The genetic alteration spectrum of the SWI/SNF complex: The oncogenic roles of BRD9 and ACTL6A
Autoři:
Xiaoxian Sima aff001; Jiangnan He aff001; Jie Peng aff002; Yanmei Xu aff003; Feng Zhang aff004; Libin Deng aff002
Působiště autorů:
Queen Mary College, Nanchang University, Nanchang, Jiangxi, P.R. China
aff001; Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, Jiangxi, P.R. China
aff002; The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
aff003; Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi, P. R. China
aff004; College of Basic Medical Science, Nanchang University, Nanchang, Jiangxi, P.R. China
aff005
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0222305
Souhrn
SWItch/Sucrose NonFermentable (SWI/SNF) is a set of multi-subunits chromatin remodeling complexes, playing important roles in a variety of biological processes. Loss-of-function mutations in the genes encoding SWI/SNF subunits have been reported in more than 20% of human cancers. Thus, it was widely considered as a tumor suppressor in the past decade. However, recent studies reported that some genes encoding subunits of SWI/SNF complexes were amplified and play oncogenic roles in human cancers. In present study, we summarized the genetic alteration spectrum of SWI/SNF complexes, and firstly systematically estimated both the copy number variations and point mutations of all 30 genes encoding the subunits in this complex. Additionally, the bioinformatics analyses were performed for two significantly amplified genes, ACTL6A and BRD9, to investigate their oncogenic roles in human cancers. Our findings may lay a foundation for the discovery of potential treatment targets in SWI/SNF complexes of cancers.
Klíčová slova:
Medicine and health sciences – Oncology – Carcinogenesis – Cancers and neoplasms – Carcinomas – Adenocarcinomas – Adenocarcinoma of the lung – Lung and intrathoracic tumors – Biology and life sciences – Genetics – Mutation – Point mutation – Gene expression – Gene amplification – Genomics – Genome complexity – Copy number variation – Biochemistry – Metabolism – Metabolic processes – Oxidative phosphorylation – Ribosomes – Cell biology – Cellular structures and organelles – Computational biology
Zdroje
1. Wang W, Cote J, Xue Y, Zhou S, Khavari PA, Biggar SR, et al. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. The EMBO journal. 1996;15(19):5370–82. Epub 1996/10/01. 8895581
2. Kadoch C, Hargreaves DC, Hodges C, Elias L, Ho L, Ranish J, et al. Proteomic and Bioinformatic Analysis of mSWI/SNF (BAF) Complexes Reveals Extensive Roles in Human Malignancy. Nature genetics. 2013;45(6):592–601. doi: 10.1038/ng.2628 23644491
3. Mashtalir N, D'Avino AR, Michel BC, Luo J, Pan J, Otto JE, et al. Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes. Cell. 2018;175(5):1272–88.e20. Epub 2018/10/23. doi: 10.1016/j.cell.2018.09.032 30343899
4. Alpsoy A, Dykhuizen EC. Glioma tumor suppressor candidate region gene 1 (GLTSCR1) and its paralog GLTSCR1-like form SWI/SNF chromatin remodeling subcomplexes. The Journal of biological chemistry. 2018;293(11):3892–903. Epub 2018/01/28. doi: 10.1074/jbc.RA117.001065 29374058
5. Pulice JL, Kadoch C. Composition and Function of Mammalian SWI/SNF Chromatin Remodeling Complexes in Human Disease. Cold Spring Harbor symposia on quantitative biology. 2016;81:53–60. Epub 2017/04/15. doi: 10.1101/sqb.2016.81.031021 28408647
6. Lu C, Allis CD. SWI/SNF complex in cancer. Nature genetics. 2017;49(2):178–9. Epub 2017/02/01. doi: 10.1038/ng.3779 28138149
7. Shain AH, Pollack JR. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. PLoS One. 2013;8(1):e55119. Epub 2013/01/29. doi: 10.1371/journal.pone.0055119 23355908
8. Saladi SV, Ross K, Karaayvaz M, Tata PR, Mou H, Rajagopal J, et al. ACTL6A Is Co-Amplified with p63 in Squamous Cell Carcinoma to Drive YAP Activation, Regenerative Proliferation, and Poor Prognosis. Cancer cell. 2017;31(1):35–49. Epub 2017/01/04. doi: 10.1016/j.ccell.2016.12.001 28041841
9. Saladi SV, Ross K, Karaayvaz M, Tata PR, Mou H, Rajagopal J, et al. ACTL6A is co-Amplified with p63 in Squamous Cell Carcinoma to Drive YAP Activation, Regenerative Proliferation and Poor Prognosis. Cancer cell. 2017;31(1):35–49. doi: 10.1016/j.ccell.2016.12.001 28041841
10. Scotto L, Narayan G, Nandula SV, Subramaniyam S, Kaufmann AM, Wright JD, et al. Integrative genomics analysis of chromosome 5p gain in cervical cancer reveals target over-expressed genes, including Drosha. Molecular cancer. 2008;7:58. Epub 2008/06/19. doi: 10.1186/1476-4598-7-58 18559093
11. Taulli R, Foglizzo V, Morena D, Coda DM, Ala U, Bersani F, et al. Failure to downregulate the BAF53a subunit of the SWI/SNF chromatin remodeling complex contributes to the differentiation block in rhabdomyosarcoma. Oncogene. 2014;33(18):2354–62. Epub 2013/06/04. doi: 10.1038/onc.2013.188 23728344
12. Zeng Z, Yang H, Xiao S. ACTL6A expression promotes invasion, metastasis and epithelial mesenchymal transition of colon cancer. BMC Cancer. 2018;18(1):1020. Epub 2018/10/24. doi: 10.1186/s12885-018-4931-3 30348114
13. Xiao S, Chang RM, Yang MY, Lei X, Liu X, Gao WB, et al. Actin-like 6A predicts poor prognosis of hepatocellular carcinoma and promotes metastasis and epithelial-mesenchymal transition. Hepatology. 2016;63(4):1256–71. Epub 2015/12/25. doi: 10.1002/hep.28417 26698646
14. Zhong PQ, Zhong L, Yao JJ, Liu DD, Yuan Z, Liu JM, et al. ACTL6A interacts with p53 in acute promyelocytic leukemia cell lines to affect differentiation via the Sox2/Notch1 signaling pathway. Cell Signal. 2019;53:390–9. Epub 2018/11/19. doi: 10.1016/j.cellsig.2018.11.009 30448346
15. Zhu B, Ueda A, Song X, Horike SI, Yokota T, Akagi T. Baf53a is involved in survival of mouse ES cells, which can be compensated by Baf53b. Sci Rep. 2017;7(1):14059. Epub 2017/10/27. doi: 10.1038/s41598-017-14362-4 29070872
16. Lu W, Fang L, Ouyang B, Zhang X, Zhan S, Feng X, et al. Actl6a protects embryonic stem cells from differentiating into primitive endoderm. Stem Cells. 2015;33(6):1782–93. Epub 2015/03/25. doi: 10.1002/stem.2000 25802002
17. Zhang Y, Cui P, Li Y, Feng G, Tong M, Guo L, et al. Mitochondrially produced ATP affects stem cell pluripotency via Actl6a-mediated histone acetylation. FASEB journal: official publication of the Federation of American Societies for Experimental Biology. 2018;32(4):1891–902. Epub 2017/12/10. doi: 10.1096/fj.201700626RR 29222327
18. Ji J, Xu R, Zhang X, Han M, Xu Y, Wei Y, et al. Actin like-6A promotes glioma progression through stabilization of transcriptional regulators YAP/TAZ. Cell Death Dis. 2018;9(5):517. Epub 2018/05/05. doi: 10.1038/s41419-018-0548-3 29725063
19. Alpsoy A, Dykhuizen EC. Glioma tumor suppressor candidate region gene 1 (GLTSCR1) and its paralog GLTSCR1-like form SWI/SNF chromatin remodeling subcomplexes. The Journal of biological chemistry. 2018;293(11):3892–903. doi: 10.1074/jbc.RA117.001065 29374058
20. Del Gaudio N, Di Costanzo A, Liu NQ, Conte L, Migliaccio A, Vermeulen M, et al. BRD9 binds cell type-specific chromatin regions regulating leukemic cell survival via STAT5 inhibition. Cell Death Dis. 2019;10(5):338. Epub 2019/04/20. doi: 10.1038/s41419-019-1570-9 31000698
21. Gatchalian J, Malik S, Ho J, Lee DS, Kelso TWR, Shokhirev MN, et al. A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells. Nat Commun. 2018;9(1):5139. Epub 2018/12/05. doi: 10.1038/s41467-018-07528-9 30510198
22. McFarland JM, Ho ZV, Kugener G, Dempster JM, Montgomery PG, Bryan JG, et al. Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nat Commun. 2018;9(1):4610. Epub 2018/11/06. doi: 10.1038/s41467-018-06916-5 30389920
23. Igoe N, Bayle ED, Tallant C, Fedorov O, Meier JC, Savitsky P, et al. Design of a Chemical Probe for the Bromodomain and Plant Homeodomain Finger-Containing (BRPF) Family of Proteins. Journal of medicinal chemistry. 2017;60(16):6998–7011. Epub 2017/07/18. doi: 10.1021/acs.jmedchem.7b00611 28714688
24. Clark PG, Vieira LC, Tallant C, Fedorov O, Singleton DC, Rogers CM, et al. LP99: Discovery and Synthesis of the First Selective BRD7/9 Bromodomain Inhibitor. Angewandte Chemie (Weinheim an der Bergstrasse, Germany). 2015;127(21):6315–9. Epub 2016/06/28. doi: 10.1002/ange.201501394 27346896
25. Michel BC, D'Avino AR, Cassel SH, Mashtalir N, McKenzie ZM, McBride MJ, et al. A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation. Nature cell biology. 2018;20(12):1410–20. Epub 2018/11/07. doi: 10.1038/s41556-018-0221-1. 30397315
Článek vyšel v časopise
PLOS One
2019 Číslo 9
- Tisícileté topoly, mokří psi, stárnoucí kočky a ospalé octomilky – „jednohubky“ z výzkumu 2024/41
- Jaké jsou aktuální trendy v léčbě karcinomu slinivky?
- Menstruační krev má značný diagnostický potenciál, mimo jiné u diabetu
- Proč jsou nemocnice nepřítelem spánku? A jak to změnit?
- Metamizol jako analgetikum první volby: kdy, pro koho, jak a proč?