The Spectrum of SWI/SNF Mutations, Ubiquitous in Human Cancers

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Shain, A Hunter ^a   Pollack, Jonathan R ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; ARID1A PROTEIN; ARID1B PROTEIN; ARID2 PROTEIN; PBRM1 PROTEIN; PROTEIN; PROTEIN P53; PROTEIN SWI; TRANSCRIPTION FACTOR EZH2; TRANSCRIPTION FACTOR SNF; UNCLASSIFIED DRUG;

ARID1A GENE; ARID1B GENE; ARID2 GENE; ARTICLE; BREAST CANCER; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHRONIC LYMPHATIC LEUKEMIA; GENE; GENE EXPRESSION; GENE FUNCTION; GENE MUTATION; GENE SEQUENCE; GLIOBLASTOMA; HEAD AND NECK CANCER; HUMAN; HYDROLYSIS; MEDULLOBLASTOMA; MULTIPLE MYELOMA; NUCLEOSOME; PBRM1 GENE; TUMOR SUPPRESSOR GENE;

CHROMOSOMAL PROTEINS, NON-HISTONE; DATA MINING; EXOME; HUMANS; MUTATION; NEOPLASMS; TRANSCRIPTION FACTORS; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84872810488     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0055119     Document Type: Article

References (50)

1. Neigeborn L, Carlson M, (1984) Genes affecting the regulation of SUC2 gene expression by glucose repression in Saccharomyces cerevisiae. Genetics 108: 845-858.
2. Stern M, Jensen R, Herskowitz I, (1984) Five SWI genes are required for expression of the HO gene in yeast. J Mol Biol 178: 853-868.
3. Wilson BG, Roberts CW, (2011) SWI/SNF nucleosome remodellers and cancer. Nat Rev Cancer 11: 481-492.
4. Weissman B, Knudsen KE, (2009) Hijacking the chromatin remodeling machinery: impact of SWI/SNF perturbations in cancer. Cancer Res 69: 8223-8230.
5. Reisman D, Glaros S, Thompson EA, (2009) The SWI/SNF complex and cancer. Oncogene 28: 1653-1668.
6. Versteege I, Sevenet N, Lange J, Rousseau-Merck MF, Ambros P, et al. (1998) Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer. Nature 394: 203-206.
7. Roberts CW, Galusha SA, McMenamin ME, Fletcher CD, Orkin SH, (2000) Haploinsufficiency of Snf5 (integrase interactor 1) predisposes to malignant rhabdoid tumors in mice. Proc Natl Acad Sci U S A 97: 13796-13800.
8. Medina PP, Carretero J, Fraga MF, Esteller M, Sidransky D, et al. (2004) Genetic and epigenetic screening for gene alterations of the chromatin-remodeling factor, SMARCA4/BRG1, in lung tumors. Genes Chromosomes Cancer 41: 170-177.
9. Medina PP, Romero OA, Kohno T, Montuenga LM, Pio R, et al. (2008) Frequent BRG1/SMARCA4-inactivating mutations in human lung cancer cell lines. Hum Mutat 29: 617-622.
10. Jones S, Wang TL, Shih Ie M, Mao TL, Nakayama K, et al. (2010) Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 330: 228-231.
11. Li M, Zhao H, Zhang X, Wood LD, Anders RA, et al. (2011) Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat Genet 43: 828-829.
12. Varela I, Tarpey P, Raine K, Huang D, Ong CK, et al. (2011) Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 469: 539-542.
13. Wang K, Kan J, Yuen ST, Shi ST, Chu KM, et al. (2011) Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat Genet 43: 1219-1223.
14. Shain AH, Giacomini CP, Matsukuma K, Karikari CA, Bashyam MD, et al. (2012) Convergent structural alterations define SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeler as a central tumor suppressive complex in pancreatic cancer. Proc Natl Acad Sci U S A 109: E252-259.
15. Wiegand KC, Shah SP, Al-Agha OM, Zhao Y, Tse K, et al. (2010) ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med 363: 1532-1543.
16. Birnbaum DJ, Birnbaum D, Bertucci F (2011) Endometriosis-associated ovarian carcinomas. N Engl J Med 364: 483-484; author reply 484-485.
17. Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, et al. (2007) The genomic landscapes of human breast and colorectal cancers. Science 318: 1108-1113.
18. Quesada V, Conde L, Villamor N, Ordonez GR, Jares P, et al. (2011) Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet 44: 47-52.
19. Wang L, Lawrence MS, Wan Y, Stojanov P, Sougnez C, et al. (2011) SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med 365: 2497-2506.
20. Lohr JG, Stojanov P, Lawrence MS, Auclair D, Chapuy B, et al. (2012) Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A 109: 3879-3884.
21. Pasqualucci L, Trifonov V, Fabbri G, Ma J, Rossi D, et al. (2011) Analysis of the coding genome of diffuse large B-cell lymphoma. Nat Genet 43: 830-837.
22. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, et al. (2011) Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 476: 298-303.
23. Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, et al. (2008) An integrated genomic analysis of human glioblastoma multiforme. Science 321: 1807-1812.
24. Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, et al. (2011) The mutational landscape of head and neck squamous cell carcinoma. Science 333: 1157-1160.
25. Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, et al. (2011) Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science 333: 1154-1157.
26. Parsons DW, Li M, Zhang X, Jones S, Leary RJ, et al. (2011) The genetic landscape of the childhood cancer medulloblastoma. Science 331: 435-439.
27. Wei X, Walia V, Lin JC, Teer JK, Prickett TD, et al. (2011) Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet 43: 442-446.
28. Nikolaev SI, Rimoldi D, Iseli C, Valsesia A, Robyr D, et al. (2011) Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma. Nat Genet 44: 133-139.
29. Stark MS, Woods SL, Gartside MG, Bonazzi VF, Dutton-Regester K, et al. (2011) Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing. Nat Genet 44: 165-169.
30. Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, et al. (2011) Initial genome sequencing and analysis of multiple myeloma. Nature 471: 467-472.
31. Yoshida K, Sanada M, Shiraishi Y, Nowak D, Nagata Y, et al. (2011) Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 478: 64-69.
32. Bettegowda C, Agrawal N, Jiao Y, Sausen M, Wood LD, et al. (2011) Mutations in CIC and FUBP1 contribute to human oligodendroglioma. Science 333: 1453-1455.
33. Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, et al. (2008) Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321: 1801-1806.
34. Wang L, Tsutsumi S, Kawaguchi T, Nagasaki K, Tatsuno K, et al. (2011) Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency. Genome Res 22: 208-219.
35. Wu J, Jiao Y, Dal Molin M, Maitra A, de Wilde RF, et al. (2011) Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways. Proc Natl Acad Sci U S A 108: 21188-21193.
36. Jiao Y, Shi C, Edil BH, de Wilde RF, Klimstra DS, et al. (2011) DAXX/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors. Science 331: 1199-1203.
37. DelBove J, Rosson G, Strobeck M, Chen J, Archer TK, et al. (2011) Identification of a core member of the SWI/SNF complex, BAF155/SMARCC1, as a human tumor suppressor gene. Epigenetics 6: 1444-1453.
38. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, et al. (2010) A method and server for predicting damaging missense mutations. Nat Methods 7: 248-249.
39. Jones S, Li M, Parsons DW, Zhang X, Wesseling J, et al. (2012) Somatic mutations in the chromatin remodeling gene ARID1A occur in several tumor types. Hum Mutat 33: 100-103.
40. Mamo A, Cavallone L, Tuzmen S, Chabot C, Ferrario C, et al. (2011) An integrated genomic approach identifies ARID1A as a candidate tumor-suppressor gene in breast cancer. Oncogene 31: 2090-2100.
41. Cornen S, Adelaide J, Bertucci F, Finetti P, Guille A, et al. (2012) Mutations and deletions of ARID1A in breast tumors. Oncogene 31: 4255-4256.
42. Xia W, Nagase S, Montia AG, Kalachikov SM, Keniry M, et al. (2008) BAF180 is a critical regulator of p21 induction and a tumor suppressor mutated in breast cancer. Cancer Res 68: 1667-1674.
43. Maitra A, Fukushima N, Takaori K, Hruban RH, (2005) Precursors to invasive pancreatic cancer. Adv Anat Pathol 12: 81-91.
44. Dal Molin M, Hong SM, Hebbar S, Sharma R, Scrimieri F, et al. (2012) Loss of expression of the SWI/SNF chromatin remodeling subunit BRG1/SMARCA4 is frequently observed in intraductal papillary mucinous neoplasms of the pancreas. Hum Pathol 43: 585-591.
45. Tsurusaki Y, Okamoto N, Ohashi H, Kosho T, Imai Y, et al. (2012) Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome. Nat Genet 44: 376-378.
46. Olivier M, Hollstein M, Hainaut P, (2010) TP53 mutations in human cancers: origins, consequences, and clinical use. Cold Spring Harb Perspect Biol 2: a001008.
47. Guan B, Wang TL, Shih Ie M, (2011) ARID1A, a factor that promotes formation of SWI/SNF-mediated chromatin remodeling, is a tumor suppressor in gynecologic cancers. Cancer Res 71: 6718-6727.
48. Wilson BG, Wang X, Shen X, McKenna ES, Lemieux ME, et al. (2010) Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation. Cancer Cell 18: 316-328.
49. Ho L, Jothi R, Ronan JL, Cui K, Zhao K, et al. (2009) An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proc Natl Acad Sci U S A 106: 5187-5191.
50. Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, et al. (2011) Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet 7: e1002008.