Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes

Nature Genetics

Volumn 44, Issue 5, 2012, Pages 570-574

  Zang, Zhi Jiang ^a,b   Cutcutache, Ioana ^c   Poon, Song Ling ^a   Zhang, Shen Li ^b   Mcpherson, John R ^c   Tao, Jiong ^b,d   Rajasegaran, Vikneswari ^a   Heng, Hong Lee ^a   Deng, Niantao ^b   Gan, Anna ^a   Lim, Kiat Hon ^e   Ong, Choon Kiat ^a   Huang, DaChuan ^a   Chin, Sze Yung ^b   Tan, Iain Beehuat ^a,b   Ng, Cedric Chuan Young ^a   Yu, Willie ^a,b   Wu, Yingting ^f   Lee, Minghui ^a   Wu, Jeanie ^a   Poh, Dianne ^b   Wan, Wei Keat ^e   Rha, Sun Young ^g   So, Jimmy ^h   Salto Tellez, Manuel ^b,i   Yeoh, Khay Guan ^j   Wong, Wai Keong ^e   Zhu, Yi Jun ^k   Futreal, P Andrew ^l   Pang, Brendan ^b,d   Ruan, Yijun ^m   Hillmer, Axel M ^m   Bertrand, Denis ^m   Nagarajan, Niranjan ^m   Rozen, Steve ^c   Teh, Bin Tean ^a,b,n   Tan, Patrick ^b,d,m   more..

^a DIVISION OF MEDICAL ONCOLOGY   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c DUKE NUS MEDICAL SCHOOL   (Singapore)

^d NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^e SINGAPORE GENERAL HOSPITAL   (Singapore)

^f SINGAPORE MIT ALLIANCE   (Singapore)

^g Yonsei University College of Medicine   (South Korea)

^h NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

ⁱ QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^j Dept Medicine Endocrinol Diabet   (Singapore)

^k NORTHWESTERN UNIVERSITY   (United States)

^l WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^m GENOME INSTITUTE OF SINGAPORE   (Singapore)

ⁿ VAN ANDEL RESEARCH INSTITUTE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARID1A PROTEIN; CADHERIN; FAT4 PROTEIN; MIXED LINEAGE LEUKEMIA PROTEIN; MLL3 PROTEIN; PIK3CA PROTEIN; PROTEIN; PROTEIN P53; UNCLASSIFIED DRUG;

ARTICLE; CANCER SCREENING; CELL ADHESION; CHROMATIN ASSEMBLY AND DISASSEMBLY; EXOME; GENE DELETION; GENE MUTATION; GENE SEQUENCE; HUMAN; HUMAN TISSUE; MOUSE; NONHUMAN; PREVALENCE; PRIORITY JOURNAL; SOMATIC MUTATION; STOMACH ADENOCARCINOMA;

ADENOCARCINOMA; CASE-CONTROL STUDIES; CELL ADHESION; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA; EXOME; GENES, TUMOR SUPPRESSOR; HUMANS; MICROSATELLITE INSTABILITY; MUTATION; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; STOMACH; STOMACH NEOPLASMS;

EID: 84860327480     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.2246     Document Type: Article

References (40)

1. Li, M. et al. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat. Genet. 43, 828-829 (2011).
2. Jones, S. et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321, 1801-1806 (2008).
3. Parsons, D.W. et al. The genetic landscape of the childhood cancer medulloblastoma. Science 331, 435-439 (2011).
4. Pleasance, E.D. et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463, 184-190 (2010).
5. Katoh, M. Dysregulation of stem cell signaling network due to germline mutation, SNP, Helicobacter pylori infection, epigenetic change and genetic alteration in gastric cancer. Cancer Biol. Ther. 6, 832-839 (2007). (Pubitemid 351574970)
6. Panani, A.D. Cytogenetic and molecular aspects of gastric cancer: clinical implications. Cancer Lett. 266, 99-115 (2008).
7. Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153-158 (2007). (Pubitemid 46398669)
8. Huang, 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).
9. Sjöblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268-274 (2006). (Pubitemid 44571966)
10. Compton, A.G. et al. Mutations in contactin-1, a neural adhesion and neuromuscular junction protein, cause a familial form of lethal congenital myopathy. Am. J. Hum. Genet. 83, 714-724 (2008).
11. Su, J.L. et al. Knockdown of contactin-1 expression suppresses invasion and metastasis of lung adenocarcinoma. Cancer Res. 66, 2553-2561 (2006).
12. Berx, G. & van Roy, F. Involvement of members of the cadherin superfamily in cancer. Cold Spring Harb. Perspect. Biol. 1, a003129 (2009).
13. Wang, Y. Wnt/Planar cell polarity signaling: a new paradigm for cancer. Mol. Cancer Ther. 8, 2103-2109 (2009).
14. Saburi, S. et al. Loss of Fat4 disrupts PCP signaling and oriented cell division and leads to cystic kidney disease. Nat. Genet. 40, 1010-1015 (2008).
15. Mao, Y. et al. Characterization of a Dchs1 mutant mouse reveals requirements for Dchs1-Fat4 signaling during mammalian development. Development 138, 947-957 (2011).
16. Mahoney, P.A. et al. The fat tumor suppressor gene in Drosophila encodes a novel member of the cadherin gene superfamily. Cell 67, 853-868 (1991). (Pubitemid 121001500)
17. Qi, C., Zhu, Y.T., Hu, L. & Zhu, Y.J. Identification of Fat4 as a candidate tumor suppressor gene in breast cancers. Int. J. Cancer 124, 793-798 (2009).
18. Ramensky, V. et al. Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 30, 3894-3900 (2002). (Pubitemid 35012462)
19. Agrawal, N. et al. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science 333, 1154-1157 (2011).
20. 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. Gut published online, doi:0.1136/gutjnl- 2011-301839 (7 February 2012).
21. Van Loo, P. et al. Allele-specific copy number analysis of tumors. Proc. Natl. Acad. Sci. USA 107, 16910-16915 (2010).
22. Cuadrado, M., Sacristán, M. & Antequera, F. Species-specific organization of CpG island promoters at mammalian homologous genes. EMBO Rep. 2, 586-592 (2001). (Pubitemid 32707704)
23. Cavallaro, U. & Christofori, G. Cell adhesion and signalling by cadherins and Ig-CAMs in cancer. Nat. Rev. Cancer 4, 118-132 (2004). (Pubitemid 38198740)
24. Yachida, S. et al. Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 467, 1114-1117 (2010).
25. Wiegand, K.C. et al. Loss of BAF250a (ARID1A) is frequent in high-grade endometrial carcinomas. J. Pathol. 224, 328-333 (2011).
26. Wang, K. et al. Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat. Genet. 43, 1219-1223 (2011).
27. Jones, S. et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 330, 228-231 (2010).
28. Wiegand, K.C. et al. ARID1A mutations in endometriosis-associated ovarian carcinomas. N. Engl. J. Med. 363, 1532-1543 (2010).
29. Van Rechem, C., Boulay, G. & Leprince, D. HIC1 interacts with a specific subunit of SWI/SNF complexes, ARID1A/BAF250A. Biochem. Biophys. Res. Commun. 385, 586-590 (2009).
30. Gao, X. et al. ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a. Proc. Natl. Acad. Sci. USA 105, 6656-6661 (2008). (Pubitemid 351754562)
31. Guan, B., Wang, T.L. & Shih, IeM. 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).
32. Neuhaus, E.M. et al. Activation of an olfactory receptor inhibits proliferation of prostate cancer cells. J. Biol. Chem. 284, 16218-16225 (2009).
33. Spicer, Z. et al. Stomachs of mice lacking the gastric H,K-ATPase α-subunit have achlorhydria, abnormal parietal cells, and ciliated metaplasia. J. Biol. Chem. 275, 21555-21565 (2000). (Pubitemid 30481861)
34. Fuereder, T. et al. Gastric cancer growth control by BEZ235 in vivo does not correlate with PI3K/mTOR target inhibition but with [18F]FLT uptake. Clin. Cancer Res. 17, 5322-5332 (2011).
35. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
36. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
37. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
38. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615 (2011).
39. Olshen, A.B. et al. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557-572 (2004). (Pubitemid 41180205)
40. Ooi, C.H. et al. Oncogenic pathway combinations predict clinical prognosis in gastric cancer. PLoS Genet. 5, e1000676 (2009).