-
Something wrong with this record ?
Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1
M. Mehnert, W. Li, C. Wu, B. Salovska, Y. Liu,
Language English Country Germany
Document type Journal Article, Research Support, Non-U.S. Gov't
- MeSH
- Chromatin physiology MeSH
- CRISPR-Cas Systems MeSH
- Gene Deletion * MeSH
- Gene Editing methods MeSH
- HeLa Cells MeSH
- Humans MeSH
- Cell Line, Tumor MeSH
- Cell Proliferation genetics MeSH
- HMGN1 Protein genetics MeSH
- Proteomics methods MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
CRISPR-Cas gene editing holds substantial promise in many biomedical disciplines and basic research. Due to the important functional implications of non-histone chromosomal protein HMG-14 (HMGN1) in regulating chromatin structure and tumor immunity, gene knockout of HMGN1 is performed by CRISPR in cancer cells and the following proteomic regulation events are studied. In particular, DIA mass spectrometry (DIA-MS) is utilized, and more than 6200 proteins (protein- FDR 1%) and more than 82 000 peptide precursors are reproducibly measured in the single MS shots of 2 h. HMGN1 protein deletion is confidently verified by DIA-MS in all of the clone- and dish- replicates following CRISPR. Statistical analysis reveals 147 proteins change their expressions significantly after HMGN1 knockout. Functional annotation and enrichment analysis indicate the deletion of HMGN1 induces histone inactivation, various stress pathways, remodeling of extracellular proteomes, cell proliferation, as well as immune regulation processes such as complement and coagulation cascade and interferon alpha/ gamma response in cancer cells. These results shed new lights on the cellular functions of HMGN1. It is suggested that DIA-MS can be reliably used as a rapid, robust, and cost-effective proteomic-screening tool to assess the outcome of the CRISPR experiments.
Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich 8093 Switzerland
Yale Cancer Biology Institute Yale University West Haven CT 06516 USA
References provided by Crossref.org
- 000
- 00000naa a2200000 a 4500
- 001
- bmc20023871
- 003
- CZ-PrNML
- 005
- 20201214131519.0
- 007
- ta
- 008
- 201125s2019 gw f 000 0|eng||
- 009
- AR
- 024 7_
- $a 10.1002/pmic.201800438 $2 doi
- 035 __
- $a (PubMed)30901150
- 040 __
- $a ABA008 $b cze $d ABA008 $e AACR2
- 041 0_
- $a eng
- 044 __
- $a gw
- 100 1_
- $a Mehnert, Martin $u Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, 8093, Switzerland.
- 245 10
- $a Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1 / $c M. Mehnert, W. Li, C. Wu, B. Salovska, Y. Liu,
- 520 9_
- $a CRISPR-Cas gene editing holds substantial promise in many biomedical disciplines and basic research. Due to the important functional implications of non-histone chromosomal protein HMG-14 (HMGN1) in regulating chromatin structure and tumor immunity, gene knockout of HMGN1 is performed by CRISPR in cancer cells and the following proteomic regulation events are studied. In particular, DIA mass spectrometry (DIA-MS) is utilized, and more than 6200 proteins (protein- FDR 1%) and more than 82 000 peptide precursors are reproducibly measured in the single MS shots of 2 h. HMGN1 protein deletion is confidently verified by DIA-MS in all of the clone- and dish- replicates following CRISPR. Statistical analysis reveals 147 proteins change their expressions significantly after HMGN1 knockout. Functional annotation and enrichment analysis indicate the deletion of HMGN1 induces histone inactivation, various stress pathways, remodeling of extracellular proteomes, cell proliferation, as well as immune regulation processes such as complement and coagulation cascade and interferon alpha/ gamma response in cancer cells. These results shed new lights on the cellular functions of HMGN1. It is suggested that DIA-MS can be reliably used as a rapid, robust, and cost-effective proteomic-screening tool to assess the outcome of the CRISPR experiments.
- 650 _2
- $a CRISPR-Cas systémy $7 D064113
- 650 _2
- $a nádorové buněčné linie $7 D045744
- 650 _2
- $a proliferace buněk $x genetika $7 D049109
- 650 _2
- $a chromatin $x fyziologie $7 D002843
- 650 12
- $a delece genu $7 D017353
- 650 _2
- $a editace genu $x metody $7 D000072669
- 650 _2
- $a protein HMGN1 $x genetika $7 D024241
- 650 _2
- $a HeLa buňky $7 D006367
- 650 _2
- $a lidé $7 D006801
- 650 _2
- $a proteomika $x metody $7 D040901
- 655 _2
- $a časopisecké články $7 D016428
- 655 _2
- $a práce podpořená grantem $7 D013485
- 700 1_
- $a Li, Wenxue $u Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA.
- 700 1_
- $a Wu, Chongde $u Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA.
- 700 1_
- $a Salovska, Barbora $u Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA. Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, 14220, Czech Republic.
- 700 1_
- $a Liu, Yansheng $u Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA. Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.
- 773 0_
- $w MED00007044 $t Proteomics $x 1615-9861 $g Roč. 19, č. 13 (2019), s. e1800438
- 856 41
- $u https://pubmed.ncbi.nlm.nih.gov/30901150 $y Pubmed
- 910 __
- $a ABA008 $b sig $c sign $y a $z 0
- 990 __
- $a 20201125 $b ABA008
- 991 __
- $a 20201214131517 $b ABA008
- 999 __
- $a ok $b bmc $g 1596190 $s 1114547
- BAS __
- $a 3
- BAS __
- $a PreBMC
- BMC __
- $a 2019 $b 19 $c 13 $d e1800438 $e 20190614 $i 1615-9861 $m Proteomics $n Proteomics $x MED00007044
- LZP __
- $a Pubmed-20201125
