Zobrazit více v PubMed
Mack J, Fulwyler Particle Separator. US patent US 3380584 A.
Kachel V, Fellner-Feldegg H and Menke E, Hydrodynamic properties of flow cytometry instruments. In Melamed MR, Lindmo T and Mendelsohn ML (Eds.), Flow cytometry and sorting, 2nd ed., Wiley, New York, 1990, pp. 27– 44. ISBN 0-471-56235-1.
Crosland-Taylor PJ, A device for counting small particles suspended in a fluid through a tube. Nature 1953. 171: 37– 38.
PubMed
Gucker FT Jr., O’Konski CT, Pickard HB and Pitts JN Jr., A photoelectronic counter for colloidal particles. J. Am. Chem. Soc 1947. 69: 2422– 2431.
PubMed
Van den Engh GJ, Flow cytometer droplet formation system. US patent US 6861265 B1.
Van den Engh GJ, Particle separating apparatus and method. US patent US 5819948 A.
Norton PO, Vane DR and Javadi S, Fixed mounted sorting cuvette with user replaceable nozzle. US patent US 7201875 B2.
Doležel J and Göhde W, Sex determination in dioecious plants Melandrium album and M. rubrum using high-resolution flow cytometry. Cytometry 1995. 19: 103– 106.
PubMed
Steen HB, Lindau T and Sorensen O, A simple, high resolution flow cytometer based on a standard fluorescence microscope. In Laerum OD, Lindmo T and Thorud E (Eds.), Proceedings of the IVth international symposium on flow cytometry (pulse cytophotometry), June 4–8, 1979. Universitetsforlaget, Bergen, Norway, 1980, pp. 31– 33, ISBN 82-00-05399-7.
Pinkel D and Stovel R, Flow chambers and sample handling. In Dilla MA, Dean PN, Laerum OD, Melame MR (Eds.), Flow cytometry: Instrumentation and data analysis, Academic Press, London, 1985, pp. 77– 128, ISBN: 0-12-712150-1
Kaduchak G et al., Ultrasonic analyte concentration and application in flow cytometry. US patent US 7340957 B2.
Kaduchak G et al., System and method for acoustic focusing hardware and implementations. US patent US 8714014 B2.
Ward M, Turner P, DeJohn M and Kaduchak G, Fundamentals of acoustic cytometry. Curr. Protoc. Cytometry 2009. 53: 1.22.1–1.22.12.
PubMed
Sweet RG, Fluid droplet recorder. US patent US 3596275 A.
Göttlinger C, Mechtold B, Meyer KL and Radbruch A, Setup of a Flow Sorter. In Radbruch A (Ed.), Flow Cytometry and Cell Sorting. Springer Laboratory, Berlin, Heidelberg: 1992, pp. 153– 158.
Petersen TW and Van den Engh G, Stability of the breakoff point in a high-speed cell sorter. Cytometry Part A 2003. 56: 63– 70.
PubMed
Kaiser T, Raba K, Scheffold A and Radbruch A, A sheath-cooling system to stabilize side-streams and drop delay during long-term sorts for FACS-Aria® cell-sorter, http://fccf.drfz.de/uploads/pdf/poster_zentrallabor_A0.pdf
Lawrence WG, Varadi G, Entine G, Podniesinski E and Wallace PK, Enhanced red and near infrared detection in flow cytometry using avalanche photodiodes. Cytometry A 2008. 73: 767– 776.
PubMed
PMC
Kester W, Understand SINAD, ENOB, SNR, THD, THD+ N, and SFDR so you don’t get lost in the noise floor. MT-003 Tutorial, 2009, http://www.analog.com/media/en/training-seminars/tutorials/MT-003.pdf.
AD9240AS by Analog Devices | Data Acquisition, Arrow.com. [Online]. Available: https://www.arrow.com/de-de/products/ad9240as/analog-devices. [Accessed: 18-Jan-2017].
Snow C, Flow cytometer electronics. Cytometry Part A 2004. 57A: 63– 69.
PubMed
Asbury CL, Uy JL and van den Engh G, Polarization of scatter and fluorescence signals in flow cytometry. Cytometry 2000. 40: 88– 101.
PubMed
Shapiro HM, Practical flow cytometry, 4th ed., John Wiley & Sons, Inc., Hoboken, NJ: 2003, pp. 184– 197.
Watson DA, Brown LO, Gaskill DF, Naivar M, Graves SW, Doorn SK and Nolan JP, A flow cytometer for the measurement of Raman spectra. Cytometry Part A 2008. 73A: 119– 128.
PubMed
Nolan JP, Condello D, Duggan E, Naivar M and Novo D, Visible and near infrared fluorescence spectral flow cytometry. Cytometry Part A 2012. 83: 253– 264.
PubMed
PMC
Wade CG, Rhyne RH, Woodruff WH, Bloch DP and Bartholomew JC, Spectra of cells in flow cytometry using a vidicon detector. J. Histochem. Cytochem 1979. 27: 1049– 1052.
PubMed
Robinson JP, Multispectral Cytometry: The Next Generation. Biophotonics International October 2004, 36– 40.
Robinson JP, Rajwa B, Gregori G, Jones V and Patsekin V, Multispectral cytometry of single bio-particles using a 32-channel detector. In Tuan Vo-Dinh T, Grundfest WS, Benaron DA, Cohn GE, (Eds.), Advanced Biomedical and Clinical Diagnostic Systems III, Edition 5692. Springer, Berlin/Heidelberg, 2005, pp. 359– 365.
Robinson JP, Rajwa B, Patsekin V, Gregori G, Jones J Multi-spectral detector and analysis system US patent US7280204 B2.
Gregori G, Patsekin V, Rajwa B, Jones J, Ragheb K, Holdman C, Robinson JP, Robinson JP, Hyperspectral cytometry at the single cell level using a 32 channel photodetector. Cytometry A 2012, 81A: 35– 44.
PubMed
Goddard G, Martin JC, Naivar M, Goodwin PM, Graves SW, Habbersett R, Nolan JP et al., Single particle high resolution spectral analysis flow cytometry. Cytometry 2006. 69A: 842– 851.
PubMed
Futamura K, Sekino M, Hata A, Ikebuchi R, Nakanishi Y, Egawa G, Kabashima K et al., Novel full-spectral flow cytometry with multiple spectrally-adjacent fluorescent proteins and fluorochromes and visualization of in vivo cellular movement. Cytometry 2015. 87: 830– 842.
PubMed
PMC
Feher K, von Volkmann K, Kirsch J, Radbruch A, Popien J and Kaiser T, Multispectral flow cytometry: The consequences of increased light collection. Cytometry 2016. 89: 681– 689.
PubMed
Phadwal K, Alegre-Abarrategui J, Watson AS, Pike L, Anbalagan S, Hammond EM, Wade-Martins R et al., A novel method for autophagy detection in primary cells: Impaired levels of macroautophagy in immunosenescent T cells. Autophagy 2012. 8: 677– 689.
PubMed
PMC
Juvet SC, Sanderson S, Hester J, Wood KJ and Bushell A, Quantification of CD4(+) T cell alloreactivity and its control by regulatory T cells using time-lapse microscopy and immune synapse detection. Am. J. Transplant 2016. 16: 1394– 1407.
PubMed
PMC
Bandura DR, Baranov VI, Ornatsky OI, Antonov A, Kinach R, Lou X, Pavlov S et al., Mass cytometry: Technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal. Chem 2009. 81: 6813– 6822.
PubMed
Bendall SC, Simonds EF, Qiu P, Amir el AD, Krutzik PO, Finck R, Bruggner RV et al., Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 2011. 332: 687– 696.
PubMed
PMC
Bendall SC, Nolan GP, Roederer M and Chattopadhyay PK, A deep profiler’s guide to cytometry. Trends Immunol. 2012. 33: 323– 332.
PubMed
PMC
Tanner SD, Baranov VI, Ornatsky OI, Bandura DR and George TC, An introduction to mass cytometry: Fundamentals and applications. Cancer Immunol. Immun 2013. 62: 955– 965.
PubMed
PMC
Newell EW, Sigal N, Bendall SC, Nolan GP and Davis MM, Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. Immunity 2012. 36: 142– 152.
PubMed
PMC
Newell EW, Sigal N, Nair N, Kidd BA, Greenberg HB and Davis MM, Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization. Nat. Biotechnol 2013. 31: 623– 629.
PubMed
PMC
Wong MT, Ong DE, Lim FS, Teng KW, McGovern N, Narayanan S, Ho WQ et al., A high-dimensional atlas of human T cell diversity reveals tissue-specific trafficking and cytokine signatures. Immunity 2016. 45: 442– 456.
PubMed
Zunder ER, Lujan E, Goltsev Y, Wernig M and Nolan GP, A continuous molecular roadmap to iPSC reprogramming through progression analysis of single-cell mass cytometry. Cell Stem Cell 2015. 16: 323– 337.
PubMed
PMC
Gaudilliere B, Fragiadakis GK, Bruggner RV, Nicolau M, Finck R, Tingle M, Silva J et al., Clinical recovery from surgery correlates with single-cell immune signatures. Sci. Transl. Med 2014. 6: 255ra131.
PubMed
PMC
Nair N, Mei HE, Chen SY, Hale M, Nolan GP, Maecker HT, Genovese M et al., Mass cytometry as a platform for the discovery of cellular biomarkers to guide effective rheumatic disease therapy. Arthritis Res. Ther 2015. 17: 127.
PubMed
PMC
Mingueneau M, Boudaoud S, Haskett S, Reynolds TL, Nocturne G, Norton E, Zhang X et al., Cytometry by time-of-flight immunophenotyping identifies a blood Sjogren’s signature correlating with disease activity and glandular inflammation. J. Allergy Clin. Immunol 2016. 137: 1809– 1821, e1812.
PubMed
Pejoski D, Tchitchek N, Rodriguez Pozo A, Elhmouzi-Younes J, Yousfi-Bogniaho R, Rogez-Kreuz C, Clayette P et al., Identification of vaccine-altered circulating B cell phenotypes using mass cytometry and a two-step clustering analysis. J. Immunol 2016. 196: 4814– 4831.
PubMed
Leipold MD, Ornatsky O, Baranov V, Whitfield C and Nitz M, Development of mass cytometry methods for bacterial discrimination. Anal. Biochem 2011. 419: 1– 8.
PubMed
Guo Y, Baumgart S, Stärk HJ, Harms H and Müller S, Mass Cytometry for Detection of Silver at the Bacterial Single Cell Level. Front Microbiol. 2017. 8: 1326.
PubMed
PMC
Yang YS, Atukorale PU, Moynihan KD, Bekdemir A, Rakhra K, Tang L, Stellacci F et al., High-throughput quantitation of inorganic nanoparticle biodistribution at the single-cell level using mass cytometry. Nat Commun. 2017. 8: 14069.
PubMed
PMC
Abdelrahman AI, Ornatsky O, Bandura D, Baranov V, Kinach R, Dai S, Thickett SC et al., Metal-containing polystyrene beads as standards for mass cytometry. J. Anal. Atom. Spectrom 2010. 25: 260– 268.
PubMed
PMC
Leipold MD, Newell EW and Maecker HT, Multiparameter phenotyping of human PBMCs using mass cytometry. In Shaw A (Ed.), Immunosenescence. Methods in Molecular Biology, vol 1343. Humana Press, New York, NY: 2015, pp. 81– 95.
PubMed
PMC
Chester C and Maecker HT, Algorithmic tools for mining high-dimensional cytometry data. J. Immunol 2015. 195: 773– 779.
PubMed
PMC
Diggins KE, Ferrell PB Jr. and Irish JM, Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data. Methods 2015. 82: 55– 63.
PubMed
PMC
Mair F, Hartmann FJ, Mrdjen D, Tosevski V, Krieg C and Becher B, The end of gating? An introduction to automated analysis of high dimensional cytometry data. Eur. J. Immunol 2016. 46: 34– 43.
PubMed
Saeys Y, Gassen SV and Lambrecht BN, Computational flow cytometry: helping to make sense of high-dimensional immunology data. Nat. Rev. Immunol 2016. 16: 449– 462.
PubMed
Cosma A, A time to amaze, a time to settle down, and a time to discover. Cytometry A 2015. 87: 795– 796.
PubMed
Giesen C, Wang HA, Schapiro D, Zivanovic N, Jacobs A, Hattendorf B, Schuffler PJ et al., Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nat. Methods 2014. 11: 417– 422.
PubMed
Angelo M, Bendall SC, Finck R, Hale MB, Hitzman C, Borowsky AD, Levenson RM et al., Multiplexed ion beam imaging of human breast tumors. Nat. Med 2014. 20: 436– 442.
PubMed
PMC
Chang Q, Ornatsky OI, Siddiqui I, Loboda A, Baranov VI and Hedley DW, Imaging Mass Cytometry. Cytometry A 2017. 91: 160– 169.
PubMed
Mei HE, Leipold MD and Maecker HT, Platinum-conjugated antibodies for application in mass cytometry. Cytometry A 2016. 89: 292– 300.
PubMed
Tricot S, Meyrand M, Sammicheli C, Elhmouzi-Younes J, Corneau A, Bertholet S, Malissen M et al., Evaluating the efficiency of isotope transmission for improved panel design and a comparison of the detection sensitivities of mass cytometer instruments. Cytometry A 2015. 87: 357– 368.
PubMed
Rahman AH, Tordesillas L and Berin MC, Heparin reduces nonspecific eosinophil staining artifacts in mass cytometry experiments. Cytometry A 2016. 89: 601– 607.
PubMed
PMC
Schulz AR, Stanislawiak S, Baumgart S, Grützkau A and Mei HE, Silver nanoparticles for the detection of cell surface antigens in mass cytometry. Cytometry Part A 2017. 91: 25– 33.
PubMed
Lin W, Hou Y, Lu Y, Abdelrahman AI, Cao P, Zhao G, Tong L et al., A high-sensitivity lanthanide nanoparticle reporter for mass cytometry: Tests on microgels as a proxy for cells. Langmuir 2014. 30: 3142– 3153.
PubMed
PMC
Tong L, Lu E, Pichaandi J, Zhao G and Winnik MA, Synthesis of uniform NaLnF4 (Ln: Sm to Ho) nanoparticles for mass cytometry. J. Phys. Chem. C 2016. 120: 6269– 6280.
Baumgart S, Schulz AR, Peddinghaus A, Stanislawiak S, Gillert S, Hirseland H, Krauthäuser S et al. Dual-labelled antibodies for flow and mass cytometry: A new tool for cross-platform comparison and enrichment of target cells for mass cytometry. Eur J Immunol. 2017. 8: 1377– 1385.
PubMed
Leipold MD and Maecker HT, Mass cytometry: Protocol for daily tuning and running cell samples on a CyTOF mass cytometer. J. Vis. Exp 2012. 69: e4398.
PubMed
PMC
Finck R, Simonds EF, Jager A, Krishnaswamy S, Sachs K, Fantl W, Pe’er D et al., Normalization of mass cytometry data with bead standards. Cytometry A 2013. 83: 483– 494.
PubMed
PMC
Bodenmiller B, Zunder ER, Finck R, Chen TJ, Savig ES, Bruggner RV, Simonds EF et al., Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators. Nat. Biotechnol 2012. 30: 858– 867.
PubMed
PMC
Mei HE, Leipold MD, Schulz AR, Chester C and Maecker HT, Barcoding of live human peripheral blood mononuclear cells for multiplexed mass cytometry. J. Immunol 2015. 194: 2022– 2031.
PubMed
PMC
Zunder ER, Finck R, Behbehani GK, Amir el AD, Krishnaswamy S, Gonzalez VD, Lorang CG et al., Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm. Nat. Protoc 2015. 10: 316– 333.
PubMed
PMC
Brodin P, Jojic V, Gao T, Bhattacharya S, Angel CJ, Furman D, Shen-Orr S et al., Variation in the human immune system is largely driven by non-heritable influences. Cell 2015. 160: 37– 47.
PubMed
PMC
Baumgart S, Peddinghaus A, Schulte-Wrede U, Mei HE and Grützkau A, OMIP-034: Comprehensive immune phenotyping of human peripheral leukocytes by mass cytometry for monitoring immunomodulatory therapies. Cytometry Part A 2016. 91: 34– 38.
PubMed
Nicholas KJ, Greenplate AR, Flaherty DK, Matlock BK, Juan JS, Smith RM, Irish JM et al., Multiparameter analysis of stimulated human peripheral blood mononuclear cells: A comparison of mass and fluorescence cytometry. Cytometry A 2016. 89: 271– 280.
PubMed
PMC
Behbehani GK, Bendall SC, Clutter MR, Fantl WJ and Nolan GP, Single-cell mass cytometry adapted to measurements of the cell cycle. Cytometry A 2012. 81: 552– 566.
PubMed
PMC
Frei AP, Bava FA, Zunder ER, Hsieh EW, Chen SY, Nolan GP and Gherardini PF, Highly multiplexed simultaneous detection of RNAs and proteins in single cells. Nat. Methods 2016. 13: 269– 275.
PubMed
PMC
Edgar LJ, Vellanki RN, Halupa A, Hedley D, Wouters BG and Nitz M, Identification of hypoxic cells using an organotellurium tag compatible with mass cytometry. Angew. Chem 2014. 53: 11473– 11477.
PubMed
Ornatsky OI, Lou X, Nitz M, Schafer S, Sheldrick WS, Baranov VI, Bandura DR et al., Study of cell antigens and intracellular DNA by identification of element-containing labels and metallointercalators using inductively coupled plasma mass spectrometry. Anal. Chem 2008. 80: 2539– 2547.
PubMed
Fienberg HG, Simonds EF, Fantl WJ, Nolan GP and Bodenmiller B, A platinum-based covalent viability reagent for single-cell mass cytometry. Cytometry A 2012. 81: 467– 475.
PubMed
PMC
Leipold MD and Maecker HT, Phenotyping of live human PBMC using CyTOFTM mass cytometry. Bio-Protocol 2015. 5: e1382.
PubMed
PMC
Horowitz A, Strauss-Albee DM, Leipold M, Kubo J, Nemat-Gorgani N, Dogan OC, Dekker CL et al., Genetic and environmental determinants of human NK cell diversity revealed by mass cytometry. Sci. Transl. Med 2013. 5: 208ra145.
PubMed
PMC
Recktenwald D and Radbruch A (Eds.), Cell separation methods and applications. Marcel Dekker Inc., New York/Basel/Hong Kong, 1998.
Miltenyi S and Pflueger E, High gradient magnetic cell sorting. In Radbruch A (Ed.), Flow cytometry and sorting. Springer-Verlag, Berlin/Heidelberg, 1992, pp. 141– 152.
Ruffert C, Magnetic bead—Magic bullet (review). Micromachines 2016. 7: 21.
PubMed
PMC
McCloskey KE, Chalmers JJ and Zborowski M, Magnetic cell separation: Characterization of magnetophoretic mobility. Anal. Chem 2003. 75: 6868– 6874.
PubMed
Boyum A, Isolation of leucocytes from human blood. Further observations. Methylcellulose, dextran, and ficoll as erythrocyteaggregating agents. Scand. J. Clin. Lab. Invest. Suppl 1968. 97: 31– 50.
PubMed
Boyum A, Isolation of lymphocytes, granulocytes and macrophages. Scand. J. Immunol 1976. Suppl 5: 9– 15.
PubMed
Yeo C, Saunders N, Locca D, Flett A, Preston M, Brookman P, Davy B et al., Ficoll-Paque versus Lymphoprep: A comparative study of two density gradient media for therapeutic bone marrow mononuclear cell preparations. Regen. Med 2009. 4: 689– 696.
PubMed
Boyum A, Brincker FH, Martinsen I, Lea T and Lovhaug D, Separation of human lymphocytes from citrated blood by density gradient (NycoPrep) centrifugation: Monocyte depletion depending upon activation of membrane potassium channels. Scand. J. Immunol 2002. 56: 76– 84.
PubMed
Kuhns DB, Priel DA, Chu J and Zarember KA, Isolation and functional analysis of human neutrophils. Curr. Protoc. Immunol 2015. 111: 7.23.1– 7.23.16.
PubMed
PMC
Maqbool M, Vidyadaran S, George E and Ramasamy R, Optimisation of laboratory procedures for isolating human peripheral blood derived neutrophils. Med. J. Malaysia 2011. 66: 296– 299.
PubMed
Bruyninckx WJ and Blancquaert AM, Isolation of horse mononuclear cells, especially of monocytes, on Isopaque-Ficoll neutral density gradient. Vet. Immunol. Immunopathol 1983. 4: 493– 504.
PubMed
Pertoft H, Fractionation of cells and subcellular particles with Percoll. J. Biochem. Biophys. Methods 2000. 44: 1– 30.
PubMed
Yu L, Warner P, Warner B, Recktenwald D, Yamanishi D, Guia A and Ghetti A, Whole blood leukocytes isolation with microfabricated filter for cell analysis, Cytometry 2011. 79A: 1009– 1015.
PubMed
Higuchi A, Wang C-T, Ling Q-D, Lee HH-C, Suresh Kumar S, Chang Y, Alarfaj AA et al., A hybrid-membrane migration method to isolate high-purity adipose-derived stem cells from fat tissues. Sci. Rep 2015. 5: 10217.
PubMed
PMC
Huang LR, Cox EC, Austin RH and Sturm JC, Continuous particle separation through deterministic lateral displacement. Science 2004. 304: 987– 990.
PubMed
Davis JA, Inglis DW, Morton KJ, Lawrence DA, Huang LR, Chou SY, Sturm JC et al., Deterministic hydrodynamics: Taking blood apart, Proc. Nat. Acad. Sci 2008. 103: 14779– 14784.
PubMed
PMC
Loutherback K, D’Silva1 J, Liu L, Wu A, Austin RH and Sturm JC, Deterministic separation of cancer cells from blood at 10 mL/min. AIP Adv. 2012. 2: 042107.1– 042107.7.
PubMed
PMC
D’Silva J, Austin H and Sturm C, Inhibition of clot formation in deterministic lateral displacement arrays for processing large volumes of blood for rare cell capture. Lab Chip 2015. 15: 2240– 2247.
PubMed
PMC
Laurell T, Petersson F and Nilsson A, Chip integrated strategies for acoustic separation and manipulation of cells and particles. Chem. Soc. Rev 2007. 36: 492– 506.
PubMed
Dykes J, Lenshof A, Åstrand-Grundström I-B, Laurell T and Scheding S, Efficient removal of platelets from peripheral blood progenitor cell products using a novel micro-chip based acoustophoretic platform. PLoS ONE 2011. 6: e23074.
PubMed
PMC
Pribush A, Meyerstein D and Meyerstein N, Kinetics of erythrocyte swelling and membrane hole formation in hypotonic media. BBA-Biomembrane 2002. 1558: 119– 132.
PubMed
Tiirikainen MI, Evaluation of red blood cell lysing solutions for the detection of intracellular antigens by flow cytometry. Cytometry 1995. 20: 341– 348.
PubMed
Wysocki LJ and Sato VL, Panning for lymphocytes: A method for cell selection. Proc. Natl. Acad. Sci. U S A 1978. 75: 2844– 2848.
PubMed
PMC
Weiner MS, Bianco C and Nussenzweig V, Enhanced binding of neuraminidase-treated sheep erythrocytes to human T lymphocytes. Blood 1973. 42: 939– 946.
PubMed
Indiviri F, Huddlestone J, Pellegrino MA and Ferroni S, Isolation of human T lymphocytes: Comparison between wool filtration and rosetting with neuraminidase (VCN) and 2-aminoethylisothiouronium (AET)-treated sheep red blood cells. J. Immunol. Methods 1980. 34: 107– 112.
PubMed
Esser C, Historical and useful methods of preselection and preparative scale cell sorting. In Recktenwald D and Radbruch A (Eds.), Cell separation methods and applications. Marcel Dekker Inc., New York/Basel/Hong Kong, 1998, pp. 1– 14.
Lepe-Zuniga JL, Zigler JS and Gery I, Toxicity of light-exposed Hepes media. J. Immunol. Methods 1987. 103: 145.
PubMed
Cowan CM and Basu S Heng BC, Comparison of enzymatic and non-enzymatic means of dissociating adherent monolayers of mesenchymal stem cells. Biol. Proced Online 2009. 11: 161– 169.
PubMed
PMC
Wiesman U, Segregating cells – Proteases in tissue culture. In Sterchi EE and Stöcker W (Eds.), Proteolytic enzymes: tools and targets. Springer, Berlin/Heidelberg, 1999, pp. 298– 311.
Stovel R,T, The influence of particles on jet breakoff. J Histochem Cytochem 1977. 25: 813– 820.
PubMed
Houtz B, Trotter J and Sasaki D, Tips on Cell Preparation for Flow Cytometric Analysis and Sorting. BD FACService Technotes 2004. 9.
Holmes KL, Fontes B, Hogarth P, Konz R, Monard S, Pletcher CH Jr., Wadley RB et al., International Society for the Advancement of Cytometry cell sorter biosafety standards. Cytometry Part A 2014. 85: 434– 453.
PubMed
PMC
Fu L-M, Yang R-J, Lin C-H, Pan Y-J and Gwo-Bin L, Electrokinetically driven micro flow cytometers with integrated fiber optics for on-line cell/particle detection. Anal. Chim. Acta 2004. 507: 163– 169.
Telleman P, Larsen UD, Philip J, Blankenstein G, and Wolff A, Cell Sorting in Microfluidic Systems. In Harrison D. Jed and Berg A. den (Eds.). Micro total analysis systems ‘98. Springer, Netherlands, 1998, pp. 39– 44.
Wang X, Chen S, Kong M, Wang Z, Costa KD, Li RA and Sun D, Enhanced cell sorting and manipulation with combined optical tweezer and microfluidic chip technologies. Lab Chip 2011. 11: 3656– 3662.
PubMed
Bhagat AA, Bow H, Hou HW, Tan SJ, Han J and Lim CT, Microfluidics for cell separation. Med. Biol. Eng. Comput 2010. 48: 999– 1014.
PubMed
Chapman GV, Instrumentation for flow cytometry. J. Immunol. Methods 2000. 243: 3– 12.
PubMed
Abate AR, Agresti JJ and Weitz DA, Microfluidic sorting with high-speed single-layer membrane valves. Appl. Phys. Lett 2010. 96: 203509.
Shemesh J, Bransky A, Khoury M and Levenberg S, Advanced microfluidic droplet manipulation based on piezoelectric actuation. Biomed. Microdevices 2010. 12: 907– 914.
PubMed
Chen CH, Cho SH, Tsai F, Erten A and Lo YH, Microfluidic cell sorter with integrated piezoelectric actuator. Biomed. Microdevices 2009. 11: 1223– 1231.
PubMed
PMC
Wang MM, Tu E, Raymond DE, Yang JM, Zhang H, Hagen N, Dees B et al., Microfluidic sorting of mammalian cells by optical force switching. Nature Biotechnology 2005. 23: 83– 87.
PubMed
Roederer M, Distributions of autofluorescence after compensation: Be panglossian, fret not. Cytometry A 2016. 89: 398– 402.
PubMed
Szalóki G and Goda K, Compensation in multicolor flow cytometry. Cytometry A 2015. 87: 982– 985.
PubMed
Novo D, Grégori G and Rajwa B, Generalized unmixing model for multispectral flow cytometry utilizing nonsquare compensation matrices. Cytometry A 2013. 83: 508– 520.
PubMed
PMC
Nguyen R, Perfetto S, Mahnke YD, Chattopadhyay P and Roederer M, Quantifying spillover spreading for comparing instrument performance and aiding in multicolor panel design. Cytometry A 2013. 83: 306– 315.
PubMed
PMC
Lee JA, Spidlen J, Boyce K, Cai J, Crosbie N, Dalphin M, Furlong J et al., MIFlowCyt: The minimum information about a Flow Cytometry Experiment. Cytometry A 2008. 73: 926– 930.
PubMed
PMC
Tung JW, Parks DR, Moore WA and Herzenberg LA, New approaches to fluorescence compensation and visualization of FACS data. Clinical Immunology 2004. 110: 277– 283.
PubMed
BD Cytometer Setup and Tracking Application Guide V3.0, BD Biosciences, San Jose, USA, 2013.
Wood J and Hoffman R, Evaluating fluorescence sensitivity on flow cytometers: An overview. Cytometry 1998. 33: 256– 259.
PubMed
Wood J, Fundamental flow cytometer properties govering sensitivity and resolution. Cytometry 1998. 33: 260– 266.
PubMed
Hoffman RA, Standardization, calibration, and control in flow cytometry. Curr. Protoc. Cytom 2005. 32: 1.3.1– 1.3.21.
PubMed
Wood JCS, Establishing and maintaining system linearity. Curr. Prot. Cytom 2009. 47: 1.4.1– 1.4.14.
PubMed
Jett JH, Martin JC and Habbersett RC, Techniques for flow cytometer alignment. Curr. Protoc. Cytom 2009. 50: 1.10.1– 1.10.7.
PubMed
Perfetto SP, Chattopadhyay PK, Wood J, Nguyen R, Ambrozak D, Hill JP and Roederer M, Q and B values are critical measurements required for inter-instrument standardization and development of multicolor flow cytometry staining panels. Cytometry 2014. 85: 1037– 1048.
PubMed
Perfetto SP, Ambrozak D, Nguyen R, Chattopadhyay P and Roederer M, Quality assurance for polychromatic flow cytometry. Nat. Prot 2006. 1: 1522– 1530.
PubMed
Steen HB, Noise, sensitivity, and resolution of flow cytometers. Cytometry 1992. 13: 822– 830.
PubMed
Friend M, Franklin GB and Quinn B, An LED pulser for measuring photomultiplier linearity. Nucl. Instr. And Meth. A 2012. 676, 66– 69.
BD FACSCanto II flow cytometer reference manual, BD Biosciences, San Jose, USA, 2006.
MACSQuant instrument user manual, V6, Miltenyi Biotec, Bergisch Gladbach, Germany, 2015.
CyFlow Cube 6 instrument operating manual, Partec GmbH, Germany, 2012.
Attune NxT acoustic focusing cytometer user guide, Life Technologies, USA part of Thermo Fisher Scientific, 2015.
Gallios flow cytometer instructions for use, Beckman Coulter, Brea, USA, 2009.
Flow cell care & maintenance; Feb
2011, Precision Cells, Inc. http://ezinearticles.com/?Flow-Cytometry—Flow-Cell-Care-and-Maintenance&id=5898431
A Guide to Absolute Counting Using the BD AccuriTM C6 Flow Cytometer, BD Biosciences, Technical Bulletin, Jan. 2012.
BD FACSDiva Software v 8.0 Reference Manual, BD Biosciences, San Jose, USA, 2004.
Roederer M, Compensation in flow cytometry. Curr. Protoc. Cytom 2002. 22: 1.14.1–1.14.20.
PubMed
Biburger M, Trenkwald I and Nimmerjahn F, Three blocks are not enough–Blocking of the murine IgG receptor FcgammaRIV is crucial for proper characterization of cells by FACS analysis. Eur. J. Immunol 2015. 45: 2694– 2697.
PubMed
Maecker HT, Frey T, Nomura LE and Trotter J, Selecting fluorochrome conjugates for maximum sensitivity. Cytometry A 2004. 62: 169– 173.
PubMed
Nüsse M, Beisker W, Kramer J, Miller BM, Schreiber GA, Viaggi S, Weller EM et al., Measurement of Micronuclei by Flow Cytometry. Methods Cell Biol. 1994. 42: 149– 158.
PubMed
Hengst J, Theorell J, Deterding K, Potthoff, Dettmer A, Ljunggren HG, Wedemeyer H and Björkström NK, High-resolution determination of human immune cell signatures from fine-needle liver aspirates. Eur. J. Immunol 2015. 45: 2154– 2157.
PubMed
Mucci I, Legitimo A, Compagnino M, Consolini R, Migliaccio P, Metelli MR and Scatena F, The methodological approach for the generation of human dendritic cells from monocytes affects the maturation state of the resultant dendritic cells. Biologicals 2009. 37: 288– 296.
PubMed
Delirezh N and Shojaeefar E, Phenotypic and functional comparison between flask adherent and magnetic activated cell sorted monocytes derived dendritic cells. Iran. J. Immunol 2012. 9: 98– 108.
PubMed
E1 E, Subasic A, Strasser A, Augustin D, Thalhammer R, Steiner I and Schwarzinger I, Lysis matters: Red cell lysis with FACS Lyse affects the flow cytometric enumeration of circulating leukemic blasts. J. Immunol. Methods 2013. 390: 127– 132.
PubMed
Lindahl PE, Principle of a counter-streaming centrifuge for the separation of particles of different sizes. Nature 1948. 161: 648– 649.
PubMed
McEwen CR, Stallard RW and Juhos ET, Separation of biological particles by centrifugal elutriation. Anal. Biochem 1968. 23: 369– 377.
PubMed
Pretlow TG 2nd and Pretlow TP, Centrifugal elutriation (counterstreaming centrifugation) of cells. Cell Biophys. 1979. 1: 195– 210.
PubMed
www.biologydiscussion.com/cell-biology/8-methods-involved-in-separation-of-whole-cells-with-diagram/3494
.
Ferrone S, Cooper NR, Pellegrino MA and Reisfeld RA, Interaction of histocompatibility (HL-A) antibodies and complement with synchronized human lymphoid cells in continuous culture. J. Exp. Med 1973. 137: 55– 68.
PubMed
PMC
Lustig H and Bianco C, Antibody-mediated cell cytotoxicity in a defined system: regulation by antigen, antibody, and complement. J. Immunol 1976. 116: 253– 260.
PubMed
www.pluriselect.com
.
www.miltenyibiotec.com
.
www.thermofisher.com/de/de/home/brands/product-brand/dynal.html
.
www.bdbiosciences.com/us/reagents/research/magnetic-cell-separation/other-species-cell-separation-reagents/cell-separation-magnet/p/552311
.
Alsayed H, Owaidah T and Al Rawas F, Validation of a modified cryopreservation method for leukemic blasts for flow cytometry assessment. Hematol. Oncol. Stem Cell Ther 2008. 1: 94– 97.
PubMed
Johnson S, Nguyen V and Coder D, Assessment of cell viability. Curr. Protoc. Cytom 2013. 64: 9.2.1– 9.2.26.
PubMed
Perfetto SP, Chattopadhyay PK, Lamoreaux L, Nguyen R, Ambrozak D, Koup RA and Roederer M, Amine-reactive dyes for dead cell discrimination in fixed samples. Curr. Protoc. Cytom 2013. 53: 9.34.1– 9.34.14.
PubMed
PMC
Combrier E, Métézeau P, Ronot X, Gachelin H and Adolphe M, Flow cytometric assessment of cell viability: A multifaceted analysis. Cytotechnology 1989. 2: 27– 37.
PubMed
Reardon AJ, Elliott JA and McGann LE, Fluorescence as an alternative to light-scatter gating strategies to identify frozen-thawed cells with flow cytometry. Cryobiology 2014. 69: 91– 99.
PubMed
Chow C, Hedley D, Grom P, Magari R, Jacobberger JW and Shankey TV, Whole Blood Fixation and Permeabilization Protocol with Red Blood Cell Lysis for Flow Cytometry of Intracellular Phosphorylated Epitopes in Leukocyte Populations. Cytometry 2005. 67: 4– 17.
PubMed
Woost PC, Solchaga LA, Meyerson HJ, Shankey TV, Goolsby CL and Jacobberger JW, High-resolution kinetics of cytokine signaling in human CD34/CD117-positive cells in unfractionated bone marrow. Blood 2011. 117: e131– e141.
PubMed
PMC
Marvin J, Swiminathan S, Kraker G, Chadburn A, Jacobberger JW and Goolsby C, Normal bone marrow signal-transduction profiles: A requisite for enhanced detection of signaling dysregulations in AML. Blood 2011. 117: e120– e130.
PubMed
PMC
Shankey TV, Forman MF, Scibelli P, Cobb J, Smith CM, Mills R, Holdiway K et al., An Optimized Whole Blood Method for Flow Cytometric Measurement of ZAP-70 Protein Expression in Chronic Lymphocytic Leukemia. Cytometry 2006. 70: 259– 269.
PubMed
Jacobberger JW, Sramkowski RM, Frisa PS, Peng Ye P, Gottlieb MA, Hedley DW, Shankey TV et al., Immunoreactivity of STAT5 phosphorylated on tyrosine as a cell-based measure of Bcr/Abl kinase activity. Cytometry 2003. 54: 75– 88.
PubMed
Krutzik PO and Nolan GP, Fluorescent cell barcoding in flow cytometry allows high-throughput drug screening and signaling profiling. Nat. methods 2006. 3: 361– 368.
PubMed
Behbehani GK, Thom C, Zunder ER, Finck R, Gaudilliere B, Fragiadakis GK, Fantl WJ et al., Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining. Cytometry A 2014. 85: 1011– 1019.
PubMed
PMC
Lai L, Ong R, Li J and Albani S, A CD45-based barcoding approach to multiplex mass-cytometry (CyTOF). Cytometry A 2015. 87: 369– 374.
PubMed
PMC
Akkaya B, Miozzo P, Holstein AH, Shevach EM, Pierce SK and Akkaya M, A simple, versatile antibody-based barcoding method for flow cytometry. J. Immunol 2016. 197: 2027– 2038.
PubMed
PMC
Catena R, Ozcan A, Zivanovic N and Bodenmiller B, Enhanced multiplexing in mass cytometry using osmium and ruthenium tetroxide species. Cytometry A 2016. 89: 491– 497.
PubMed
Zivanovic N, Jacobs A and Bodenmiller B, A practical guide to multiplexed mass cytometry. Curr. Top. Microbiol. Immunol 2013. 377: 95– 109.
PubMed
Yamanaka YJ, Szeto GL, Gierahn TM, Forcier TL, Benedict KF, Brefo MS, Lauffenburger DA et al., Cellular barcodes for efficiently profiling single-cell secretory responses by microengraving. Anal. Chem 2012. 84: 10531– 10536.
PubMed
PMC
Krutzik PO, Clutter MR, Trejo A and Nolan GP, Fluorescent cell barcoding for multiplex flow cytometry. Curr. Protoc. Cytom 2011. 55: 6.31.1– 6.31.15.
PubMed
PMC
Krutzik PO, Crane JM, Clutter MR and Nolan GP, High-content single-cell drug screening with phosphospecific flow cytometry. Nat. Chem. Biol 2008. 4: 132– 142.
PubMed
Frischbutter S, Schultheis K, Patzel M, Radbruch A and Baumgrass R, Evaluation of calcineurin/NFAT inhibitor selectivity in primary human Th cells using bar-coding and phospho-flow cytometry. Cytometry A 2012. 81: 1005– 1011.
PubMed
Simard C, Cloutier M and Neron S, Feasibility study: Phosphospecific flow cytometry enabling rapid functional analysis of bone marrow samples from patients with multiple myeloma. Cytometry Part B, Clin. Cytom 2014. 86: 139– 144.
PubMed
Simard C, Cloutier M and Neron S, Rapid determination of IL-6 specific activity by flow cytometry. J. Immunol. Methods 2014. 415: 63– 65.
PubMed
Spurgeon BE, Aburima A, Oberprieler NG, Tasken K and Naseem KM, Multiplexed phosphospecific flow cytometry enables large-scale signaling profiling and drug screening in blood platelets. J. Thromb. Haemost 2014. 12: 1733– 1743.
PubMed
Bernardo SM, Allen CP, Waller A, Young SM, Oprea T, Sklar LA and Lee SA, An automated high-throughput cell-based multiplexed flow cytometry assay to identify novel compounds to target Candida albicans virulence-related proteins. PLoS One 2014. 9: e110354.
PubMed
PMC
Clark MA, Goheen MM, Spidale NA, Kasthuri RS, Fulford A and Cerami C, RBC barcoding allows for the study of erythrocyte population dynamics and P. falciparum merozoite invasion. PLoS One 2014. 9: e101041.
PubMed
PMC
Becher B, Schlitzer A, Chen J, Mair F, Sumatoh HR, Teng KW, Low D et al., High-dimensional analysis of the murine myeloid cell system. Nat. Immunol 2014. 15: 1181– 1189.
PubMed
McCarthy RL, Mak DH, Burks JK and Barton MC, Rapid monoisotopic cisplatin based barcoding for multiplexed mass cytometry. Sci. Rep 2017. 7: 3779.
PubMed
PMC
Irish JM, Myklebust JH, Alizadeh AA, Houot R, Sharman JP, Czerwinski DK, Nolan GP et al., B-cell signaling networks reveal a negative prognostic human lymphoma cell subset that emerges during tumor progression. Proc. Natl. Acad. Sci. U. S. A 2010. 107: 12747– 12754.
PubMed
PMC
Lujan E, Zunder ER, Ng YH, Goronzy IN, Nolan GP and Wernig M, Early reprogramming regulators identified by prospective isolation and mass cytometry. Nature 2015. 521: 352– 356.
PubMed
PMC
Chattopadhyay PK and Roederer M, Cytometry: Today’s technology and tomorrow’s horizons. Methods 2012. 57: 251– 258.
PubMed
PMC
Roederer M, Spectral compensation for flow cytometry: Visualization artifacts, limitations, and caveats. Cytometry 2001. 45, 194– 205.
PubMed
Perfetto SP and Roederer M, Increased immunofluorescence sensitivity using 532 nm laser excitation. Cytometry A 2007. 71, 73– 79.
PubMed
Chattopadhyay PK, Melenhorst JJ, Ladell K, Gostick E, Scheinberg P, Barrett AJ, Wooldridge L et al., Techniques to improve the direct ex vivo detection of low frequency antigen-specific CD8+ T cells with peptide-major histocompatibility complex class I tetramers. Cytometry A 2008. 73: 1001– 1009.
PubMed
PMC
Lugli E, Troiano L and Cossarizza A, Investigating T cells by polychromatic flow cytometry. In Libero G (Ed.) T cell protocols. Methods in Molecular Biology, vol 514. Humana Press, New York, NY: 2009, pp. 47– 63.
PubMed
Ferraresi R, Troiano L, Roat E, Lugli E, Nemes E, Nasi M, Pinti M et al., Essential requirement of reduced glutathione (GSH) for the anti-oxidant effect of the flavonoid quercetin. Free Radic. Res 2005. 39: 1249– 1258.
PubMed
Mahnke YD and Roederer M, Optimizing a multicolor immunophenotyping assay. Clin. Lab. Med 2007. 27: 469– 485.
PubMed
PMC
Lugli E, Gattinoni L, Roberto A, Mavilio D, Price DA, Restifo NP and Roederer M, Identification, isolation and in vitro expansion of human and nonhuman primate T stem cell memory cells. Nat. Protoc 2013. 8: 33– 42.
PubMed
PMC
Lugli E, Zanon V, Mavilio D and Roberto A FACS analysis of memory T lymphocytes. In Lugli E (Ed.) T-cell differentiation. Methods in Molecular Biology, vol 1514. Humana Press, New York, NY, 2017.
PubMed
Boehm T, McCurley N, Sutoh Y, Schorpp M, Kasahara M and Cooper MD, VLR-based adaptive immunity. Annu. Rev. Immunol 2012. 30: 203– 220.
PubMed
PMC
Pancer Z, Amemiya CT, Ehrhardt GR, Ceitlin J, Gartland GL and Cooper MD, Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature 2004. 430: 174– 180.
PubMed
Velikovsky CA, Deng L, Tasumi S, Iyer LM, Kerzic MC, Aravind L, Pancer Z et al., Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen. Nat. Struct. Mol. Biol 2009. 16: 725– 730.
PubMed
PMC
Han BW, Herrin BR, Cooper MD and Wilson IA, Antigen recognition by variable lymphocyte receptors. Science 2008. 321: 1834– 1837.
PubMed
PMC
Herrin BR, Alder MN, Roux KH, Sina C, Ehrhardt GR, Boydston JA, Turnbough CL Jr. et al., Structure and specificity of lamprey monoclonal antibodies. Proc. Natl. Acad. Sci. U. S. A 2008. 105: 2040– 2045.
PubMed
PMC
Yu C, Liu Y, Chan JT, Tong J, Li Z, Shi M, Davani D et al. Identification of human plasma cells with a lamprey monoclonal antibody. JCI Insight. 2016. 1: e84738.
PubMed
PMC
Haas J, Roth S, Arnold K, Kiefer F, Schmidt T, Bordoli L and Schwede T, The protein model portal–a comprehensive resource for protein structure and model information. Database (Oxford) 2013. 2013: bat031.
PubMed
PMC
Alder MN, Rogozin IB, Iyer LM, Glazko GV, Cooper MD and Pancer Z, Diversity and function of adaptive immune receptors in a jawless vertebrate. Science 2005. 310: 1970– 1973.
PubMed
Yu C, Ali S, St-Germain J, Liu Y, Yu X, Jaye DL, Moran MF et al., Purification and identification of cell surface antigens using lamprey monoclonal antibodies. J. Immunol. Methods 2012. 386: 43– 49.
PubMed
PMC
Bøyum A, Løvhaug D, Tresland L and Nordlie EM, Separation of leucocytes: Improved cell purity by fine adjustments of gradient medium density and osmolality. Scand. J. Immunol 1991. 34: 697– 712.
PubMed
Loos H, Blok-Schut B, van Doorn R, Hoksbergen R, Brutel de la Rivière A and Meerhof L, A method for the recognition and separation of human blood monocytes on density gradients. Blood 1976. 48: 731– 742.
PubMed
BD FACSAria user’s guide, BD Biosciences, San Jose, USA, 2006.
Wixforth A, Acoustically driven programmable microfluidics for biological and chemical applications. J. Lab. Automat 2006. 11: 399– 405.
Kaiser T, Raba K, Sickert M, Radbruch A and Scheffold A, Integration of an ultrasonic wave device in a FACS-Aria cell sorter for continuous, non-invasive mixing of cell suspensions. Poster, Budapest, 2008. ISAC congress. 10.13140/RG.2.1.1760.2966
DOI
Radbruch A (Ed.), Flow cytometry and cell sorting, 2nd ed., Springer, Berlin/Heidelberg: 2000.
Freyer JP, Fillak D and Jett JH, Use of xantham gum to suspend large particles during flow cytometric analysis and sorting. Cytometry 1989. 10: 803– 806.
PubMed
Leslie DS, Johnston WW, Daly L, Ring DB, Shpall EJ, Peters WP and Bast RC Jr., Detection of breast carcinoma cells in human bone marrow using fluorescence-activated cell sorting and conventional cytology. Am. J. Clin. Pathol 1990. 94: 8– 13.
PubMed
Frantz CN, Ryan DH, Cheung NV, Duerst RE and Wilbur DC, Sensitive detection of rare metastatic human neuroblastoma cells in bone marrow by two-color immunofluorescence and cell sorting. Prog. Clin. Biol. Res 1988. 271: 249– 262.
PubMed
Ryan DH, Mitchell SJ, Hennessy LA, Bauer KD, Horan PK and Cohen HJ, Improved detection of rare CALLA-positive cells in peripheral blood using multiparameter flow cytometry. J. Immunol. Methods 1984. 74: 115– 128.
PubMed
Visser JW and De Vries P, Identification and purification of murine hematopoietic stem cells by flow cytometry. Methods Cell Biol. 1990. 33: 451– 468.
PubMed
Cory JM, Ohlsson-Wilhelm BM, Brock EJ, Sheaffer NA, Steck ME, Eyster ME and Rapp F, Detection of human immunodeficiency virus-infected lymphoid cells at low frequency by flow cytometry. J. Immunol. Methods 1987. 105: 71– 78.
PubMed
Jensen RH and Leary JF, Mutagenesis as measured by flow cytometry and cell sorting. In Melamed MR, Mendelsohn ML and Lindmo T (Eds.) Flow cytometry and sorting, 2nd ed., Wiley-LISS, NY, 1990.
Cossarizza A and Cousins D, Overcoming challenges in cellular analysis: Multiparameter analysis of rare cells. Science 2015. 347: 443.
Gross HJ, Verwer B, Houck D, Hoffman RA and Recktenwald D, Model study detecting breast cancer cells in peripheral blood mononuclear cells at frequencies as low as 10(−7). Proc. Natl. Acad. Sci. U. S. A 1995. 92: 537– 541.
PubMed
PMC
Donnenberg AD and Donnenberg VS, Rare-event analysis in flow cytometry. Clin. Lab. Med 2007. 27: 627– 652.
PubMed
De Biasi S, Bianchini E, Nasi M, Digaetano M, Gibellini L, Carnevale G, Borghi V et al., Th1 and Th17 pro-inflammatory profile characterizes iNKT cells in virologically suppressed HIV+ patients with low CD4/CD8 ratio. AIDS 2016. 30: 2599– 2610.
PubMed
Duda DG, Cohen KS, Scadden DT and Jain RK, A protocol for phenotypic detection and enumeration of circulating endothelial cells and circulating progenitor cells in human blood. Nat. Protoc 2007. 2: 805– 810.
PubMed
PMC
Mancuso P, Antoniotti P, Quarna J, Calleri A, Rabascio C, Tacchetti C and Braidotti P, Validation of a standardized method for enumerating circulating endothelial cells and progenitors: Flow cytometry and molecular and ultrastructural analyses. Clin. Cancer Res 2009. 15: 267– 273.
PubMed
Van Craenenbroeck EM, Conraads VM, Van Bockstaele DR, Haine SE, Vermeulen K, Van Tendeloo VF and Vrints CJ, Quantification of circulating endothelial progenitor cells: A methodological comparison of six flow cytometric approaches. J. Immunol. Methods 2008. 332: 31– 40.
PubMed
Estes ML, Mund JA, Ingram DA and Case J, Identification of endothelial cells and progenitor cell subsets in human peripheral blood. Curr. Protoc. Cytom 2010. 52: 9.33.1– 9.33.11.
PubMed
De Biasi S, Cerri S, Bianchini E, Gibellini L, Persiani E, Montanari G and Luppi F, Levels of circulating endothelial cells are low in idiopathic pulmonary fibrosis and are further reduced by anti-fibrotic treatments. BMC Med. 2015. 13: 277.
PubMed
PMC
Cox C, Reeder JE, Robinson RD, Suppes SB and Wheeless LL, Comparison of frequency distribution in flow cytometry. Cytometry 1988. 9: 291– 298.
PubMed
Haight FA, Handbook of the Poisson distribution. John Wiley & Sons, New York, 1967.
Roederer M, How many events is enough? Are you positive? Cytometry 2008. 73: 384– 385
PubMed
Perfetto SP, Ambrozak D, Nguyen R, Chattopadhyay PK and Roederer M, Quality assurance for polychromatic flow cytometry using a suite of calibration beads. Nat. Protocols 2012. 7: 2067– 2079.
PubMed
Rockefeller University BD FACSAria2–3 Water-Cooled Sort Collection Integrated Tube Holder 5-15-5-5 | NIH 3D Print Exchange. Available at: http://3dprint.nih.gov/discover/3dpx-002415. (Accessed:
20th April 2016)
Sasaki DT, Tichenor EH, Lopez F, Combs J, Uchida N, Smith CR, Stokdijk W, et al., Development of a clinically applicable high-speed flow cytometer for the isolation of transplantable human hematopoietic stem cells. J. Hematother 1995. 4: 503– 514.
PubMed
Kvistborg P, Gouttefangeas C, Aghaeepour N, Cazaly A, Chattopadhyay PK, Chan C, Eckl J et al., Thinking outside the gate: single-cell assessments in multiple dimensions. Immunity 2015. 42: 591– 592.
PubMed
PMC
Aghaeepour N, Finak G, The FlowCAP Consortium, The DREAM Consortium, Hoos H, Mosmann TR, Brinkman R et al., Critical assessment of automated flow cytometry data analysis techniques. Nat. Methods 2013. 10: 228– 238.
PubMed
PMC
Aghaeepour N, Nikolic R, Hoos HH and Brinkman RR, Rapid cell population identification in flow cytometry data. Cytometry Part A 2011. 79A: 6– 13.
PubMed
PMC
Bashashati A and Brinkman RR, A Survey of Flow Cytometry Data Analysis Methods. Adv. Bioinformatics 2009. 2009: 584603.
PubMed
PMC
Finak G, Bashashati A, Brinkman R and Gottardo R, Merging mixture components for cell population identification in flow cytometry. Adv. Bioinformatics 2009. 2009: 247646.
PubMed
PMC
Mosmann TR, Naim I, Rebhahn J, Datta S, Cavenaugh JS, Weaver JM and Sharma G, SWIFT-scalable clustering for automated identification of rare cell populations in large, high-dimensional flow cytometry datasets, Part 2: Biological evaluation. Cytometry A 2014. 85: 422– 433.
PubMed
PMC
Finak G, Langweiler M, Jaimes M, Malek M, Taghiyar J, Korin Y, Raddassi K et al., Standardizing flow cytometry immunophenotyping analysis from the human immunophenotyping consortium. Sci. Rep 2016. 6: 20686.
PubMed
PMC
Qian Y, Wei C, Eun-Hyung Lee F, Campbell J, Halliley J, Lee JA, Cai J et al., Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data. Cytometry B Clin. Cytom 2010. 78 : S69– S82.
PubMed
PMC
Qiu P, Simonds EF, Bendall SC, Gibbs KD Jr., Bruggner RV, Linderman MD, Sachs K et al., Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat. Biotechnol 2011. 29: 886– 891.
PubMed
PMC
Naim I, Datta S, Rebhahn J, Cavenaugh JS, Mosmann TR and Sharma G, SWIFT-scalable clustering for automated identification of rare cell populations in large, high-dimensional flow cytometry datasets, Part 1: Algorithm design. Cytometry A 2014. 85: 408– 421.
PubMed
PMC
Fletez-Brant K, Spidlen J, Brinkman RR, Roederer M and Chattopadhyay PK, flowClean: Automated identification and removal of fluorescence anomalies in flow cytometry data. Cytometry A 2016. 89: 461– 471.
PubMed
PMC
Finak G, Perez JM, Weng A and Gottardo R, Optimizing transformations for automated, high throughput analysis of flow cytometry data. BMC Bioinformatics 2010. 11: 546.
PubMed
PMC
Finak G, Perez JM and Gottardo R, flowTrans: Parameter optimization for flow cytometry data transformation. R package version 1.24.0 2010.
Hahne F, Khodabakhshi AH, Bashashati A, Wong CJ, Gascoyne RD, Weng AP, Seyfert-Margolis V et al., Per-channel basis normalization methods for flow cytometry data. Cytometry A 2010. 77: 121– 131.
PubMed
PMC
Finak G, Jiang W, Krouse K, Wei C, Sanz I, Phippard D, Asare A et al., High-throughput flow cytometry data normalization for clinical trials. Cytometry A 2014. 85: 277– 286.
PubMed
PMC
Amir el AD, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, Shenfeld DK et al., viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nat. Biotechnol 2013. 31: 545– 552.
PubMed
PMC
Benjamini Y and Hochberg Y, Controlling the false discovery rate—A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol 1995. 57: 289– 300.
Almudevar A, Multiple hypothesis testing: A methodological overview. In Yakovlev A, Klebanov L and Gaile D (Eds.) Statistical methods for microarray data analysis. Methods in Molecular Biology, vol 972. Humana Press, New York, NY: 2013, pp. 37– 55.
PubMed
Rebhahn JA, Roumanes DR, Qi Y, Khan A, Thakar J, Rosenberg A, Lee FE et al., Competitive SWIFT cluster templates enhance detection of aging changes. Cytometry A 2016. 89: 59– 70.
PubMed
PMC
Aghaeepour N, Chattopadhyay PK, Ganesan A, O’Neill K, Zare H, Jalali A, Hoos HH et al., Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays. Bioinformatics 2012. 28: 1009– 1016.
PubMed
PMC
O’Neill K, Aghaeepour N, Špidlen J and Brinkman RR, Flow cytometry bioinformatics. PLoS Comput. Biol 2013. 9: e1003365.
PubMed
PMC
Maecker H, Rinfret A, D’Souza P, Darden J, Roig E, Landry C, Hayes P, et al. Standardization of cytokine flow cytometry assays. BMC Immunol. 2005. 6: 13.
PubMed
PMC
Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN et al., A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes. Cytometry 2016. 89: 16– 21.
PubMed
PMC
Weber LM and Robinson MD, Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data. Cytometry A 2016. 89: 1084– 1096.
PubMed
Finak G, Frelinger J, Jiang W, Newell EW, Ramey J, Davis MM, Kalams SA et al., OpenCyto: An open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis. PLoS Comput. Biol 2014. 10: e1003806.
PubMed
PMC
Malek M, Taghiyar MJ, Chong L, Finak G, Gottardo R and Brinkman RR, flowDensity: Reproducing manual gating of flow cytometry data by automated density-based cell population identification. Bioinformatics 2015. 31: 606– 607.
PubMed
PMC
Naim I, Datta S, Sharma G, Cavenaugh JS and Mosmann TR, Swift: Scalable weighted iterative sampling for flow cytometry clustering. In 2010 IEEE International Conference on acoustics, speech, and signal processing: proceedings. IEEE, Piscataway, NJ: 2010, pp. 509– 512.
Maaten LVD and Hinton G, Visualizing data using t-SNE. J. Mach. Learn. Res 2008. 9: 2579– 2605.
Aghaeepour N, Jalali A, O’Neill K, Chattopadhyay PK, Roederer M, Hoos HH and Brinkman RR, RchyOptimyx: Cellular hierarchy optimization for flow cytometry. Cytometry Part A 2012. 81: 1022– 1030.
PubMed
PMC
O’Neill K, Jalali A, Aghaeepour N, Hoos H and Brinkman RR, Enhanced flowType/RchyOptimyx: A bioconductor pipeline for discovery in high-dimensional cytometry data. Bioinformatics 2014. 30: 1329– 1330.
PubMed
PMC
Tong DL, Ball GR and Pockley AG, gEM/GANN: A multivariate computational strategy for auto-characterizing relationships between cellular and clinical phenotypes and predicting disease progression time using high-dimensional flow cytometry data. Cytometry 2015. 87: 616– 623.
PubMed
Gassen SV, Vens C, Dhaene T, Lambrecht BN and Saeys Y, FloReMi: Flow density survival regression using minimal feature redundancy. Cytometry A 2015. 89: 22– 29.
PubMed
Spidlen J, Barsky A, Breuer K, Carr P, Nazaire MD, Hill BA, Qian Y et al., GenePattern flow cytometry suite. Source Code Biol. Med 2013. 8: 14.
PubMed
PMC
Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T and Scheuermann RH, Automated analysis of flow cytometry data comes of age. Cytometry A 2016. 89: 16– 21.
PubMed
Dean PN and Jett JJ, Mathematical analysis of DNA distributions derived from flow microfluorometry. J. Cell. Biol 1974. 60: 523– 527.
PubMed
PMC
Gray JW, Cell cycle analysis from computer synthesis of deoxyribonucleic acid histograms. J. Histochem. Cytochem 1974. 22: 642– 650.
PubMed
Watson JV, The application of age distribution theory in the analysis of cytofluorimetric DNA-histogram data. Cell Tissue Kinet. 1977. 10: 157– 169.
PubMed
Watson JV, Chambers SH and Smith PJ, A pragmatic approach to the analysis of DNA histograms with a definable G1 peak. Cytometry 1987. 8: 1– 8.
PubMed
Rosenblatt JI, Hokanson JA, McLaughlin SR and Leary JF, Theoretical basis for sampling statistics useful for detecting and isolating rare cells using flow cytometry and cell sorting. Cytometry 1997. 27: 233– 238.
PubMed
Poisson SD, Recherches sur la probabilité des jugements en matière criminelle et en matière civile: précédées des règles générales du calcul des probabilités. Bachelier, Paris, France, 1837.
Gosset WS, The probable error of a mean. Biometrica 1908. 6: 1– 25.
Fisher RA, Statistical methods for research workers. Oliver & Boyd, Edinburgh, U.K., 1925.
Watson JV, Flow cytometry data analysis: basic concepts and statistics, Cambridge University Press, Cambridge, UK, 2005
Fisher RA and Yates F, Statistical tables for biological, medical and agricultural research. Oliver and Boyd, Edinburgh, UK, 1963. p. 86.
Snedecor GW, Statistical methods 4th ed., Iowa State College Press, Ames, Iowa, 1946
Wilcoxon F, Individual comparisons by ranking methods. Biometrics Bull. 1945. 1: 80– 83.
PubMed
Mann HB and Whitney DR, On a test of whether one of two random variables is stochastically larger than the other. Ann. Math. Stat 1947. 18: 50– 60.
Siegel S and Castellón NJ, Non-parametric statistics for the behavioral sciences, 2nd ed McGraw-Hill, New York, 1988, Chapter 6.
Young IT, Proof without prejudice: use of the Kolmogorov-Smirnov test for the analysis of histograms from flow systems and other sources. J. Histochem. Cytochem 1977. 25: 935– 941.
PubMed
Kendall MG, Rank and product-moment correlation. Biometrika 1949. 36: 177– 193.
PubMed
Watson JV, Proof without prejudice revisited: Immunofluorescence histogram analysis using cumulative frequency subtraction plus ratio analysis of means. Cytometry 2001. 43: 55– 68.
PubMed
Melzer S, Zachariae S, Bocsi J, Engel C, Löffler M and Tárnok A, Reference intervals for leukocyte subsets in adults: Results from a population-based study using 10-color flow cytometry. Cytometry B Clin. Cytom 2015. 88: 270– 281.
PubMed
Bocsi J, Melzer S, Dähnert I and Tárnok A, OMIP-023: 10-color, 13 antibody panel for in-depth phenotyping of human peripheral blood leukocytes. Cytometry A 2014. 85: 781– 784.
PubMed
Loeffler M, Engel C, Ahnert P, Alfermann D, Arelin K, Baber R, Beutner F et al., The LIFE-Adult-Study: Objectives and design of a population-based cohort study with 10 000 deeply phenotyped adults in Germany. BMC Public Health 2015. 15: 691.
PubMed
PMC
Moher D, Glasziou P, Chalmers I, Nasser M, Bossuyt PM, Korevaar DA, Graham ID et al., Increasing value and reducing waste in biomedical research: Who’s listening? Lancet 2015. 387: 1573– 1586.
PubMed
Tárnok A, End of year note, again (Redux ad infinitum?). Cytometry A 2015. 87: 1065– 1066.
PubMed
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA et al., Promoting coherent minimum reporting guidelines for biological and biomedical investigations: The MIBBI project. Nat. Biotechnol 2008. 26: 889– 896.
PubMed
PMC
Spidlen J, Breuer K and Brinkman R, Preparing a minimum information about a flow cytometry experiment (miflowcyt) compliant manuscript using the International Society for Advancement of Cytometry (ISAC) FCS file repository (FlowRepository.org). Curr. Prot. Cytom
2012. 61: 10.18.1– 10.18.26.
PubMed
Roederer M and Tárnok A, OMIPs–Orchestrating multiplexity in polychromatic science. Cytometry A 2010. 77: 811– 812.
PubMed
Tárnok A, New Year’s note 2016. Cytometry A 2016. 89: 7– 8.
PubMed
O’Neill K and Brinkman RR, Publishing code is essential for reproducible flow cytometry bioinformatics. Cytometry A 2016. 89: 10– 11.
PubMed
Thomson Reuters. Collaborative Science - Solving the Issues of Discovery, Attribution and Measurement in Data Sharing. 2012. http://wokinfo.com/products_tools/multidisciplinary/dci/collaborative_science_essay.pdf
Piwowar HA and Chapman WW, A review of journal policies for sharing research data. Proceedings ELPUB 2008
Conference on Electronic Publishing, 2008, http://elpub.scix.net/data/works/att/001_elpub2008.content.pdf
Fecher B, Friesike S and Hebing M, What drives academic data sharing? PLoS One 2015. 10: e0118053.
PubMed
PMC
Nicol A, Caruso J and Archambault É, Open data access policies and strategies in the European research area and beyond. Science-Metrix, Inc. Produced for the European Commission DG Research & Innovation, 2013, http://www.science-metrix.com/pdf/SM_EC_OA_Data.pdf
National Institute of Health. NIH Data Sharing Policy. http://grants.nih.gov/grants/policy/data_sharing/
PLOS. PLOS’ New Data Policy: Public Access to Data. http://blogs.plos.org/everyone/2014/02/24/plos-new-data-policy-public-access-data-2/
Chen TJ and Kotecha N, Cytobank: Providing an analytics platform for community cytometry data analysis and collaboration. Curr. Top. Microbiol. Immunol 2014. 377: 127– 157.
PubMed
Kotecha N, Krutzik PO and Irish JM, Web-based analysis and publication of flow cytometry experiments. Curr. Protoc. Cytom 2010. 53: 10.17.1– 10.17.24.
PubMed
PMC
Spidlen J, Breuer K, Rosenberg C, Kotecha N and Brinkman RR, FlowRepository: A resource of annotated flow cytometry datasets associated with peer-reviewed publications. Cytometry A 2012. 81: 727– 731.
PubMed
Kong YM, Dahlke C, Xiang Q, Qian Y, Karp D and Scheuermann RH, Toward an ontology-based framework for clinical research databases. J. Biomed. Inform 2011. 44: 48– 58.
PubMed
PMC
Bhattacharya S, Andorf S, Gomes L, Dunn P, Schaefer H, Pontius J, Berger P et al., ImmPort: Disseminating data to the public for the future of immunology. Immunol. Res 2014. 58: 234– 239.
PubMed
Brusic V, Gottardo R, Kleinstein SH, Davis MM and HIPC steering committee. Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium. Nat. Biotechnol 2014. 32: 146– 148.
PubMed
PMC
Van der Maaten L and Hinton G, Visualizing data using t-SNE. J. Machine Learn. Res 2008. 9: 2579– 2605.
el-AD A, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, Shenfeld DK et al., viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nat. Biotechnol 2013. 31: 545– 52.
PubMed
PMC
U.S. Department of Health & Human Services. Summary of the HIPAA Privacy Rule. http://www.hhs.gov/sites/default/files/privacysummary.pdf
Zimmermann J, Hübschmann T, Schattenberg F, Schumann J, Durek P, Riedel R and Friedrich M, High-resolution microbiota flow cytometry reveals dynamic colitis-associated changes in fecal bacterial composition. Eur J Immunol. 2016. 46: 1300– 1303.
PubMed
PMC
Boyd WA, Smith MV and Freedman JH, Caenorhabditis elegans as a model in developmental toxicology. Methods Cell Biol. 2012. 889: 15– 24.
PubMed
PMC
Steffen A, Ludwig B and Krautz C, Bornstein S, Solimena M, Functional assessment of automatically sorted pancreatic islets using large particle flow cytometry. Islets 2011. 3: 267– 270.
PubMed
PMC
Li CY, Wood DK, Huang JH and Bhatia SN, Flow-based pipeline for systematic modulation and analysis of 3D tumor microenviornments. Lab Chip 2013. 13: 1969– 1978.
PubMed
PMC
Karp JM, Yeh J, Eng G, Fukuda J, Blumling J, Suh KY, Cheng J et al., Controlling size, shape and homogeneity of embryoid bodies using poly(ethylene glycol) microwells. Lab Chip 2007. 7: 786– 794.
PubMed
Coder DM, Assessment of cell viability. Curr. Protoc. Cytom 2001. 15: 9.2.1– 9.2.14.
PubMed
Perfetto SP, Chattopadhyay PK, Lamoreaux L, Nguyen R, Ambrozak D, Koup RA and Roederer M, Amine=reactive dyes: An effective tool to discriminate live and dead cells in polychromatic flow cytometry. J. Immunol. Methods 2006. 313: 199– 208.
PubMed
Zuba-Surman EK, Kucia M and Ratajczak MZ, Decoding the dots: The ImageStream system (ISS) as a novel and powerful tool for flow cytometric analysis. Cent. Eur. J. Biol 2008. 3: 1– 10.
Vindelov LL, Christensen IJ and Nissen NI, A detergent-trypsin method for the preparation of nuclei for flow cytometric DNA analysis. Cytometry 1983. 3: 323– 327.
PubMed
Hedley DW, Friedlander ML, Taylor IW, Rugg CA and Musgrove EA, Method for analysis of cellular DNA content of paraffin-embedded pathological material using flow cytometry. J. Histochem. Cytochem 1983. 31: 1333– 1335.
PubMed
Baerlocher GM, Vulto I and Lansdorp PM, Flow cytometry and FISH to measure the average length of telomeres (flow FISH). Nat. Protoc 2006. 1: 2365– 2376.
PubMed
Cerveira J, Begum J, Di Marco Barros R, ven der Veen A and Filby A, An imaging flow-cytometry-based approach to measuring the spatiotemporal calcium mobilization in activated T cells. J. Immunol. Methods 2015. 423: 120– 130.
PubMed
Degtyarev M, Reichelt M and Lin K, Novel quantitative autophagy analysis by organelle flow cytometry after cell sonication. PLoS One 2014. 9: e87707.
PubMed
PMC
Poot M, Gibson LL and Singer VL, Detection of apoptosis in live cells by MitoTracker CMXRos and SYTO dye flow cytometry. Cytometry 1997. 27: 358– 364.
PubMed
Poot M, Analysis of intracellular organelles by flow cytometry or microscopy. Curr. Protoc. Cytom 2001. 14: 9.4.1– 9.4.24.
PubMed
Chikte S, Panchal N and Warnes G, Use of LysoTracker dyes: A flow cytometric study of autophagy. Cytometry A 2014. 85: 169– 178.
PubMed
Lu Q, Haragopal H, Slepchenko KG, Stork C and Li YV, Intracellular zinc distribution in mitochondria, ER and the Golgi apparatus. Int. J. Physiol. Pathophysiol. Pharmacol 2016. 8: 35– 43.
PubMed
PMC
Warnes G, Flow cytometric assays for the study of autophagy. Methods 2015. 82: 21– 28.
PubMed
Salvioli S, Ardizzoni A, Franceschi C and Cossarizza A, JC-1, but not DiOC6(3) or rhodamine 123, is a reliable fluorescent probe to assess AW changes in intact cells: implications for studies on mitochondrial functionality during apoptosis. FEBS Lett. 1997. 411: 77– 82.
PubMed
Bailey S and Macardle PJ, Flow cytometric comparison of Indo-1 to Fluo-3 and Fura Red excited with low power lasers for detecting Ca(2+) flux. J. Immunol. Methods 2006. 311: 220– 225.
PubMed
Leverrier S, Bergamaschi D and Ghali L, Role of HPV E6 proteins in preventing UVB-induced release of pro-apoptotic factors from the mitochondria. Apoptosis 2007. 12: 549– 560.
PubMed
Dolezel J, Vrana J, Safar J, Bartos J, Kubalakova M and Simkova H, Chromosomes in the flow to simplify genome analysis. Funct. Integr. Genomics 2012. 12: 397– 416.
PubMed
PMC
Davies DC, Monard SP and Young BD, Chromosome analysis and sorting by flow cytometry, 3rd ed. In Ormerod MG (Ed.) Flow cytometry: a practical approach. Oxford University Press, Oxford, UK, 2000.
Gribble SM, Ng BL, Prigmore E, Fitzgerald T and Carter NP, Array painting: A protocol for the rapid analysis of aberrant chromosomes using DNA microarrays. Nat. Protoc 2009. 4: 1722– 1736.
PubMed
PMC
Scheffold A, Radbruch A and Assenmacher M, Phenotyping and separation of leukocyte populations based on affinity labelling. Immunol. Infect 2002. 32: 23– 58.
Bradbury AM and Plückthun A, Antibodies: Validate recombinants once. Nature 2015. 520: 295.
PubMed
Jain R and Gray DH, Isolation of thymic epithelial cells and analysis by flow cytometry. Curr Protoc Immunol. 2014. 107: 3.26.1– 3.26.15.
PubMed
Grützkau A, Krüger-Krasagakes S, Baumeister H, Schwarz C, Kögel H, Welker P, Lippert U et al., Synthesis, storage, and release of vascular endothelial growth factor/vascular permeability factor (VEGF/VPF) by human mast cells: Implications for the biological significance of VEGF206. Mol. Biol. Cell 1998. 9: 875– 884.
PubMed
PMC
Worthington Biochemical Corporation tissue dissociation guide, Worthington Biochemical Corporation, 2008.
Wong KHK, Sandlin RD, Carey TR, Miller KL, Shank AT, Oklu R, Maheswaran S et al., The role of physical stabilization in whole blood preservation. Sci. Rep 2016. 6: 21023.
PubMed
PMC
Plate MM, Louzao R, Steele PM, Greengrass V, Morris LM, Lewis J, Barnett D et al., Evaluation of the blood stabilizers TransFix and Cyto-Chex BCT for low-cost CD4 T-cell methodologies. Viral Immunol. 2009. 22: 329– 332.
PubMed
Thomas TE, Miller CL and Eaves CJ, Purification of hematopoietic stem cells for further biological study. Methods 1999. 17: 202– 218.
PubMed
Van der Toom EE, Verdone JE, Gorin MA and Pienta KJ, Technical challenges in the isolation and analysis of circulating tumor cells. Oncotarget 2016. 7: 62754– 62766.
PubMed
PMC
Donnenberg VS and Donnenberg AD, Identification, rare-event detection and analysis of dendritic cell subsets in bronchio-alveolar lavage fluid and peripheral blood by flow cytometry. Front. Biosci 2003. 8: s1175– s1180.
PubMed
Bacher P and Scheffold A, New technologies for monitoring human antigen-specific T cells and regulatory T cells by flow-cytometry. Curr. Opin. Pharmacol 2015. 23: 17– 24.
PubMed
Hayashida K, Bartlett AH, Chen Y and Park PW, Molecular and cellular mechanisms of ectodomain shedding. Anat. Rec. (Hoboken) 2010. 293: 925– 937.
PubMed
PMC
Berhanu D, Mortari F, De Rosa SC and Roederer M, Optimized lymphocyte isolation methods for analysis of chemokine receptor expression. J. Immunol. Methods 2003. 279: 199– 207.
PubMed
Kivisäkk P, Liu Z, Trebst C, Tucky B, Wu L, Stine J, Mack M et al., Flow cytometric analysis of chemokine receptor expression on cerebrospinal fluid leukocytes. Methods 2003. 29: 319– 325.
PubMed
Liu H, Rhodes M, Wiest DL and Vignali DA, On the dynamic of TCR:CD3 complex cell surface expression and downmodulation. Immunity 2000. 192: 1529– 1534.
PubMed
Mueller A, Kelly E and Strange PG, Pathways for internalization and recycling of the chemokine receptor CCR5. Blood 2002. 99: 785– 791.
PubMed
Campana S, De Pasquale C, Carrega P, Ferlazzo G and Bonaccorsi I, Cross-dressing: An alternative mechanism for antigen presentation. Immunol. Lett 2015. 168: 349– 354.
PubMed
Anselmo A, Mazzon C, Borroni EM, Bonecchi R, Graham GJ and Locati M, Flow cytometry applications for the analysis of chemokine receptor expression and function. Cytometry A 2014. 85: 292– 301.
PubMed
Fan J, Nishanian P, Breen EC, McDonald M and Fahey JL, Cytokine gene expression in normal human lymphocytes in response to stimulation. Clin. Diagn. Lab. Immunol 1998. 5: 335– 340.
PubMed
PMC
Löhning M, Richter A and Stamm T, Establishment of memory for IL-10 expression in developing T helper 2 cells requires repetitive IL-4 costimulation and does not impair proliferation. Proc. Natl. Acad. Sci. USA 2003. 100: 12307– 12312.
PubMed
PMC
Sanos SL, Vonarbourg C, Mortha A and Diefenbach A, Control of epithelial cell function by interleukin-22-producing RORgammat+ innate lymphoid cells. Immunology 2011. 132: 453– 465.
PubMed
PMC
Nussbaum JC, Van Dyken SJ and von Moltke J, Type 2 innate lymphoid cells control eosinophil homeostasis. Nature 2013. 502: 245– 248.
PubMed
PMC
Robinson D, Shibuya K, Mui A, Zonin F, Murphy E, Sana T, Hartley SB et al., IGIF does not drive Th1 development but synergizes with IL-12 for interferon-gamma production and activates IRAK and NFκB. Immunity 1997. 7: 571– 581.
PubMed
Sattler A, Wagner U, Rossol M, Sieper J, Wu P, Krause A, Schmidt WA et al., Cytokine-induced human IFN-γ-secreting effector-memory Th cells in chronic autoimmune inflammation. Blood 2009. 113: 1948– 1956.
PubMed
Zimmermann J, Radbruch A and Chang HD, A Ca(2+) concentration of 1.5 mM, as present in IMDM but not in RPMI, is critical for maximal response of Th cells to PMA/ionomycin. Eur. J. Immunol 2015. 45: 1270– 1273.
PubMed
PMC
Lohning M, Richter A, Stamm T, Hu-Li J, Assenmacher M, Paul WE and Radbruch A, Establishment of memory for IL-10 expression in developing T helper 2 cells requires repetitive IL-4 costimulation and does not impair proliferation. Proc. Natl. Acad. Sci. U. S. A 2003. 100: 12307– 12312.
PubMed
PMC
Assenmacher M, Schmitz J and Radbruch A, Flow cytometric determination of cytokines in activated murine T helper lymphocytes: Expression of interleukin-10 in interferon-gamma and in interleukin-4-expressing cells. Eur. J. Immunol 1994. 24: 1097– 1101.
PubMed
Lorenz H, Hailey DW, Wunder C and Lippincott-Schwartz J, The fluorescence protease protection (FPP) assay to determine protein localization and membrane topology. Nat. Protoc 2006. 1: 276– 279.
PubMed
Francis G, Kerem Z, Makkar HP and Becker K, The biological action of saponins in animal systems: A review. Br. J. Nutr 2002. 88: 587– 605.
PubMed
Moller BK, Andresen BS, Christensen EI and Petersen CM, Surface membrane CD4 turnover in phorbol ester stimulated T-lymphocytes. Evidence of degradation and increased synthesis. FEBS Lett. 1990. 276: 59– 62.
PubMed
Boyer C, Auphan N, Luton F, Malburet JM, Barad M, Bizozzero JP, Reggio H and Schmitt-Verhulst AM, T cell receptor/CD3 complex internalization following activation of a cytolytic T cell clone: Evidence for a protein kinase C-independent staurosporine-sensitive step. Eur. J. Immunol 1991. 21: 1623– 1634.
PubMed
Grupillo M, Lakomy R, Geng X, Styche A, Rudert WA, Trucco M and Fan Y, An improved intracellular staining protocol for efficient detection of nuclear proteins in YFP-expressing cells. Biotechniques 2011. 51: 417– 420.
PubMed
Heinen AP, Wanke F, Moos S, Attig S, Luche H, Pal PP, Budisa N et al., Improved method to retain cytosolic reporter protein fluorescence while staining for nuclear proteins. Cytometry A 2014. 85: 621– 627.
PubMed
Robinson JP, Patsekin V, Holdman C, Ragheb K, Sturgis J, Fatig R, Avramova LV et al., High-throughput secondary screening at the single-cell level. J. Lab. Automat 2012. 18: 85– 98.
PubMed
PMC
Robinson JP, Durack G and Kelley S, An innovation in flow cytometry data collection & analysis producing a correlated multiple sample analysis in a single file. Cytometry 1991. 12: 82– 90.
PubMed
Newell E, Bendall S, Hong D, Lewis D, Nolan G and Davis M, Surveying the Influenza-specific Cytotoxic T Cell Response in Humans and Mice Using Mass-cytometry (CyTOF) and Combinatorial Tetramer Staining. Clin. Immunol 2010. 135: S104– S104.
Rajwa B, Venkatapathi M, Ragheb K, Banada PP, Hirleman ED, Lary T and Robinson JP Automated classification of bacterial particles in flow by multiangle scatter measurement and a support vector machine classifier. Cytometry Part A 2008. 73A: 369– 379.
PubMed
Costa ES, Pedreira CE, Barrena S, Lecrevisse Q, Flores J, Quijano S, Almeida J, Del CG-M et al., Automated pattern-guided principal component analysis vs expert-based immunophenotypic classification of B-cell chronic lymphoproliferative disorders: A step forward in the standardization of clinical immunophenotyping. Leukemia 2010. 24: 1927– 1933.
PubMed
PMC
Dundar M, Akova F, Yerebakan HZ and Rajwa B, A non-parametric Bayesian model for joint cell clustering and cluster matching: Identification of anomalous sample phenotypes with random effects. BMC Bioinformatics 2014. 15: 314.
PubMed
PMC
Bagwell CB, Hunsberger BC, Herbert DJ, Munson ME, Hill BL, Bray CM and Preffer FI, Probability state modeling theory. Cytometry A 2015. 87: 646– 660.
PubMed
Robinson JP, Rajwa B, Patsekin V and Davisson VJ, Computational Analysis of High Throughput flow cytometry data. Expert Opin. Drug Deliv 2012. 7: 679– 693.
PubMed
PMC
Fulton RJ, McDade RL, Smith PL, Kienker LJ and Kettman JR Jr. Advanced multiplexed analysis with the FlowMetrix system. Clin. Chem 1997. 43: 1749– 1756.
PubMed
Robinson JP, Patsekin V, Gregori G, Rajwa B and Jones J, Multispectral flow cytometry: Next generation tools for automated classification. Microsc. Microanal 2005. 11: 2– 3.
Altman JD, Moss PA and Goulder PJ, Phenotypic analysis of antigen-specific T lymphocytes. Science 1996. 274: 94– 96.
PubMed
Newell EW, Klein LO, Yu W and Davis MM, Simultaneous detection of many T-cell specificities using combinatorial tetramer staining. Nat. Methods 2009. 6: 497– 499.
PubMed
PMC
Hadrup SR, Bakker AH, Shu CJ, Andersen RS, van Veluw J, Hombrink P, Castermans E et al., Parallel detection of antigen-specific T-cell responses by multidimensional encoding of MHC multimers. Nat. Methods 2009. 6: 520– 526.
PubMed
Toebes M, Coccoris M, Bins A, Rodenko B, Gomez R, Nieuwkoop NJ, van de Kasteele W et al., Design and use of conditional MHC class I ligands. Nat. Med 2006. 12: 246– 251.
PubMed
Kvistborg P, Philips D, Kelderman S, Hageman L, Ottensmeier C, Joseph-Pietras D, Welters MJ et al., Anti-CTLA-4 therapy broadens the melanoma-reactive CD8+ T cell response. Sci. Transl. Med 2014. 6: 254ra128.
PubMed
Kvistborg P, Shu CJ, Heemskerk B, Fankhauser M, Thrue CA, Toebes M, van Rooij N et al., TIL therapy broadens the tumor-reactive CD8(+) T cell compartment in melanoma patients. Oncoimmunology 2012. 1: 409– 418.
PubMed
PMC
Rizvi NA, Hellmann MD, Snyder A, Kvistborg P, Makarov V, Havel JJ, Lee W et al., Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 2015. 348: 124– 128.
PubMed
PMC
van Rooij N, van Buuren MM, Philips D, Velds A, Toebes M, Heemskerk B, van Dijk LJ et al., Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma. J. Clin. Oncol 2013. 31: e439– e442.
PubMed
PMC
van Buuren MM, Calis JJ and Schumacher TN, High sensitivity of cancer exome-based CD8 T cell neo-antigen identification. Oncoimmunology 2014. 3: e28836.
PubMed
PMC
Schneck JP, Monitoring antigen-specific T cells using MHC-Ig dimers. Immunol. Invest 2000. 29: 163– 169.
PubMed
Selin LK, Vergilis K, Welsh RM and Nahill SR, Reduction of otherwise remarkably stable virus-specific cytotoxic T lymphocyte memory by heterologous viral infections. J. Exp. Med 1996. 183: 2489– 2499.
PubMed
PMC
Martinez RJ, Andargachew R, Martinez HA and Evavold BD, Low-affinity CD4+ T cells are major responders in the primary immune response. Nat. Commun 2016. 7: 13848.
PubMed
PMC
Engelhardt KR, Richter K, Baur K, Staeheli P and Hausmann J, The functional avidity of virus-specific CD8+ T cells is down-modulated in Borna disease virus-induced immunopathology of the central nervous system. Eur. J. Immun 2005. 35: 487– 497.
PubMed
Xiao Z, Mescher MF and Jameson SC, Detuning CD8 T cells: Down-regulation of CD8 expression, tetramer binding, and response during CTL activation. J. Exp. Med 2007. 204: 2667– 2677.
PubMed
PMC
Bakker AH and Schumacher TN, MHC multimer technology: Current status and future prospects. Curr. Opin. Immun 2005. 17: 428– 433.
PubMed
McMichael AJ and O’Callaghan CA, A new look at T cells. J. Exp. Med 1998. 187: 1367– 1371.
PubMed
PMC
Ogg GS, King AS, Dunbar PR and McMichael AJ, Isolation of HIV-1-specific cytotoxic T lymphocytes using human leukocyte antigen-coated beads. AIDS 1999. 13: 1991– 1993.
PubMed
Luxembourg AT, Borrow P, Teyton L, Brunmark AB, Peterson PA and Jackson MR, Biomagnetic isolation of antigen-specific CD8+ T cells usable in immunotherapy. Nat. Biotechnol 1998. 16: 281– 285.
PubMed
Xu XN, Purbhoo MA, Chen N, Mongkolsapaya J, Cox JH, Meier UC, Tafuro S et al., A novel approach to antigen-specific deletion of CTL with minimal cellular activation using alpha3 domain mutants of MHC class I/peptide complex. Immunity 2001. 14: 591– 602.
PubMed
Whelan JA, Dunbar PR, Price DA, Purbhoo MA, Lechner F, Ogg GS, Griffiths G et al., Specificity of CTL interactions with peptide-MHC class I tetrameric complexes is temperature dependent. J. Immunol 1999. 163: 4342– 4348.
PubMed
Daniels MA and Jameson SC, Critical role for CD8 in T-cell receptor binding and activation by peptide/major histocompatibility complex multimers. J. Exp. Med 2000. 191: 335– 346.
PubMed
PMC
Knabel M, Franz TJ, Schiemann M, Wulf A, Villmow B, Schmidt B, Bernhard H et al., Reversible MHC multimer staining for functional isolation of T-cell populations and effective adoptive transfer. Nat. Med 2002. 8: 631– 637.
PubMed
Stemberger C, Dreher S, Tschulik C, Piossek C, Bet J, Yamamoto TN, Schiemann M et al., Novel serial positive enrichment technology enables clinical multiparameter cell sorting. PLoS One 2012. 7: e35798.
PubMed
PMC
Nauerth M, Weissbrich B, Knall R, Franz T, Dossinger G, Bet J, Paszkiewicz PJ et al., TCR-ligand koff rate correlates with the protective capacity of antigen-specific CD8+ T cells for adoptive transfer. Sci. Transl. Med 2013. 5: 192ra87.
PubMed
PMC
Haanen JB, Wolkers MC, Kruisbeek AM and Schumacher TN, Selective expansion of cross-reactive CD8(+) memory T cells by viral variants. J. Exp. Med 1999. 190: 1319– 1328.
PubMed
PMC
Lund-Johansen F, Bjerknes R and Laerum OD, Flow cytometric assay for the measurement of human bone marrow phenotype, function and cell cycle. Cytometry 1990. 11: 610– 616.
PubMed
Vollers SS and Stern LJ, Class II major histocompatibility complex tetramer staining: progress, problems, and prospects. Immunology 2008. 123: 305– 313.
PubMed
PMC
James EA, LaFond R, Durinovic-Bello I and Kwok W, Visualizing antigen specific CD4+ T cells using MHC class II tetramers. J. Vis. Exp 2009. 25: e1167.
PubMed
PMC
Scheffold A, Busch DH and Kern F, Detection of Atigen-specific T-Cells using Major Histocompatibility Complex Multimers or Functional Parameters. In Sack U, Tárnok A and Rothe G (Eds). Cellular diagnostics: basics, methods and clinical applications of flow cytometry. Karger, Basel, 2009, pp. 476– 502.
Chattopadhyay PK, Gierahn TM, Roederer M and Love JC, Single-cell technologies for monitoring immune systems. Nat. Immunol 2014. 15: 128– 135.
PubMed
PMC
Chattopadhyay PK and Roederer M, A mine is a terrible thing to waste: High content, single cell technologies for comprehensive immune analysis. Am. J. Transplant 2015. 15: 1155– 1161.
PubMed
Newell EW and Davis MM, Beyond model antigens: High-dimensional methods for the analysis of antigen-specific T cells. Nat. Biotechnol 2014. 32: 149– 157.
PubMed
PMC
Bacher P and Scheffold A, Flow-cytometric analysis of rare antigen-specific T cells. Cytometry A 2013. 83: 692– 701.
PubMed
Kutscher S, Dembek CJ, Deckert S, Russo C, Körber N, Bogner JR, Geisler F et al., Overnight resting of PBMC changes functional signatures of antigen specific T- cell responses: Impact for immune monitoring within clinical trials. PLoS One 2013. 8: e76215.
PubMed
PMC
Owen RE, Sinclair E, Emu B, Heitman JW, Hirschkorn DF, Epling CL, Tan QX et al., Loss of T cell responses following long-term cryopreservation. J. Immunol. Methods 2007. 326: 93– 115.
PubMed
PMC
Romer PS, Berr S, Avota E, Na SY, Battaglia M, ten Berge I, Einsele H et al., Preculture of PBMCs at high cell density increases sensitivity of T-cell responses, revealing cytokine release by CD28 superagonist TGN1412. Blood 2011. 118: 6772– 6782.
PubMed
Wegner J, Hackenberg S, Scholz CJ, Chuvpilo S, Tyrsin D, Matskevich AA, Grigoleit GU et al., High-density preculture of PBMCs restores defective sensitivity of circulating CD8 T cells to virus- and tumor-derived antigens. Blood 2015. 126: 185– 194.
PubMed
Lamoreaux L, Roederer M and Koup R, Intracellular cytokine optimization and standard operating procedure. Nat. Protoc 2006. 1: 1507– 1516.
PubMed
Maecker HT, Rinfret A, D’Souza P, Darden J, Roig E, Landry C, Hayes P, et al., Standardization of cytokine flow cytometry assays. BMC Immunol. 2005. 6: 13.
PubMed
PMC
Brosterhus H, Brings S, Leyendeckers H, Manz RA, Miltenyi S, Radbruch A, Assenmacher M, and Schmitz J, Enrichment and detection of live antigen-specific CD4(+) and CD8(+) T cells based on cytokine secretion. Eur. J. Immunol 1999. 29: 4053– 4059.
PubMed
Manz R, Assenmacher M, Pfluger E, Miltenyi S and Radbruch A, Analysis and sorting of live cells according to secreted molecules, relocated to a cell-surface affinity matrix. Proc. Natl. Acad. Sci. U. S. A 1995. 92: 1921– 1925.
PubMed
PMC
Jung T, Schauer U, Heusser C, Neumann C and Rieger C, Detection of intracellular cytokines by flow cytometry. J. Immunol. Methods 1993. 159: 197– 207.
PubMed
O’Neil-Andersen NJ and Lawrence DA, Differential modulation of surface and intracellular protein expression by T cells after stimulation in the presence of monensin or brefeldin A. Clin. Diagn. Lab. Immunol 2002. 9: 243– 250.
PubMed
PMC
Bacher P, Schink C, Teutschbein J, Kniemeyer O, Assenmacher M, Brakhage AA and Scheffold A, Antigen-reactive T cell enrichment for direct, high-resolution analysis of the human naive and memory T helper cell repertoire. J. Immunol 2013. 190: 3967– 3976.
PubMed
Chattopadhyay PK, Yu J and Roederer M, A live-cell assay to detect antigen-specific CD4+ T cells with diverse cytokine profiles. Nat. Med 2005. 11: 1113– 1117.
PubMed
Frentsch M, Arbach O, Kirchhoff D, Moewes B, Worm M, Rothe M, Scheffold A et al., Direct access to CD4+ T cells specific for defined antigens according to CD154 expression. Nat. Med 2005. 11: 1118– 1124.
PubMed
Bacher P, Heinrich F, Stervbo U, Nienen M, Vahldieck M, Iwert C, Vogt K, et al., Regulatory T cell specificity directs tolerance versus allergy against aeroantigens in humans. Cell 2016. 167: 1067– 1078.
PubMed
Bacher P, Kniemeyer O, Schonbrunn A, Sawitzki B, Assenmacher M, Rietschel E, Steinbach A, et al., Antigen-specific expansion of human regulatory T cells as a major tolerance mechanism against mucosal fungi. Mucosal. Immunol 2014. 7: 916– 928.
PubMed
Schoenbrunn A, Frentsch M, Kohler S, Keye J, Dooms H, Moewes B, Dong J, et al., A Converse 4–1BB and CD40 ligand expression pattern delineates activated regulatory T cells (Treg) and conventional T cells enabling direct isolation of alloantigen-reactive natural Foxp3+ Treg. J. Immunol 2012. 189: 5985– 5994.
PubMed
Seddiki N, Cook L, Hsu DC, Phetsouphanh C, Brown K, Xu Y, Kerr SJ et al., Human antigen-specific CD4+ CD25+ CD134+ CD39+ T cells are enriched for regulatory T cells and comprise a substantial proportion of recall responses. Eur. J. Immunol 2014. 44: 1644– 1661.
PubMed
Cook L, Munier CML, Seddiki N, van Bockel D, Ontiveros N, Hardy MY, Gillies JK, et al., Circulating gluten-specific FOXP3+CD39+ regulatory T cells have impaired suppressive function in patients with celiac disease. J. Allergy Clin. Immunol 2017. 10.1016/j.jaci.2017.02.015
PubMed
DOI
Wehler TC, Karg M, Distler E, Konur A, Nonn M, Meyer RG, Huber C, et al., Rapid identification and sorting of viable virus-reactive CD4(+) and CD8(+) T cells based on antigen-triggered CD137 expression. J. Immunol. Methods 2008. 339: 23– 37.
PubMed
Wölfl M, Kuball J, Eyrich M, Schlegel PG and Greenberg PD, Use of CD137 to study the full repertoire of CD8+ T cells without the need to know epitope specificities. Cytometry A 2008. 73: 1043– 1049.
PubMed
PMC
Wölfl M, Kuball J, Ho WY, Nguyen H, Manley TJ, Bleakley M, and Greenberg PD, Activation-induced expression of CD137 permits detection, isolation, and expansion of the full repertoire of CD8+ T cells responding to antigen without requiring knowledge of epitope specificities. Blood 2007. 110: 201– 210.
PubMed
PMC
Reddy M, Eirikis E, Davis C, Davis HM and Prabhakar U, Comparative analysis of lymphocyte activation marker expression and cytokine secretion profile in stimulated human peripheral blood mononuclear cell cultures: an in vitro model to monitor cellular immune function. J. Immunol. Methods 2004. 293: 127– 142.
PubMed
Zaunders JJ, Munier ML, Seddiki N, Pett S, Ip S, Bailey M, Xu Y et al., High levels of human antigen-specific CD4+ T cells in peripheral blood revealed by stimulated coexpression of CD25 and CD134 (OX40). J. Immunol 2009. 183: 2827– 2836.
PubMed
Redmond WL, Ruby CE and Weinberg AD, The role of OX40-mediated co-stimulation in T-cell activation and survival. Crit. Rev. Immunol 2009. 29: 187– 201.
PubMed
PMC
Betts MR, Brenchley JM, Price DA, De Rosa SC, Douek DC, Roederer M, and Koup RA, Sensitive and viable identification of antigen-specific CD8+ T cells by a flow cytometric assay for degranulation. J. Immunol. Methods 2003. 281: 65– 78.
PubMed
Betts MR and Koup RA, Detection of T-cell degranulation: CD107a and b. Methods Cell Biol. 2004. 75: 497– 512.
PubMed
Day CL, Seth NP, Lucas M, Appel H, Gauthier L, Lauer GM, Robbins GK, et al., Ex vivo analysis of human memory CD4 T cells specific for hepatitis C virus using MHC class II tetramers. J Clin Invest 2003. 112: 831– 842.
PubMed
PMC
Miltenyi S, Muller W, Weichel W and Radbruch A, High gradient magnetic cell separation with MACS. Cytometry 1990. 11: 231– 238.
PubMed
Moon JJ, Chu HH, Pepper M, McSorley SJ, Jameson SC, Kedl RM, and Jenkins MK, Naive CD4(+) T cell frequency varies for different epitopes and predicts repertoire diversity and response magnitude. Immunity 2007. 27: 203– 213.
PubMed
PMC
Obar JJ, Khanna KM and Lefrancois L, Endogenous naive CD8+ T cell precursor frequency regulates primary and memory responses to infection. Immunity 2008. 28: 859– 869.
PubMed
PMC
Krensky AM, The HLA system, antigen processing and presentation. Kidney Int. Suppl 1997. 58: S2– S7.
PubMed
Kern F, Faulhaber N, Frommel C, Khatamzas E, Prosch S, Schonemann C, Kretzschmar I, et al., Analysis of CD8 T cell reactivity to cytomegalovirus using protein-spanning pools of overlapping pentadecapeptides. Eur. J. Immunol 2000. 30: 1676– 1682.
PubMed
Maecker HT, Dunn HS, Suni MA, Khatamzas E, Pitcher CJ, Bunde T, Persaud N, et al., Use of overlapping peptide mixtures as antigens for cytokine flow cytometry. J. Immunol. Methods 2001. 255: 27– 40.
PubMed
Eberl G, Renggli J, Men Y, Roggero MA, Lopez JA and Corradin G, Extracellular processing and presentation of a 69-mer synthetic polypetide to MHC class I-restricted T cells. Mol. Immunol 1999. 36: 103– 112.
PubMed
Sherman LA, Burke TA and Biggs JA, Extracellular processing of peptide antigens that bind class I major histocompatibility molecules. J. Exp. Med 1992. 175: 1221– 1226.
PubMed
PMC
Macey MG, Flow cytometry: Principles and applications. Totowa, NJ, Humana Press, 2007.
Alanio C, Lemaitre F, Law HK, Hasan M and Albert ML, Enumeration of human antigen-specific naive CD8+ T cells reveals conserved precursor frequencies. Blood 2010. 115: 3718– 3725.
PubMed
Campion SL, Brodie TM, Fischer W, Korber BT, Rossetti A, Goonetilleke N, McMichael AJ, et al., Proteome-wide analysis of HIV-specific naive and memory CD4(+) T cells in unexposed blood donors. J. Exp. Med 2014. 211: 1273– 1280.
PubMed
PMC
Geiger R, Duhen T, Lanzavecchia A and Sallusto F, Human naive and memory CD4+ T cell repertoires specific for naturally processed antigens analyzed using libraries of amplified T cells. J. Exp. Med 2009. 206: 1525– 1534.
PubMed
PMC
Su LF, Kidd BA, Han A, Kotzin JJ and Davis MM, Virus-specific CD4(+) Memory-Phenotype T cells are abundant in unexposed adults. Immunity 2013. 38: 373– 383.
PubMed
PMC
Nauerth M, Stemberger C, Mohr F, Weissbrich B, Schiemann M, Germeroth L, and Busch DH, Flow cytometry-based TCR-ligand Koff -rate assay for fast avidity screening of even very small antigen-specific T cell populations ex vivo. Cytometry A 2016. 89: 816– 825.
PubMed
Pockley AG, Foulds GA, Oughton JA, Kerkvliet NI and Multhoff G, Immune cell phenotyping using flow cytometry. Curr. Protoc. Toxicol 2015. 66: 18.8.1– 18.8.34.
PubMed
Darzynkiewicz Z, Halicka HD, Zhao H, Analysis of cellular DNA content by flow and laser scanning cytometry. Adv. Exp. Med. Biol 2010. 676: 137– 147.
PubMed
PMC
Hamelik RM and Krishan A, Click-iT assay with improved DNA distribution histograms. Cytometry Part A 2009. 75: 862– 865.
PubMed
Krishan A and Hamelik RM, Click-iT proliferation assay with improved DNA histograms. Curr. Protoc. Cytom 2010. 52: 7.36.1– 7.36.7.
PubMed
Lyons AB and Parish CR, Determination of lymphocyte division by flow cytometry. J. Immunol. Methods 1994. 171: 131– 137.
PubMed
Wersto RP, Chrest FJ, Leary JF, Morris C, Stetler-Stevenson MA and Gabrielson E, Doublet discrimination in DNA cell-cycle analysis. Cytometry 2001. 46: 296– 306.
PubMed
Hopkinson K, Williams EA, Fairburn B, Forster S, Flower DJ, Saxton JM et al., A MitoTracker® green-based flow cytometric assay for natural killer cell activity: Variability, the influence of platelets and a comparison of analytical approaches. Exp. Hematol 2007. 35: 350– 357.
PubMed
Edward R and Dimmick I, Compensation-free dead cell exclusion: Multi-beam excitation of the far-red DNA binding viability dye DRAQ7.(TECH2P. 873). J. Immunol 2014. 192: 135.4.
Pieper IL, Radley G, Chan CH, Friedmann Y, Foster G and Thornton CA, Quantification methods for human and large animal leukocytes using DNA dyes by flow cytometry. Cytometry Part A 2016. 89: 565– 574.
PubMed
van Engeland M, Nieland LJ, Ramaekers FC, Schutte B and Reutelingsperger CP, Annexin V-affinity assay: A review on an apoptosis detection system based on phosphatidylserine exposure. Cytometry 1998. 31: 1– 9.
PubMed
Gehrmann M, Doss BT, Wagner M, Zettlitz KA, Kontermann RE, Foulds G et al., A novel expression and purification system for the production of enzymatic and biologically active human granzyme B. J. Immunol. Methods 2011. 371: 8– 17.
PubMed
Gehrmann M, Stangl S, Kirschner A, Foulds GA, Sievert W, Doss BT et al., Immunotherapeutic targeting of membrane HSP70-expressing tumors using recombinant human granzyme B. PLoS One 2012. 7: e41341.
PubMed
PMC
Shalini S, Dorstyn L, Dawar S and Kumar S, Old, new and emerging functions of caspases. Cell Death Differ. 2015. 22: 526– 539.
PubMed
PMC
Galluzzi L, Lopez-Soto A, Kumar S and Kroemer G, Caspases connect cell-death signaling to organismal homeostasis. Immunity 2016. 44: 221– 231.
PubMed
Wallace DC, Mitochondria and cancer. Nat. Rev. Cancer 2012. 12: 685– 698.
PubMed
PMC
Wallace DC, Mitochondrial diseases in man and mouse. Science 1999. 283: 1482– 1488.
PubMed
Brand MD and Nicholls DG, Assessing mitochondrial dysfunction in cells. Biochem. J 2011. 435: 297– 312.
PubMed
PMC
Cottet-Rousselle C, Ronot X, Leverve X and Mayol JF, Cytometric assessment of mitochondria using fluorescent probes. Cytometry A 2011. 79: 405– 425.
PubMed
Lay AWL and Burton AC, Direct measurement of potential difference across the human red blood cell membrane. Biophys. J 1969. 9: 115– 121.
PubMed
PMC
Perry SW, Norman JP, Barbieri J, Brown EB and Gelbard HA, Mitochondrial membrane potential probes and the proton gradient: A practical usage guide. Biotechniques 2011. 50: 98– 115.
PubMed
PMC
Petit PX, Susin SA, Zamzami N, Mignotte B and Kroemer G, Mitochondria and programmed cell death: Back to the future. FEBS Lett. 1996. 396: 7– 13.
PubMed
Rottenberg H and Wu S, Quantitative assay by flow cytometry of the mitochondrial membrane potential in intact cells. Biochim. Biophys. Acta 1998. 1404: 393– 404.
PubMed
Johnson LV, Walsh ML and Chen LB, Localization of mitochondria in living cells with rhodamine 123. Proc. Natl. Acad. Sci. U. S. A 1980. 77: 990– 994.
PubMed
PMC
Troiano L, Granata AR, Cossarizza A, Kalashnikova G, Bianchi R, Pini G, Tropea F, et al., Mitochondrial membrane potential and DNA stainability in human sperm cells: A flow cytometry analysis with implications for male infertility. Exp. Cell. Res 1998. 241: 384– 393.
PubMed
Ehrenberg B, Montana V, Wei MD, Wuskell JP and Loew LM, Membrane potential can be determined in individual cells from the nernstian distribution of cationic dyes. Biophys. J 1988. 53: 785– 794.
PubMed
PMC
Nicholls DG and Ward MW, Mitochondrial membrane potential and neuronal glutamate excitotoxicity: Mortality and millivolts. Trends Neurosci. 2000. 23: 166– 174.
PubMed
Cossarizza A, Baccarani-Contri M and Kalashnikova G and Franceschi C, A new method for the cytofluorimetric analysis of mitochondrial membrane potential using the J-aggregate forming lipophilic cation 5,5′,6,6′-tetrachloro-1,1′,3,3′-tetraethylbenzimidazolcarbocyanine iodide (JC-1). Biochem. Biophys. Res. Commun 1993. 197: 40– 45.
PubMed
Smiley ST, Reers M, Mottola-Hartshorn C, Lin M, Chen A, Smith TW, Steele GD, et al., Intracellular heterogeneity in mitochondrial membrane potentials revealed by a J-aggregate-forming lipophilic cation JC-1. Proc. Natl. Acad. Sci. U. S. A 1991. 88: 3671– 3675.
PubMed
PMC
Reers M, Smith TW and Chen LB, J-aggregate formation of a carbocyanine as a quantitative fluorescent indicator of membrane potential. Biochemistry 1991. 30: 4480– 4486.
PubMed
Moudy AM, Handran SD, Goldberg MP, Ruffin N, Karl I, Kranz-Eble P, DeVivo DC, et al., Abnormal calcium homeostasis and mitochondrial polarization in a human encephalomyopathy. Proc. Natl. Acad. Sci. U. S. A 1995. 92: 729– 733.
PubMed
PMC
Perelman A, Wachtel C, Cohen M, Haupt S, Shapiro H and Tzur A, JC-1: Alternative excitation wavelengths facilitate mitochondrial membrane potential cytometry. Cell Death Dis. 2012. 3: e430.
PubMed
PMC
De Biasi S, Gibellini L and Cossarizza A, Uncompensated Polychromatic Analysis of Mitochondrial Membrane Potential Using JC-1 and Multilaser Excitation. Curr. Prot. Cytom 2015. 72: 7.32.1– 7.32.11.
PubMed
Troiano L, Ferraresi R, Lugli E, Nemes E, Roat E, Nasi M, Pinti M, et al., Multiparametric analysis of cells with different mitochondrial membrane potential during apoptosis by polychromatic flow cytometry. Nat. Protoc 2007. 2: 2719– 2727.
PubMed
Poot M, Zhang YZ, Kramer JA, Wells KS, Jones LJ, Hanzel DK, Lugade AG, et al., Analysis of mitochondrial morphology and function with novel fixable fluorescent stains. J. Histochem. Cytochem 1996. 44: 1363– 1372.
PubMed
Septinus M, Seiffert W and Zimmermann HW, Hydrophobic acridine dyes for fluorescence staining of mitochondria in living cells. 1. Thermodynamic and spectroscopic properties of 10-n-alkylacridine orange chlorides. Histochemistry 1983. 79: 443– 456.
PubMed
Dickinson BC, Lin VS and Chang CJ, Preparation and use of MitoPY1 for imaging hydrogen peroxide in mitochondria of live cells. Nat. Protoc 2013. 8: 1249– 1259.
PubMed
PMC
Mukhopadhyay P, Rajesh M, Hasko G, Hawkins BJ, Madesh M and Pacher P, Simultaneous detection of apoptosis and mitochondrial superoxide production in live cells by flow cytometry and confocal microscopy. Nat. Protoc 2007. 2: 2295– 2301.
PubMed
PMC
Mukhopadhyay P, Rajesh M, Yoshihiro K, Hasko G and Pacher P, Simple quantitative detection of mitochondrial superoxide production in live cells. Biochem. Biophys. Res. Commun 2007. 358: 203– 208.
PubMed
PMC
Robinson KM, Janes MS, Pehar M, Monette JS, Ross MF, Hagen TM, Murphy MP, et al., Selective fluorescent imaging of superoxide in vivo using ethidium-based probes. Proc. Natl. Acad. Sci. U. S. A 2006. 103: 15038– 15043.
PubMed
PMC
Cossarizza A, Ferraresi R, Troiano L, Roat E, Gibellini L, Bertoncelli L, Nasi M, et al., Simultaneous analysis of reactive oxygen species and reduced glutathione content in living cells by polychromatic flow cytometry. Nat. Protoc 2009. 4: 1790– 1797.
PubMed
Gibellini L, Pinti M, Bartolomeo R, De Biasi S, Cormio A, Musicco C, Carnevale G, et al., Inhibition of Lon protease by triterpenoids alters mitochondria and is associated to cell death in human cancer cells. Oncotarget 2015. 6: 25466– 25483.
PubMed
PMC
Hawkins BJ, Madesh M, Kirkpatrick CJ and Fisher AB, Superoxide flux in endothelial cells via the chloride channel-3 mediates intracellular signaling. Mol. Biol. Cell 2007. 18: 2002– 2012.
PubMed
PMC
Iuso A, Scacco S, Piccoli C, Bellomo F, Petruzzella V, Trentadue R, Minuto M, et al., Dysfunctions of cellular oxidative metabolism in patients with mutations in the NDUFS1 and NDUFS4 genes of complex I. Biol. Chem 2006. 281: 10374– 10380.
PubMed
Rezvani HR, Dedieu S, North S, Belloc F, Rossignol R, Letellier T, de Verneuil H, et al., Hypoxia-inducible factor-1alpha, a key factor in the keratinocyte response to UVB exposure. J. Biol. Chem 2007. 282: 16413– 16422.
PubMed
Gordon S, Phagocytosis: An immunobiologic process. Immunity 2016. 44: 463– 475.
PubMed
Cooper EL, Kauschke E and Cossarizza A, Digging for innate immunity since Darwin and Metchnikoff. Bioessays 2002. 24: 319– 333.
PubMed
Navarre WW and Zychlinsky A, Pathogen-induced apoptosis of macrophages: a common end for different pathogenic strategies. Cell Microbiol. 2000. 2: 265– 273.
PubMed
Savill J, Recognition and phagocytosis of cells undergoing apoptosis. Br. Med. Bull 1997. 53: 491– 508.
PubMed
Brown GC, Vilalta A and Fricker M, Phagoptosis—Cell death By phagocytosis—Plays central roles in physiology, host defense and pathology. Curr. Mol. Med 2015. 15: 842– 851.
PubMed
Lunov O, Syrovets T, Loos C, Beil J, Delacher M, Tron K, Nienhaus GU, et al., Differential uptake of functionalized polystyrene nanoparticles by human macrophages and a monocytic cell line. ACS Nano 2011. 5: 1657– 1669.
PubMed
Valet G, Jenssen HL, Krefft M and Ruhenstroth-Baued G, Flow-cytometric measurements of the transmembrane potential, the surface charge density and the phagocytic activity of guinea pig macrophages after incubation with lymphokines. Blut 1981. 42: 379– 382.
PubMed
Dunn PA and Tyrer HW, Quantitation of neutrophil phagocytosis, using fluorescent latex beads. Correlation of microscopy and flow cytometry. J. Lab. Clin. Med 1981. 98: 374– 381.
PubMed
Bjerknes R and Bassøe CF, Human leukocyte phagocytosis of zymosan particles measured by flow cytometry. Acta Pathol. Microbiol. Immunol. Scand. C 1983. 91: 341– 348.
PubMed
Lehmann AK, Sørnes S and Halstensen A, Phagocytosis: Measurement by flow cytometry. J. Immunol. Methods 2000. 243: 229– 242.
PubMed
Bassøe CF, Assessment of phagocyte functions by flow cytometry. Curr. Prot. Cytometry 2002. 21: 9.19.1– 9.19.22.
PubMed
Simons ER, Measurement of phagocytosis and of the phagosomal environment in polymorphonuclear phagocytes by flow cytometry. Curr. Protoc. Cytom 2010. 51: 9.31.1– 9.31.10.
PubMed
PMC
Sokolovska A, Becker CE and Stuart LM, Measurement of phagocytosis, phagosome acidification, and intracellular killing of Staphylococcus aureus. Curr. Protoc. Immunol 2012. 99: 14.30.1– 14.30.12.
PubMed
Elbim C and Lizard G, Flow cytometric investigation of neutrophil oxidative burst and apoptosis physiological and pathological situation. Cytometry Part A 2009. 75A: 475– 481.
PubMed
Thomason J, Archer T, Mackin A, Stokes J and Pinchuk L, Applications of flow cytometry in veterinary research and small animal clinical practice. J. Vet. Med. Res 2014. 1: 1004– 1012.
Keogh MJ, Spoon T, Ridgway SH, Jensen E, Van Bonn W and Romano TA, Simultaneous measurement of phagocytosis and respiratory burst of leukocytes in whole blood from bottlenose dolphins (Tursiops truncatus) utilizing flow cytometry. Vet. Immunol. Immunopathol 2011. 144: 468– 475.
PubMed
Frankenberg T, Kirschnek S, Häcker H and Häcker G, Phagocytosis-induced apoptosis of macrophages is linked to uptake, killing and degradation of bacteria. Eur. J. Immunol 2008. 38: 204– 215.
PubMed
Tartaro K, VanVolkenburg M, Wilkie D, Coskran TM, Kreeger JM, Kawabata TT, and Casinghino S, Development of a fluorescence-based in vivo phagocytosis assay to measure mononuclear phagocyte system function in the rat. J. Immunotoxicol 2015. 12: 239– 246.
PubMed
Webb C, McCord K and Dow S, Neutrophil function in septic dogs. J. Vet. Intern. Med 2007. 21: 982– 989.
PubMed
Rossi G, Capitani L, Ceciliani F, Restelli L and Paltrinieri S, Hyposialylated α1-acid glycoprotein inhibits phagocytosis of feline neutrophils. Res. Vet. Sci 2013. 95: 465– 471.
PubMed
PMC
Moya SL, Gómez MA, Boyle LA, Mee JF, O’Brien B and Arkins S, Effects of milking frequency on phagocytosis and oxidative burst activity of phagocytes from primiparous and multiparous dairy cows during early lactation. J. Dairy. Sci 2008. 91: 587– 595.
PubMed
Stent G, Reece JC, Baylis DC, Ivinson K, Paukovics G, Thomson M, and Cameron PU, Heterogeneity of freshly isolated human tonsil dendritic cells demonstrated by intracellular markers, phagocytosis, and membrane dye transfer. Cytometry 2002. 48: 167– 176.
PubMed
Becker S, Halme J and Haskill S, Heterogeneity of human peritoneal macrophages: Cytochemical and flow cytometric studies. J Reticuloendothelial Soc. 1983. 33: 127– 138.
PubMed
Jersmann HPA, Ross KA, Vivers S, Brown SB, Haslett C and Dransfield I, Phagocytosis of apoptotic cells by human macrophages: Analysis by multiparameter flow cytometry. Cytometry A 2003. 51A: 7– 15.
PubMed
Linehan E, Dombrowski Y, Snoddy R, Fallon PG, Kissenpfennig A and Fitzgerald DC, Aging impairs peritoneal but not bone marrow-derived macrophage phagocytosis. Aging Cell 2014. 13: 699– 708.
PubMed
PMC
Fuller-Espie SL, Using flow cytometry to measure phagocytic uptake in earthworms. J. Microbiol. Biol. Educ 2010. 11: 144– 151.
PubMed
PMC
http://www.lgcstandards-atcc.org/
Sustrova T, Ondrackova P, Leva L and Sladek Z, Isolation techniques of neutrophils and peripheral blood mononuclear cells for the comparative experiments in humans and pigs model organisms in flow cytometry. Mendelnet. 2014. pp. 516– 521.
Carneiro C, Vaz C, Carvalho-Pereira J, Pais C and Sampaio P, A new method for yeast phagocytosis analysis by flow cytometry. J. Microbiol. Methods 2014. 101: 56– 62.
PubMed
Murciano C, Villamón E, O’Connor JE, Gozalbo D and Gil ML, Killed Candida albicans yeasts and hyphae inhibit gamma interferon release by murine natural killer cells. Infect. Immun 2006. 74: 1403– 1406.
PubMed
PMC
Anding K, Rost JM, Jacobs E and Daschner FD, Flow cytometric measurements of neutrophil functions: The dependence on the stimulus to cell ratio. FEMS Immunol. Med. Microbiol 2003. 35: 147– 152.
PubMed
Chan CL, Rénia L and Tan KSW, A simplified, sensitive phagocytic assay for malaria cultures facilitated by flow cytometry of differentially-stained cell populations. PLoS One 2012. 7: e38523.
PubMed
PMC
Lee CY, Herant M and Heinrich M, Target-specific mechanics of phagocytosis: Protrusive neutrophil response to zymosan differs from the uptake of antibody-tagged pathogens. Cell Sci. 2011. 124: 1106– 1114.
PubMed
PMC
Salih HR, Husfeld L and Adam D, Simultaneous cytofluorometric measurement of phagocytosis, burst production and killing of human phagocytes using Candida albicans and Staphylococcus aureus as target organisms. Clin. Microbiol. Infect 2000. 6: 251– 258.
PubMed
Li F, Yang M, Wang L, Tian F, Qin M, Shah PK, and Sharifi BG, Autofluorescence contributes to false-positive intracellular Foxp3 staining in macrophages: A lesson learned from flow cytometry. J. Immunol. Methods 2012. 386: 101– 107.
PubMed
PMC
Yáñez A, Flores A, Murciano C, O’Connor JE, Gozalbo D and Gil ML, Signalling through TLR2/MyD88 induces differentiation of murine bone marrow stem and progenitor cells to functional phagocytes in response to Candida albicans. Cell Microbiol. 2010. 12: 114– 128.
PubMed
Bicker H, Höflich C, Wolk K, Vogt K, Volk HD and Sabat R, A simple assay to measure phagocytosis of live bacteria. Clin. Chem 2008. 54: 911– 915.
PubMed
Schreiner L, Huber-Lang M, Weiss ME, Hohmann H, Schmolz M and Schneider EM, Phagocytosis and digestion of pH-sensitive fluorescent dye (Eos-FP) transfected E. coli in whole blood assays from patients with severe sepsis and septic shock. J. Cell Commun. Signal 2011. 5: 135– 144.
PubMed
PMC
Bajno L and Grinstein S, Fluorescent proteins: Powerful tools in phagocyte biology. J. Immunol. Methods 1999. 232: 67– 75.
PubMed
Zawada AM, Rogacev KS, Schirmer SH, Sester M, Böhm M, Fliser D, and Heine GH, Monocyte heterogeneity in human cardiovascular disease. Immunobiology 2012. 217: 1273– 1284.
PubMed
Schrijvers DM, Martinet W, De Meyer GRY, Andries L, Herman and Kockx MM, Flow cytometric evaluation of a model for phagocytosis of cells undergoing apoptosis. J. Immunol. Methods 2004. 287: 101– 108.
PubMed
Basiji DA, Ortyn WE, Liang L, Venkatachalam V and Morrissey P, Cellular image analysis and imaging by flow cytometry. Clin. Lab. Med 2007. 27: 653– 670.
PubMed
PMC
McFarlin BK, Williams RR, Venable AS, Dwyer KC and Haviland DL, Image-based cytometry reveals three distinct subsets of activated granulocytes based on phagocytosis and oxidative burst. Cytometry A 2013. 83A: 745– 751.
PubMed
Pul R, Morbiducci F, Škuljec J, Skripuletz T, Singh V, Diederichs U, Garde N, et al., Glatiramer acetate increases phagocytic activity of human monocytes in vitro and in multiple sclerosis patients. PLoS One 2012. 7: e51867.
PubMed
PMC
Cuervo AM and Wong E, Chaperone-mediated autophagy:roles in disease and aging. Cell Research 2014. 24: 92– 104.
PubMed
PMC
Li W, Li J and Bao J, Microautophagy: Lesser-known self-eating. Cell. Mol. Life. Sci 2011. 69: 1125– 1136.
PubMed
PMC
Boya P, Reggiori F and Codogno P, Emerging regulation and functions of Autophagy. Nature Cell Biology 2013. 15: 713– 720.
PubMed
PMC
Mizushima N, Yoshimori T and Ohsumi Y, The role of Atg proteins in autophagosome formation. Annu. Rev. Cell. Dev. Biol 2011. 27: 107– 132.
PubMed
Pasquier B, Autophagy inhibitors. Cell Mol. Life Sci 2016. 73: 985– 1001.
PubMed
PMC
Shintani T and Klionsky DJ, Autophagy in health and disease: A double-edged sword. Science 2006. 306: 990– 995.
PubMed
PMC
Yamamoto A, Tagawa Y, Yoshimori T, Moriyama Y, Masaki R and Tashiro Y, Bafilomycin A1 prevents maturation of autophagic vacuoles by inhibiting fusion between autophagosomes and lysosomes in rat hepatoma cell line, H-4-II-E cells. Cell Struct. Funct 1998. 23: 33– 42.
PubMed
Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, Adachi H, et al., Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy 2016. 12: 1– 222.
PubMed
PMC
Eng KE, Panas MD, Karlsson Hedestam GB and McInerney GM, A novel quantitative flow cytometry-based assay for autophagy. Autophagy 2010. 6: 634– 641.
PubMed
Puleston DJ, Zhang H, Powell TJ, Lipina E, Sims S, Panse I, Watson AS, et al., Autophagy is a critical regulator of memory CD8(+) T cell formation. Elife 2014. 3: e03706.
PubMed
PMC
Watson AS, Riffelmacher T, Stranks A, Williams O, De Boer J, Cain K, MacFarlane M, et al., Autophagy limits proliferation and glycolytic metabolism in acute myeloid leukemia. Cell Death Discov. 2015. 1: 15008.
PubMed
PMC
Song YM, Song SO, Jung YK, Kang ES, Cha BS, Lee HC, and Lee BW, Dimethyl sulfoxide reduces hepatocellular lipid accumulation through autophagy induction. Autophagy 2012. 8: 1085– 1097.
PubMed
PMC
Caro LH, Plomp PJ, Wolvetang EJ, Kerkhof C and Maijer AJ, 3-methyladenine, an inhibitor of autophagy, has multiple effects on metabolism. Eur. J. Biochem 1988. 175: 325– 329.
PubMed
Klionsky DJ, Elazar Z, Seglen PO and Rubinsztein DC, Does bafilomycin A1 block the fusion of autophagosomes with lysosomes?. Autophagy. 2008. 4: 849– 850.
PubMed
Demishtein A, Porat Z, Elazar Z and Shvets E, Applications of flow cytometry for measurement of autophagy. Methods 2015. 75: 87– 95.
PubMed
Mueller SN, Gebhardt T, Carbone FR and Heath WR, Memory T cell subsets, migration patterns, and tissue residence. Annu. Rev. Immunol 2013. 31: 137– 161.
PubMed
Masopust D and Schenkel JM, The integration of T cell migration, differentiation and function. Nat. Rev. Immunol 2013. 13: 309– 320.
PubMed
Murali-Krishna K, Altman JD, Suresh M, Sourdive DJ, Zajac AJ, Miller JD, Slansky J, et al., Counting antigen-specific CD8 T cells: A reevaluation of bystander activation during viral infection. Immunity 1998. 8: 177– 187.
PubMed
Masopust D, Vezys V, Marzo AL and Lefrancois L, Preferential localization of effector memory cells in nonlymphoid tissue. Science 2001. 291: 2413– 2417.
PubMed
Barber DL, Wherry EJ and Ahmed R, Cutting edge: Rapid in vivo killing by memory CD8 T cells. J. Immunol 2003. 171: 27– 31.
PubMed
Brunner KT, Mauel J, Cerottini JC and Chapuis B, Quantitative assay of the lytic action of immune lymphoid cells on 51-Cr-labelled allogeneic target cells in vitro; inhibition by isoantibody and by drugs. Immunology 1968. 14: 181– 196.
PubMed
PMC
Liu L, Chahroudi A, Silvestri G, Wernett ME, Kaiser WJ, Safrit JT, Komoriya A, et al., Visualization and quantification of T cell-mediated cytotoxicity using cell-permeable fluorogenic caspase substrates. Nat. Med 2002. 8: 185– 189.
PubMed
He L, Wu X, Meylan F, Olson DP, Simone J, Hewgill D, Siegel R, et al., Monitoring caspase activity in living cells using fluorescent proteins and flow cytometry. Am. J. Pathol 2004. 164: 1901– 1913.
PubMed
PMC
Sheehy ME, McDermott AB, Furlan SN, Klenerman P and Nixon DF, A novel technique for the fluorometric assessment of T lymphocyte antigen specific lysis. J. Immunol. Methods 2001. 249: 99– 110.
PubMed
Michonneau D, Sagoo P, Breart B, Garcia Z, Celli S and Bousso P, The PD-1 Axis enforces an anatomical segregation of CTL activity that creates tumor niches after allogeneic hematopoietic stem cell transplantation. Immunity 2016. 44: 143– 154.
PubMed
Aichele P, Brduscha-Riem K, Oehen S, Odermatt B, Zinkernagel RM, Hengartner H, and Pircher H, Peptide antigen treatment of naive and virus-immune mice: antigen-specific tolerance versus immunopathology. Immunity 1997. 6: 519– 529.
PubMed
Coles RM, Mueller SN, Heath WR, Carbone FR and Brooks AG, Progression of armed CTL from draining lymph node to spleen shortly after localized infection with herpes simplex virus 1. J. Immunol 2002. 168: 834– 838.
PubMed
Scandella E, Bolinger B, Lattmann E, Miller S, Favre S, Littman DR, Finke D, et al., Restoration of lymphoid organ integrity through the interaction of lymphoid tissue-inducer cells with stroma of the T cell zone. Nat. Immunol 2008. 9: 667– 675.
PubMed
Taubenberger JK and Morens DM, The pathology of influenza virus infections. Annu. Rev. Pathol 2008. 3: 499– 522.
PubMed
PMC
Ringelhan M, O’Connor T, Protzer U and Heikenwalder M, The direct and indirect roles of HBV in liver cancer: Prospective markers for HCC screening and potential therapeutic targets. J. Pathol 2015. 235: 355– 367.
PubMed
Schrepfer S, Deuse T, Reichenspurner H, Fischbein MP, Robbins RC and Pelletier MP, Stem cell transplantation: The lung barrier. Transplant. Proc 2007. 39: 573– 576.
PubMed
Wabnitz GH, Balta E, Schindler S, Kirchgessner H, Jahraus B, Meuer S and Samstag Y, The pro-oxidative drug WF-10 inhibits serial killing by primary human cytotoxic T-cells. Cell Death Discov. 2016. 2: 16057.
PubMed
PMC
Wabnitz GH, Kirchgessner H and Samstag Y, Imaging Flow Cytometry for Multiparametric Analysis of Molecular Mechanism Involved in the Cytotoxicity of Human CD8+ T-cells. J. Cell Biochem 2017. 118: 2528– 2533.
PubMed
Spielberg SP, Boxer LA, Oliver JM, Allen JM and Schulman JD, Oxidative damage to neutrophils in glutathione synthetase deficiency. Br. J. Haematol 1979. 42: 215– 223.
PubMed
Min-Wen JC, Jun-Hao ET and Shyh-Chang N, Stem cell mitochondria during aging. Semin. Cell Dev. Biol 2016. 52: 110– 118.
PubMed
Watanabe R, Fujii H, Shirai T, Saito S, Ishii T and Harigae H, Autophagy plays a protective role as an anti-oxidant system in human T cells and represents a novel strategy for induction of T-cell apoptosis. Eur. J. Immunol 2014. 44: 2508– 2520.
PubMed
Chen L, Peng F, Li G, Jie X, Cai K, Cai C, Zhong Y, et al., The studies on the cytotoxicity in vitro, cellular uptake, cell cycle arrest and apoptosis-inducing properties of ruthenium methylimidazole. J. Inorg. Biochem 2016. 156: 64– 74.
PubMed
Alfadda AA and Sallam RM, Reactive oxygen species in health and disease. J. Biomed. Biotechnol 2012. 2012: 936486.
PubMed
PMC
Ilkun O and Boudina S, Cardiac dysfunction and oxidative stress in the metabolic syndrome: an update on antioxidant therapies. Curr. Pharm. Des 2013. 19: 4806– 4817.
PubMed
PMC
Zhou T, Chuang CC and Zuo L, Molecular Characterization of Reactive Oxygen Species in Myocardial Ischemia-Reperfusion Injury. Biomed. Res. Int 2015. 2015: 864946.
PubMed
PMC
Gabelloni ML, Sabbione F, Jancic C, Fuxman Bass J, Keitelman I, Iula L, Oleastro M, et al., NADPH oxidase derived reactive oxygen species are involved in human neutrophil IL-1 β secretion but not in inflammasome activation. Eur. J. Immunol 2013. 43: 3324– 3335.
PubMed
Vogel DY, Kooij G, Heijnen PD, Breur M, Peferoen LA, van der Valk P, de Vries HE, et al., GM-CSF promotes migration of human monocytes across the blood brain barrier. Eur. J. Immunol 2015. 45: 1808– 1819.
PubMed
Autréaux BD and Toledano MB, ROS as signalling molecules: Mechanisms that generate specificity in ROS homeostasis. Nat. Rev. Mol. Cell Biol 2007. 8: 813– 824.
PubMed
Ray PD, Huang BW and Tsuji Y, Reactive oxygen species (ROS) homeostasis and redox regulation in cellular signaling. Cell Signal 2012. 24: 981– 990.
PubMed
PMC
Solaini G, Baracca A, Lenaz G and Sgarbi G, Hypoxia and mitochondrial oxidative metabolism. Biochim. Biophys. Acta 2010. 1797: 1171– 1177.
PubMed
Wang L, Duan Q, Wang T, Ahmed M, Zhang N, Li Y, Li L, et al., Mitochondrial respiratory chain inhibitors involved in ROS production induced by acute high concentrations of iodide and the effects of SOD as a protective factor. Oxid. Med. Cell. Longevity 2015. 2015: 217670.
PubMed
PMC
Halliwell B and Gutteridge JMC, Oxygen toxicity, oxygen radicals, transition metals and disease. Biochem. J 1984. 219: 1– 14.
PubMed
PMC
Diacovich L and Gorvel JP, Bacterial manipulation of innate immunity to promote infection. Nat. Rev. Microbiol 2010. 8: 117– 128.
PubMed
Belaaouaj A, Neutrophil elastase-mediated killing of bacteria: lessons from targeted mutagenesis. Microbes Infect. 2002. 4: 1259– 1264.
PubMed
Gonzalez-Navajas JM, Corr MP and Raz E, The immediate protective response to microbial challenge. Eur. J. Immunol 2014. 44: 2536– 2549.
PubMed
Rahal A, Kumar A, Singh V, Yadav B, Tiwari R, Chakraborty S, and Dhama K, Oxidative stress, prooxidants, and antioxidants: The interplay. BioMed Res. Int 2014. 2014: 761264.
PubMed
PMC
Schieber M and Chandel NS, ROS function in redox signaling and oxidative stress. Curr. Biol 2014. 24: 453– 462.
PubMed
PMC
Wu Z, Zhao Y and Zhao B, Superoxide anion, uncoupling proteins and Alzheimer’s disease. J. Clin. Biochem. Nutr 2010. 46: 187– 194.
PubMed
PMC
Baehner RL, Murrmann SK, Davis J and Johnston RB, The role of superoxide anion and hydrogen peroxide in phagocytosis-associated oxidative metabolic reactions. J. Clin. Invest 1975. 56: 571– 576.
PubMed
PMC
Kohen R and Nyska A, Oxidation of biological systems: Oxidative stress phenomena, antioxidants, redox reactions, and methods for their quantification. Toxicol. Pathol 2002. 30: 620– 650.
PubMed
Tafazoli S and O’Brien PJ, Amodiaquine-induced oxidative stress in a hepatocyte inflammation model. Toxicology 2009. 256: 101– 109.
PubMed
Okado-Matsumoto A and Fridovich I, Assay of superoxide dismutase: cautions relevant to the use of cytochrome c, a sulfonated tetrazolium, and cyanide. Anal. Biochem 2001. 298: 337– 342.
PubMed
Trevithick JR and Dzialoszynski T, A new technique for enhancing luminol luminescent detection of free radicals and reactive oxygen species. Biochem. Mol. Biol. Int 1994. 33: 1179– 1190.
PubMed
Soh N, Recent advances in fluorescent probes for the detection of reactive oxygen species. Anal. Bioanal. Chem 2006. 386: 532– 543.
PubMed
Emmendorffer A, Hecht M, Lohmann-Matthes ML and Roesler JA, Fast and easy method to determine the production of reactive oxygen intermediates by human and murine phagocytes using dihydrorhodamine 123. J. Immunol. Methods 1990. 131: 269– 275.
PubMed
Amini P, Stojkov D, Wang X, Wicki S, Kaufmann T, Wong WW, Simon HU, et al., Formation can occur independently of RIPK3 and MLKL signaling. Eur. J. Immunol 2016. 46: 178– 184.
PubMed
PMC
Sheyn U, Rosenwasser S, Ben-dor S, Porat Z and Vardi A, Modulation of host ROS metabolism is essential for viral infection of a bloom-forming coccolithophore in the ocean. ISME J. 2016. 10: 1742– 1754.
PubMed
PMC
van Eeden SF, Klut ME, Walker BA and Hogg JC, The use of flow cytometry to measure neutrophil function. J. Immunol. Methods 1999. 32: 23– 43.
PubMed
Fornas O, Garcia J and Petriz J, Flow cytometry counting of CD34+ cells in whole blood. Nat. Med 2000. 6: 833– 836.
PubMed
Berridge MJ, Lipp P and Bootman MD, The versatility and universality of calcium signalling. Nat. Rev. Mol. Cell Biol 2000. 1: 11– 21.
PubMed
Feske S, Okamura H, Hogan PG and Rao A, Ca2+/calcineurin signalling in cells of the immune system. Biochem. Biophys. Res. Commun 2003. 311: 1117– 1132.
PubMed
Gwack Y, Feske S, Srikanth S, Hogan PG and Rao A, Signalling to transcription: Store-operated Ca2+ entry and NFAT activation in lymphocytes. Cell Calcium 2007. 42: 145– 156.
PubMed
Varga-Szabo D, Braun A and Nieswandt B, Calcium signaling in platelets. J. Thrombosis haemostasis JTH 2009. 7: 1057– 1066.
PubMed
Armstrong DL, Erxleben C and White JA, Patch clamp methods for studying calcium channels. Methods Cell Biol. 2010. 99: 183– 197.
PubMed
Grynkiewicz G, Poenie M and Tsien RY, A new generation of Ca2+ indicators with greatly improved fluorescence properties. J. Biol. Chem 1985. 260: 3440– 3450.
PubMed
Kao JP, Harootunian AT and Tsien RY, Photochemically generated cytosolic calcium pulses and their detection by fluo-3. J. Biol. Chem 1989. 264: 8179– 8184.
PubMed
Paredes RM, Etzler JC, Watts LT, Zheng W and Lechleiter JD, Chemical calcium indicators. Methods 2008. 46: 143– 151.
PubMed
PMC
Foerster C, Voelxen N, Rakhmanov M, Keller B, Gutenberger S, Goldacker S, Thiel J, et al., B cell receptor-mediated calcium signaling is impaired in B lymphocytes of type Ia patients with common variable immunodeficiency. J. Immunol 2010. 184: 7305– 7313.
PubMed
Dolmetsch RE, Lewis RS, Goodnow CC and Healy JI, Differential activation of transcription factors induced by Ca2+ response amplitude and duration. Nature 1997. 386: 855– 858.
PubMed
Griesbeck M, Ziegler S, Laffont S, Smith N, Chauveau L, Tomezsko P, Sharei A, et al., Sex differences in plasmacytoid dendritic cell levels of IRF5 drive higher IFNα production in women. J. Immunol 2015. 195: 5327– 5336.
PubMed
PMC
Martrus G, Niehrs A, Cornelis R, Rechtien A, García-Beltran W, Lütgehetmann M, Hoffmann C, et al., Kinetics of HIV-1 Latency Reversal Quantified on the Single-Cell Level Using a Novel Flow-Based Technique. J. Virol. Sep 2016. 90: 9018– 9028.
PubMed
PMC
Baxter AE, Niessl J, Fromentin R, Richard J, Porichis F, Charlebois R, Massanella M, et al., Single-cell characterization of viral translation-competent reservoirs in HIV-infected individuals. Cell Host Microbe 2016. 20: 368– 380.
PubMed
PMC
Garcia-Beltran WF, Hölzemer A, Martrus G, Chung AW, Pacheco Y, Simoneau CR, Rucevic M, et al., Open conformers of HLA-F are high-affinity ligands of the activating NK-cell receptor KIR3DS1. Nat. Immunol. Sep 2016. 17: 1067– 1074.
PubMed
PMC
Thaler B, Hohensinner PJ, Krychtiuk KA, Matzneller P, Koller L, Brekalo M, Maurer G, et al., Differential in vivo activation of monocyte subsets during low-grade inflammation through experimental endotoxemia in humans. Sci. Rep 2016. 6: 30162.
PubMed
PMC
Krutzik PO and Nolan GP, Intracellular phospho-protein staining techniques for flow cytometry: Monitoring single cell signaling events. Cytometry 2003. 55: 61– 70.
PubMed
Pozarowski P and Darzykiewicz Z, Analysis of cell cycle by flow cytometry. In Schönthal AH, (Ed.) Checkpoint controls and cancer. Methods in Molecular Biology, vol 281. Humana Press, Totowa, NJ: 2004, 301– 311.
PubMed
Schmid I and Sakamoto KM, Analysis of DNA content and green fluorescent protein expression. Curr. Protoc. Cytom 2001. 16: 7.16.1– 7.16.10.
PubMed
Lanier LL and Warner NL, Paraformaldehyde fixation of hematopoietic cells for quantitative flow cytometry (FACS) analysis. J. Immunol. Methods 1981. 47: 25– 30.
PubMed
Filby A, Seddon B, Kleczkowska J, Salmond R, Tomlinson P, Smida M, Lindquist JA, et al., Fyn regulates the duration of TCR engagement needed for commitment to effector function. The J. Immunol 2007. 179: 4635– 4644.
PubMed
Hori S, Nomura T and Sakaguchi S, Control of regulatory T cell development by the transcription factor Foxp3. Science 2003. 299: 1057– 1061.
PubMed
Liu W, Putnam AL, Xu-yu Z, Szot GL, Lee MR, Zhu S, Gottlieb PA, et al., CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells. JEM 2006. 203: 1701– 1711.
PubMed
PMC
Filby A, Perucha E, Summers H, Rees P, Chana P, Heck S, Lord GM, et al., An imaging flow cytometric method for measuring cell division history and molecular symmetry during mitosis. Cytometry Part A 2011. 79: 496– 506.
PubMed
Baecher-Allan C, Viglietta V and Hafler DA, Human CD4+CD25+ regulatory T cells. Semin. Immunol 2004. 16: 89– 98.
PubMed
Watson M, Chow S, Barsyte D, Arrowsmith C, Shankey TV, Minden M, and Hedley D, The study of epigenetic mechanisms based on the analysis of histone modification patterns by flow cytometry. Cytometry 2013. 85: 78– 87.
PubMed
Guha M and Mackman N, LPS induction of gene expression in human monocytes. Cell. Signal 2001. 13: 85– 94.
PubMed
Gantke T, Sriskantharajah S and Ley SC, Regulation and function of TPL-2, an IκB kinase-regulated MAP Kinase Kinase. Cell Res. 2011. 21: 131– 134.
PubMed
PMC
Dufner A and Thomas G, Ribosomal S6 kinase signaling and the control of translation. Exp. Cell Res 1999. 253: 100– 109.
PubMed
G1 F. and Nunès JA, Analysis of signaling events by dynamic phosphoflow cytometry. Sci. Signal 2009. 2: pl3.
PubMed
West MA, Koons A, Crandall M, Skinner R, Worley M and Shapiro MB, Whole blood leukocyte mitogen activated protein kinases activation differentiates intensive care unit patients with systemic inflammatory response syndrome and sepsis. J. Trauma 2007. 62: 805– 811.
PubMed
Donnelly RP and Finlay DK, Glucose, glycolysis and lymphocyte responses. Mol. Immunol 2015. 68: 513– 519.
PubMed
Caro-Maldonado a, Wang R, Nichols AG, Kuraoka M, Milasta S, Sun LD, Gavin AL, et al., Metabolic reprogramming is required for antibody production that is suppressed in anergic but exaggerated in chronically BAFF-exposed B cells. J. Immunol 2014. 192: 3626– 3636.
PubMed
PMC
Warburg O, On the origin of cancer cells. Science 1956. 123: 309– 314.
PubMed
Hale LP, Braun RODD, Gwinn WM, Greer PK, Dewhirst MW, Laura P, Braun RODD, et al., Hypoxia in the thymus: Role of oxygen tension in thymocyte survival. Am. J. Physiol. Heart Circ. Physiol 2002. 282: H1467– H1477.
PubMed
Parmar K, Mauch P, Vergilio J-A, Sackstein R and Down JD, Distribution of hematopoietic stem cells in the bone marrow according to regional hypoxia. Proc. Natl. Acad. Sci. U. S. A 2007. 104: 5431– 5436.
PubMed
PMC
Chandel NS, McClintock DS, Feliciano CE, Wood TM, Melendez JA, Rodriguez AM, Schumacker PT, Reactive oxygen species generated at mitochondrial Complex III stabilize hypoxia-inducible factor-1α. J. Biol. Chem 2000. 275: 25130– 25138.
PubMed
Bigarella CL, Liang R and Ghaffari S, Stem cells and the impact of ROS signaling. Development 2014. 141: 4206– 4218.
PubMed
PMC
Jang K-J, Mano H, Aoki K, Hayashi T, Muto A, Nambu Y, Takahashi K, et al., Mitochondrial function provides instructive signals for activation-induced B-cell fates. Nat. Commun 2015. 6: 6750.
PubMed
PMC
Korchak HM, Rich AM, Wilkenfeld C, Rutherford LE and Weissmann G, A carboxyanine dye, DiOC6(3), acts as a mitochondrial probe in human neutrophils. Biochem. Biophys. Res. Commun 1982. 108: 1495– 1501.
PubMed
Avramidou A, Kroczek C, Lang C, Schuh W, Jäck H-M and Mielenz D, The novel adaptor protein Swiprosin-1 enhances BCR signals and contributes to BCR-induced apoptosis. Cell Death Differ. 2007. 14: 1936– 1947.
PubMed
Eruslanov E and Kusmartsev S, Identification of ROS using oxidized DCFDA and flow-cytometry. In Armstrong D (Ed.) Advanced protocols in oxidative stress II. Methods in Molecular Biology, vol 594. Humana Press, New York, NY: 2010, pp. 57– 72.
PubMed
Kalyanaraman B, Darley-Usmar V, Davies KJA, Dennery PA, Forman HJ, Grisham MB, Mann GE, et al., Measuring reactive oxygen and nitrogen species with fluorescent probes: Challenges and limitations. Free Radic. Biol. Med 2012. 52: 1– 6.
PubMed
PMC
Hempel SL, Buettner GR, O’Malley YQ, Wessels D. a. and Flaherty DM, Dihydrofluorescein diacetate is superior for detecting intracellular oxidants: Comparison with 2’,7′-dichlorodihydrofluorescein diacetate, 5 (and 6)-caboxy-2′,7′-dichlorodihydrofluorescein diacetate, and dihydrorhodamine 123. Free Radic. Biol. Med 1999. 27: 146– 159.
PubMed
Tzur A, Moore JK, Jorgensen P, Shapiro HM and Kirschner MW, Optimizing optical flow cytometry for cell volume-based sorting and analysis. PLoS One 2011. 6: e16053.
PubMed
PMC
Henzi T and Schwaller B, Antagonistic regulation of parvalbumin expression and mitochondrial calcium handling capacity in renal epithelial cells. PLoS One 2015. 10: e0142005.
PubMed
PMC
Martina MN, Noel S, Saxena A, Rabb H and Hamad AR, Double negative (DN) αβ T cells: misperception and overdue recognition. Immunol Cell Biol. 2015. 93: 305– 310.
PubMed
PMC
Gerlach C, van Heijst JW, Sie D, Armstrong N, Kerkhoven RM, Zehn D, et al., One naive T-cell, multiple fates in CD8+ T-cell differentiation. J. Exp. Med 2010. 207: 1235– 1246.
PubMed
PMC
Stemberger C, Huster KM, Koffler M, Anderl F, Schiemann M, Wagner H, and Busch DH, A single naive CD8+ T-cell precursor can develop into diverse effector and memory subsets. Immunity 2007. 27: 985– 997.
PubMed
Appay V, van Lier RA, Sallusto F and Roederer M, Phenotype and function of human T lymphocyte subsets: Consensus and issues. Cytometry A 2008. 73: 975– 983.
PubMed
Costantini A, Mancini S, Giuliodoro S, Butini L, Regnery CM, Silvestri G, and Montroni M, Effects of cryopreservation on lymphocyte immunophenotype and function. J. Immunol. Methods 2003. 278: 145– 155.
PubMed
Hamann D, Baars PA, Rep MH, Hooibrink B, Kerkhof-Garde SR, Klein MR, and van Lier RA, Phenotypic and functional separation of memory and effector human CD8+ T-cells. J. Exp. Med 1997. 186: 1407– 1418.
PubMed
PMC
Appay V, Dunbar PR, Callan M, Klenerman P, Gillespie GM, Papagno L, Ogg GS, et al., Memory CD8+ T-cells vary in differentiation phenotype in different persistent virus infections. Nat. Med 2002. 8: 379– 385.
PubMed
Sallusto F, Lenig D, Forster R, Lipp M and Lanzavecchia A, Two subsets of memory T lymphocytes with distinct homing potentials and effector functions. Nature 1999. 401: 708– 712.
PubMed
van Aalderen MC, Remmerswaal EB, Verstegen NJ, Hombrink P, ten Brinke A, Pircher H, Kootstra NA et al., Infection history determines the differentiation state of human CD8+ T cells. J Virol. 2015. 89: 5110– 5123.
PubMed
PMC
van Leeuwen EM, Remmerswaal EB, Vossen MT, Rowshani AT, Wertheim-van Dillen PM, van Lier RA, and ten Berge IJ, Emergence of a CD4+. J. Immunol 2004. 173: 1834– 1841.
PubMed
Oja AE, Vieira Braga FA, Remmerswaal EB, Kragten NA, Hertoghs KM, Zuo J, Moss PA et al., The Transcription Factor Hobit Identifies Human Cytotoxic CD4+ T Cells. Front Immunol. 2017. 8: 325.
PubMed
PMC
Sallusto F, Lenig D, Mackay CR and Lanzavecchia A, Flexible programs of chemokine receptor expression on human polarized T Helper 1 and 2 lymphocytes. J. Exp. Med 1998. 187: 875– 883.
PubMed
PMC
Mahnke YD, Beddall MH and Roederer M, OMIP-017: human CD4(+) helper T-cell subsets including follicular helper cells. Cytometry A 2013. 83: 439– 440.
PubMed
PMC
Zheng W and Flavell RA, The transcription factor GATA-3 is necessary and sufficient for Th2 cytokine gene expression in CD4 T-cells. Cell 1997. 89: 587– 596.
PubMed
Ouyang W, Ranganath SH, Weindel K, Bhattacharya D, Murphy TL, Sha WC, and Murphy KM, Inhibition of Th1 development mediated by GATA-3 through an IL-4-independent mechanism. Immunity 1998. 9: 745– 755.
PubMed
Kanhere A, Hertweck A, Bhatia U, Gokmen MR, Perucha E, Jackson I, Lord GM, et al., T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements. Nat. Commun 2012. 3: 1268.
PubMed
PMC
Staudt V, Bothur E, Klein M, Lingnau K, Reuter S, Grebe N, Gerlitzki B, et al., Interferon-regulatory factor 4 is essential for the developmental program of T helper 9 cells. Immunity 2010. 33: 192– 202.
PubMed
Maggi L, Santarlasci V, Capone M, Peired A, Frosali F, Crome SQ, Querci V et al., CD161 is a marker of all human IL-17-producing T-cell subsets and is induced by RORC. Eur J Immunol. 2010. 40: 2174– 2181.
PubMed
Zielinski CE, Mele F, Aschenbrenner D, Jarrossay D, Ronchi F, Gattorno M, Monticelli S et al., Pathogen-induced human TH17 cells produce IFN-γ or IL-10 and are regulated by IL-1β. Nature 2012. 484: 514– 518.
PubMed
Cosmi L, Maggi L, Santarlasci V, Liotta F and Annunziato F, T helper cells plasticity in inflammation. Cytometry A 2014. 85: 36– 42.
PubMed
Acosta-Rodriguez EV, Rivino L, Geginat J, Jarrossay D, Gattorno M, Lanzavecchia A, Sallusto F, et al., Surface phenotype and antigenic specificity of human interleukin 17-producing T helper memory cells. Nat Immunol 2007. 8: 639– 646.
PubMed
Gagliani N, Amezcua Vesely MC, Iseppon A, Brockmann L, Xu H, Palm NW, de Zoete MR et al., Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation. Nature 2015. 523: 221– 225.
PubMed
PMC
Ivanov II, McKenzie BS, Zhou L, Tadokoro CE, Lepelley A, Lafaille JJ, Cua DJ, et al., The orphan nuclear receptor RORgammat directs the differentiation program of proinflammatory IL-17+ T helper cells. Cell 2006. 126: 1121– 1133.
PubMed
Basu R, O’Quinn DB, Silberger DJ, Schoeb TR, Fouser L, Ouyang W, Hatton RD, et al., Th22 cells are an important source of IL-22 for host protection against enteropathogenic bacteria. Immunity 2012. 37: 1061– 1075.
PubMed
PMC
Duhen T, Geiger R, Jarrossay D, Lanzavecchia A and Sallusto F, Production of interleukin 22 but not interleukin 17 by a subset of human skin-homing memory T-cells. Nat. Immunol 2009. 10: 857– 863.
PubMed
Morita R, Schmitt N, Bentebibel SE, Ranganathan R, Bourdery L, Zurawski G, Foucat E, et al., Human blood CXCR5(+)CD4(+) T-cells are counterparts of T follicular cells and contain specific subsets that differentially support antibody secretion. Immunity 2011. 34: 108– 121.
PubMed
PMC
Glatman ZA, Taylor JJ, King IL, Marshall FA, Mohrs M and Pearce EJ, T follicular helper cells differentiate from Th2 cells in response to helminth antigens. J. Exp. Med 2009. 206: 991– 999.
PubMed
PMC
Huster KM, Busch V, Schiemann M, Linkemann K, Kerksiek KM, Wagner H, and Busch DH, Selective expression of IL-7 receptor on memory T-cells identifies early CD40L-dependent generation of distinct CD8+ memory T-cell subsets. Proc. Natl. Acad. Sci. U. S. A 2004. 101: 5610– 5615.
PubMed
PMC
Hand TW, Morre M and Kaech SM, Expression of IL-7 receptor alpha is necessary but not sufficient for the formation of memory CD8 T-cells during viral infection. Proc. Natl. Acad. Sci. U. S. A 2007. 104: 11730– 11735.
PubMed
PMC
Shay T, Jojic V, Zuk O, Rothamel K, Puyraimond-Zemmour D, Feng T, Wakamatsu E, et al., Conservation and divergence in the transcriptional programs of the human and mouse immune systems. Proc. Natl. Acad. Sci. U. S. A 2013. 110: 2946– 2951.
PubMed
PMC
Kaech SM and Cui W, Transcriptional control of effector and memory CD8+ T-cell differentiation. Nat. Rev. Immunol 2012. 12: 749– 761.
PubMed
PMC
Joshi NS, Cui W, Chandele A, Lee HK, Urso DR, Hagman J, Gapin L, et al., Inflammation directs memory precursor and short-lived effector CD8(+) T-cell fates via the graded expression of T-bet transcription factor. Immunity 2007. 27: 281– 295.
PubMed
PMC
Intlekofer AM, Takemoto N, Wherry EJ, Longworth SA, Northrup JT, Palanivel VR, Mullen AC, et al., Effector and memory CD8+ T-cell fate coupled by T-bet and eomesodermin. Nat. Immunol 2005. 6: 1236– 1244.
PubMed
Vieira Braga FA, Hertoghs KM, Kragten NA, Doody GM, Barnes NA, Remmerswaal EB, Hsiao CC, et al., Blimp-1 homolog Hobit identifies effector-type lymphocytes in humans. Eur. J. Immunol 2015. 45: 2945– 2958.
PubMed
Fontenot JD, Gavin MA and Rudensky AY, Foxp3 programs the development and function of CD4+CD25+ regulatory T-cells. Nat. Immunol 2003. 4: 330– 336.
PubMed
Kim HJ, Barnitz RA, Kreslavsky T, Brown FD, Moffett H, Lemieux ME, Kaygusuz Y et al., Stable inhibitory activity of regulatory T cells requires the transcription factor Helios. Science 2015. 350: 334– 339.
PubMed
PMC
Thornton AM, Korty PE, Tran DQ, Wohlfert EA, Murray PE, Belkaid Y, and Shevach EM, Expression of Helios, an Ikaros transcription factor family member, differentiates thymic-derived from peripherally induced Foxp3+ T regulatory cells. J. Immunol 2010. 184: 3433– 3441.
PubMed
PMC
Beura LK, Hamilton SE, Bi K, Schenkel JM, Odumade OA, Casey KA, Thompson EA, et al., Normalizing the environment recapitulates adult human immune traits in laboratory mice. Nature 2016. 532: 512– 516.
PubMed
PMC
Akondy RS, Monson ND, Miller JD, Edupuganti S, Teuwen D, Wu H, Quyyumi F, et al., The yellow fever virus vaccine induces a broad and polyfunctional human memory CD8+ T-cell response. J. Immunol 2009. 183: 7919– 7930.
PubMed
PMC
Schulz AR, Mälzer JN, Domingo C, Jürchott K, Grützkau A, Babel N, Nienen M, et al., Low thymic activity and dendritic cell numbers are associated with the immune response to primary viral infection in elderly humans. J. Immunol 2015. 195: 4699– 4711.
PubMed
van Leeuwen EM, de Bree GJ, Remmerswaal EB, Yong SL, Tesselaar K, ten Berge IJ, and van Lier RA, IL-7 receptor alpha chain expression distinguishes functional subsets of virus-specific human CD8+ T-cells. Blood 2005. 106: 2091–2091.
PubMed
Mueller SN and Mackay LK, Tissue-resident memory T-cells: Local specialists in immune defence. Nat. Rev. Immunol 2016. 16: 79– 89.
PubMed
Anderson KG, Mayer-Barber K, Sung H, Beura L, James BR, Taylor JJ, Qunaj L, et al., Intravascular staining for discrimination of vascular and tissue leukocytes. Nat. Protoc 2014. 9: 209– 222.
PubMed
PMC
Zhou L, Chong MM and Littman DR, Plasticity of CD4+ T-cell lineage differentiation. Immunity 2009. 30: 646– 655.
PubMed
Mittrucker HW, Visekruna A and Huber M, Heterogeneity in the differentiation and function of CD8(+) T-cells. Arch. Immunol. Ther. Exp. (Warsz) 2014. 62: 449– 458.
PubMed
Mosmann TR, Cherwinski H, Bond MW, Giedlin MA and Coffman RL, Two types of murine helper T-cell clone. I. Definition according to profiles of lymphokine activities and secreted proteins. J. Immunol 1986. 136: 2348– 2357.
PubMed
Hsieh CS, Macatonia SE, Tripp CS, Wolf SF, O’Garra A and Murphy KM, Development of TH1 CD4+ T-cells through IL-12 produced by Listeria-induced macrophages. Science 1993. 260: 547– 549.
PubMed
Lighvani AA, Frucht DM, Jankovic D, Yamane H, Aliberti J, Hissong BD, and Nguyen BV, T-bet is rapidly induced by interferon-gamma in lymphoid and myeloid cells. Proc. Natl. Acad. Sci. U. S. A 2001. 98: 15137– 15142.
PubMed
PMC
Szabo SJ, Kim ST, Costa GL, Zhang X, Fathman CG and Glimcher LH, A novel transcription factor, T-bet, directs Th1 lineage commitment. Cell 2000. 100: 655– 669.
PubMed
Le Gros G, Ben-Sasson SZ, Seder R, Finkelman FD and Paul WE, Generation of interleukin 4 (IL-4)-producing cells in vivo and in vitro: IL-2 and IL-4 are required for in vitro generation of IL-4-producing cells. J. Exp. Med 1990. 172: 921– 929.
PubMed
PMC
Swain SL, Weinberg AD, English M and Huston G, IL-4 directs the development of Th2-like helper effectors. J. Immunol 1990. 145: 3796– 3806.
PubMed
Cua DJ, Sherlock J, Chen Y, Murphy CA, Joyce B, Seymour B, and Lucian L, Interleukin-23 rather than interleukin-12 is the critical cytokine for autoimmune inflammation of the brain. Nature 2003. 421: 744– 748.
PubMed
Murphy CA, Langrish CL, Chen Y, Blumenschein W, McClanahan T, Kastelein RA, Sedgwick JD, et al., Divergent pro- and antiinflammatory roles for IL-23 and IL-12 in joint autoimmune inflammation. J. Exp. Med 2003. 198: 1951– 1957.
PubMed
PMC
Iwakura Y, Ishigame H, Saijo S and Nakae S, Functional specialization of interleukin-17 family members. Immunity 2011. 34: 149– 162.
PubMed
Harrington LE, Hatton RD, Mangan PR, Turner H, Murphy TL, Murphy KM, and Weaver CT, Interleukin 17-producing CD4+ effector T-cells develop via a lineage distinct from the T helper type 1 and 2 lineages. Nat. Immunol 2005. 6: 1123– 1132.
PubMed
Baba N, Rubio M, Kenins L, Regairaz C, Woisetschlager M, Carballido JM, and Sarfati M, The aryl hydrocarbon receptor (AhR) ligand VAF347 selectively acts on monocytes and naive CD4(+) Th cells to promote the development of IL-22-secreting Th cells. Hum. Immunol 2012. 73: 795– 800.
PubMed
Gerlach K, Hwang Y, Nikolaev A, Atreya R, Dornhoff H, Steiner S, Lehr HA, et al., TH9 cells that express the transcription factor PU.1 drive T-cell-mediated colitis via IL-9 receptor signaling in intestinal epithelial cells. Nat. Immunol 2014. 15: 676– 686.
PubMed
Chtanova T, Tangye SG, Newton R, Frank N, Hodge MR, Rolph MS, and Mackay CR, T follicular helper cells express a distinctive transcriptional profile, reflecting their role as non-Th1/Th2 effector cells that provide help for B-cells. J. Immunol 2004. 173: 68– 78.
PubMed
Mackay LK, Minnich M, Kragten NA, Liao Y, Nota B, Seillet C, Zaid A, et al., Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes. Science 2016. 352: 459– 463.
PubMed
Grewal IS, Xu J and Flavell RA, Impairment of antigen-specific T-cell priming in mice lacking CD40 ligand. Nature 1995. 378: 617– 620.
PubMed
Garside P, Ingulli E, Merica RR, Johnson JG, Noelle RJ and Jenkins MK, Visualization of specific B and T lymphocyte interactions in the lymph node. Science 1998. 281: 96– 99.
PubMed
Lord GM, Rao RM, Choe H, Sullivan BM, Lichtman AH, Luscinskas FW, and Glimcher LH, T-bet is required for optimal proinflammatory CD4+ T-cell trafficking. Blood 2005. 106: 3432– 3439.
PubMed
PMC
Sundrud MS, Grill SM, Ni D, Nagata K, Alkan SS, Subramaniam A, and Unutmaz D, Genetic reprogramming of primary human T-cells reveals functional plasticity in Th cell differentiation. J. Immunol 2003. 171: 3542– 3549.
PubMed
Hirota K, Yoshitomi H, Hashimoto M, Maeda S, Teradaira S, Sugimoto N, Yamaguchi T, et al., Preferential recruitment of CCR6-expressing Th17 cells to inflamed joints via CCL20 in rheumatoid arthritis and its animal model. J. Exp. Med 2007. 204: 2803– 2812.
PubMed
PMC
Breitfeld D, Ohl L, Kremmer E, Ellwart J, Sallusto F, Lipp M, Förster R, Follicular B helper T-cells express CXC chemokine receptor 5, localize to B-cell follicles, and support immunoglobulin production. J. Exp. Med 2000. 192: 1545– 1552.
PubMed
PMC
Frentsch M, Stark R, Matzmohr N, Meier S, Durlanik S, Schulz AR, Stervbo U, et al., CD40L expression permits CD8+ T-cells to execute immunologic helper functions. Blood 2013. 122: 405– 412.
PubMed
PMC
Odendahl M, Jacobi A, Hansen A, Feist E, Hiepe F, Burmester GR, Lipsky PE, et al., Disturbed peripheral B lymphocyte homeostasis in systemic lupus erythematosus. J. Immunol 2000. 165: 5970– 5979.
PubMed
Anderson KC, Bates MP, Slaughenhoupt BL, Pinkus GS, Schlossman SF and Nadler LM, Expression of human B-cell-associated antigens on leukemias and lymphomas: A model of human B-cell differentiation. Blood 1984. 63: 1424– 1433.
PubMed
Stashenko P, Nadler LM, Hardy R and Schlossman SF, Characterization of a human B lymphocyte-specific antigen. J. Immunol 1980. 125: 1678– 1685.
PubMed
LeBien TW and Tedder TF, B lymphocytes: How they develop and function. Blood 2008. 112: 1570– 1580.
PubMed
PMC
Sims GP, Ettinger R, Shirota Y, Yarboro CH, Illei GG and Lipsky PE, Identification and characterization of circulating human transitional B-cells. Blood 2005. 105: 4390– 4398.
PubMed
PMC
Klein U, Rajewsky K and Kuppers R, Human immunoglobulin (Ig)M+IgD+ peripheral blood B-cells expressing the CD27 cell surface antigen carry somatically mutated variable region genes: CD27 as a general marker for somatically mutated (memory) B-cells. J. Exp. Med 1998. 188: 1679– 1689.
PubMed
PMC
Kuppers R, Klein U, Hansmann ML and Rajewsky K, Cellular origin of human B-cell lymphomas. N. Engl. J. Med 1999. 341: 1520– 1529.
PubMed
Agematsu K, Hokibara S, Nagumo H and Komiyama A, CD27: A memory B-cell marker. Immunol. Today 2000. 21: 204– 206.
PubMed
Agematsu K, Nagumo H, Yang FC, B-cell subpopulations separated by CD27 and crucial collaboration of CD27+ B-cells and helper T-cells in immunoglobulin production. Eur. J. Immunol 1997. 27: 2073– 2079.
PubMed
Mei HE, Wirries I, Frolich D, Brisslert M, Giesecke C, Grun JR, Alexander T, et al., A unique population of IgG-expressing plasma cells lacking CD19 is enriched in human bone marrow. Blood 2015. 125: 1739– 1748.
PubMed
Jacobi AM and Dorner T, B-cell-directed therapy in patients with connective tissue diseases. Dtsch. Med. Wochenschr 2012. 137: 1755– 1757.
PubMed
Pascual V, Liu YJ, Magalski A, de Bouteiller O, Banchereau J and Capra JD, Analysis of somatic mutation in five B-cell subsets of human tonsil. J. Exp. Med 1994. 180: 329– 339.
PubMed
PMC
Kikutani H, Suemura M, Owaki H, Nakamura H, Sato R, Yamasaki K, Barsumian EL, et al., Fc epsilon receptor, a specific differentiation marker transiently expressed on mature B-cells before isotype switching. J. Exp. Med 1986. 164: 1455– 1469.
PubMed
PMC
Clark EA and Lane PJ, Regulation of human B-cell activation and adhesion. Annu. Rev. Immunol 1991. 9: 97– 127.
PubMed
Jacobi AM, Reiter K, Mackay M, Aranow C, Hiepe F, Radbruch A, Hansen A, et al., Activated memory B-cell subsets correlate with disease activity in systemic lupus erythematosus: delineation by expression of CD27, IgD, and CD95. Arthritis Rheum. 2008. 58: 1762– 1773.
PubMed
Wehr C, Eibel H, Masilamani M, Illges H,Schlesier M, Peter HH, and Warnatz K, A new CD21low B-cell population in the peripheral blood of patients with SLE. Clin. Immunol 2004. 113: 161– 171.
PubMed
Tedder TF, Zhou LJ and Engel P, The CD19/CD21 signal transduction complex of B lymphocytes. Immunol. Today 1994. 15: 437– 442.
PubMed
Radbruch AG, Muehlinghaus EO, Luger A, Inamine A, Smith KG, Dörner T, and Hiepe F, Competence and competition: The challenge of becoming a long-lived plasma cell. Nat. Rev. Immunol 2006. 6: 741– 750.
PubMed
Mei HEI, Wirries D, Frolich M, Brisslert M, Giesecke C, Grun JR, Alexander T, et al., A unique population of IgG-expressing plasma cells lacking CD19 is enriched in human bone marrow. Blood 2015. 125: 1739– 1748.
PubMed
Hoyer BFK, Moser AE, Hauser A, Peddinghaus A, Voigt C, Eilat D, Radbruch A, et al., Short-lived plasmablasts and long-lived plasma cells contribute to chronic humoral autoimmunity in NZB/W mice. J. Exp. Med 2004. 199: 1577– 1584.
PubMed
PMC
Tellier J and Nutt SL, Standing out from the crowd: How to identify plasma cells. Eur. J. Immunol 2017. 47: 1276– 1279.
PubMed
Pracht K, Meinzinger J, Daum P, Schulz SR, Reimer D, Hauke M, Roth E, et al., A new staining protocol for detection of murine antibody-secreting plasma cell subsets by flow cytometry. Eur. J. Immunol 2017. 47: 1389– 1392.
PubMed
Wilmore JR, Jones DD and Allman D, Protocol for improved resolution of plasma cell subpopulations by flow cytometry. Eur. J. Immunol 2017. 47: 1386– 1388.
PubMed
PMC
Odendahl MH, Mei BF, Hoyer AM, Jacobi AM, Hansen A, Muehlinghaus G, Berek C, et al., Generation of migratory antigen-specific plasma blasts and mobilization of resident plasma cells in a secondary immune response. Blood 2005. 105: 1614– 1621.
PubMed
Stohl WF, Hiepe KM, Latinis M, Thomas M, Scheinberg MA, Clarke A, Aranow C, et al., Belimumab reduces autoantibodies, normalizes low complement, and reduces select B-cell populations in patients with systemic lupus erythematosus. Arthritis Rheum. 2012. 64: 2328– 2337.
PubMed
PMC
Martinez-Murillo P, Pramanik L, Sundling C, Hultenby K, Wretenberg P, Spångberg M and Karlsson Hedestam GB, CD138 and CD31 double-positive cells comprise the functional antibody-secreting plasma cell compartment in primate bone marrow. Front. Immunol 2016. 7: 242.
PubMed
PMC
Manz RA, Thiel A and Radbruch A, Lifetime of plasma cells in the bone marrow. Nature 1997. 388: 133– 134.
PubMed
Weisel FJ, Zuccarino-Catania GV, Chikina M and Shlomchik MJ, A Temporal Switch in the Germinal Center Determines Differential Output of Memory B and Plasma Cells. Immunity 2016. 44: 116– 130.
PubMed
PMC
Jacobi AMH, Mei BF, Hoyer IM, Mumtaz IM, Thiele K, Radbruch A, Burmester GR, et al., HLA-DRhigh/CD27high plasmablasts indicate active disease in patients with systemic lupus erythematosus. Ann. Rheum. Dis 2010. 69: 305– 308.
PubMed
Hoyer BF, Mumtaz IM, Loddenkemper K, Bruns A, Sengler C, Hermann KG, Maza S, et al., Takayasu arteritis is characterised by disturbances of B-cell homeostasis and responds to B-cell depletion therapy with rituximab. Ann. Rheum. Dis 2012. 71: 75– 79.
PubMed
Espeli M, Bokers S, Giannico G, Dickinson HA, Bardsley V, Fogo AB, and Smith KG, Local renal autoantibody production in lupus nephritis. J. Am. Soc. Nephrol. JASN 2011. 22: 296– 305.
PubMed
PMC
Halliley JL, Tipton CM, Liesveld J, Rosenberg AF, Darce J, Gregoretti IV, Popova L, et al., Long-lived plasma cells are contained within the CD19(−)CD38(hi)CD138(+) subset in human bone marrow. Immunity 2015. 43: 132– 145.
PubMed
PMC
Spits H, Artis D, Colonna M, Diefenbach A, Di Santo JP, Eberl G, Koyasu S, et al., Innate lymphoid cells—A proposal for uniform nomenclature. Nat. Rev. Immunol 2013. 13: 145– 149.
PubMed
Spits H and Cupedo T, Innate lymphoid cells: Emerging insights in development, lineage relationships, and function. Annu. Rev. Immunol 2012. 30: 647– 675.
PubMed
Biron CA, Nguyen KB, Pien GC, Cousens LP and Salazar-Mather TP, Natural killer cells in antiviral defense: Function and regulation by innate cytokines. Annu. Rev. Immunol 1999. 17: 189– 220.
PubMed
Daussy C, Faure F, Mayol K, Viel S, Gasteiger G, Charrier E, Bienvenu J, et al., T-bet and Eomes instruct the development of two distinct natural killer cell lineages in the liver and in the bone marrow. J. Exp. Med 2014. 211: 563– 577.
PubMed
PMC
Klose CS, Flach M, Mohle L, Rogell L, Hoyler T, Ebert K, Fabiunke C, et al., Differentiation of type 1 ILCs from a common progenitor to all helper-like innate lymphoid cell lineages. Cell 2014. 157: 340– 356.
PubMed
Sojka DK, Plougastel-Douglas B, Yang L, Pak-Wittel MA, Artyomov MN, Ivanova Y, Zhong C, et al., Tissue-resident natural killer (NK) cells are cell lineages distinct from thymic and conventional splenic NK cells. Elife 2014. 3: e01659.
PubMed
PMC
Walker JA and McKenzie AN, Development and function of group 2 innate lymphoid cells. Curr. Opin. Immunol 2013. 25: 148– 155.
PubMed
PMC
Montaldo E, Juelke K and Romagnani C, Group 3 innate lymphoid cells (ILC3s): Origin, differentiation, and plasticity in humans and mice. Eur. J. Immunol 2015. 45: 2171– 2182.
PubMed
Robinette ML, Fuchs A, Cortez VS, Lee JS, Wang Y, Durum SK, Gilfillan S, et al., Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets. Nat. Immunol 2015. 16: 306– 317.
PubMed
PMC
Kim S, Iizuka K, Kang HS, Dokun A, French AR, Greco S, and Yokoyama WM, In vivo developmental stages in murine natural killer cell maturation. Nat. Immunol 2002. 3: 523– 528.
PubMed
Hayakawa Y and Smyth MJ, CD27 dissects mature NK cells into two subsets with distinct responsiveness and migratory capacity. J. Immunol 2006. 176: 1517– 1524.
PubMed
Chiossone L, Chaix J, Fuseri N, Roth C, Vivier E and Walzer T, Maturation of mouse NK cells is a 4-stage developmental program. Blood 2009. 113: 5488– 5496.
PubMed
Nagler A, Lanier LL, Cwirla S and Phillips JH, Comparative studies of human FcRIII-positive and negative natural killer cells. J. Immunol 1989. 143: 3183– 3191.
PubMed
Bjorkstrom NK, Riese P, Heuts F, Andersson S, Fauriat C, Ivarsson MA, Bjorklund AT, et al., Expression patterns of NKG2A, KIR, and CD57 define a process of CD56dim NK-cell differentiation uncoupled from NK-cell education. Blood 2010. 116: 3853– 3864.
PubMed
Lopez-Verges S, Milush JM, Pandey S, York VA, Arakawa-Hoyt J, Pircher H, Norris PJ, et al., CD57 defines a functionally distinct population of mature NK cells in the human CD56dimCD16+ NK-cell subset. Blood 2010. 116: 3865– 3874.
PubMed
PMC
Juelke K, Killig M, Luetke-Eversloh M, Parente E, Gruen J, Morandi B, Ferlazzo G, et al., CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells. Blood 2010. 116: 1299– 1307.
PubMed
Mebius RE, Organogenesis of lymphoid tissues. Nat. Rev. Immunol 2003. 3: 292– 303.
PubMed
Cella M, Fuchs A, Vermi W, Facchetti F, Otero K, Lennerz JKM, Doherty JM, et al., A human natural killer cell subset provides an innate source of IL-22 for mucosal immunity. Nature 2009. 457: 722– 725.
PubMed
PMC
Cupedo T, Crellin NK, Papazian N, Rombouts EJ, Weijer K, Grogan JL, Fibbe WE, et al., Human fetal lymphoid tissue-inducer cells are interleukin 17-producing precursors to RORC+ CD127+ natural killer-like cells. Nat. Immunol 2009. 10: 66– 74.
PubMed
Sanos SL, Bui VL, Mortha A, Oberle K, Heners C,Johner C, and Diefenbach A, ROR gamma t and commensal microflora are required for the differentiation of mucosal interleukin 22-producing NKp46(+) cells. Nat. Immunol 2009. 10: 83– 91.
PubMed
PMC
Satoh-Takayama N, Vosshenrich CAJ, Lesjean-Pottier S, Sawa S, Lochner M, Rattis F, Mention JJ, et al., Microbial Flora Drives Interleukin 22 Production in Intestinal NKp46(+) Cells that Provide Innate Mucosal Immune Defense. Immunity 2008. 29: 958– 970.
PubMed
Luci C, Reynders A, Ivanov II, Cognet C, Chiche L, Chasson L, Hardwigsen J, et al., Influence of the transcription factor ROR gamma t on the development of NKp46(+) cell populations in gut and skin. Nat. Immunol 2009. 10: 75– 82.
PubMed
Fort MM, Cheung J, Yen D, Li J, Zurawski SM, Lo S, Menon S, et al., IL-25 induces IL-4, IL-5, and IL-13 and Th2-associated pathologies in vivo. Immunity 2001. 15: 985– 995.
PubMed
Moro K, Yamada T, Tanabe M, Takeuchi T, Ikawa T, Kawamoto H, Furusawa J, et al., Innate production of T(H)2 cytokines by adipose tissue-associated c-Kit(+)Sca-1(+) lymphoid cells. Nature 2010. 463: 540– 544.
PubMed
Neill DR, Wong SH, Bellosi A, Flynn RJ, Daly M, Langford TK, Bucks C, et al., Nuocytes represent a new innate effector leukocyte that mediates type-2 immunity. Nature 2010. 464: 1367– 1370.
PubMed
PMC
Price AE, Liang HE, Sullivan BM, Reinhardt RL, Eisley CJ,Erle DJ, and Locksley RM, Systemically dispersed innate IL-13-expressing cells in type 2 immunity. Proc. Natl. Acad. Sci. U. S. A 2010. 107: 11489– 11494.
PubMed
PMC
Mjosberg JM, Trifari S, Crellin NK, Peters CP, van Drunen CM, Piet B, Fokkens WJ, et al., Human IL-25- and IL-33-responsive type 2 innate lymphoid cells are defined by expression of CRTH2 and CD161. Nat. Immunol 2011. 12: 1055– 1062.
PubMed
Fuchs A, Vermi W, Lee JS, Lonardi S, Gilfillan S, Newberry RD, Cella M, et al., Intraepithelial type 1 innate lymphoid cells are a unique subset of IL-12- and IL-15-responsive IFN-gamma-producing cells. Immunity 2013. 38: 769– 781.
PubMed
PMC
Bernink JH, Peters CP, Munneke M, te Velde AA, Meijer SL, Weijer K, Hreggvidsdottir HS, et al., Human type 1 innate lymphoid cells accumulate in inflamed mucosal tissues. Nat. Immunol 2013. 14: 221– 229.
PubMed
Gasteiger G, Fan X, Dikiy S, Lee SY and Rudensky AY, Tissue residency of innate lymphoid cells in lymphoid and nonlymphoid organs. Science 2015. 350: 981– 985.
PubMed
PMC
Hoyler T, Klose CS, Souabni A, Turqueti-Neves A, Pfeifer D, Rawlins EL, Voehringer D, et al., The transcription factor GATA-3 controls cell fate and maintenance of type 2 innate lymphoid cells. Immunity 2012. 37: 634– 648.
PubMed
PMC
Serafini N, Klein Wolterink RG, Satoh-Takayama N, Xu W, Vosshenrich CA, Hendriks RW, and Di Santo JP, Gata3 drives development of RORgammat+ group 3 innate lymphoid cells. J. Exp. Med 2014. 211: 199– 208.
PubMed
PMC
Sawa S, Cherrier M, Lochner M, Satoh-Takayama N, Fehling HJ, Langa F, Di Santo JP, et al., Lineage relationship analysis of RORgammat+ innate lymphoid cells. Science 2010. 330: 665– 669.
PubMed
Rankin LC, Groom JR, Chopin M, Herold MJ, Walker JA, Mielke LA, McKenzie AN, et al., The transcription factor T-bet is essential for the development of NKp46+ innate lymphocytes via the Notch pathway. Nat. Immunol 2013. 14: 389– 395.
PubMed
PMC
Klose CS, Kiss EA, Schwierzeck V, Ebert K, Hoyler T, d’Hargues Y, Goppert N, et al., A T-bet gradient controls the fate and function of CCR6-RORgammat+ innate lymphoid cells. Nature 2013. 494: 261– 265.
PubMed
Vonarbourg C, Mortha A, Bui VL, Hernandez PP, Kiss EA, Hoyler T, Flach M, et al., Regulated expression of nuclear receptor RORgammat confers distinct functional fates to NK cell receptor-expressing RORgammat(+) innate lymphocytes. Immunity 2010. 33: 736– 751.
PubMed
PMC
Villanova F, Flutter B, Tosi I, Grys K, Sreeneebus H, Perera GK, Chapman A, et al., Characterization of innate lymphoid cells in human skin and blood demonstrates increase of NKp44+ ILC3 in psoriasis. J. Invest. Dermatol 2014. 134: 984– 991.
PubMed
PMC
Teunissen MB, Munneke JM, Bernink JH, Spuls PI, Res PC, Te Velde A, Cheuk S, et al., Composition of innate lymphoid cell subsets in the human skin: Enrichment of NCR(+) ILC3 in lesional skin and blood of psoriasis patients. J. Invest. Dermatol 2014. 134: 2351– 2360.
PubMed
Wojno ED, Monticelli LA, Tran SV, Alenghat T, Osborne LC, Thome JJ, Willis C, et al., The prostaglandin D(2) receptor CRTH2 regulates accumulation of group 2 innate lymphoid cells in the inflamed lung. Mucosal Immunol. 2015. 8: 1313– 1323.
PubMed
PMC
Marquardt N, Beziat V, Nystrom S, Hengst J, Ivarsson MA, Kekalainen E, Johansson H, et al., Cutting edge: Identification and characterization of human intrahepatic CD49a+ NK cells. J. Immunol 2015. 194: 2467– 2471.
PubMed
Vacca P, Montaldo E, Croxatto D, Loiacono F, Canegallo F, Venturini PL, Moretta L, et al., Identification of diverse innate lymphoid cells in human decidua. Mucosal Immunol. 2015. 8: 254– 264.
PubMed
Montaldo E, Vacca P, Chiossone L, Croxatto D, Loiacono F, Martini S, Ferrero S, et al., Unique eomes(+) NK cell subsets are present in uterus and decidua during early pregnancy. Front. Immunol 2015. 6: 646.
PubMed
PMC
Ryon JJ, Isolation of mononuclear cells from tonsillar tissue. Curr. Protoc. Immunol 2009. 86: 7.8.1– 7.8.4.
PubMed
Paclik D, Stehle C, Lahmann A, Hutloff A and Romagnani C, ICOS regulates the pool of group 2 innate lymphoid cells under homeostatic and inflammatory conditions in mice. Eur. J. Immunol 2015. 45: 2766– 2772.
PubMed
Herberman RB, Nunn ME, Holden HT and Lavrin DH, Natural cytotoxic reactivity of mouse lymphoid cells against syngeneic and allogeneic tumors. II. Characterization of effector cells. Int. J. Cancer 1975. 16: 230– 239.
PubMed
Ljunggren HG and Kärre K, In search of the ‘missing self’: MHC molecules and NK cell recognition. Immunol. Today 1990. 11: 237– 244.
PubMed
Moretta A, Bottino C, Mingari MC, Biassoni R and Moretta L, What is a natural killer cell?. Nat. Immunol 2002. 3: 6– 8.
PubMed
Vivier E, Tomasello E, Baratin M, Walzer T and Ugolini S, Functions of natural killer cells. Nat. Immunol 2008. 9: 503– 510.
PubMed
Lopez-Botet M, Perez-Villar JJ, Carretero M, Rodriguez A, Melero I, Bellon T, Llano M, et al., Structure and function of the CD94 C-type lectin receptor complex involved in recognition of HLA class I molecules. Immunol. Rev 1997. 155: 165– 174.
PubMed
Braud VM, Allan DS, O’Callaghan CA, Soderstrom K, D’Andrea A, Ogg GS, Lazetic S, et al., HLA-E binds to natural killer cell receptors 94/NKG2A, B and C. Nature 1998. 391: 795– 799.
PubMed
Moretta A, Bottino C, Vitale M, Pende D, Biassoni R, Mingari MC, and Moretta L, Receptors for HLA-class I molecules in human Natural Killer cells. Ann. Rev. Immunol 1996. 14: 619– 648.
PubMed
Parham P, MHC class I molecules and KIRs in human history, health and survival. Nat. Rev. Immunol 2005. 5: 201– 214.
PubMed
Moretta A, Bottino C, Vitale M, Pende D, Cantoni C, Mingari MC, Biassoni R, et al., Activating receptors and coreceptors involved in human natural killer cell-mediated cytolysis. Annu. Rev. Immunol 2001. 19: 197– 223.
PubMed
Vivier E, Raulet DH, Moretta A, Caligiuri MA, Zitvogel L, Lanier LL, Yokoyama WM, et al., Innate or adaptive immunity? The example of natural killer cells. Science 2011. 331: 44– 49.
PubMed
PMC
Raulet DH, Roles of the NKG2D immunoreceptor and its ligands. Nat. Rev. Immunol 2003. 3: 781– 790.
PubMed
Moretta A, Sivori S, Vitale M, Pende D, Morelli L, Augugliaro R, Bottino C, et al., Existence of both inhibitory(p58) and activatory (p50) receptors for HLA. C molecules in human natural killer cells. J. Exp. Med 1995. 182: 875– 884.
PubMed
PMC
Wagtmann N, Biassoni R, Cantoni C, Verdiani S, Malnati MS, Vitale M, Bottino C, et al., Molecular clones of the p58 natural killer cell receptor reveal Ig-related molecules with diversity in both the extra- and intracellular domains. Immunity 1995. 2: 439– 449.
PubMed
Sivori S, Cantoni C, Parolini S, Marcenaro E, Moretta L and Moretta A, IL21 induces both rapid maturation of human CD34+ cell precursors towards NK cells and acquisition of surface killer Ig-like receptors. Eur. J. Immunol 2003. 33: 3439– 3447.
PubMed
Freud AG and Caligiuri MA, Human natural killer cell development. Immunol. Rev 2006. 214: 56– 72.
PubMed
Caligiuri MA, Zmuidzinas A, Manley TJ, Levine H, Smith KA and Ritz J, Functional consequences of interleukin 2 receptor expression on resting human lymphocytes: Identification of a novel natural killer cell subset with high affinity receptors. J. Exp. Med 1990. 171: 1509– 1526.
PubMed
PMC
Carson WE, Fehniger TA and Caligiuri MA, CD56bright natural killer cell subsets: Characterization of distinct functional responses to interleukin-2 and the C-kit ligand. Eur. J. Immunol 1997. 27: 354– 360.
PubMed
Frey M, Packianathan NB, Fehniger TA, Ross ME, Wang WC, Stewart CC, Caligiuri MA, et al., Differential expression and function of L-selectin on CD56bright and CD56dim natural killer cell subsets. J. Immunol 1998. 161: 400– 408.
PubMed
Campbell JJ, Qin S, Unutmaz D, Soler D, Murphy KE, Hodge MR, Wu L, et al., Unique subpopulations of CD56+ NK and NK-T peripheral blood lymphocytes identified by chemokine receptor expression repertoire. J. Immunol 2001. 166: 6477– 6482.
PubMed
Robertson MJ, Role of chemokines in the biology of natural killer cells. J. Leukoc. Biol 2002. 71: 173– 183.
PubMed
Lima M, Leander M, Santos M, Santos AH, Lau C, Queirós ML, Gonçalves M, et al., Chemokine receptor expression on normal blood CD56+ NK-cells elucidates cell partners that comigrate during the innate and adaptive immune responses and identifies a transitional NK-cell population. J. Immunol. Res 2015. 2015: 839684.
PubMed
PMC
De Maria A, Bozzano F, Cantoni C and Moretta L, Revisiting human natural killer cell subset function revealed cytolytic CD56 dim CD16+ NK cells as rapid producers of abundant IFN-γ on activation. Proc. Natl. Acad. Sci. U. S. A 2011. 108: 728– 732.
PubMed
PMC
Fauriat C, Long EO, Ljunggren HG and Bryceson YT, Regulation of human NK-cell cytokine and chemokine production by target cell recognition. Blood 2010. 115: 2167– 2176.
PubMed
PMC
Del Zotto G, Marcenaro E, Vacca P, Sivori S, Pende D, Della Chiesa M, Moretta F, et al., Markers and function of human NK cells in normal and pathological conditions. Cytometry B Clin. Cytom 2017. 92: 100– 114.
PubMed
Björkström NK, Riese P, Heuts F, Andersson S, Fauriat C, Ivarsson MA, Björklund AT, et al., Expression patterns of NKG2A, KIR, and CD57 define a process of CD56dim NK-cell differentiation uncoupled from NK-cell education. Blood 2010. 116: 3853– 3864.
PubMed
Guma M, Angulo A, Vilches C, Gomez-Lozano N, Malats N and Lopez-Botet M, Imprint of human cytomegalovirus infection on the NK cell receptor repertoire. Blood 2004. 104: 3664– 3671.
PubMed
Della Chiesa M, Falco M, Podestà M, Locatelli F, Moretta L, Frassoni F, and Moretta A, Phenotypic and functional heterogeneity of human NK cells developing after umbilical cord blood transplantation: A role for human cytomegalovirus? Blood 2012. 119: 399– 410.
PubMed
Malmberg KJ, Beziat V and Ljunggren HG, Spotlight on NKG2C and the human NK-cell response to CMV infection. Eur. J. Immunol 2012. 42: 3141– 3145.
PubMed
Muccio L, Bertaina A, Falco M, Pende D, Meazza R, Lopez-Botet M, Moretta L, et al., Analysis of memory-like natural killer cells in human cytomegalovirus-infected children undergoing αβ+T and B cell-depleted hematopoietic stem cell transplantation for hematological malignancies. Haematologica 2016. 101: 371– 381.
PubMed
PMC
Pesce S, Greppi M, Tabellini G, Rampinelli F, Parolini S, Olive D, Moretta L, et al., Identification of a subset of human natural killer cells expressing high levels of programmed death 1: A phenotypic and functional characterization. J. Allergy Clin. Immunol 2017. 139: 335– 46.
PubMed
Sivori S, Falco M, Marcenaro E, Parolini S, Biassoni R, Bottino C, Moretta L, et al., Early expression of triggering receptors and regulatory role of 2B4 in human natural killer cell precursors undergoing in vitro differentiation. Proc. Natl. Acad. Sci. U. S. A 2002. 99: 4526– 4531.
PubMed
PMC
Vacca P, Pietra G, Falco M, Romeo E, Bottino C, Bellora F, Prefumo F, et al., Analysis of natural killer cells isolated from human decidua: Evidence that 2B4 (CD244) functions as an inhibitory receptor and blocks NK-cell function. Blood 2006. 108: 4078– 4085.
PubMed
Vacca P, Vitale C, Montaldo E, Conte R, Cantoni C, Fulcheri E, Darretta V, et al., CD34+ hematopoietic precursors are present in human decidua and differentiate into natural killer cells upon interaction with stromal cells. Proc. Natl. Acad. Sci. U. S. A 2011. 108: 2402– 2407.
PubMed
PMC
Hanna J, Goldman-Wohl D, Hamani Y, Avraham I, Greenfield C, Natanson-Yaron S, Prus D, et al., Decidual NK cells regulate key developmental processes at the human fetal-maternal interface. Nat. Med 2006. 12: 1065– 1074.
PubMed
Fehniger TA, Cooper MA, Nuovo GJ, Cella M, Facchetti F, Colonna M, and Caligiuri MA, CD56bright natural killer cells are present in human lymph nodes and are activated by T cell derived IL-2: A potential new link between adaptive and innate immunity. Blood 2003. 101: 3052.
PubMed
Ferlazzo G, Thomas D, Lin SL, Goodman K, Morandi B, Muller WA, Moretta A, et al., The abundant NK cells in human secondary lymphoid tissues require activation to express killer cell Ig-like receptors and become cytolytic. J. Immunol 2004. 172: 1455– 1462.
PubMed
van Furth R and Cohn ZA, The origin and kinetics of mononuclear phagocytes. J. Exp. Med 1968. 128: 415– 435.
PubMed
PMC
Mildner A and Jung S, Development and function of dendritic cell subsets. Immunity 2014. 40: 642– 656.
PubMed
Merad M, Sathe P, Helft J, Miller J and Mortha A, The dendritic cell lineage: Ontogeny and function of dendritic cells and their subsets in the steady state and the inflamed setting. Annu. Rev. Immunol 2013. 31: 563– 604.
PubMed
PMC
Ginhoux F and Jung S, Monocytes and macrophages: Developmental pathways and tissue homeostasis. Nat. Rev. Immunol 2014. 14: 392– 404.
PubMed
Varol C, Mildner A and Jung S, Macrophages: Development and tissue specialization. Annu. Rev. Immunol 2015. 33: 643– 675.
PubMed
Guilliams M, Ginhoux F, Jakubzick C, Naik SH, Onai N, Schraml BU, Segura E, et al., Dendritic cells, monocytes and macrophages: A unified nomenclature based on ontogeny. Nat. Rev. Immunol 2014. 14: 571– 578.
PubMed
PMC
Geissmann F, Jung S and Littman DR, Blood monocytes consist of two principal subsets with distinct migratory properties. Immunity 2003. 19: 71– 82.
PubMed
Hettinger J, Richards DM, Hansson J, Barra MM, Joschko A-C, Krijgsveld J, and Feuerer M, Origin of monocytes and macrophages in a committed progenitor. Nat. Immunol 2013. 14: 821– 830.
PubMed
Fogg DK, Sibon C, Miled C, Jung S, Aucouturier P, Littman DR, Cumano A, et al., A clonogenic bone marrow progenitor specific for macrophages and dendritic cells. Science 2006. 311: 83– 87.
PubMed
Varol C, Landsman L, Fogg DK, Greenshtein L, Gildor B, Margalit R, Kalchenko V, et al., Monocytes give rise to mucosal, but not splenic, conventional dendritic cells. J. Exp. Med 2007. 204: 171– 180.
PubMed
PMC
Mildner A, Yona S and Jung S, A close encounter of the third kind: Monocyte-derived cells. Adv. Immunol 2013. 120: 69– 103.
PubMed
Yona S, Kim K-W, Wolf Y, Mildner A, Varol D, Breker M, Strauss-Ayali D, et al., Fate mapping reveals origins and dynamics of monocytes and tissue macrophages under homeostasis. Immunity 2013. 38: 79– 91.
PubMed
PMC
Auffray C, Fogg D, Garfa M, Elain G, Join-Lambert O, Kayal S, Sarnacki S, et al., Monitoring of blood vessels and tissues by a population of monocytes with patrolling behavior. Science 2007. 317: 666– 670.
PubMed
Wynn TA, Chawla A and Pollard JW, Macrophage biology in development, homeostasis and disease. Nature 2013. 496: 445– 455.
PubMed
PMC
Amit I, Winter DR and Jung S, The role of the local environment and epigenetics in shaping macrophage identity and their effect on tissue homeostasis. Nat. Immunol 2016. 17: 18– 25.
PubMed
Bar-On L and Jung S, Defining dendritic cells by conditional and constitutive cell ablation. Immunol. Rev 2010. 234: 76– 89.
PubMed
Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, Mildner A, et al., Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 2014. 343: 776– 779.
PubMed
PMC
Gross M, Salame T-M and Jung S, Guardians of the gut—Murine intestinal macrophages and dendritic cells. Front. Immunol 2015. 6: 254.
PubMed
PMC
Palframan RT, Jung S, Cheng G, Weninger W, Luo Y, Dorf M, Littman DR, et al., Inflammatory chemokine transport and presentation in HEV: A remote control mechanism for monocyte recruitment to lymph nodes in inflamed tissues. J. Exp. Med 2001. 194: 1361– 1373.
PubMed
PMC
Zigmond E, Samia-Grinberg S, Pasmanik-Chor M, Brazowski E, Shibolet O, Halpern Z, and Varol C, Infiltrating monocyte-derived macrophages and resident kupffer cells display different ontogeny and functions in acute liver injury. J. Immunol 2014. 193: 344– 353.
PubMed
Scott CL, Zheng F, De Baetselier P, Martens L, Saeys Y, De Prijck S, Lippens S, et al., Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells. Nat. Commun 2016. 7: 10321.
PubMed
PMC
Ginhoux F, Greter M, Leboeuf M, Nandi S, See P, Gokhan S, Mehler MF, et al., Supporting Fate mapping analysis reveals that adult microglia derive from primitive macrophages. Science 2010. 330: 841– 845.
PubMed
PMC
Prinz M, Priller J, Sisodia SS and Ransohoff RM, Heterogeneity of CNS myeloid cells and their roles in neurodegeneration. Nat. Neurosci 2011. 14: 1227– 1235.
PubMed
Niess JH, Brand S, Gu X, Landsman L, Jung S, McCormick BA, Vyas JM, et al., CX3CR1-mediated dendritic cell access to the intestinal lumen and bacterial clearance. Science 2005. 307: 254– 258.
PubMed
Varol C, Yona S and Jung S, Origins and tissue-context-dependent fates of blood monocytes. Immunol. Cell Biol 2009. 87: 30– 38.
PubMed
Bogunovic M, Ginhoux F, Helft J, Shang L, Hashimoto D, Greter M, Liu K, et al., Origin of the lamina propria dendritic cell network. Immunity 2009. 31: 513– 525.
PubMed
PMC
Tamoutounour S, Henri S, Lelouard H, de Bovis B, de Haar C, van der Woude CJ, Woltman AM, et al., CD64 distinguishes macrophages from dendritic cells in the gut and reveals the Th1-inducing role of mesenteric lymph node macrophages during colitis. Eur. J. Immunol 2012. 42: 3150– 3166.
PubMed
Bain CC, Bravo-Blas A, Scott CL, Perdiguero EG, Geissmann F, Henri S, Malissen B, et al., Constant replenishment from circulating monocytes maintains the macrophage pool in the intestine of adult mice. Nat. Immunol 2014. 15: 929– 937.
PubMed
PMC
Welty NE, Staley C, Ghilardi N, Sadowsky MJ, Igyártó BZ and Kaplan DH, Intestinal lamina propria dendritic cells maintain T cell homeostasis but do not affect commensalism. J. Exp. Med 2013. 210: 2011– 2024.
PubMed
PMC
Cerovic V, Bain CC, Mowat AM and Milling SWF, Intestinal macrophages and dendritic cells: What’s the difference?. Trends Immunol. 2014. 35: 270– 277.
PubMed
Guilliams M and van de Laar L, A Hitchhiker’s guide to myeloid cell subsets: Practical implementation of a novel mononuclear phagocyte classification system. Front. Immunol 2015. 6: 406.
PubMed
PMC
Malissen B, Tamoutounour S and Henri S, The origins and functions of dendritic cells and macrophages in the skin. Nat. Rev. Immunol 2014. 14: 417– 428.
PubMed
Guilliams M, Lambrecht BN and Hammad H, Division of labor between lung dendritic cells and macrophages in the defense against pulmonary infections. Mucosal Immunol. 2013. 6: 464– 473.
PubMed
Hoff J, Methods of blood collection in the mouse. Lab. Anim 2000. 29: 47– 53.
Munoz LE, Maueroder C, Chaurio R, Berens C, Herrmann M and Janko C, Colourful death: Six-parameter classification of cell death by flow cytometry–dead cells tell tales. Autoimmunity 2013. 46: 336– 341.
PubMed
Maueröder C, Chaurio RA, Dumych T, Podolska M, Lootsik MD, Culemann S, Friedrich RP, et al., A blast without power—Cell death induced by the tuberculosis-necrotizing toxin fails to elicit adequate immune responses. Cell Death Differ. 2016. 23: 1016– 1025.
PubMed
PMC
Casanova-Acebes M, Pitaval C, Weiss LA, Nombela-Arrieta C, Chevre R, A-Gonzalez N, Kunisaki Y, et al., Rhythmic modulation of the hematopoietic niche through neutrophil clearance. Cell 2013. 153: 1025– 1035.
PubMed
PMC
Bianco P, Cao X, Frenette PS, Mao JJ, Robey PG,Simmons PJ, and Wang CY, The meaning, the sense and the significance: Translating the science of mesenchymal stem cells into medicine. Nat. Med 2013. 19: 35– 42.
PubMed
PMC
Frenette PS, Pinho S, Lucas D and Scheiermann C, Mesenchymal stem cell: Keystone of the hematopoietic stem cell niche and a stepping-stone for regenerative medicine. Annu. Rev. Immunol 2013. 31: 285– 316.
PubMed
Mendelson A and Frenette PS, Hematopoietic stem cell niche maintenance during homeostasis and regeneration. Nat. Med 2014. 20: 833– 846.
PubMed
PMC
Ding L and Morrison SJ, Haematopoietic stem cells and early lymphoid progenitors occupy distinct bone marrow niches. Nature 2013. 495: 231– 235.
PubMed
PMC
Ding L, Saunders TL, Enikolopov G and Morrison SJ, Endothelial and perivascular cells maintain haematopoietic stem cells. Nature 2012. 481: 457– 462.
PubMed
PMC
Greenbaum A, Hsu YM, Day RB, Schuettpelz LG, Christopher MJ, Borgerding JN, Nagasawa T, et al., CXCL12 in early mesenchymal progenitors is required for haematopoietic stem-cell maintenance. Nature 2013. 495: 227– 230.
PubMed
PMC
Kunisaki Y, Bruns I, Scheiermann C, Ahmed J, Pinho S, Zhang D, Mizoguchi T, et al., Arteriolar niches maintain haematopoietic stem cell quiescence. Nature 2013. 502: 637– 643.
PubMed
PMC
Dominici M, Le Blanc K, Mueller I, Slaper-Cortenbach I, Marini F, Krause D, Deans R, et al., Minimal criteria for defining multipotent mesenchymal stromal cells. The International Society for Cellular Therapy position statement. Cytotherapy 2006. 8: 315– 317.
PubMed
Morikawa S, Mabuchi Y, Kubota Y, Nagai Y, Niibe K, Hiratsu E, Suzuki S, et al., Prospective identification, isolation, and systemic transplantation of multipotent mesenchymal stem cells in murine bone marrow. J. Exp. Med 2009. 206: 2483– 2496.
PubMed
PMC
Pinho S, Lacombe J, Hanoun M, Mizoguchi T, Bruns I,Kunisaki Y, and Frenette PS, PDGFRalpha and CD51 mark human nestin + sphere-forming mesenchymal stem cells capable of hematopoietic progenitor cell expansion. J. Exp. Med 2013. 210: 1351– 1367.
PubMed
PMC
Sacchetti B, Funari A, Michienzi S, Di Cesare S, Piersanti S, Saggio I, Tagliafico E, et al., Self-renewing osteoprogenitors in bone marrow sinusoids can organize a hematopoietic microenvironment. Cell 2007. 131: 324– 336.
PubMed
Suire C, Brouard N, Hirschi K and Simmons PJ, Isolation of the stromal-vascular fraction of mouse bone marrow markedly enhances the yield of clonogenic stromal progenitors. Blood 2012. 119: e86– e95.
PubMed
PMC
Mendez-Ferrer S, Michurina TV, Ferraro F, Mazloom AR, Macarthur BD, Lira SA, Scadden DT, et al., Mesenchymal and haematopoietic stem cells form a unique bone marrow niche. Nature 2010. 466: 829– 834.
PubMed
PMC
Mizoguchi T, Pinho S, Ahmed J, Kunisaki Y, Hanoun M, Mendelson A, Ono N, et al., Osterix marks distinct waves of primitive and definitive stromal progenitors during bone marrow development. Dev. Cell 2014. 29: 340– 349.
PubMed
PMC
Park D, Spencer JA, Koh BI, Kobayashi T, Fujisaki J, Clemens TL, Lin CP, et al., Endogenous bone marrow MSCs are dynamic, fate-restricted participants in bone maintenance and regeneration. Cell Stem Cell 2012. 10: 259– 272.
PubMed
PMC
Sugiyama T, Kohara H, Noda M and Nagasawa T, Maintenance of the hematopoietic stem cell pool by CXCL12-CXCR4 chemokine signaling in bone marrow stromal cell niches. Immunity 2006. 25: 977– 988.
PubMed
Zhou BO, Yue R, Murphy MM, Peyer JG and Morrison SJ, Leptin-receptor-expressing mesenchymal stromal cells represent the main source of bone formed by adult bone marrow. Cell Stem Cell 2014. 15: 154– 168.
PubMed
PMC
Morrison SJ, Uchida N and Weissman IL, The biology of hematopoietic stem cells. Annu. Rev. Cell Dev. Biol 1995. 11: 35– 71.
PubMed
Spangrude GJ, Brooks DM and Tumas DB, Long-term repopulation of irradiated mice with limiting numbers of purified hematopoietic stem cells: In vivo expansion of stem cell phenotype but not function. Blood 1995. 85: 1006– 1016.
PubMed
Cheshier SH, Morrison SJ, Liao X and Weissman IL, In vivo proliferation and cell cycle kinetics of long-term self-renewing hematopoietic stem cells. Proc. Natl. Acad. Sci. U. S. A 1999. 96: 3120– 3125.
PubMed
PMC
Calvi LM, Adams GB, Weibrecht KW, Weber JM, Olson DP, Knight MC, Martin RP, et al., Osteoblastic cells regulate the haematopoietic stem cell niche. Nature 2003. 425: 841– 846.
PubMed
Arai F, Hirao A, Ohmura M, Sato H, Matsuoka S, Takubo K, Ito K, et al., Tie2/angiopoietin-1 signaling regulates hematopoietic stem cell quiescence in the bone marrow niche. Cell 2004. 118: 149– 161.
PubMed
Zhang J, Niu C and Ye L, Identification of the haematopoietic stem cell niche and control of the niche size. Nature 2003. 425: 836– 841.
PubMed
Kajikhina K and Melchers F, Chemokine polyreactivity of IL7Rα+CSF-1R+ lympho-myeloid progenitors in the developing fetal liver. Sci. Rep 2015. 5: 12817.
PubMed
PMC
Mikkola HK and Orkin SH, The journey of developing hematopoietic stem cells. Development 2006. 133: 3733– 3744.
PubMed
Ciriza J and García-Ojeda ME, Expression of migration-related genes is progressively upregulated in murine Lineage-Sca-1+c-Kit+ population from the fetal to adult stages of rdevelopment. Stem Cell Res. Ther 2010. 1: 14.
PubMed
PMC
Simsek T, Kocabas F, Zheng J, Deberardinis RJ, Mahmoud AI, Olson EN, Schneider JW, et al., The distinct metabolic profile of hematopoietic stem cells reflects their location in a hypoxic niche. Cell Stem Cell 2010. 7: 380– 390.
PubMed
PMC
Spangrude GJ, Heimfeld S and Weissman IL, Purification and characterization of mouse hematopoietic stem cells. Science 1988. 241: 58– 62.
PubMed
Ikuta K and Weissman IL, Evidence that hematopoietic stem cells express mouse c-kit but do not depend on steel factor for their generation. Proc. Natl. Acad. Sci. U. S. A 1992. 89: 1502– 1506.
PubMed
PMC
Morrison SJ and Weissman IL, The long-term repopulating subset of hematopoietic stem cells is deterministic and isolatable by phenotype. Immunity 1994. 1: 661– 673.
PubMed
Okada S, Nakauchi H, Nagayoshi K, Nishikawa S, Miura Y and Suda T, In vivo and in vitro stem cell function of c-kit- and Sca-1-positive murine hematopoietic cells. Blood 1992. 80: 3044– 3050.
PubMed
Kiel MJ, Yilmaz OH, Iwashita T, Yilmaz OH, Terhorst C and Morrison SJ, SLAM family receptors distinguish hematopoietic stem and progenitor cells and reveal endothelial niches for stem cells. Cell 2005. 121: 1109– 1121.
PubMed
Papathanasiou P, Attema JL, Karsunky H, Xu J, Smale ST and Weissman IL, Evaluation of the long-term reconstituting subset of hematopoietic stem cells with CD150. Stem Cells 2009. 27: 2498– 2508.
PubMed
PMC
Yilmaz OH, Kiel MJ, and Morrison SJ, SLAM family markers are conserved among hematopoietic stem cells from old and reconstituted mice and markedly increase their purity. Blood 2006. 107: 924– 930.
PubMed
PMC
Balazs AB, Fabian AJ, Esmon CT and Mulligan RC, Endothelial protein C receptor (CD201) explicitly identifies hematopoietic stem cells in murine bone marrow. Blood 2006. 107: 2317– 2321.
PubMed
PMC
Osawa M, Hanada KI, Hamada H and Nakauchi H, Long-term lymphohematopoietic reconstitution by a single CD34–low/negative hematopoietic stem cell. Science 1996. 273: 242– 245.
PubMed
Jones RJ, Collector MI, Barber JP, Vala MS, Fackler MJ, May WS, Griffin CA, et al., Characterization of mouse lymphohematopoietic stem cells lacking spleen colony-forming activity. Blood 1996. 88: 487– 491.
PubMed
Zhou S, Schuetz JD, Bunting KD, Colapietro AM and Sampath J, The ABC transporter Bcrp1/ABCG2 is expressed in a wide variety of stem cells and is a molecular determinant of the side-population phenotype. Nat. Med 2001. 7: 1028– 1034.
PubMed
Ergen AV, Jeong M, Lin KK, Challen GA and Goodell MA, Isolation and characterization of mouse side population cells. In Helgason C and Miller C (Eds.) Basic cell culture protocols. Methods in Molecular Biology, vol 946. Humana Press, New York, NY: 2013. 151– 162.
PubMed
Herbein G, Sovalat H, Wunder E, Baerenzung M, Bachorz J, Lewandowski H, Schweitzer C, et al., Isolation and identification of two CD34+ cell subpopulations from normal human peripheral blood. Stem Cells 1994. 12: 187– 197.
PubMed
Majeti R, Park CJ and Weissman IL, Identification of a hierarchy of multipotent hematopoietic progenitors in human cord blood. Cell Stem Cell 2007. 1: 635– 645.
PubMed
PMC
Tornack J, Reece S, Bauer WM, Vogelzang A, Bandermann S, Zedler U, Stingl G, et al., Human and mouse hematopoietic stem cells are a depot for dormant Mycobacterium tuberculosis. PLoS One 2017. 12: e0169119.
PubMed
PMC
Lansdorp PM, Sutherland HJ and Eaves CJ, Selective expression of CD45 isoforms on functional subpopulations of CD34+ hemopoietic cells from human bone marrow. J. Exp. Med 1990. 172: 363– 366.
PubMed
PMC
van Dongen JJM, Lhermitte L, Böttcher S, Almeida J, van der Velden JVH, Flores-Montero J, Rawstron A, et al., EuroFlow antibody panels for standardized n-dimensional flow cytometric immunophenotyping of normal, reactive and malignant leukocytes. Leukemia 2012. 26: 1908– 1975.
PubMed
PMC
Streitz M, Miloud T, Kapinsky M, Reed MR, Magari R, Geissler EK, Hutchinson JA, et al., Standardization of whole blood immune phenotype monitoring for clinical trials: Panels and methods from the ONE study. Transplant Res. 2013. 2: 17.
PubMed
PMC
Alix-Panabières C and Pantel K, Challenges in circulating tumour cell research. Nat. Rev. Cancer 2014. 14: 623– 631.
PubMed
Schumacher T and Schreiber RD, Neoantigens in cancer immunotherapy. Science 2015. 348: 69– 74.
PubMed
Grizzi F, Mirandola L, Qehajaj D, Cobos E, Figueroa JA and Chiriva-Internati M, Cancer-testis antigens and immunotherapy in the light of cancer complexity. Int. Rev. Immunol 2015. 34: 143– 153.
PubMed
Garrido F, Aptsiauri N, Doorduijn EM, Garcia Lora AM and van Hall T, The urgent need to recover MHC class I in cancers for effective immunotherapy. Curr. Opin. Immunol 2016. 39: 44– 51.
PubMed
PMC
Raulet DH, Gasser S, Gowen BG, Deng W and Jung H, Regulation of ligands for the NKG2D activating receptor. Annu. Rev. Immunol 2013. 31: 413– 441.
PubMed
PMC
Sers C, Kuner R, Fak CS, Lund P, Sueltmann H, Braun M, Buness A, et al., Down-regulation of HLA Class I and NKG2D ligands through a concerted action of MAPK and DNA methyltransferases in colorectal cancer cells. Int. J. Cancer 2009. 125: 1626– 1639.
PubMed
Luo Z, Wu RR, Lv L, Li P, Zhang LY, Hao QL, Li W, Prognostic value of CD44 expression in non-small cell lung cancer: A systematic review. Int. J. Clin. Exp. Pathol 2014. 7: 3632– 3646.
PubMed
PMC
Paulis YW, Huijbers EJ, van der Schaft DW, Soetekouw PM, Pauwels P, Tjan-Heijnen VC, Griffioen AW, CD44 enhances tumor aggressiveness by promoting tumor cell plasticity. Oncotarget 2015. 6: 19634– 19646.
PubMed
PMC
http://www.cancerresearchuk.org/about-cancer/what-is-cancer/how-cancer-starts/types-of-cancer#carcinomas
.
Weng YR, Cui Y and Fang JY, Biological functions of Cytokeratin 18 in cancer. Mol. Cancer Res 2012. 10: 485– 493.
PubMed
Appert-Collin A, Hubert P, Crémel G and Bennasroune A, Role of ErbB receptors in cancer cell migration and invasion. Front. Pharmacol 2015. 6: 283.
PubMed
PMC
http://www.cancer.org/cancer/breastcancer/detailedguide/breast-cancer-breast-cancer-types
.
Park JW, Lee JK, Phillips JW, Huang P, Cheng D, Huang J, Witte ON, Prostate epithelial cell of origin determines cancer differentiation state in an organoid transformation assay. Proc. Natl. Acad. Sci. U. S. A 2016. 113: 4482– 4487.
PubMed
PMC
http://screening.iarc.fr/colpochap.php?chap=2
.
https://www.iarc.fr/en/publications/pdfs-online/pat-gen/bb2/bb2-chap1.pdf
.
http://www.cancer.org/cancer/bladdercancer/detailedguide/bladder-cancer-what-is-bladder-cancer
.
Hruban RH and Fukushima N, Pancreatic adenocarcinoma: Update on the surgical pathology of carcinomas of ductal origin and PanINs. Mod. Pathol 2007. 20: 61– 70.
PubMed
http://www.cancer.net/cancer-types/sarcoma-soft-tissue/overview
.
DuBois SG, Epling CL, Teague J, Matthay KK and Sinclair E, Flow cytometric detection of Ewing sarcoma cells in peripheral blood and bone marrow. Pediatr Blood Cancer 2010. 54: 13– 18.
PubMed
PMC
Avey D, Brewers B and Zhu F, Recent advances in the study of Kaposi’s sarcoma-associated herpesvirus replication and athogenesis. Virol. Sin 2015. 30: 130– 145.
PubMed
PMC
Deel MD, Li JJ, Crose LE and Linardic CM, A Review: Molecular aberrations within hippo signaling in bone and soft-tissue sarcomas. Front. Oncol 2015. 5: 190.
PubMed
PMC
Sullivan RJ, The role of mitogen-activated protein targeting in melanoma beyond BRAFV600. Curr. Opin. Oncol 2016. 28: 185– 191.
PubMed
Sucker A, Zhao F, Real B, Heeke C, Bielefeld N, Maßen S, Horn S, et al., Genetic evolution of T cell resistance in the course of melanoma progression. Clin. Cancer Res 2014. 20: 6593– 6604.
PubMed
PMC
Lakshmikanth T, Burke S, Ali TH, Kimpfler S, Ursini F, Ruggeri L, Capanni M, et al., NCRs and DNAM-1 mediate NK cell recognition and lysis of human and mouse melanoma cell lines in vitro and in vivo. J. Clin. Invest 2009. 119: 1251– 1263.
PubMed
PMC
Binder DC, Davis AA and Wainwright DA, Immunotherapy for cancer in the central nervous system: Current and future directions. Oncoimmunology 2015. 5: e1082027.
PubMed
PMC
Razavi SM, Lee KE, Jin BE, Aujla PS, Gholamin S and Li G, Immune evasion strategies of glioblastoma. Front. Surg 2016. 3: 11.
PubMed
PMC
Seifert M, Garbe M, Friedrich B, Mittelbronn M, and Klink B, Comparative transcriptomics reveals similarities and differences between astrocytoma grades. BMC Cancer 2015. 15: 952.
PubMed
PMC
Dranoff G, Experimental mouse tumour models: What can be learnt about human cancer immunology? Nat. Rev. Immunol 2012. 12: 61– 66.
PubMed
Morton JJ, Bird G, Fefaeli Y and Jimeno A, Humanized mouse xenograft models: Narrowing the tumor-microenvironment gap. Cancer Res. 2016. Sep 1. pii: canres.1260.2016. [Epub ahead of print].
PubMed
PMC
Hanahan D and Weinberg RA, Hallmarks of cancer—The next generation. Cell 2011. 144: 646– 674.
PubMed
Galuzzi L, Vacchelli E, Bravo-San Pedro JM, Buqué A, Senovilla L, Baracco EE, Bloy N, et al., Classification of current anticancer immunotherapies. Oncotarget 2015. 5: 12472– 12508.
PubMed
PMC
