Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer (original) (raw)
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
Zang, Z.J. et al. Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nat. Genet.44, 570–574 (2012). ArticleCASPubMed Google Scholar
Pleasance, E.D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature463, 191–196 (2010). ArticleCASPubMed Google Scholar
Dulak, A.M. et al. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nat. Genet.45, 478–486 (2013). ArticleCASPubMedPubMed Central Google Scholar
Youn, A. & Simon, R. Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics27, 175–181 (2011). ArticleCASPubMed Google Scholar
Garcia, E., Carvalho, F., Amorim, A. & David, L. MUC6 gene polymorphism in healthy individuals and in gastric cancer patients from northern Portugal. Cancer Epidemiol. Biomarkers Prev.6, 1071–1074 (1997). CASPubMed Google Scholar
Kwon, J.A. et al. Short rare MUC6 minisatellites-5 alleles influence susceptibility to gastric carcinoma by regulating gene. Hum. Mutat.31, 942–949 (2010). ArticleCASPubMed Google Scholar
Zheng, H. et al. MUC6 down-regulation correlates with gastric carcinoma progression and a poor prognosis: an immunohistochemical study with tissue microarrays. J. Cancer Res. Clin. Oncol.132, 817–823 (2006). ArticleCASPubMed Google Scholar
Koo, B.K. et al. Tumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors. Nature488, 665–669 (2012). ArticleCASPubMed Google Scholar
Sehgal, R.N., Gumbiner, B.M. & Reichardt, L.F. Antagonism of cell adhesion by an α-catenin mutant, and of the Wnt-signaling pathway by α-catenin in Xenopus embryos. J. Cell Biol.139, 1033–1046 (1997). ArticleCASPubMedPubMed Central Google Scholar
Bogaerts, S., Vanlandschoot, A., van Hengel, J. & van Roy, F. Nuclear translocation of αN-catenin by the novel zinc finger transcriptional repressor ZASC1. Exp. Cell Res.311, 1–13 (2005). ArticleCASPubMed Google Scholar
Majewski, I.J. et al. An α-E-catenin (CTNNA1) mutation in hereditary diffuse gastric cancer. J. Pathol.229, 621–629 (2013). ArticleCASPubMed Google Scholar
van den Brink, G.R. et al. Sonic hedgehog regulates gastric gland morphogenesis in man and mouse. Gastroenterology121, 317–328 (2001). ArticleCASPubMed Google Scholar
Ramalho-Santos, M., Melton, D.A. & McMahon, A.P. Hedgehog signals regulate multiple aspects of gastrointestinal development. Development127, 2763–2772 (2000). CASPubMed Google Scholar
Blank, M.C. et al. Multiple developmental programs are altered by loss of Zic1 and Zic4 to cause Dandy-Walker malformation cerebellar pathogenesis. Development138, 1207–1216 (2011). ArticleCASPubMedPubMed Central Google Scholar
Park, S.H., Kim, Y.S., Park, B.K., Hougaard, S. & Kim, S.J. Sequence-specific enhancer binding protein is responsible for the differential expression of ERT/ESX/ELF-3/ESE-1/jen gene in human gastric cancer cell lines: implication for the loss of TGF-β type II receptor expression. Oncogene20, 1235–1245 (2001). ArticleCASPubMed Google Scholar
Nakanishi, Y. et al. Dclk1 distinguishes between tumor and normal stem cells in the intestine. Nat. Genet.45, 98–103 (2013). ArticleCASPubMed Google Scholar
Ahuja, N. et al. Association between CpG island methylation and microsatellite instability in colorectal cancer. Cancer Res.57, 3370–3374 (1997). CASPubMed Google Scholar
Kang, G.H. et al. CpG island methylation in premalignant stages of gastric carcinoma. Cancer Res.61, 2847–2851 (2001). CASPubMed Google Scholar
Oue, N. et al. Reduced expression of the TSP1 gene and its association with promoter hypermethylation in gastric carcinoma. Oncology64, 423–429 (2003). ArticleCASPubMed Google Scholar
Dvorsky, R., Blumenstein, L., Vetter, I.R. & Ahmadian, M.R. Structural insights into the interaction of ROCKI with the switch regions of RhoA. J. Biol. Chem.279, 7098–7104 (2004). ArticleCASPubMed Google Scholar
Maesaki, R. et al. The structural basis of Rho effector recognition revealed by the crystal structure of human RhoA complexed with the effector domain of PKN/PRK1. Mol. Cell4, 793–803 (1999). ArticleCASPubMed Google Scholar
Sahai, E., Alberts, A.S. & Treisman, R. RhoA effector mutants reveal distinct effector pathways for cytoskeletal reorganization, SRF activation and transformation. EMBO J.17, 1350–1361 (1998). ArticleCASPubMedPubMed Central Google Scholar
Bae, C.D., Min, D.S., Fleming, I.N. & Exton, J.H. Determination of interaction sites on the small G protein RhoA for phospholipase D. J. Biol. Chem.273, 11596–11604 (1998). ArticleCASPubMed Google Scholar
Barker, N. et al. Lgr5+ve stem cells drive self-renewal in the stomach and build long-lived gastric units in vitro. Cell Stem Cell6, 25–36 (2010). ArticleCASPubMed Google Scholar
Sato, T. et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature459, 262–265 (2009). ArticleCASPubMed Google Scholar
Watanabe, K. et al. A ROCK inhibitor permits survival of dissociated human embryonic stem cells. Nat. Biotechnol.25, 681–686 (2007). ArticleCASPubMed Google Scholar
Deng, N. et al. A comprehensive survey of genomic alterations in gastric cancer reveals systematic patterns of molecular exclusivity and co-occurrence among distinct therapeutic targets. Gut61, 673–684 (2012). ArticleCASPubMed Google Scholar
Kimura, Y. et al. Genetic alterations in 102 primary gastric cancers by comparative genomic hybridization: gain of 20q and loss of 18q are associated with tumor progression. Mod. Pathol.17, 1328–1337 (2004). ArticleCASPubMed Google Scholar
Mermel, C.H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol.12, R41 (2011). ArticleCASPubMedPubMed Central Google Scholar
Tuncel, H. et al. PARP6, a mono(ADP-ribosyl) transferase and a negative regulator of cell proliferation, is involved in colorectal cancer development. Int. J. Oncol.41, 2079–2086 (2012). ArticleCASPubMed Google Scholar
Pang, J.C. et al. KIAA0495/PDAM is frequently downregulated in oligodendroglial tumors and its knockdown by siRNA induces cisplatin resistance in glioma cells. Brain Pathol.20, 1021–1032 (2010). ArticleCASPubMedPubMed Central Google Scholar
Fujii, Y. et al. CDX1 confers intestinal phenotype on gastric epithelial cells via induction of stemness-associated reprogramming factors SALL4 and KLF5. Proc. Natl. Acad. Sci. USA109, 20584–20589 (2012). ArticlePubMedPubMed Central Google Scholar
Mutoh, H. et al. Cdx1 induced intestinal metaplasia in the transgenic mouse stomach: comparative study with Cdx2 transgenic mice. Gut53, 1416–1423 (2004). ArticleCASPubMedPubMed Central Google Scholar
Rau, T.T. et al. Methylation-dependent activation of CDX1 through NF-κB: a link from inflammation to intestinal metaplasia in the human stomach. Am. J. Pathol.181, 487–498 (2012). ArticleCASPubMedPubMed Central Google Scholar
Kwon, O.H. et al. Aberrant upregulation of ASCL2 by promoter demethylation promotes the growth and resistance to 5-fluorouracil of gastric cancer cells. Cancer Sci.104, 391–397 (2013). ArticleCASPubMedPubMed Central Google Scholar
van der Flier, L.G. et al. Transcription factor achaete scute-like 2 controls intestinal stem cell fate. Cell136, 903–912 (2009). ArticleCASPubMed Google Scholar
Wang, J. et al. Cadherin-17 induces tumorigenesis and lymphatic metastasis in gastric cancer through activation of NFκB signaling pathway. Cancer Biol. Ther.14, 262–270 (2013). ArticleCASPubMedPubMed Central Google Scholar
Nagl, N.G. Jr., Zweitzig, D.R., Thimmapaya, B., Beck, G.R. Jr. & Moran, E. The c-myc gene is a direct target of mammalian SWI/SNF-related complexes during differentiation-associated cell cycle arrest. Cancer Res.66, 1289–1293 (2006). ArticleCASPubMed Google Scholar
Guan, B., Wang, T.L. & Shih Ie, 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
Matsusaka, K. et al. Classification of Epstein-Barr virus–positive gastric cancers by definition of DNA methylation epigenotypes. Cancer Res.71, 7187–7197 (2011). ArticleCASPubMed Google Scholar
Zouridis, H. et al. Methylation subtypes and large-scale epigenetic alterations in gastric cancer. Sci. Transl. Med.4, 156ra140 (2012). ArticleCASPubMed Google Scholar
Matsuzaki, K. et al. The relationship between global methylation level, loss of heterozygosity, and microsatellite instability in sporadic colorectal cancer. Clin. Cancer Res.11, 8564–8569 (2005). ArticleCASPubMed Google Scholar
Wilson, A.S., Power, B.E. & Molloy, P.L. DNA hypomethylation and human diseases. Biochim. Biophys. Acta1775, 138–162 (2007). CASPubMed Google Scholar
Sahai, E. & Marshall, C.J. RHO-GTPases and cancer. Nat. Rev. Cancer2, 133–142 (2002). ArticlePubMed Google Scholar
Braga, V.M., Machesky, L.M., Hall, A. & Hotchin, N.A. The small GTPases Rho and Rac are required for the establishment of cadherin-dependent cell-cell contacts. J. Cell Biol.137, 1421–1431 (1997). ArticleCASPubMedPubMed Central Google Scholar
Coleman, M.L. & Olson, M.F. Rho GTPase signalling pathways in the morphological changes associated with apoptosis. Cell Death Differ.9, 493–504 (2002). ArticleCASPubMed Google Scholar
Coleman, M.L. et al. Membrane blebbing during apoptosis results from caspase-mediated activation of ROCK I. Nat. Cell Biol.3, 339–345 (2001). ArticleCASPubMed Google Scholar
Cox, E.A., Sastry, S.K. & Huttenlocher, A. Integrin-mediated adhesion regulates cell polarity and membrane protrusion through the Rho family of GTPases. Mol. Biol. Cell12, 265–277 (2001). ArticleCASPubMedPubMed Central Google Scholar
Sahai, E. & Marshall, C.J. Differing modes of tumour cell invasion have distinct requirements for Rho/ROCK signalling and extracellular proteolysis. Nat. Cell Biol.5, 711–719 (2003). ArticleCASPubMed Google Scholar
Yoshioka, K., Nakamori, S. & Itoh, K. Overexpression of small GTP-binding protein RhoA promotes invasion of tumor cells. Cancer Res.59, 2004–2010 (1999). CASPubMed Google Scholar
Sahai, E., Garcia-Medina, R., Pouyssegur, J. & Vial, E. Smurf1 regulates tumor cell plasticity and motility through degradation of RhoA leading to localized inhibition of contractility. J. Cell Biol.176, 35–42 (2007). ArticleCASPubMedPubMed Central Google Scholar
Matsuoka, T. et al. RhoA/ROCK signaling mediates plasticity of scirrhous gastric carcinoma motility. Clin. Exp. Metastasis28, 627–636 (2011). ArticleCASPubMed Google Scholar
Sakata-Yanagimoto, M. et al. Somatic RHOA mutation in angioimmunoblastic T cell lymphoma. Nat. Genet.46, 171–175 (2014). ArticleCASPubMed Google Scholar
Palomero, T. et al. Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas. Nat. Genet.46, 166–170 (2014). ArticleCASPubMedPubMed Central Google Scholar
Yoo, H.Y. et al. A recurrent inactivating mutation in RHOA GTPase in angioimmunoblastic T cell lymphoma. Nat. Genet.46, 371–375 (2014). ArticleCASPubMed Google Scholar
Saunders, C.T. et al. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics28, 1811–1817 (2012). ArticleCASPubMed Google Scholar
Staaf, J. et al. Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics9, 409 (2008). ArticleCASPubMedPubMed Central Google Scholar
Wang, K. et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res.17, 1665–1674 (2007). ArticleCASPubMedPubMed Central Google Scholar
Olshen, A.B., Venkatraman, E.S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics5, 557–572 (2004). ArticlePubMed Google Scholar
Yau, C. et al. A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data. Genome Biol.11, R92 (2010). CASPubMedPubMed Central Google Scholar
Wang, K. et al. Genomic landscape of copy number aberrations enables the identification of oncogenic drivers in hepatocellular carcinoma. Hepatology58, 706–717 (2013). ArticleCASPubMed Google Scholar
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. & Tanabe, M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res.40, D109–D114 (2012). CASPubMed Google Scholar