Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes (original) (raw)
Ferlay, J. et al. Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int. J. Cancer127, 2893–2917 (2010). ArticleCASPubMed Google Scholar
Sherman, M.E. Theories of endometrial carcinogenesis: a multidisciplinary approach. Mod. Pathol.13, 295–308 (2000). ArticleCASPubMed Google Scholar
Hamilton, C.A. et al. Uterine papillary serous and clear cell carcinomas predict for poorer survival compared to grade 3 endometrioid corpus cancers. Br. J. Cancer94, 642–646 (2006). ArticleCASPubMedPubMed Central Google Scholar
Hendrickson, M., Ross, J., Eifel, P., Martinez, A. & Kempson, R. Uterine papillary serous carcinoma: a highly malignant form of endometrial adenocarcinoma. Am. J. Surg. Pathol.6, 93–108 (1982). ArticleCASPubMed Google Scholar
McConechy, M.K. et al. Subtype-specific mutation of PPP2R1A in endometrial and ovarian carcinomas. J. Pathol.223, 567–573 (2011). ArticleCASPubMed Google Scholar
Rudd, M.L. et al. A unique spectrum of somatic PIK3CA (p110α) mutations within primary endometrial carcinomas. Clin. Cancer Res.17, 1331–1340 (2011). ArticleCASPubMedPubMed Central Google Scholar
Hayes, M.P., Douglas, W. & Ellenson, L.H. Molecular alterations of EGFR and PIK3CA in uterine serous carcinoma. Gynecol. Oncol.113, 370–373 (2009). ArticleCASPubMedPubMed Central Google Scholar
National Cancer Institute, SEER Program. SEER Survival Monograph: Cancer Survival Among Adults: U.S. SEER Program, 1988–2001. Patient and Tumor Characteristics (eds. Ries, L.A.G., Young, J.L., Keel, G.E., Eisner, M.P., Lin, Y.D. & Horner, M.-J.) (National Cancer Institute, SEER Program, Bethesda, MD, 2007).
Zhang, Y., LeRoy, G., Seelig, H.P., Lane, W.S. & Reinberg, D. The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities. Cell95, 279–289 (1998). ArticleCASPubMed Google Scholar
Li, J., Lin, Q., Wang, W., Wade, P. & Wong, J. Specific targeting and constitutive association of histone deacetylase complexes during transcriptional repression. Genes Dev.16, 687–692 (2002). ArticleCASPubMedPubMed Central Google Scholar
Tong, J.K., Hassig, C.A., Schnitzler, G.R., Kingston, R.E. & Schreiber, S.L. Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex. Nature395, 917–921 (1998). ArticleCASPubMed Google Scholar
Xue, Y. et al. NURD, a novel complex with both ATP-dependent chromatin-remodeling and histone deacetylase activities. Mol. Cell2, 851–861 (1998). ArticleCASPubMed Google Scholar
Hall, J.A. & Georgel, P.T. CHD proteins: a diverse family with strong ties. Biochem. Cell Biol.85, 463–476 (2007). ArticleCASPubMed Google Scholar
Polo, S.E., Kaidi, A., Baskcomb, L., Galanty, Y. & Jackson, S.P. Regulation of DNA-damage responses and cell-cycle progression by the chromatin remodelling factor CHD4. EMBO J.29, 3130–3139 (2010). ArticleCASPubMedPubMed Central Google Scholar
Smeenk, G. et al. The NuRD chromatin-remodeling complex regulates signaling and repair of DNA damage. J. Cell Biol.190, 741–749 (2010). ArticleCASPubMedPubMed Central Google Scholar
Chou, D.M. et al. A chromatin localization screen reveals poly (ADP ribose)–regulated recruitment of the repressive polycomb and NuRD complexes to sites of DNA damage. Proc. Natl. Acad. Sci. USA107, 18475–18480 (2010). ArticleCASPubMedPubMed Central Google Scholar
Larsen, D.H. et al. The chromatin-remodeling factor CHD4 coordinates signaling and repair after DNA damage. J. Cell Biol.190, 731–740 (2010). ArticleCASPubMedPubMed Central Google Scholar
Boerkoel, C.F. et al. Mutant chromatin remodeling protein SMARCAL1 causes Schimke immuno-osseous dysplasia. Nat. Genet.30, 215–220 (2002). ArticleCASPubMed Google Scholar
Tsurusaki, Y. et al. Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome. Nat. Genet.44, 376–378 (2012). ArticleCASPubMed Google Scholar
Van Houdt, J.K. et al. Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome. Nat. Genet.44, 445–449 (2012). ArticleCASPubMed Google Scholar
Welcker, M. & Clurman, B.E. FBW7 ubiquitin ligase: a tumour suppressor at the crossroads of cell division, growth and differentiation. Nat. Rev. Cancer8, 83–93 (2008). ArticleCASPubMed Google Scholar
Cassia, R. et al. Cyclin E gene (CCNE) amplification and hCDC4 mutations in endometrial carcinoma. J. Pathol.201, 589–595 (2003). ArticleCASPubMed Google Scholar
Spruck, C.H. et al. hCDC4 gene mutations in endometrial cancer. Cancer Res.62, 4535–4539 (2002). CASPubMed Google Scholar
Suehiro, Y. et al. Aneuploidy predicts outcome in patients with endometrial carcinoma and is related to lack of CDH13 hypermethylation. Clin. Cancer Res.14, 3354–3361 (2008). ArticleCASPubMed Google Scholar
Forbes, S.A. et al. The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr. Protoc. Hum. Genet.Ch. 10, Unit 10.11 (2008). Google Scholar
Reva, B., Antipin, Y. & Sander, C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res.39, e118 (2011). ArticleCASPubMedPubMed Central Google Scholar
Wertz, I.E. et al. Sensitivity to antitubulin chemotherapeutics is regulated by MCL1 and FBW7. Nature471, 110–114 (2011). ArticleCASPubMed Google Scholar
Barbieri, C.E. et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat. Genet.44, 685–689 (2012). ArticleCASPubMedPubMed Central Google Scholar
Li, C. et al. Tumor-suppressor role for the SPOP ubiquitin ligase in signal-dependent proteolysis of the oncogenic co-activator SRC-3/AIB1. Oncogene30, 4350–4364 (2011). ArticleCASPubMedPubMed Central Google Scholar
Glaeser, M., Floetotto, T., Hanstein, B., Beckmann, M.W. & Niederacher, D. Gene amplification and expression of the steroid receptor coactivator SRC3 (AIB1) in sporadic breast and endometrial carcinomas. Horm. Metab. Res.33, 121–126 (2001). ArticleCASPubMed Google Scholar
Huang, D.W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc.4, 44–57 (2009). ArticleCAS Google Scholar
Huang, D.W., Sherman, B.T. & Lempicki, R.A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res.37, 1–13 (2009). ArticleCAS Google Scholar
Dalgliesh, G.L. et al. Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature463, 360–363 (2010). ArticleCASPubMedPubMed Central Google Scholar
Fujimoto, A. et al. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat. Genet.44, 760–764 (2012). CASPubMed Google Scholar
Gui, Y. et al. Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat. Genet.43, 875–878 (2011). ArticleCASPubMedPubMed Central Google Scholar
Guichard, C. et al. Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma. Nat. Genet.44, 694–698 (2012). ArticleCASPubMedPubMed Central Google Scholar
Jiao, Y. et al. DAXX/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors. Science331, 1199–1203 (2011). ArticleCASPubMedPubMed Central Google Scholar
Ong, C.K. et al. Exome sequencing of liver fluke–associated cholangiocarcinoma. Nat. Genet.44, 690–693 (2012). ArticleCASPubMed Google Scholar
Parsons, D.W. et al. The genetic landscape of the childhood cancer medulloblastoma. Science331, 435–439 (2011). ArticleCASPubMed Google Scholar
Schwartzentruber, J. et al. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature482, 226–231 (2012). ArticleCASPubMed Google Scholar
Shain, A.H. et al. Convergent structural alterations define SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeler as a central tumor suppressive complex in pancreatic cancer. Proc. Natl. Acad. Sci. USA109, E252–E259 (2012). ArticleCASPubMed Google Scholar
Varela, I. et al. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature469, 539–542 (2011). ArticleCASPubMedPubMed Central Google Scholar
Wang, K. et al. Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat. Genet.43, 1219–1223 (2011). ArticleCASPubMed Google Scholar
Ogryzko, V.V., Schiltz, R.L., Russanova, V., Howard, B.H. & Nakatani, Y. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell87, 953–959 (1996). ArticleCASPubMed Google Scholar
Huang, J., Zhao, Y.L., Li, Y., Fletcher, J.A. & Xiao, S. Genomic and functional evidence for an ARID1A tumor suppressor role. Genes Chromosom. Cancer46, 745–750 (2007). ArticleCASPubMed Google Scholar
Guan, B., Wang, T.L. & Shih, I.M. ARID1A, a factor that promotes formation of SWI/SNF-mediated chromatin remodeling, is a tumor suppressor in gynecologic cancers. Cancer Res.71, 6718–6727 (2011). ArticleCASPubMedPubMed Central Google Scholar
Guan, B. et al. Mutation and loss of expression of ARID1A in uterine low-grade endometrioid carcinoma. Am. J. Surg. Pathol.35, 625–632 (2011). ArticlePubMedPubMed Central Google Scholar
McConechy, M.K. et al. Use of mutation profiles to refine the classification of endometrial carcinomas. J. Pathol.228, 20–30 (2012). CASPubMedPubMed Central Google Scholar
Wiegand, K.C. et al. Loss of BAF250a (ARID1A) is frequent in high-grade endometrial carcinomas. J. Pathol.224, 328–333 (2011). ArticleCASPubMed Google Scholar
Urick, M.E. et al. PIK3R1 (p85α) is somatically mutated at high frequency in primary endometrial cancer. Cancer Res.71, 4061–4067 (2011). ArticleCASPubMedPubMed Central Google Scholar
Kuhn, E. et al. Identification of molecular pathway aberrations in uterine serous carcinoma by genome-wide analyses. J. Natl. Cancer Inst.104, 1503–1513 (2012). ArticleCASPubMedPubMed Central Google Scholar
Teer, J.K. et al. Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res.20, 1420–1431 (2010). ArticleCASPubMedPubMed Central Google Scholar
Teer, J.K., Green, E.D., Mullikin, J.C. & Biesecker, L.G. VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computer. Bioinformatics28, 599–600 (2012). ArticleCASPubMed Google Scholar
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J.R. Stat. Soc.57, 289–300 (1995). Google Scholar
Sjöblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science314, 268–274 (2006). ArticleCASPubMed Google Scholar
Rubin, A.F. & Green, P. Comment on “The consensus coding sequences of human breast and colorectal cancers”. Science317, 1500 (2007). ArticleCASPubMed Google Scholar