction between AP-5 and the hereditary spastic paraplegia proteins SPG11 and SPG15. Mol Biol Cell. 2013. Aug;24(16):2558–69. doi:10.1091/mbc.E13-03-0170. PubMed PMID: 23825025; PubMed Central PMCID: PMCPMC3744948. PubMed DOI PMC

Chang J, Lee S, Blackstone C.. Spastic paraplegia proteins spastizin and spatacsin mediate autophagic lysosome reformation. J Clin Invest. 2014. Dec;124(12):5249–62. doi:10.1172/JCI77598. PubMed PMID: 25365221; PubMed Central PMCID: PMCPMC4348974. PubMed DOI PMC

Ghidoni R, Houri JJ, Giuliani A, et al. The metabolism of sphingo(glyco)lipids is correlated with the differentiation-dependent autophagic pathway in HT-29 cells. Eur J Biochem/FEBS. 1996. Apr 15;237(2):454–9. PubMed PMID: 8647085; eng. PubMed

Lavieu G, Scarlatti F, Sala G, et al. Is autophagy the key mechanism by which the sphingolipid rheostat controls the cell fate decision? Autophagy. 2007. Jan-Feb;3(1):45–47. PubMed PMID: 17035732; eng. PubMed

Young MM, Wang HG.. Sphingolipids as Regulators of Autophagy and Endocytic Trafficking. Adv Cancer Res. 2018;140:27–60. doi: 10.1016/bs.acr.2018.04.008. PubMed PMID: 30060813. PubMed DOI

Tommasino C, Marconi M, Ciarlo L, et al. Autophagic flux and autophagosome morphogenesis require the participation of sphingolipids. Apoptosis. 2015. May;20(5):645–57. doi: 10.1007/s10495-015-1102-8. PubMed PMID: 25697338. PubMed DOI

Chakraborty P, Vaena SG, Thyagarajan K, et al. Pro-survival lipid sphingosine-1-phosphate metabolically programs T cells to limit anti-tumor activity. Cell Rep. 2019. Aug 13;28(7):1879–1893 e7. doi: 10.1016/j.celrep.2019.07.044. PubMed PMID: 31412253; PubMed Central PMCID: PMCPMC6889821. PubMed DOI PMC

Panneer Selvam S, De Palma RM, Oaks JJ, et al. Binding of the sphingolipid S1P to hTERT stabilizes telomerase at the nuclear periphery by allosterically mimicking protein phosphorylation. Sci Signal. 2015. Jun 16;8(381):ra58. doi: 10.1126/scisignal.aaa4998. PubMed PMID: 26082434; PubMed Central PMCID: PMCPMC4492107. PubMed DOI PMC

Chang CL, Ho MC, Lee PH, et al. S1P(5) is required for sphingosine 1-phosphate-induced autophagy in human prostate cancer PC-3 cells. Am J Physiol Cell Physiol. 2009. Aug;297(2):C451–8. doi: 10.1152/ajpcell.00586.2008. PubMed PMID: 19474291. PubMed DOI

Dai L, Bai A, Smith CD, et al. ABC294640, a novel sphingosine kinase 2 inhibitor, induces oncogenic virus-infected cell autophagic death and represses tumor growth. Mol Cancer Ther. 2017. Dec;16(12):2724–2734. doi: 10.1158/1535-7163.MCT-17-0485. PubMed PMID: 28939554; PubMed Central PMCID: PMCPMC5716930. PubMed DOI PMC

Orsini M, Chateauvieux S, Rhim J, et al. Sphingolipid-mediated inflammatory signaling leading to autophagy inhibition converts erythropoiesis to myelopoiesis in human hematopoietic stem/progenitor cells. Cell Death Differ. 2019. Sep;26(9):1796–1812. doi: 10.1038/s41418-018-0245-x. PubMed PMID: 30546074; PubMed Central PMCID: PMCPMC6748125. PubMed DOI PMC

Sheng R, Zhang TT, Felice VD, et al. Preconditioning stimuli induce autophagy via sphingosine kinase 2 in mouse cortical neurons. J Biol Chem. 2014. Jul 25;289(30):20845–57. doi: 10.1074/jbc.M114.578120. PubMed PMID: 24928515; PubMed Central PMCID: PMCPMC4110292. PubMed DOI PMC

Song DD, Zhang TT, Chen JL, et al. Sphingosine kinase 2 activates autophagy and protects neurons against ischemic injury through interaction with Bcl-2 via its putative BH3 domain. Cell Death Dis. 2017. Jul 6;8(7):e2912. doi: 10.1038/cddis.2017.289. PubMed PMID: 28682313; PubMed Central PMCID: PMCPMC5550846. PubMed DOI PMC

Song DD, Zhou JH, Sheng R.. Regulation and function of sphingosine kinase 2 in diseases. Histol Histopathol. 2018. May;33(5):433–445. doi: 10.14670/HH-11-939. PubMed PMID: 29057430. PubMed DOI

Serhan CN. Pro-resolving lipid mediators are leads for resolution physiology. Nature. 2014. Jun 5;510(7503):92–101. doi:10.1038/nature13479. PubMed PMID: 24899309; PubMed Central PMCID: PMCPMC4263681. PubMed DOI PMC

Leuti A, Maccarrone M, Chiurchiu V.. Proresolving lipid mediators: endogenous modulators of oxidative stress. Oxid Med Cell Longev. 2019;2019:8107265. doi:10.1155/2019/8107265. PubMed PMID: 31316721; PubMed Central PMCID: PMCPMC6604337. PubMed DOI PMC

Prieto P, Rosales-Mendoza CE, Terron V, et al. Activation of autophagy in macrophages by pro-resolving lipid mediators. Autophagy. 2015;11(10):1729–44. doi:10.1080/15548627.2015.1078958. PubMed PMID: 26506892; PubMed Central PMCID: PMCPMC4824594. PubMed DOI PMC

Rong Y, McPhee C, Deng S, et al. Spinster is required for autophagic lysosome reformation and mTOR reactivation following starvation. Proc Natl Acad Sci U S A. 2011. May 10;108(19):7826–31. doi:10.1073/pnas.1013800108. PubMed PMID: 21518918; PubMed Central PMCID: PMC3093520. eng. PubMed DOI PMC

Sun C, Enkhjargal B, Reis C, et al. Osteopontin-enhanced autophagy attenuates early brain injury via FAK-ERK pathway and improves long-term outcome after subarachnoid hemorrhage in rats. Cells 2019. Aug 27;8(9). doi:10.3390/cells8090980. PubMed PMID: 31461955; PubMed Central PMCID: PMCPMC6769958. PubMed DOI PMC

Wen X, Gatica D, Yin Z, et al. The transcription factor Spt4-Spt5 complex regulates the expression of ATG8 and ATG41. Autophagy. 2020. Sep 8:in press. doi:10.1080/15548627.2019.1659573. PubMed PMID: 31462158. PubMed DOI PMC

Chen Q, Yue F, Li W, et al. Potassium bisperoxo (1,10-phenanthroline) oxovanadate (bpV(phen)) induces apoptosis and pyroptosis and disrupts the P62-HDAC6 interaction to suppress the acetylated microtubule-dependent degradation of auto-phagosomes. J Biol Chem. 2015. Sep 11;290:26051–8. doi:10.1074/jbc.M115.653568. PubMed PMID: 26363065. PubMed DOI PMC

Zhang Y, Mun SR, Linares JF, et al. Mechanistic insight into the regulation of SQSTM1/p62. Autophagy. 2019. Apr;15(4):735–737. doi:10.1080/15548627.2019.1569935. PubMed PMID: 30653391; PubMed Central PMCID: PMCPMC6526835. PubMed DOI PMC

Itakura E, Mizushima N.. p62 Targeting to the autophagosome formation site requires self-oligomerization but not LC3 binding. J Cell Biol. 2011. Jan 10;192(1):17–27. doi:10.1083/jcb.201009067. PubMed PMID: 21220506; PubMed Central PMCID: PMCPMC3019556. PubMed DOI PMC

Wurzer B, Zaffagnini G, Fracchiolla D, et al. Oligomerization of p62 allows for selection of ubiquitinated cargo and isolation membrane during selective autophagy. eLife. 2015. Sep 28;4:e08941. doi:10.7554/eLife.08941. PubMed PMID: 26413874; PubMed Central PMCID: PMCPMC4684078. PubMed DOI PMC

Kwon DH, Kim L, Song HK.. pH-dependent regulation of SQSTM1/p62 during autophagy. Autophagy. 2019. Jan;15(1):180–181. doi:10.1080/15548627.2018.1532264. PubMed PMID: 30290711; PubMed Central PMCID: PMCPMC6287675. PubMed DOI PMC

Sun D, Wu R, Zheng J, et al. Polyubiquitin chain-induced p62 phase separation drives autophagic cargo segregation. Cell Res. 2018. Apr;28(4):405–415. doi:10.1038/s41422-018-0017-7. PubMed PMID: 29507397; PubMed Central PMCID: PMCPMC5939046. PubMed DOI PMC

Zaffagnini G, Savova A, Danieli A, et al. p62 filaments capture and present ubiquitinated cargos for autophagy. EMBO J. 2018. Mar 1;37(5). doi:10.15252/embj.201798308. PubMed PMID: 29343546; PubMed Central PMCID: PMCPMC5830917. PubMed DOI PMC

Nguyen TD, Shaid S, Vakhrusheva O, et al. Loss of the selective autophagy receptor p62 impairs murine myeloid leukemia progression and mitophagy. Blood. 2019. Jan 10;133(2):168–179. doi:10.1182/blood-2018-02-833475. PubMed PMID: 30498063. PubMed DOI

Shi J, Wong J, Piesik P, et al. Cleavage of sequestosome 1/p62 by an enteroviral protease results in disrupted selective autophagy and impaired NFKB signaling. Autophagy. 2013. Oct;9(10):1591–603. doi:10.4161/auto.26059. PubMed PMID: 23989536. PubMed DOI

Shi J, Fung G, Piesik P, et al. Dominant-negative function of the C-terminal fragments of NBR1 and SQSTM1 generated during enteroviral infection. Cell Death Differ. 2014. Sep;21(9):1432–41. doi:10.1038/cdd.2014.58. PubMed PMID: 24769734; PubMed Central PMCID: PMCPMC4131175. PubMed DOI PMC

Tambe Y, Yamamoto A, Isono T, et al. The drs tumor suppressor is involved in the maturation process of autophagy induced by low serum. Cancer Lett. 2009. Sep 28;283(1):74–83. doi:10.1016/j.canlet.2009.03.028. PubMed PMID: 19368996. PubMed DOI

Mesquita FS, Thomas M, Sachse M, et al. The Salmonella deubiquitinase SseL inhibits selective autophagy of cytosolic aggregates. PLoS Pathog. 2012;8(6):e1002743. doi:10.1371/journal.ppat.1002743. PubMed PMID: 22719249; PubMed Central PMCID: PMC3375275. PubMed DOI PMC

Luna-Dulcey L, Tomasin R, Naves MA, et al. Autophagy-dependent apoptosis is triggered by a semi-synthetic [6]-gingerol analogue in triple negative breast cancer cells. Oncotarget. 2018. Jul 20;9(56):30787–30804. doi:10.18632/oncotarget.25704. PubMed PMID: 30112107; PubMed Central PMCID: PMCPMC6089392. PubMed DOI PMC

Shen S, Niso-Santano M, Adjemian S, et al. Cytoplasmic STAT3 represses autophagy by inhibiting PKR activity. Mol Cell. 2012. Dec 14;48(5):667–80. doi:10.1016/j.molcel.2012.09.013. PubMed PMID: 23084476. PubMed DOI

Wang CW. Stationary phase lipophagy as a cellular mechanism to recycle sterols during quiescence. Autophagy. 2014;10(11):2075–6. doi:10.4161/auto.36137. PubMed PMID: 25484090; PubMed Central PMCID: PMC4502705. PubMed DOI PMC

Kuang XL, Liu Y, Chang Y, et al. Inhibition of store-operated calcium entry by sub-lethal levels of proteasome inhibition is associated with STIM1/STIM2 degradation. Cell Calcium. 2016. Apr;59(4):172–80. doi:10.1016/j.ceca.2016.01.007. PubMed PMID: 26960935. PubMed DOI

Zhou J, Song J, Wu S.. Autophagic degradation of stromal interaction molecule 2 mediates disruption of neuronal dendrites by endoplasmic reticulum stress. J Neurochem. 2019. Nov;151(3):351–369. doi:10.1111/jnc.14712. PubMed PMID: 31038732. PubMed DOI

Liu Y, Gordesky-Gold B, Leney-Greene M, et al. Inflammation-induced, STING-dependent autophagy restricts zika virus infection in the drosophila brain. Cell Host Microbe. 2018. Jul 11;24(1):57–68 e3. doi: 10.1016/j.chom.2018.05.022. PubMed PMID: 29934091; PubMed Central PMCID: PMCPMC6173519. PubMed DOI PMC

Watson RO, Bell SL, MacDuff DA, et al. The cytosolic sensor cGAS detects mycobacterium tuberculosis DNA to induce type I interferons and activate autophagy. Cell Host Microbe. 2015. Jun 10;17(6):811–819. doi:10.1016/j.chom.2015.05.004. PubMed PMID: 26048136; PubMed Central PMCID: PMCPMC4466081. PubMed DOI PMC

Aden K, Tran F, Ito G, et al. ATG16L1 orchestrates interleukin-22 signaling in the intestinal epithelium via cGAS-STING. J Exp Med. 2018. Nov 5;215(11):2868–2886. doi:10.1084/jem.20171029. PubMed PMID: 30254094; PubMed Central PMCID: PMCPMC6219748. PubMed DOI PMC

Prabakaran T, Bodda C, Krapp C, et al. Attenuation of cGAS-STING signaling is mediated by a p62/SQSTM1-dependent autophagy pathway activated by TBK1. EMBO J. 2018. Apr 13;37(8). doi:10.15252/embj.201797858. PubMed PMID: 29496741; PubMed Central PMCID: PMCPMC5897779. PubMed DOI PMC

Gui X, Yang H, Li T, et al. Autophagy induction via STING trafficking is a primordial function of the cGAS pathway. Nature. 2019. Mar;567(7747):262–266. doi:10.1038/s41586-019-1006-9. PubMed PMID: 30842662. PubMed DOI PMC

Wilkinson DS, Jariwala JS, Anderson E, et al. Phosphorylation of LC3 by the Hippo Kinases STK3/STK4 Is Essential for Autophagy. Mol Cell. 2015. Jan 8;57(1):55–68. doi:10.1016/j.molcel.2014.11.019. PubMed PMID: 25544559. PubMed DOI PMC

Maejima Y, Kyoi S, Zhai P, et al. Mst1 inhibits autophagy by promoting the interaction between Beclin1 and Bcl-2. Nat Med. 2013. Nov;19(11):1478–88. doi:10.1038/nm.3322. PubMed PMID: 24141421; PubMed Central PMCID: PMC3823824. PubMed DOI PMC

Huang T, Kim CK, Alvarez AA, et al. MST4 phosphorylation of ATG4B regulates autophagic activity, tumorigenicity, and radioresistance in glioblastoma. Cancer cell. 2017. Dec 11;32(6):840–855 e8. doi:10.1016/j.ccell.2017.11.005. PubMed PMID: 29232556; PubMed Central PMCID: PMCPMC5734934. PubMed DOI PMC

Joffre C, Dupont N, Hoa L, et al. The pro-apoptotic STK38 kinase is a new beclin1 partner positively regulating autophagy. Curr Biol. 2015. Oct 5;25(19):2479–92. doi:10.1016/j.cub.2015.08.031. PubMed PMID: 26387716; PubMed Central PMCID: PMCPMC4598746. PubMed DOI PMC

Tokumitsu H, Inuzuka H, Ishikawa Y, et al. STO-609, a specific inhibitor of the Ca(2+)/calmodulin-dependent protein kinase kinase. J Biol Chem. 2002. May 3;277(18):15813–8. doi:10.1074/jbc.M201075200. PubMed PMID: 11867640. PubMed DOI

Anderson KA, Ribar TJ, Lin F, et al. Hypothalamic CaMKK2 contributes to the regulation of energy balance. Cell Metab. 2008. May;7(5):377–88. doi:10.1016/j.cmet.2008.02.011. PubMed PMID: 18460329. PubMed DOI

Monteiro P, Gilot D, Langouet S, et al. Activation of the aryl hydrocarbon receptor by the calcium/calmodulin-dependent protein kinase kinase inhibitor 7-oxo-7H-benzimidazo[2,1-a]benz[de]isoquinoline-3-carboxylic acid (STO-609). Drug Metab Dispos. 2008. Dec;36(12):2556–63. doi:10.1124/dmd.108.023333. PubMed PMID: 18755850. PubMed DOI

Kimura T, Jia J, Claude-Taupin A, et al. Cellular and molecular mechanism for secretory autophagy. Autophagy. 2017. Jun 3;13(6):1084–1085. doi:10.1080/15548627.2017.1307486. PubMed PMID: 28368721; PubMed Central PMCID: PMCPMC5486376. PubMed DOI PMC

Lu Y, Zhang Z, Sun D, et al. Syntaxin 13, a genetic modifier of mutant CHMP2B in frontotemporal dementia, is required for autophagosome maturation. Mol Cell. 2013. Oct 24;52(2):264–71. doi:10.1016/j.molcel.2013.08.041. PubMed PMID: 24095276; PubMed Central PMCID: PMC3825790. PubMed DOI PMC

Diao J, Liu R, Rong Y, et al. ATG14 promotes membrane tethering and fusion of auto-phagosomes to endolysosomes. Nature. 2015. Apr 23;520(7548):563–6. doi:10.1038/nature14147. PubMed PMID: 25686604; PubMed Central PMCID: PMCPMC4442024. PubMed DOI PMC

Arasaki K, Nagashima H, Kurosawa Y, et al. MAP1B-LC1 prevents autophagosome formation by linking syntaxin 17 to microtubules. EMBO Rep. 2018. Aug;19(8). doi:10.15252/embr.201745584. PubMed PMID: 29925525; PubMed Central PMCID: PMCPMC6073212. PubMed DOI PMC

Wang C, Wang H, Zhang D, et al. Phosphorylation of ULK1 affects autophagosome fusion and links chaperone-mediated autophagy to macroautophagy. Nat Commun. 2018. Aug 28;9(1):3492. doi:10.1038/s41467-018-05449-1. PubMed PMID: 30154410; PubMed Central PMCID: PMCPMC6113293. PubMed DOI PMC

Saleeb RS, Kavanagh DM, Dun AR, et al. A VPS33A-binding motif on syntaxin 17 controls autophagy completion in mammalian cells. J Biol Chem. 2019. Mar 15;294(11):4188–4201. doi:10.1074/jbc.RA118.005947. PubMed PMID: 30655294; PubMed Central PMCID: PMCPMC6422071. PubMed DOI PMC

Tian X, Zheng P, Zhou C, et al. DIPK2A promotes STX17- and VAMP7-mediated autophagosome-lysosome fusion by binding to VAMP7B. Autophagy. 2019. Jul 4:1–14. doi:10.1080/15548627.2019.1637199. PubMed PMID: 31251111. PubMed DOI PMC

Kumar S, Jain A, Farzam F, et al. Mechanism of Stx17 recruitment to auto-phagosomes via IRGM and mammalian Atg8 proteins. J Cell Biol. 2018. Mar 5;217(3):997–1013. doi:10.1083/jcb.201708039. PubMed PMID: 29420192; PubMed Central PMCID: PMCPMC5839791. PubMed DOI PMC

Bustos V, Pulina MV, Bispo A, et al. Phosphorylated Presenilin 1 decreases beta-amyloid by facilitating autophagosome-lysosome fusion. Proc Natl Acad Sci U S A. 2017. Jul 3;114(27):7148–7153. doi:10.1073/pnas.1705240114. PubMed PMID: 28533369; PubMed Central PMCID: PMCPMC5502640. PubMed DOI PMC

McLelland GL, Lee SA, McBride HM, et al. Syntaxin-17 delivers PINK1/parkin-dependent mitochondrial vesicles to the endolysosomal system. J Cell Biol. 2016. Aug 1;214(3):275–91. doi:10.1083/jcb.201603105. PubMed PMID: 27458136; PubMed Central PMCID: PMCPMC4970327. PubMed DOI PMC

Kimura H, Arasaki K, Ohsaki Y, et al. Syntaxin 17 promotes lipid droplet formation by regulating the distribution of acyl-CoA synthetase 3. J Lipid Res. 2018. May;59(5):805–819. doi:10.1194/jlr.M081679. PubMed PMID: 29549094; PubMed Central PMCID: PMCPMC5928434. PubMed DOI PMC

Zhou C, Qian X, Hu M, et al. STYK1 promotes autophagy through enhancing the assembly of autophagy-specific class III phosphatidylinositol 3-kinase complex I. Autophagy. 2019. Nov 7:1–21. doi:10.1080/15548627.2019.1687212. PubMed PMID: 31696776. PubMed DOI PMC

Herman-Antosiewicz A, Johnson DE, Singh SV.. Sulforaphane causes autophagy to inhibit release of cytochrome C and apoptosis in human prostate cancer cells. Cancer Res. 2006. Jun 1;66(11):5828–35. doi:10.1158/0008-5472.CAN-06-0139. PubMed PMID: 16740722. PubMed DOI

Vyas AR, Hahm ER, Arlotti JA, et al. Chemoprevention of prostate cancer by d,l-sulforaphane is augmented by pharmacological inhibition of autophagy. Cancer Res. 2013. Oct 1;73(19):5985–95. doi:10.1158/0008-5472.CAN-13-0755. PubMed PMID: 23921360; PubMed Central PMCID: PMCPMC3790864. PubMed DOI PMC

Lee JH, Jeong JK, Park SY.. Sulforaphane-induced autophagy flux prevents prion protein-mediated neurotoxicity through AMPK pathway. Neuroscience. 2014. Oct 10;278:31–9. doi:10.1016/j.neuroscience.2014.07.072. PubMed PMID: 25130556. PubMed DOI

Wang H, Wang F, Wu S, et al. Traditional herbal medicine-derived sulforaphene promotes mitophagic cell death in lymphoma cells through CRM1-mediated p62/SQSTM1 accumulation and AMPK activation. Chem Biol Interact. 2018. Feb 1;281:11–23. doi:10.1016/j.cbi.2017.12.017. PubMed PMID: 29247643. PubMed DOI

Webber JL, Tooze SA.. Coordinated regulation of autophagy by p38alpha MAPK through mAtg9 and p38IP. EMBO J. 2010. Jan 6;29(1):27–40. doi:10.1038/emboj.2009.321. PubMed PMID: 19893488; PubMed Central PMCID: PMC2808369. eng. PubMed DOI PMC

Lopergolo A, Nicolini V, Favini E, et al. Synergistic cooperation between sunitinib and cisplatin promotes apoptotic cell death in human medullary thyroid cancer. J Clin Endocrinol Metab. 2014. Feb;99(2):498–509. doi:10.1210/jc.2013-2574. PubMed PMID: 24276455. PubMed DOI

Abdel-Aziz AK, Abdel-Naim AB, Shouman S, et al. From resistance to sensitivity: insights and implications of biphasic modulation of autophagy by sunitinib. Front Pharmacol. 2017;8:718. doi:10.3389/fphar.2017.00718. PubMed PMID: 29066973; PubMed Central PMCID: PMCPMC5641351. PubMed DOI PMC

Elgendy M, Abdel-Aziz AK, Renne SL, et al. Dual modulation of MCL-1 and mTOR determines the response to sunitinib. J Clin Invest. 2017. Jan 3;127(1):153–168. doi:10.1172/JCI84386. PubMed PMID: 27893461; PubMed Central PMCID: PMCPMC5199697. PubMed DOI PMC

Nikoletopoulou V, Sidiropoulou K, Kallergi E, et al. Modulation of autophagy by BDNF underlies synaptic plasticity. Cell Metab. 2017. Jul 5;26(1):230–242 e5. doi:10.1016/j.cmet.2017.06.005. PubMed PMID: 28683289. PubMed DOI

Okerlund ND, Schneider K, Leal-Ortiz S, et al. Bassoon controls presynaptic autophagy through Atg5. Neuron. 2017. Feb 22;93(4):897–913 e7. doi:10.1016/j.neuron.2017.01.026. PubMed PMID: 28231469. PubMed DOI

Liang Y, Sigrist S.. Autophagy and proteostasis in the control of synapse aging and disease. Curr Opin Neurobiol. 2018. Feb;48:113–121. doi:10.1016/j.conb.2017.12.006. PubMed PMID: 29274917. PubMed DOI

Liang Y. Emerging concepts and functions of autophagy as a regulator of synaptic components and plasticity. Cells. 2019. Jan 9;8(1). doi:10.3390/cells8010034. PubMed PMID: 30634508; PubMed Central PMCID: PMCPMC6357011. PubMed DOI PMC

Rowland AM, Richmond JE, Olsen JG, et al. Presynaptic terminals independently regulate synaptic clustering and autophagy of GABAA receptors in Caenorhabditis elegans. J Neurosci. 2006. Feb 8;26(6):1711–20. doi:10.1523/JNEUROSCI.2279-05.2006. PubMed PMID: 16467519; PubMed Central PMCID: PMCPMC6793639. PubMed DOI PMC

Shehata M, Matsumura H, Okubo-Suzuki R, et al. Neuronal stimulation induces autophagy in hippocampal neurons that is involved in AMPA receptor degradation after chemical long-term depression. J Neurosci. 2012. Jul 25;32(30):10413–22. doi:10.1523/JNEUROSCI.4533-11.2012. PubMed PMID: 22836274; PubMed Central PMCID: PMCPMC6703735. PubMed DOI PMC

Ashrafi G, Schlehe JS, LaVoie MJ, et al. Mitophagy of damaged mitochondria occurs locally in distal neuronal axons and requires PINK1 and Parkin. J Cell Biol. 2014. Sep 1;206(5):655–70. doi:10.1083/jcb.201401070. PubMed PMID: 25154397; PubMed Central PMCID: PMCPMC4151150. PubMed DOI PMC

Hoffmann S, Orlando M, Andrzejak E, et al. Light-activated ROS production induces synaptic autophagy. J Neurosci. 2019. Mar 20;39(12):2163–2183. doi:10.1523/JNEUROSCI.1317-18.2019. PubMed PMID: 30655355; PubMed Central PMCID: PMCPMC6433757. PubMed DOI PMC

Vanhauwaert R, Kuenen S, Masius R, et al. The SAC1 domain in synaptojanin is required for autophagosome maturation at presynaptic terminals. EMBO J. 2017. May 15;36(10):1392–1411. doi:10.15252/embj.201695773. PubMed PMID: 28331029; PubMed Central PMCID: PMCPMC5430236. PubMed DOI PMC

Criollo A, Niso-Santano M, Malik SA, et al. Inhibition of autophagy by TAB2 and TAB3. EMBO J. 2011. Dec 14;30(24):4908–20. doi:10.1038/emboj.2011.413. PubMed PMID: 22081109; PubMed Central PMCID: PMC3243630. PubMed DOI PMC

Takaesu G, Kobayashi T, Yoshimura A.. TGFbeta-activated kinase 1 (TAK1)-binding proteins (TAB) 2 and 3 negatively regulate autophagy. J Biochem. 2012. Feb;151(2):157–66. doi:10.1093/jb/mvr123. PubMed PMID: 21976705. PubMed DOI

Biering SB, Choi J, Halstrom RA, et al. Viral Replication Complexes Are Targeted by LC3-Guided Interferon-Inducible GTPases. Cell Host Microbe. 2017. Jul 12;22(1):74–85 e7. doi:10.1016/j.chom.2017.06.005. PubMed PMID: 28669671; PubMed Central PMCID: PMCPMC5591033. PubMed DOI PMC

Nagahara Y, Takeyoshi M, Sakemoto S, et al. Novel tamoxifen derivative Ridaifen-B induces Bcl-2 independent autophagy without estrogen receptor involvement. Biochem Biophys Res Commun. 2013. Jun 14;435(4):657–63. doi:10.1016/j.bbrc.2013.05.040. PubMed PMID: 23688426. PubMed DOI

Torres-Lopez L, Maycotte P, Linan-Rico A, et al. Tamoxifen induces toxicity, causes autophagy, and partially reverses dexamethasone resistance in Jurkat T cells. J Leukoc Biol. 2019. May;105(5):983–998. doi:10.1002/JLB.2VMA0818-328R. PubMed PMID: 30645008. PubMed DOI

Bose JK, Huang CC, Shen CK.. Regulation of autophagy by neuropathological protein TDP-43. J Biol Chem. 2011. Dec 30;286(52):44441–8. doi:10.1074/jbc.M111.237115. PubMed PMID: 22052911; PubMed Central PMCID: PMC3247982. PubMed DOI PMC

Fu T, Liu J, Wang Y, et al. Mechanistic insights into the interactions of NAP1 with the SKICH domains of NDP52 and TAX1BP1. Proc Natl Acad Sci U S A. 2018. Dec 11;115(50):E11651–E11660. doi:10.1073/pnas.1811421115. PubMed PMID: 30459273; PubMed Central PMCID: PMCPMC6294882. PubMed DOI PMC

Newman AC, Scholefield CL, Kemp AJ, et al. TBK1 kinase addiction in lung cancer cells is mediated via autophagy of Tax1bp1/Ndp52 and non-canonical NF-kappaB signalling. PLoS One. 2012;7(11):e50672. doi:10.1371/journal.pone.0050672. PubMed PMID: 23209807; PubMed Central PMCID: PMC3510188. PubMed DOI PMC

Petkova DS, Verlhac P, Rozieres A, et al. Distinct contributions of autophagy receptors in measles virus replication. Viruses. 2017. May 22;9(5). doi:10.3390/v9050123. PubMed PMID: 28531150; PubMed Central PMCID: PMCPMC5454435. PubMed DOI PMC

Dibble CC, Elis W, Menon S, et al. TBC1D7 is a third subunit of the TSC1-TSC2 complex upstream of mTORC1. Mol Cell. 2012. Aug 24;47(4):535–46. doi:10.1016/j.molcel.2012.06.009. PubMed PMID: 22795129; PubMed Central PMCID: PMC3693578. PubMed DOI PMC

Alfaiz AA, Micale L, Mandriani B, et al. TBC1D7 mutations are associated with intellectual disability, macrocrania, patellar dislocation, and celiac disease. Hum Mutat. 2014. Apr;35(4):447–51. doi:10.1002/humu.22529. PubMed PMID: 24515783. PubMed DOI

Capo-Chichi JM, Tcherkezian J, Hamdan FF, et al. Disruption of TBC1D7, a subunit of the TSC1-TSC2 protein complex, in intellectual disability and megalencephaly. J Med Genet. 2013. Nov;50(11):740–4. doi:10.1136/jmedgenet-2013-101680. PubMed PMID: 23687350. PubMed DOI

Liao Y, Li M, Chen X, et al. Interaction of TBC1D9B with mammalian ATG8 homologues regulates autophagic flux. Sci Rep. 2018. Sep 10;8(1):13496. doi:10.1038/s41598-018-32003-2. PubMed PMID: 30202024; PubMed Central PMCID: PMCPMC6131546. PubMed DOI PMC

Gallo LI, Liao Y, Ruiz WG, et al. TBC1D9B functions as a GTPase-activating protein for Rab11a in polarized MDCK cells. Mol Biol Cell. 2014. Nov 15;25(23):3779–97. doi:10.1091/mbc.E13-10-0604. PubMed PMID: 25232007; PubMed Central PMCID: PMCPMC4230784. PubMed DOI PMC

Hirano S, Uemura T, Annoh H, et al. Differing susceptibility to autophagic degradation of two LC3-binding proteins: SQSTM1/p62 and TBC1D25/OATL1. Autophagy. 2016;12(2):312–26. doi:10.1080/15548627.2015.1124223. PubMed PMID: 26902585; PubMed Central PMCID: PMCPMC4836008. PubMed DOI PMC

Pomerantz JL, Baltimore D.. NF-kappaB activation by a signaling complex containing TRAF2, TANK and TBK1, a novel IKK-related kinase. EMBO J. 1999. Dec 1;18(23):6694–704. doi:10.1093/emboj/18.23.6694. PubMed PMID: 10581243; PubMed Central PMCID: PMC1171732. eng. PubMed DOI PMC

Neill T, Torres A, Buraschi S, et al. Decorin induces mitophagy in breast carcinoma cells via peroxisome proliferator-activated receptor gamma coactivator-1alpha (PGC-1alpha) and mitostatin. J Biol Chem. 2014. Feb 21;289(8):4952–68. doi:10.1074/jbc.M113.512566. PubMed PMID: 24403067; PubMed Central PMCID: PMC3931056. PubMed DOI PMC

Ogawa M, Yoshikawa Y, Kobayashi T, et al. A tecpr1-dependent selective autophagy pathway targets bacterial pathogens. Cell Host Microbe. 2011. May 19;9(5):376–89. doi:10.1016/j.chom.2011.04.010. PubMed PMID: 21575909; eng. PubMed DOI

Zhang H, Yan S, Khambu B, et al. Dynamic MTORC1-TFEB feedback signaling regulates hepatic autophagy, steatosis and liver injury in long-term nutrient oversupply. Autophagy. 2018;14(10):1779–1795. doi:10.1080/15548627.2018.1490850. PubMed PMID: 30044707; PubMed Central PMCID: PMCPMC6135624. PubMed DOI PMC

Oz-Levi D, Ben-Zeev B, Ruzzo EK, et al. Mutation in TECPR2 reveals a role for autophagy in hereditary spastic paraparesis. Am J Hum Genet. 2012. Dec 7;91(6):1065–72. doi:10.1016/j.ajhg.2012.09.015. PubMed PMID: 23176824; PubMed Central PMCID: PMC3516605. PubMed DOI PMC

Oz-Levi D, Gelman A, Elazar Z, et al. TECPR2: a new autophagy link for neurodegeneration. Autophagy. 2013. May;9(5):801–2. doi:10.4161/auto.23961. PubMed PMID: 23439247; PubMed Central PMCID: PMC3669195. PubMed DOI PMC

Delorme-Axford E, Popelka H, Klionsky DJ.. TEX264 is a major receptor for mammalian reticulophagy. Autophagy. 2019. Oct;15(10):1677–1681. doi:10.1080/15548627.2019.1646540. PubMed PMID: 31362563; PubMed Central PMCID: PMCPMC6735500. PubMed DOI PMC

Wang P, Nolan TM, Yin Y, et al. Identification of transcription factors that regulate ATG8 expression and autophagy in Arabidopsis. Autophagy. 2020. Jan;16(1):123–139. doi:10.1080/15548627.2019.1598753. PubMed PMID: 30909785; PubMed Central PMCID: PMCPMC6984607. PubMed DOI PMC

Huang S, Lu W, Ge D, et al. A new microRNA signal pathway regulated by long noncoding RNA TGFB2-OT1 in autophagy and inflammation of vascular endothelial cells. Autophagy. 2015;11(12):2172–83. doi:10.1080/15548627.2015.1106663. PubMed PMID: 26565952; PubMed Central PMCID: PMCPMC4835209. PubMed DOI PMC

D’Eletto M, Farrace MG, Falasca L, et al. Transglutaminase 2 is involved in autophagosome maturation. Autophagy. 2009. Nov;5(8):1145–54. PubMed PMID: 19955852. PubMed

Salazar M, Carracedo A, Salanueva IJ, et al. Cannabinoid action induces autophagy-mediated cell death through stimulation of ER stress in human glioma cells. J Clin Invest. 2009. May;119(5):1359–72. PubMed PMID: 19425170; PubMed Central PMCID: PMC2673842. PubMed PMC

Salazar M, Lorente M, Garcia-Taboada E, et al. The pseudokinase tribbles homologue-3 plays a crucial role in cannabinoid anticancer action. Biochim Biophys Acta. 2013. Oct;1831(10):1573–8. doi:10.1016/j.bbalip.2013.03.014. PubMed PMID: 23567453. PubMed DOI

Velasco G, Sanchez C, Guzman M.. Towards the use of cannabinoids as antitumour agents. Nat Rev Cancer. 2012. Jun;12(6):436–44. doi:10.1038/nrc3247. PubMed PMID: 22555283. PubMed DOI

Yuzwa SA, Macauley MS, Heinonen JE, et al. A potent mechanism-inspired O-GlcNAcase inhibitor that blocks phosphorylation of tau in vivo. Nat Chem Biol. 2008. Aug;4(8):483–90. doi:10.1038/nchembio.96. PubMed PMID: 18587388. PubMed DOI

Zhu Y, Shan X, Safarpour F, et al. Pharmacological Inhibition of O-GlcNAcase Enhances Autophagy in Brain through an mTOR-Independent Pathway. ACS Chem Neurosci. 2018. Jun 20;9(6):1366–1379. doi:10.1021/acschemneuro.8b00015. PubMed PMID: 29460617. PubMed DOI

Bensaad K, Cheung EC, Vousden KH.. Modulation of intracellular ROS levels by TIGAR controls autophagy. EMBO J. 2009. Oct 7;28(19):3015–26. doi:10.1038/emboj.2009.242. PubMed PMID: 19713938; PubMed Central PMCID: PMC2736014. eng. PubMed DOI PMC

Lok CN, Sy LK, Liu F, et al. Activation of autophagy of aggregation-prone ubiquitinated proteins by timosaponin A-III. J Biol Chem. 2011. Sep 9;286(36):31684–96. doi:10.1074/jbc.M110.202531. PubMed PMID: 21757721; PubMed Central PMCID: PMC3173142. PubMed DOI PMC

Lin H, Yan J, Wang Z, et al. Loss of immunity-supported senescence enhances susceptibility to hepatocellular carcinogenesis and progression in Toll-like receptor 2-deficient mice. Hepatology. 2013. Jan;57(1):171–82. doi:10.1002/hep.25991. PubMed PMID: 22859216. PubMed DOI

Lin H, Hua F, Hu ZW.. Autophagic flux, supported by toll-like receptor 2 activity, defends against the carcinogenesis of hepatocellular carcinoma. Autophagy. 2012. Dec, 8(12):1859–61. doi:10.4161/auto.22094. PubMed PMID: 22996042; PubMed Central PMCID: PMCPMC3541305. PubMed DOI PMC

Wang Z, Yan J, Lin H, et al. Toll-like receptor 4 activity protects against hepatocellular tumorigenesis and progression by regulating expression of DNA repair protein Ku70 in mice. Hepatology 2013. May;57(5):1869–81. doi:10.1002/hep.26234. PubMed PMID: 23299825. PubMed DOI

Wang Z, Lin H, Hua F, et al. Repairing DNA damage by XRCC6/KU70 reverses TLR4-deficiency-worsened HCC development via restoring senescence and autophagic flux. Autophagy. 2013. Jun 1;9(6):925–7. doi:10.4161/auto.24229. PubMed PMID: 23518600; PubMed Central PMCID: PMCPMC3672303. PubMed DOI PMC

Wu RN, Yu TY, Zhou JC, et al. Targeting HMGB1 ameliorates cardiac fibrosis through restoring TLR2-mediated autophagy suppression in myocardial fibroblasts. Int J Cardiol. 2018. Sep 15;267:156–162. doi:10.1016/j.ijcard.2018.04.103. PubMed PMID: 29957254. PubMed DOI

Oka T, Hikoso S, Yamaguchi O, et al. Mitochondrial DNA that escapes from autophagy causes inflammation and heart failure. Nature. 2012. May 10;485(7397):251–5. doi:10.1038/nature10992. PubMed PMID: 22535248; PubMed Central PMCID: PMCPMC3378041. PubMed DOI PMC

He P, Peng Z, Luo Y, et al. High-throughput functional screening for autophagy-related genes and identification of TM9SF1 as an autophagosome-inducing gene. Autophagy. 2009. Jan 1;5(1):52–60. PubMed PMID: 19029833; eng. PubMed

Sun L, Meng Z, Zhu Y, et al. TM9SF4 is a novel factor promoting autophagic flux under amino acid starvation. Cell Death Differ. 2018. Feb;25(2):368–379. doi:10.1038/cdd.2017.166. PubMed PMID: 29125601; PubMed Central PMCID: PMCPMC5762850. PubMed DOI PMC

Maurel M, Obacz J, Avril T, et al. Control of anterior GRadient 2 (AGR2) dimerization links endoplasmic reticulum proteostasis to inflammation. EMBO Mol Med. 2019. Jun;11(6). doi:10.15252/emmm.201810120. PubMed PMID: 31040128; PubMed Central PMCID: PMCPMC6554669. PubMed DOI PMC

Morita K, Hama Y, Izume T, et al. Genome-wide CRISPR screen identifies TMEM41B as a gene required for autophagosome formation. J Cell Biol. 2018. Nov 5;217(11):3817–3828. doi:10.1083/jcb.201804132. PubMed PMID: 30093494; PubMed Central PMCID: PMCPMC6219718. PubMed DOI PMC

Shoemaker CJ, Huang TQ, Weir NR, et al. CRISPR screening using an expanded toolkit of autophagy reporters identifies TMEM41B as a novel autophagy factor. PLoS Biol. 2019. Apr;17(4):e2007044. doi:10.1371/journal.pbio.2007044. PubMed PMID: 30933966; PubMed Central PMCID: PMCPMC6459555. PubMed DOI PMC

Moretti F, Bergman P, Dodgson S, et al. TMEM41B is a novel regulator of autophagy and lipid mobilization. EMBO Rep. 2018. Sep;19(9). doi:10.15252/embr.201845889. PubMed PMID: 30126924; PubMed Central PMCID: PMCPMC6123663. PubMed DOI PMC

Boada-Romero E, Letek M, Fleischer A, et al. TMEM59 defines a novel ATG16L1-binding motif that promotes local activation of LC3. EMBO J. 2013. Feb 20;32(4):566–82. doi:10.1038/emboj.2013.8. PubMed PMID: 23376921; PubMed Central PMCID: PMC3579146. PubMed DOI PMC

Boada-Romero E, Serramito-Gomez I, Sacristan MP, et al. The T300A Crohn’s disease risk polymorphism impairs function of the WD40 domain of ATG16L1. Nat Commun. 2016. Jun 8;7:11821. doi:10.1038/ncomms11821. PubMed PMID: 27273576; PubMed Central PMCID: PMCPMC4899871. PubMed DOI PMC

Sun Y, Chen Y, Zhang J, et al. TMEM74 promotes tumor cell survival by inducing autophagy via interactions with ATG16L1 and ATG9A. Cell Death Dis. 2017. Aug 31;8(8):e3031. doi:10.1038/cddis.2017.370. PubMed PMID: 29048433; PubMed Central PMCID: PMCPMC5596558. PubMed DOI PMC

Mrschtik M, O’Prey J, Lao LY, et al. DRAM-3 modulates autophagy and promotes cell survival in the absence of glucose. Cell Death Differ. 2015. Oct;22(10):1714–26. doi:10.1038/cdd.2015.26. PubMed PMID: 25929859; PubMed Central PMCID: PMCPMC4563785. PubMed DOI PMC

Mrschtik M, O’Prey J, Lao LY, et al. DRAM-3 modulates autophagy and promotes cell survival in the absence of glucose. Cell Death Differ. 2017. Aug;24(8):1470. doi:10.1038/cdd.2017.57. PubMed PMID: 28665403; PubMed Central PMCID: PMCPMC5520458. PubMed DOI PMC

Shi CS, Kehrl JH.. Traf6 and A20 differentially regulate TLR4-induced autophagy by affecting the ubiquitination of Beclin 1 [Research Support, N.I.H., Intramural]. Autophagy. 2010. Oct;6(7):986–7. doi:10.4161/auto.6.7.13288. PubMed PMID: 20798608; PubMed Central PMCID: PMC3039745. eng. PubMed DOI PMC

Matsuzawa Y, Oshima S, Takahara M, et al. TNFAIP3 promotes survival of CD4 T cells by restricting MTOR and promoting autophagy. Autophagy. 2015. Jul 3;11(7):1052–62. doi:10.1080/15548627.2015.1055439. PubMed PMID: 26043155. PubMed DOI PMC

Slowicka K, Serramito-Gomez I, Boada-Romero E, et al. Physical and functional interaction between A20 and ATG16L1-WD40 domain in the control of intestinal homeostasis. Nat Commun. 2019. Apr 23;10(1):1834. doi:10.1038/s41467-019-09667-z. PubMed PMID: 31015422; PubMed Central PMCID: PMCPMC6478926. PubMed DOI PMC

Shah JA, Emery R, Lee B, et al. TOLLIP deficiency is associated with increased resistance to Legionella pneumophila pneumonia. Mucosal Immunol. 2019. Nov;12(6):1382–1390. doi:10.1038/s41385-019-0196-7. PubMed PMID: 31462698; PubMed Central PMCID: PMCPMC6824992. PubMed DOI PMC

Shah JA, Vary JC, Chau TT, et al. Human TOLLIP regulates TLR2 and TLR4 signaling and its polymorphisms are associated with susceptibility to tuberculosis. J Iimmunol. 2012. Aug 15;189(4):1737–46. doi:10.4049/jimmunol.1103541. PubMed PMID: 22778396; PubMed Central PMCID: PMCPMC3428135. PubMed DOI PMC

Jacinto E. What controls TOR? IUBMB life. 2008. Aug;60(8):483–96. doi:10.1002/iub.56. PubMed PMID: 18493947; eng. PubMed DOI

Peterson TR, Laplante M, Thoreen CC, et al. DEPTOR is an mTOR inhibitor frequently overexpressed in multiple myeloma cells and required for their survival. Cell. 2009. May 29;137(5):873–86. doi:10.1016/j.cell.2009.03.046. PubMed PMID: 19446321; PubMed Central PMCID: PMC2758791. eng. PubMed DOI PMC

Abe K, Yano T, Tanno M, et al. mTORC1 inhibition attenuates necroptosis through RIP1 inhibition-mediated TFEB activation. Biochim Biophys Acta Mol Basis Dis. 2019. Dec 1;1865(12):165552. doi:10.1016/j.bbadis.2019.165552. PubMed PMID: 31499159. PubMed DOI

Pearce LR, Huang X, Boudeau J, et al. Identification of Protor as a novel Rictor-binding component of mTOR complex-2. Biochem J. 2007. Aug 1;405(3):513–22. doi: BJ20070540 [pii] doi:10.1042/BJ20070540. PubMed PMID: 17461779; PubMed Central PMCID: PMC2267312. eng. PubMed DOI PMC

Vlahakis A, Graef M, Nunnari J, et al. TOR complex 2-Ypk1 signaling is an essential positive regulator of the general amino acid control response and autophagy. Proc Natl Acad Sci U S A. 2014. Jul 22;111(29):10586–91. doi:10.1073/pnas.1406305111. PubMed PMID: 25002487; PubMed Central PMCID: PMC4115538. PubMed DOI PMC

Renna M, Bento CF, Fleming A, et al. IGF-1 receptor antagonism inhibits autophagy. Hum Mol Genet. 2013. Nov 15;22(22):4528–44. doi:10.1093/hmg/ddt300. PubMed PMID: 23804751; PubMed Central PMCID: PMC3889807. PubMed DOI PMC

Arias E, Koga H, Diaz A, et al. Lysosomal mTORC2/PHLPP1/Akt regulate chaperone-mediated autophagy. Mol Cell. 2015. Jul 16;59(2):270–84. doi:10.1016/j.molcel.2015.05.030. PubMed PMID: 26118642; PubMed Central PMCID: PMC4506737. PubMed DOI PMC

Bonfili L, Cuccioloni M, Cecarini V, et al. Ghrelin induces apoptosis in colon adenocarcinoma cells via proteasome inhibition and autophagy induction. Apoptosis. 2013. Oct;18(10):1188–200. doi:10.1007/s10495-013-0856-0. PubMed PMID: 23632965. PubMed DOI

Zecchini S, Proietti Serafini F, Catalani E, et al. Dysfunctional autophagy induced by the pro-apoptotic natural compound climacostol in tumour cells. Cell Death Dis. 2018. Dec 19;10(1):10. doi:10.1038/s41419-018-1254-x. PubMed PMID: 30584259; PubMed Central PMCID: PMCPMC6315039. PubMed DOI PMC

Sancho A, Duran J, Garcia-Espana A, et al. DOR/Tp53inp2 and Tp53inp1 constitute a metazoan gene family encoding dual regulators of autophagy and transcription. PLoS One. 2012;7(3):e34034. doi:10.1371/journal.pone.0034034. PubMed PMID: 22470510; PubMed Central PMCID: PMC3314686. PubMed DOI PMC

Seillier M, Peuget S, Gayet O, et al. TP53INP1, a tumor suppressor, interacts with LC3 and ATG8-family proteins through the LC3-interacting region (LIR) and promotes autophagy-dependent cell death. Cell Death Differ. 2012. Sep;19(9):1525–35. doi:10.1038/cdd.2012.30. PubMed PMID: 22421968; PubMed Central PMCID: PMC3422476. PubMed DOI PMC

Mauvezin C, Sancho A, Ivanova S, et al. DOR undergoes nucleo-cytoplasmic shuttling, which involves passage through the nucleolus. FEBS Lett. 2012. Sep 21;586(19):3179–86. doi:10.1016/j.febslet.2012.06.032. PubMed PMID: 22750142. PubMed DOI

Mauvezin C, Orpinell M, Francis VA, et al. The nuclear cofactor DOR regulates autophagy in mammalian and Drosophila cells. EMBO Rep. 2010. Jan;11(1):37–44. doi:10.1038/embor.2009.242. PubMed PMID: 20010805; PubMed Central PMCID: PMCPMC2816618. PubMed DOI PMC

Nowak J, Archange C, Tardivel-Lacombe J, et al. The TP53INP2 protein is required for autophagy in mammalian cells. Mol Biol Cell. 2009. Feb;20(3):870–81. doi:10.1091/mbc.E08-07-067; PubMed PMID: 19056683. PubMed Central PMCID: PMC2633384. eng. PubMed DOI PMC

Sala D, Ivanova S, Plana N, et al. Autophagy-regulating TP53INP2 mediates muscle wasting and is repressed in diabetes. J Clin Invest. 2014. May 1;124(5):1914–27. doi:10.1172/JCI72327. PubMed PMID: 24713655; PubMed Central PMCID: PMC4001546. PubMed DOI PMC

Romero M, Sabate-Perez A, Francis VA, et al. TP53INP2 regulates adiposity by activating beta-catenin through autophagy-dependent sequestration of GSK3beta. Nat Cell Biol. 2018. Apr;20(4):443–454. doi:10.1038/s41556-018-0072-9. PubMed PMID: 29593329. PubMed DOI

Lin PH, Duann P, Komazaki S, et al. Lysosomal two-pore channel subtype 2 (TPC2) regulates skeletal muscle autophagic signaling. J Biol Chem. 2015. Feb 6;290(6):3377–89. doi:10.1074/jbc.M114.608471. PubMed PMID: 25480788; PubMed Central PMCID: PMC4319008. PubMed DOI PMC

Kobayashi A, Hashizume C, Dowaki T, et al. Therapeutic potential of mitotic interaction between the nucleoporin Tpr and aurora kinase A. Cell cycle. 2015;14(9):1447–58. doi:10.1080/15384101.2015.1021518. PubMed PMID: 25789545; PubMed Central PMCID: PMCPMC4614903. PubMed DOI PMC

Zou S, Chen Y, Liu Y, et al. Trs130 participates in autophagy through GTPases Ypt31/32 in Saccharomyces cerevisiae. Traffic. 2013. Feb;14(2):233–46. doi:10.1111/tra.12024. PubMed PMID: 23078654; PubMed Central PMCID: PMC3538905. PubMed DOI PMC

DeBosch BJ, Heitmeier MR, Mayer AL, et al. Trehalose inhibits solute carrier 2A (SLC2A) proteins to induce autophagy and prevent hepatic steatosis. Sci Signal. 2016. Feb 23;9(416):ra21. doi:10.1126/scisignal.aac5472. PubMed PMID: 26905426; PubMed Central PMCID: PMCPMC4816640. PubMed DOI PMC

Pahari S, Negi S, Aqdas M, et al. Induction of autophagy through CLEC4E in combination with TLR4: an innovative strategy to restrict the survival of Mycobacterium tuberculosis. Autophagy. 2020. Jun;16(6):1021–1043. doi:10.1080/15548627.2019.1658436. PubMed PMID: 31462144. PubMed DOI PMC

Hua F, Li K, Yu JJ, et al. TRB3 links insulin/IGF to tumour promotion by interacting with p62 and impeding autophagic/proteasomal degradations. Nat Commun. 2015;6:7951. doi:10.1038/ncomms8951. PubMed PMID: 26268733. PubMed DOI PMC

Salazar M, Carracedo A, Salanueva IJ, et al. TRB3 links ER stress to autophagy in cannabinoid anti-tumoral action. Autophagy. 2009. Oct, 5(7):1048–9. PubMed PMID: 19652543. PubMed

Zhang XW, Zhou JC, Peng D, et al. Disrupting the TRIB3-SQSTM1 interaction reduces liver fibrosis by restoring autophagy and suppressing exosome-mediated HSC activation. Autophagy. 2019. Jul 9:1–15. doi:10.1080/15548627.2019.1635383. PubMed PMID: 31286822. PubMed DOI PMC

Francisco R, Perez-Perarnau A, Cortes C, et al. Histone deacetylase inhibition induces apoptosis and autophagy in human neuroblastoma cells. Cancer Lett. 2012. May 1;318(1):42–52. doi:10.1016/j.canlet.2011.11.036. PubMed PMID: 22186300. PubMed DOI

Wang C, Yu Z, Shi X, et al. Triclosan enhances the clearing of pathogenic intracellular salmonella or candida albicans but disturbs the intestinal microbiota through mTOR-independent autophagy. Front Cell Infect Microbiol. 2018;8:49. doi:10.3389/fcimb.2018.00049. PubMed PMID: 29515975; PubMed Central PMCID: PMCPMC5826388. PubMed DOI PMC

Lo CH, Lim CK, Ding Z, et al. Targeting the ensemble of heterogeneous tau oligomers in cells: A novel small molecule screening platform for tauopathies. Alzheimers Dement. 2019. Nov;15(11):1489–1502. doi:10.1016/j.jalz.2019.06.4954. PubMed PMID: 31653529; PubMed Central PMCID: PMCPMC7038631. PubMed DOI PMC

Ribeiro CM, Sarrami-Forooshani R, Setiawan LC, et al. Receptor usage dictates HIV-1 restriction by human TRIM5alpha in dendritic cell subsets. Nature. 2016. Dec 15;540(7633):448–452. doi:10.1038/nature20567. PubMed PMID: 27919079. PubMed DOI

Imam S, Talley S, Nelson RS, et al. TRIM5alpha degradation via autophagy is not required for retroviral restriction. J Virol. 2016. Jan 13;90(7):3400–10. doi:10.1128/JVI.03033-15. PubMed PMID: 26764007; PubMed Central PMCID: PMCPMC4794682. PubMed DOI PMC

Sebastian S, Luban J.. TRIM5alpha selectively binds a restriction-sensitive retroviral capsid. Retrovirology. 2005. Jun 20;2:40. doi:10.1186/1742-4690-2-40. PubMed PMID: 15967037; PubMed Central PMCID: PMCPMC1166576. PubMed DOI PMC

Keown JR, Black MM, Ferron A, et al. A helical LC3-interacting region mediates the interaction between the retroviral restriction factor Trim5alpha and mammalian autophagy-related ATG8 proteins. J Biol Chem. 2018. Nov 23;293(47):18378–18386. doi:10.1074/jbc.RA118.004202. PubMed PMID: 30282803; PubMed Central PMCID: PMCPMC6254359. PubMed DOI PMC

Jena KK, Kolapalli SP, Mehto S, et al. TRIM16 controls assembly and degradation of protein aggregates by modulating the p62-NRF2 axis and autophagy. EMBO J. 2018. Sep 14;37(18). doi:10.15252/embj.201798358. PubMed PMID: 30143514; PubMed Central PMCID: PMCPMC6138442. PubMed DOI PMC

Mandell MA, Jain A, Kumar S, et al. TRIM17 contributes to autophagy of midbodies while actively sparing other targets from degradation. J Cell Sci. 2016. Oct 1;129(19):3562–3573. doi:10.1242/jcs.190017. PubMed PMID: 27562068; PubMed Central PMCID: PMCPMC5087653. PubMed DOI PMC

Wang W, Xia Z, Farre JC, et al. TRIM37 deficiency induces autophagy through deregulating the MTORC1-TFEB axis. Autophagy. 2018;14(9):1574–1585. doi:10.1080/15548627.2018.1463120. PubMed PMID: 29940807; PubMed Central PMCID: PMCPMC6135569. PubMed DOI PMC

Micale L, Fusco C, Augello B, et al. Williams-Beuren syndrome TRIM50 encodes an E3 ubiquitin ligase. Eur J Human Genet. 2008. Sep;16(9):1038–49. doi:10.1038/ejhg.2008.68. PubMed PMID: 18398435; PubMed Central PMCID: PMC2680067. PubMed DOI PMC

Fusco C, Micale L, Augello B, et al. HDAC6 mediates the acetylation of TRIM50. Cell Signal. 2014. Feb;26(2):363–9. doi:10.1016/j.cellsig.2013.11.036. PubMed PMID: 24308962. PubMed DOI

Fusco C, Micale L, Egorov M, et al. The E3-ubiquitin ligase TRIM50 interacts with HDAC6 and p62, and promotes the sequestration and clearance of ubiquitinated proteins into the aggresome. PLoS One. 2012;7(7):e40440. doi:10.1371/journal.pone.0040440. PubMed PMID: 22792322; PubMed Central PMCID: PMC3392214. PubMed DOI PMC

Bodine SC, Latres E, Baumhueter S, et al. Identification of ubiquitin ligases required for skeletal muscle atrophy. Science. 2001. Nov 23;294(5547):1704–8. doi:10.1126/science.1065874. PubMed PMID: 11679633. PubMed DOI

Centner T, Yano J, Kimura E, et al. Identification of muscle specific ring finger proteins as potential regulators of the titin kinase domain. J Mol Biol. 2001. Mar 2;306(4):717–26. doi:10.1006/jmbi.2001.4448. PubMed PMID: 11243782. PubMed DOI

Gatliff J, East D, Crosby J, et al. TSPO interacts with VDAC1 and triggers a ROS-mediated inhibition of mitochondrial quality control. Autophagy. 2014;10(12):2279–96. doi:10.4161/15548627.2014.991665. PubMed PMID: 25470454; PubMed Central PMCID: PMC4502750. PubMed DOI PMC

Huang JH, Liu CY, Wu SY, et al. NLRX1 facilitates histoplasma capsulatum-Induced LC3-associated phagocytosis for cytokine production in macrophages. Front Immunol. 2018;9:2761. doi:10.3389/fimmu.2018.02761. PubMed PMID: 30559741; PubMed Central PMCID: PMCPMC6286976. PubMed DOI PMC

Lima RT, Sousa D, Paiva AM, et al. Modulation of autophagy by a thioxanthone decreases the viability of melanoma cells. Molecules. 2016. Oct 10;21(10). doi:10.3390/molecules21101343. PubMed PMID: 27735867; PubMed Central PMCID: PMCPMC6274546. PubMed DOI PMC

Palmeira A, Vasconcelos MH, Paiva A, et al. Dual inhibitors of P-glycoprotein and tumor cell growth: (re)discovering thioxanthones. Biochem Pharmacol. 2012. Jan 1;83(1):57–68. doi:10.1016/j.bcp.2011.10.004. PubMed PMID: 22044878. PubMed DOI

DeSilva DR, Jones EA, Favata MF, et al. Inhibition of mitogen-activated protein kinase kinase blocks T cell proliferation but does not induce or prevent anergy. J Immunol 1998. May 1;160(9):4175–81. PubMed PMID: 9574517. PubMed

Geisler S, Vollmer S, Golombek S, et al. UBE2N, UBE2L3 and UBE2D2/3 ubiquitin-conjugating enzymes are essential for parkin-dependent mitophagy. J Cell Sci. 2014. Jun 6;127:3280–3293. doi:10.1242/jcs.146035. PubMed PMID: 24906799. PubMed DOI

Fiesel FC, Moussaud-Lamodiere EL, Ando M, et al. A specific subset of E2 ubiquitin-conjugating enzymes regulate Parkin activation and mitophagy differently. J Cell Sci. 2014. Aug 15;127\(Pt 16):3488–504. doi:10.1242/jcs.147520. PubMed PMID: 24928900; PubMed Central PMCID: PMC4132391. PubMed DOI PMC

Newton K, Matsumoto ML, Wertz IE, et al. Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies. Cell. 2008. Aug 22;134(4):668–78. doi:10.1016/j.cell.2008.07.039. PubMed PMID: 18724939. PubMed DOI

Muller M, Kotter P, Behrendt C, et al. Synthetic quantitative array technology identifies the Ubp3-Bre5 deubiquitinase complex as a negative regulator of mitophagy. Cell Rep. 2015. Feb 24;10(7):1215–25. doi:10.1016/j.celrep.2015.01.044. PubMed PMID: 25704822. PubMed DOI

Rothenberg C, Srinivasan D, Mah L, et al. Ubiquilin functions in autophagy and is degraded by chaperone-mediated autophagy. Hum Mol Genet. 2010. Aug 15;19(16):3219–32. doi:10.1093/hmg/ddq231. PubMed PMID: 20529957; PubMed Central PMCID: PMCPMC2908472. PubMed DOI PMC

Wu JJ, Cai A, Greenslade JE, et al. ALS/FTD mutations in UBQLN2 impede autophagy by reducing autophagosome acidification through loss of function. Proc Natl Acad Sci U S A. 2020. Jun 30;117(26):15230–15241. doi:10.1073/pnas.1917371117. PubMed PMID: 32513711. PubMed DOI PMC

Chan EY, Kir S, Tooze SA.. siRNA screening of the kinome identifies ULK1 as a multidomain modulator of autophagy. J Biol Chem. 2007. Aug 31;282(35):25464–74. doi:10.1074/jbc.M703663200. PubMed PMID: 17595159; eng. PubMed DOI

Mizushima N. The role of the Atg1/ULK1 complex in autophagy regulation. Curr Opinion Cell Biol 2010. Jan 5;22:132–139. doi:10.1016/j.ceb.2009.12.004. PubMed PMID: 20056399; Eng. PubMed DOI

Martin KR, Celano SL, Solitro AR, et al. A potent and selective ULK1 inhibitor suppresses autophagy and sensitizes cancer cells to nutrient stress. iScience. 2018. Oct 26;8:74–84. doi: 10.1016/j.isci.2018.09.012. PubMed PMID: 30292171; PubMed Central PMCID: PMCPMC6172447. PubMed DOI PMC

Ogura K, Wicky C, Magnenat L, et al. Caenorhabditis elegans unc-51 gene required for axonal elongation encodes a novel serine/threonine kinase. Genes Dev. 1994. Oct 15;8(20):2389–400. doi: 10.1101/gad.8.20.2389. PubMed PMID: 7958904. PubMed DOI

He J, Johnson JL, Monfregola J, et al. Munc13-4 interacts with syntaxin 7 and regulates late endosomal maturation, endosomal signaling, and TLR9-initiated cellular responses. Mol Biol Cell. 2016. Feb 1;27(3):572–87. doi: 10.1091/mbc.E15-05-0283. PubMed PMID: 26680738; PubMed Central PMCID: PMCPMC4751605. PubMed DOI PMC

Zhang J, He J, Johnson JL, et al. Cross-regulation of defective endolysosome trafficking and enhanced autophagy through TFEB in UNC13D deficiency. Autophagy. 2019. Oct;15(10):1738–1756. doi: 10.1080/15548627.2019.1596475. PubMed PMID: 30892133; PubMed Central PMCID: PMCPMC6735675. PubMed DOI PMC

Munch C. The different axes of the mammalian mitochondrial unfolded protein response. BMC Biol. 2018. Jul 26;16(1):81. doi: 10.1186/s12915-018-0548-x. PubMed PMID: 30049264; PubMed Central PMCID: PMCPMC6060479. PubMed DOI PMC

von Stockum S, Sanchez-Martinez A, Corra S, et al. Inhibition of the deubiquitinase USP8 corrects a Drosophila PINK1 model of mitochondria dysfunction. Life Sci Alliance. 2019. Apr;2(2). doi: 10.26508/lsa.201900392. PubMed PMID: 30988163; PubMed Central PMCID: PMCPMC6467245. PubMed DOI PMC

Cornelissen T, Haddad D, Wauters F, et al. The deubiquitinase USP15 antagonizes Parkin-mediated mitochondrial ubiquitination and mitophagy. Hum Mol Genet. 2014. May 22. doi: 10.1093/hmg/ddu244. PubMed PMID: 24852371. PubMed DOI PMC

Thayer JA, Awad O, Hegdekar N, et al. The PARK10 gene USP24 is a negative regulator of autophagy and ULK1 protein stability. Autophagy. 2020. Jan;16(1):140–153. doi: 10.1080/15548627.2019.1598754. PubMed PMID: 30957634; PubMed Central PMCID: PMCPMC6984603. PubMed DOI PMC

Bingol B, Tea JS, Phu L, et al. The mitochondrial deubiquitinase USP30 opposes parkin-mediated mitophagy. Nature. 2014. Jun 19;510(7505):370–5. doi: 10.1038/nature13418. PubMed PMID: 24896179. PubMed DOI

Liang JR, Martinez A, Lane JD, et al. USP30 deubiquitylates mitochondrial Parkin substrates and restricts apoptotic cell death. EMBO Rep. 2015. May;16(5):618–27. doi: 10.15252/embr.201439820. PubMed PMID: 25739811; PubMed Central PMCID: PMCPMC4428036. PubMed DOI PMC

Wang Y, Serricchio M, Jauregui M, et al. Deubiquitinating enzymes regulate PARK2-mediated mitophagy. Autophagy. 2015. Apr 3;11(4):595–606. doi: 10.1080/15548627.2015.1034408. PubMed PMID: 25915564; PubMed Central PMCID: PMCPMC4502823. PubMed DOI PMC

Taillebourg E, Gregoire I, Viargues P, et al. The deubiquitinating enzyme USP36 controls selective autophagy activation by ubiquitinated proteins. Autophagy. 2012. May 1;8(5):767–79. doi: 10.4161/auto.19381. PubMed PMID: 22622177. PubMed DOI

Pirooz SD, He S, Zhang T, et al. UVRAG is required for virus entry through combinatorial interaction with the class C-Vps complex and SNAREs. Proc Natl Acad Sci U S A. 2014. Feb 18;111(7):2716–21. doi: 10.1073/pnas.1320629111. PubMed PMID: 24550300; PubMed Central PMCID: PMC3932887. PubMed DOI PMC

Oku M, Nishimura T, Hattori T, et al. Role of Vac8 in formation of the vacuolar sequestering membrane during micropexophagy. Autophagy. 2006. Oct-Dec;2(4):272–9. PubMed PMID: 16874085. PubMed

Gatica D, Damasio A, Pascual C, et al. The carboxy terminus of yeast Atg13 binds phospholipid membrane via motifs that overlap with the Vac8-interacting domain. Autophagy. 2020. Jun;16(6):1007–1020. doi: 10.1080/15548627.2019.1648117. PubMed PMID: 31352862. PubMed DOI PMC

Kosta A, Roisin-Bouffay C, Luciani MF, et al. Autophagy gene disruption reveals a non-vacuolar cell death pathway in Dictyostelium. J Biol Chem. 2004. Nov 12;279(46):48404–9. doi: 10.1074/jbc.M408924200. PubMed PMID: 15358773. PubMed DOI

Yamada Y, Cyclic Schaap P.. AMP induction of Dictyostelium prespore gene expression requires autophagy. Dev Biol. 2019. Aug 15;452(2):114–126. doi: 10.1016/j.ydbio.2019.04.017. PubMed PMID: 31051160; PubMed Central PMCID: PMCPMC6598861. PubMed DOI PMC

Klionsky DJ, Herman PK, Emr SD.. The fungal vacuole: composition, function, and biogenesis. Microbiol Rev 1990. Sep;54(3):266–92. PubMed PMID: 2215422; PubMed Central PMCID: PMC372777. PubMed PMC

Hoffman M, Chiang H-L.. Isolation of degradation-deficient mutants defective in the targeting of fructose-1,6-bisphosphatase into the vacuole for degradation in Saccharomyces cerevisiae. Genetics. 1996. Aug;143(4):1555–66. PubMed PMID: 8844145; PubMed Central PMCID: PMC1207420. eng. PubMed PMC

Zhang C, Lee S, Peng Y, et al. PINK1 triggers autocatalytic activation of Parkin to specify cell fate decisions. Curr Biol. 2014. Aug 18;24(16):1854–65. doi: 10.1016/j.cub.2014.07.014. PubMed PMID: 25088558; PubMed Central PMCID: PMC4143385. PubMed DOI PMC

Darsow T, Rieder SE, Emr SD.. A multispecificity syntaxin homologue, Vam3p, essential for autophagic and biosynthetic protein transport to the vacuole. J Cell Biol. 1997. Aug 11;138(3):517–29. PubMed PMID: 9245783; PubMed Central PMCID: PMC2141632. eng. PubMed PMC

Fader CM, Sanchez DG, Mestre MB, et al. TI-VAMP/VAMP7 and VAMP3/cellubrevin: two v-SNARE proteins involved in specific steps of the autophagy/multivesicular body pathways [Research Support, Non-U.S. Gov’t]. Biochim Biophys Acta. 2009. Dec;1793(12):1901–16. doi: 10.1016/j.bbamcr.2009.09.011. PubMed PMID: 19781582; eng. PubMed DOI

Moreau K, Ravikumar B, Renna M, et al. Autophagosome precursor maturation requires homotypic fusion. Cell. 2011. Jul 22;146(2):303–17. doi: 10.1016/j.cell.2011.06.023. PubMed PMID: 21784250; eng. PubMed DOI PMC

Furuta N, Fujita N, Noda T, et al. Combinational soluble N-ethylmaleimide-sensitive factor attachment protein receptor proteins VAMP8 and Vti1b mediate fusion of antimicrobial and canonical auto-phagosomes with lysosomes. Mol Biol Cell. 2010. Mar;21(6):1001–10. doi: 10.1091/mbc.E09-08-0693. PubMed PMID: 20089838; PubMed Central PMCID: PMC2836953. eng. PubMed DOI PMC

Zhao YG, Liu N, Miao G, et al. The ER contact proteins VAPA/B interact with multiple autophagy proteins to modulate autophagosome biogenesis. Curr Biol. 2018. Apr 23;28(8):1234–1245 e4. doi: 10.1016/j.cub.2018.03.002. PubMed PMID: 29628370. PubMed DOI

Ju JS, Fuentealba RA, Miller SE, et al. Valosin-containing protein (VCP) is required for autophagy and is disrupted in VCP disease. J Cell Biol. 2009. Dec 14;187(6):875–88. doi: 10.1083/jcb.200908115. PubMed PMID: 20008565; PubMed Central PMCID: PMC2806317. eng. PubMed DOI PMC

Tresse E, Salomons FA, Vesa J, et al. VCP/p97 is essential for maturation of ubiquitin-containing auto-phagosomes and this function is impaired by mutations that cause IBMPFD. Autophagy. 2010. Feb;6(2):217–27. PubMed PMID: 20104022; PubMed Central PMCID: PMC2929010. eng. PubMed PMC

Arhzaouy K, Strucksberg KH, Tung SM, et al. Heteromeric p97/p97R155C complexes induce dominant negative changes in wild-type and autophagy 9-deficient Dictyostelium strains. PLoS One. 2012;7(10):e46879. doi: 10.1371/journal.pone.0046879. PubMed PMID: 23056506; PubMed Central PMCID: PMCPMC3463532. PubMed DOI PMC

Papadopoulos C, Kirchner P, Bug M, et al. VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy. EMBO J. 2017. Jan 17;36(2):135–150. doi: 10.15252/embj.201695148. PubMed PMID: 27753622; PubMed Central PMCID: PMCPMC5242375. PubMed DOI PMC

Yuan J, Zhang Y, Sheng Y, et al. MYBL2 guides autophagy suppressor VDAC2 in the developing ovary to inhibit autophagy through a complex of VDAC2-BECN1-BCL2L1 in mammals. Autophagy. 2015;11(7):1081–98. doi: 10.1080/15548627.2015.1040970. PubMed PMID: 26060891; PubMed Central PMCID: PMCPMC4590641. PubMed DOI PMC

Yamamoto S, Kuramoto K, Wang N, et al. Autophagy differentially regulates insulin production and insulin sensitivity. Cell Rep. 2018. Jun 12;23(11):3286–3299. doi: 10.1016/j.celrep.2018.05.032. PubMed PMID: 29898399; PubMed Central PMCID: PMCPMC6054876. PubMed DOI PMC

Kaelin WG, Jr. The von Hippel-Lindau tumour suppressor protein: O2 sensing and cancer. Nat Rev Cancer. 2008. Nov;8(11):865–73. doi: 10.1038/nrc2502. PubMed PMID: 18923434. PubMed DOI

Dong N, Zhu Y, Lu Q, et al. Structurally distinct bacterial TBC-like GAPs link Arf GTPase to Rab1 inactivation to counteract host defenses. Cell. 2012. Aug 31;150(5):1029–41. doi: 10.1016/j.cell.2012.06.050. PubMed PMID: 22939626. PubMed DOI

Ogawa M, Yoshimori T, Suzuki T, et al. Escape of intracellular Shigella from autophagy. Science. 2005. Feb 4;307(5710):727–31. doi: 10.1126/science.1106036. PubMed PMID: 15576571. PubMed DOI

Vaccaro MI, Ropolo A, Grasso D, et al. A novel mammalian trans-membrane protein reveals an alternative initiation pathway for autophagy. Autophagy. 2008. Apr 1;4(3):388–90. [pii]. PubMed PMID: 18253086; eng. PubMed

Calvo-Garrido J, King JS, Munoz-Braceras S, et al. Vmp1 regulates PtdIns3P signaling during autophagosome formation in Dictyostelium discoideum. Traffic. 2014. Nov;15(11):1235–46. doi: 10.1111/tra.12210. PubMed PMID: 25131297. PubMed DOI

Molejon MI, Ropolo A, Re AL, et al. The VMP1-Beclin 1 interaction regulates autophagy induction. Sci Rep. 2013;3:1055. doi: 10.1038/srep01055. PubMed PMID: 23316280; PubMed Central PMCID: PMC3542764. PubMed DOI PMC

Nickerson DP, Brett CL, Merz AJ.. Vps-C complexes: gatekeepers of endolysosomal traffic. Current opinion in cell biology. 2009. Aug;21(4):543–51. doi: 10.1016/j.ceb.2009.05.007. PubMed PMID: 19577915; PubMed Central PMCID: PMC2807627. PubMed DOI PMC

Clancey LF, Beirl AJ, Linbo TH, et al. Maintenance of melanophore morphology and survival is cathepsin and vps11 dependent in zebrafish. PLoS One. 2013;8(5):e65096. doi: 10.1371/journal.pone.0065096. PubMed PMID: 23724125; PubMed Central PMCID: PMC3664566. PubMed DOI PMC

Munoz-Braceras S, Tornero-Ecija AR, Vincent O, et al. VPS13A is closely associated with mitochondria and is required for efficient lysosomal degradation. Dis Model Mech. 2019. Feb 22;12(2). doi: 10.1242/dmm.036681. PubMed PMID: 30709847; PubMed Central PMCID: PMCPMC6398486. PubMed DOI PMC

Kumar N, Leonzino M, Hancock-Cerutti W, et al. VPS13A and VPS13C are lipid transport proteins differentially localized at ER contact sites. J Cell Biol. 2018. Oct 1;217(10):3625–3639. doi: 10.1083/jcb.201807019. PubMed PMID: 30093493; PubMed Central PMCID: PMCPMC6168267. PubMed DOI PMC

Rzepnikowska W, Flis K, Kaminska J, et al. Amino acid substitution equivalent to human chorea-acanthocytosis I2771R in yeast Vps13 protein affects its binding to phosphatidylinositol 3-phosphate. Hum Mol Genet. 2017. Apr 15;26(8):1497–1510. doi: 10.1093/hmg/ddx054. PubMed PMID: 28334785; PubMed Central PMCID: PMCPMC5393151. PubMed DOI PMC

Kolakowski D, Kaminska J, Zoladek T.. The binding of the APT1 domains to phosphoinositides is regulated by metal ions in vitro. Biochim Biophys Acta Biomembr. 2020. Sep 1;1862(9):183349. doi: 10.1016/j.bbamem.2020.183349. PubMed PMID: 32407779. PubMed DOI

Anding AL, Wang C, Chang TK, et al. Vps13D Encodes a Ubiquitin-Binding Protein that Is Required for the Regulation of Mitochondrial Size and Clearance. Curr Biol CB 2018. Jan 22;28(2):287–295 e6. doi: 10.1016/j.cub.2017.11.064. PubMed PMID: 29307555; PubMed Central PMCID: PMCPMC5787036. PubMed DOI PMC

Huotari J, Helenius A.. Endosome maturation. EMBO J. 2011. Aug 31;30(17):3481–500. doi: 10.1038/emboj.2011.286. PubMed PMID: 21878991; PubMed Central PMCID: PMCPMC3181477. PubMed DOI PMC

Khatter D, Raina VB, Dwivedi D, et al. The small GTPase Arl8b regulates assembly of the mammalian HOPS complex on lysosomes. J Cell Sci. 2015. May 1;128(9):1746–61. doi: 10.1242/jcs.162651. PubMed PMID: 25908847; PubMed Central PMCID: PMCPMC4432227. PubMed DOI PMC

Pu J, Schindler C, Jia R, et al. BORC, a multisubunit complex that regulates lysosome positioning. Dev Cell. 2015. Apr 20;33(2):176–88. doi: 10.1016/j.devcel.2015.02.011. PubMed PMID: 25898167; PubMed Central PMCID: PMCPMC4788105. PubMed DOI PMC

Ruan Q, Harrington AJ, Caldwell KA, et al. VPS41, a protein involved in lysosomal trafficking, is protective in Caenorhabditis elegans and mammalian cellular models of Parkinson’s disease. Neurobiol Dis. 2010. Feb;37(2):330–8. doi: 10.1016/j.nbd.2009.10.011. PubMed PMID: 19850127; PubMed Central PMCID: PMCPMC2818321. PubMed DOI PMC

Harrington AJ, Yacoubian TA, Slone SR, et al. Functional analysis of VPS41-mediated neuroprotection in Caenorhabditis elegans and mammalian models of Parkinson’s disease. J Neurosci Off J Soc Neurosci 2012. Feb 8;32(6):2142–53. doi: 10.1523/JNEUROSCI.2606-11.2012. PubMed PMID: 22323726; PubMed Central PMCID: PMCPMC6621695. PubMed DOI PMC

Uttenweiler A, Schwarz H, Neumann H, et al. The vacuolar transporter chaperone (VTC) complex is required for microautophagy. Mol Biol Cell. 2007. Jan;18(1):166–75. doi: 10.1091/mbc.E06-08-0664. PubMed PMID: 17079729; PubMed Central PMCID: PMC1751332. eng. PubMed DOI PMC

Horos R, Buscher M, Kleinendorst R, et al. The Small Non-coding Vault RNA1-1 Acts as a Riboregulator of Autophagy. Cell. 2019. Feb 21;176(5):1054–1067 e12. doi: 10.1016/j.cell.2019.01.030. PubMed PMID: 30773316. PubMed DOI

Simonsen A, Birkeland HC, Gillooly DJ, et al. Alfy, a novel FYVE-domain-containing protein associated with protein granules and autophagic membranes. J Cell Sci. 2004. Aug 15;117\(Pt 18):4239–51. doi: 10.1242/jcs.01287jcs.01287 [pii]. PubMed PMID: 15292400; eng. PubMed DOI

Napoli E, Song G, Panoutsopoulos A, et al. Beyond autophagy: a novel role for autism-linked Wdfy3 in brain mitophagy. Sci Rep. 2018. Jul 27;8(1):11348. doi: 10.1038/s41598-018-29421-7. PubMed PMID: 30054502; PubMed Central PMCID: PMCPMC6063930. PubMed DOI PMC

Clausen TH, Lamark T, Isakson P, et al. p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy. Autophagy. 2010. Apr;6(3):330–44. PubMed PMID: 20168092; eng. PubMed

Kast DJ, Zajac AL, Holzbaur EL, et al. WHAMM Directs the Arp2/3 Complex to the ER for Autophagosome Biogenesis through an Actin Comet Tail Mechanism. Curr Biol. 2015. Jun 29;25(13):1791–7. doi: 10.1016/j.cub.2015.05.042. PubMed PMID: 26096974; PubMed Central PMCID: PMC4489997. PubMed DOI PMC

Dai A, Yu L, Wang HW.. WHAMM initiates autolysosome tubulation by promoting actin polymerization on autolysosomes. Nat Commun. 2019. Aug 16;10(1):3699. doi: 10.1038/s41467-019-11694-9. PubMed PMID: 31420534; PubMed Central PMCID: PMCPMC6697732. PubMed DOI PMC

Haack TB, Hogarth P, Kruer MC, et al. Exome sequencing reveals de novo WDR45 mutations causing a phenotypically distinct, X-linked dominant form of NBIA. Am J Hum Genet. 2012. Dec 7;91(6):1144–9. doi: 10.1016/j.ajhg.2012.10.019. PubMed PMID: 23176820; PubMed Central PMCID: PMC3516593. PubMed DOI PMC

Abidi A, Mignon-Ravix C, Cacciagli P, et al. Early-onset epileptic encephalopathy as the initial clinical presentation of WDR45 deletion in a male patient. Eur J Human Genet. 2015. Jul 15. doi: 10.1038/ejhg.2015.159. PubMed PMID: 26173968. PubMed DOI PMC

Saitsu H, Nishimura T, Muramatsu K, et al. De novo mutations in the autophagy gene WDR45 cause static encephalopathy of childhood with neurodegeneration in adulthood. Nat Genet. 2013. Apr;45(4):445–9, 449e1. doi: 10.1038/ng.2562. PubMed PMID: 23435086. PubMed DOI

Biagosch CA, Hensler S, Kühn R, et al. ALEN-mediated mutagenesis as a tool to generate disease models for diseases caused by dominant de novo mutations. Eur J Human Gen EJHG 2014;22:153.

Gallolu Kankanamalage S, Lee AY, Wichaidit C, et al. Multistep regulation of autophagy by WNK1. Proc Natl Acad Sci U S A. 2016. Dec 13;113(50):14342–14347. doi: 10.1073/pnas.1617649113. PubMed PMID: 27911840; PubMed Central PMCID: PMCPMC5167150. PubMed DOI PMC

Maiese K, Chong ZZ, Shang YC, et al. Targeting disease through novel pathways of apoptosis and autophagy. Expert Opin Ther Targets. 2012. Dec;16(12):1203–14. doi: 10.1517/14728222.2012.719499. PubMed PMID: 22924465; PubMed Central PMCID: PMC3500415. PubMed DOI PMC

Petherick KJ, Williams AC, Lane JD, et al. Autolysosomal beta-catenin degradation regulates Wnt-autophagy-p62 crosstalk. EMBO J. 2013. Jul 3;32(13):1903–16. doi: 10.1038/emboj.2013.123. PubMed PMID: 23736261; PubMed Central PMCID: PMC3981178. PubMed DOI PMC

Sasazawa Y, Kanagaki S, Tashiro E, et al. Xanthohumol impairs autophagosome maturation through direct inhibition of valosin-containing protein. ACS Chem Biol. 2012. May 18;7(5):892–900. doi: 10.1021/cb200492h. PubMed PMID: 22360440. PubMed DOI

Kaser A, Blumberg RS.. Endoplasmic reticulum stress in the intestinal epithelium and inflammatory bowel disease. Semin Immunol. 2009. Jun;21(3):156–63. doi: 10.1016/j.smim.2009.01.001. PubMed PMID: 19237300; eng. PubMed DOI PMC

Levine B. Eating oneself and uninvited guests: autophagy-related pathways in cellular defense. Cell. 2005. Jan 28;120(2):159–62. PubMed PMID: 15680321. PubMed

Criollo A, Maiuri MC, Tasdemir E, et al. Regulation of autophagy by the inositol trisphosphate receptor [Research Support, Non-U.S. Gov’t]. Cell Death Differ. 2007. May;14(5):1029–39. doi: 10.1038/sj.cdd.4402099. PubMed PMID: 17256008; eng. PubMed DOI

Huang X, Wu Z, Mei Y, et al. XIAP inhibits autophagy via XIAP-Mdm2-p53 signalling. EMBO J. 2013. Aug 14;32(16):2204–16. doi: 10.1038/emboj.2013.133. PubMed PMID: 23749209; PubMed Central PMCID: PMCPMC3746193. PubMed DOI PMC

Huang X, Wang XN, Yuan XD, et al. XIAP facilitates breast and colon carcinoma growth via promotion of p62 depletion through ubiquitination-dependent proteasomal degradation. Oncogene. 2019. Feb;38(9):1448–1460. doi: 10.1038/s41388-018-0513-8. PubMed PMID: 30275562. PubMed DOI

Martin AP, Jacquemyn M, Lipecka J, et al. STK38 kinase acts as XPO1 gatekeeper regulating the nuclear export of autophagy proteins and other cargoes. EMBO Rep. 2019. Nov 5;20(11):e48150. doi: 10.15252/embr.201948150. PubMed PMID: 31544310; PubMed Central PMCID: PMCPMC6832005. PubMed DOI PMC

Liang XH, Yu J, Brown K, et al. Beclin 1 contains a leucine-rich nuclear export signal that is required for its autophagy and tumor suppressor function. Cancer res 2001. Apr 15;61(8):3443–9. PubMed PMID: 11309306. PubMed

Delorme-Axford E, Abernathy E, Lennemann NJ, et al. The exoribonuclease Xrn1 is a post-transcriptional negative regulator of autophagy. Autophagy. 2018;14(5):898–912. doi: 10.1080/15548627.2018.1441648. PubMed PMID: 29465287; PubMed Central PMCID: PMCPMC6070002. PubMed DOI PMC

Kweon Y, Rothe A, Conibear E, et al. Ykt6p is a multifunctional yeast R-SNARE that is required for multiple membrane transport pathways to the vacuole, Mol Biol Cell. 2003 May;14(5):1868–81. doi: 10.1091/mbc.E02-10-0687. PubMed PMID: 12802061; PubMed Central PMCID: PMC165083. eng. PubMed DOI PMC

Takats S, Glatz G, Szenci G, et al. Non-canonical role of the SNARE protein Ykt6 in autophagosome-lysosome fusion. PLoS Genet. 2018. Apr;14(4):e1007359. doi: 10.1371/journal.pgen.1007359. PubMed PMID: 29694367; PubMed Central PMCID: PMCPMC5937789. PubMed DOI PMC

Kriegenburg F, Bas L, Gao J, et al. The multi-functional SNARE protein Ykt6 in autophagosomal fusion processes. Cell cycle. 2019. Mar - Apr;18(6–7):639–651. doi: 10.1080/15384101.2019.1580488. PubMed PMID: 30836834; PubMed Central PMCID: PMCPMC6464585. PubMed DOI PMC

Cebollero E, van der Vaart A, Zhao M, et al. Phosphatidylinositol-3-phosphate clearance plays a key role in autophagosome completion. Curr Biol. 2012. Sep 11;22(17):1545–53. doi: 10.1016/j.cub.2012.06.029. PubMed PMID: 22771041; PubMed Central PMCID: PMC3615650. PubMed DOI PMC

Cheng J, Fujita A, Yamamoto H, et al. Yeast and mammalian auto-phagosomes exhibit distinct phosphatidylinositol 3-phosphate asymmetries. Nat Commun. 2014;5:3207. doi: 10.1038/ncomms4207. PubMed PMID: 24492518. PubMed DOI

Huang J, Birmingham CL, Shahnazari S, et al. Antibacterial autophagy occurs at PI(3)P-enriched domains of the endoplasmic reticulum and requires Rab1 GTPase. Autophagy. 2011. Jan;7(1):17–26. PubMed PMID: 20980813; eng. PubMed PMC

Zoppino FC, Militello RD, Slavin I, et al. Autophagosome formation depends on the small GTPase Rab1 and functional ER exit sites [Research Support, Non-U.S. Gov’t]. Traffic. 2010. Sep;11(9):1246–61. doi: 10.1111/j.1600-0854.2010.01086.x. PubMed PMID: 20545908; eng. PubMed DOI

Vantaggiato C, Crimella C, Airoldi G, et al. Defective autophagy in spastizin mutated patients with hereditary spastic paraparesis type 15. Brain. 2013. Oct;136(Pt 10):3119–39. doi: 10.1093/brain/awt227. PubMed PMID: 24030950; PubMed Central PMCID: PMC3784282. PubMed DOI PMC

Khandelwal VK, Mitrofan LM, Hyttinen JM, et al. Oxidative stress plays an important role in zoledronic acid-induced autophagy. Physiol Res 2014;63 Suppl 4:S601–12. PubMed PMID: 25669691. PubMed

Schneider EM, Lorezn M, Walther P.. Autophagy as a hallmark of hemophagocytic diseases In: Gorbunov N, editor. Autophagy: Principles, Regulation and Roles in Disease: Nova Science Publishers; 2012.

Ryhanen T, Hyttinen JM, Kopitz J, et al. Crosstalk between Hsp70 molecular chaperone, lysosomes and proteasomes in autophagy-mediated proteolysis in human retinal pigment epithelial cells. J Cell Mol Med. 2009. Sep;13(9B):3616–31. doi: 10.1111/j.1582-4934.2008.00577.x. PubMed PMID: 19017362; eng. PubMed DOI PMC

Cheong JK, Zhang F, Chua PJ, et al. Casein kinase 1alpha-dependent feedback loop controls autophagy in RAS-driven cancers. J Clin Invest. 2015. Apr;125(4):1401–18. doi: 10.1172/JCI78018. PubMed PMID: 25798617; PubMed Central PMCID: PMCPMC4396475. PubMed DOI PMC

Amadoro G, Corsetti V, Florenzano F, et al. Morphological and bioenergetic demands underlying the mitophagy in post-mitotic neurons: the pink-parkin pathway. Front Aging Neurosci. 2014;6:18. doi: 10.3389/fnagi.2014.00018. PubMed PMID: 24600391; PubMed Central PMCID: PMC3927396. PubMed DOI PMC

Kang C, Avery L.. Systemic regulation of starvation response in Caenorhabditis elegans. Genes Dev. 2009. Jan 1;23(1):12–7. doi: 10.1101/gad.1723409. PubMed PMID: 19136622; PubMed Central PMCID: PMC2632168. eng. PubMed DOI PMC

Find record

Citation metrics

Archiving options