Distinct subtypes of gastric cancer defined by molecular characterization include novel mutational signatures with prognostic capability

Cancer Research

Volumn 76, Issue 7, 2016, Pages 1724-1732

  Li, Xiangchun ^a,b   Wu, William K K ^a,c   Xing, Rui ^d   Hwong, Sunny ^a   Liu, Yuexin ^e   Fang, Xiaodong ^b   Zhang, Yanlin ^f   Wang, Mengyao ^b   Wang, Jiaqian ^b   Li, Lin ^b   Zhou, Yong ^b   Tang, Senwei ^a   Peng, Shaoliang ^g   Qiu, Kunlong ^b   Chen, Longyun ^b   Chen, Kexin ^e   Yang, Huanming ^b   Zhang, Wei ^h   Chan, Matthew T V ^c   Lu, Youyong ^d   Sung, Joseph J Y ^a   Yu, Jun ^a   more..

^a CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^b BGI SHENZHEN   (China)

^c CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^d PEKING UNIVERSITY CANCER HOSPITAL AND INSTITUTE   (China)

^e TIANJIN MEDICAL UNIVERSITY   (China)

^f CITY UNIVERSITY OF HONG KONG   (Hong Kong)

^g NATIONAL UNIVERSITY OF DEFENSE TECHNOLOGY   (China)

^h UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AKAP6 GENE; ARTICLE; BRCA2 GENE; CANCER PATIENT; CANCER PROGNOSIS; CANCER STAGING; CANCER SURVIVAL; CNBD1 GENE; COL14A1 GENE; CONTROLLED STUDY; FANCM GENE; FRAMESHIFT MUTATION; GENE; GENE EXPRESSION; GENE MUTATION; HUMAN; HUMAN CELL; ITGAV GENE; MISSENSE MUTATION; MSH3 GENE; NBEA GENE; NONSENSE MUTATION; POINT MUTATION; PREVALENCE; PRIORITY JOURNAL; PRKDC GENE; SMAD4 GENE; SOMATIC MUTATION; STOMACH CANCER; SURVIVAL RATE; XIRP2 GENE; FEMALE; GENETIC PREDISPOSITION; GENETICS; MALE; MORTALITY; MUTATION; PROGNOSIS; STOMACH TUMOR;

FEMALE; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MALE; MUTATION; PROGNOSIS; STOMACH NEOPLASMS;

EID: 84963739887     PISSN: 00085472     EISSN: 15387445     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-15-2443     Document Type: Article

References (48)

1. Ferlay J, Soerjomataram I, Ervik M, Dikshit R, Eser S, Mathers C, et al. GLOBOCAN 2012: estimated cancer incidence, mortality and prevalence worldwide in 2012, Section of cancer information. IARC, Lyon, France. v1.0.
2. Lauren P. The two histological main types of gastric carcinoma: diffuse and so-called intestinal-type carcinoma. Acta Pathol Microbiol Scand 1965; 64:31-49.
3. Yamashita K, Sakuramoto S, Katada N, Futawatari N, Moriya H, Hirai K, et al. Diffuse type advanced gastric cancer showing dismal prognosis is characterized by deeper invasion and emerging peritoneal cancer cell: The latest comparative study to intestinal advanced gastric cancer. Hepatogastroenterology 2009;56:276-81.
4. Marrelli D, Roviello F, DeManzoni G, Morgagni P, DiLeo A, Saragoni L, et al. Different patterns of recurrence in gastric cancer depending on Lauren's histological type: longitudinal study. World J Surg 2002;26: 1160-5.
5. Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature 2009;458:719-24.
6. Vogelstein B, Kinzler KW. Cancer genes and the pathways they control. Nat Med 2004;10:789-99.
7. Helleday T, Eshtad S, Nik-Zainal S. Mechanisms underlying mutational signatures in human cancers. Nat Rev Genet 2014;15: 585-98.
8. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, et al. Signatures of mutational processes in human cancer. Nature 2013; 500:415-21.
9. Burns MB, Temiz NA, Harris RS. Evidence for APOBEC3B mutagenesis in multiple human cancers. Nat Genet 2013;45:977-83.
10. Roberts SA, Lawrence MS, Klimczak LJ, Grimm SA, Fargo D, Stojanov P, et al. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat Genet 2013;45:970-6.
11. Henderson S, Chakravarthy A, Su X, Boshoff C, Fenton TR. APOBECmediated cytosine deamination links PIK3CA helical domain mutations to human papillomavirus-driven tumor development. Cell Rep 2014;7: 1833-41.
12. Wang K, Kan J, Yuen ST, Shi ST, Chu KM, Law S, et al. Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat Genet 2011;43:1219-23.
13. Zang ZJ, Cutcutache I, Poon SL, Zhang SL, McPherson JR, Tao J, et al. Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nat Genet 2012; 44:570-4.
14. Bass AJ, Thorsson V, Shmulevich I, Reynolds SM, Miller M, Bernald B, et al. Comprehensive molecular characterization of gastric adenocarcinoma. Nature 2014;513:202-9.
15. Wang K, Yuen ST, Xu J, Lee SP, Yan HH, Shi ST, et al. Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer. Nat Genet 2014;46:573-82.
16. Kakiuchi M, Nishizawa T, Ueda H, Gotoh K, Tanaka A, Hayashi A, et al. Recurrent gain-of-function mutations of RHOA in diffuse-type gastric carcinoma. Nat Genet 2014;46:583-7.
17. Chen K, Yang D, Li X, Sun B, Song F, Cao W, et al. Mutational landscape of gastric adenocarcinoma in Chinese : implications for prognosis and therapy. Proc Natl Acad Sci 2015;6:1-6.
18. Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 2014;505:495-501.
19. Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010;38:1-7.
20. Wang H, Song M. Ckmeans.1d.dp: Optimal k-means clustering in one dimension by dynamic programming. R J 2011;3:29-33.
21. Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, et al. Mutational heterogeneity in cancer and the search for new cancerassociated genes. Nature 2013;499:214-8.
22. Liu X, Jian X, Boerwinkle E. dbNSFP v2.0: A database of human nonsynonymous SNVs and their functional predictions and annotations.Hum Mutat 2013;34:2393-402.
23. Kandoth C, Mclellan MD, Vandin F, Ye K, Niu B, Lu C, et al. Mutational landscape and significance across 12 major cancer types. Nature 2013; 502:333-9.
24. Klijn C, Durinck S, Stawiski EW, Havery PM, Jiang Z, Liu H, et al. A comprehensive transcriptional portrait of human cancer cell lines. Nat Biotechnol 2015;33:306-12.
25. Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep 2013;3:2650.
26. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, et al. A census of human cancer genes. Nat Rev Cancer 2004;4: 177-83.
27. Brunet J, Tamayo P, Golub TR, Mesirov JP. Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci U S A 2004;101:4164-9.
28. Gao Y, Church G. Improving molecular cancer class discovery through sparse non-negative matrix factorization. Bioinformatics 2005;21: 3970-5.
29. Kim H, Park H. Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis. Bioinformatics 2007;23:1495-502.
30. Gaujoux R, Seoighe C. A flexible R package for nonnegative matrix factorization. BMC Bioinformatics 2010;11:367.
31. Yu J, Wu WKK, Li X, He J, Li XX, Ng SS, et al. Novel recurrently mutated genes and a prognostic mutation signature in colorectal cancer. Gut 2015;64:636-45.
32. Cancer T, Atlas G. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012;487:330-7.
33. Bass AJ, Laird PW, Shmulevich I, Thorsson V, Schultz N, Sheth M, et al. Comprehensive Molecular Characterization of Gastric Adenocarcinoma. Nature 2014;513:202-9.
34. Alexandrov LB, Nik-Zainal S, Wedge DC, Campbell PJ, Stratton MR. Deciphering signatures of mutational processes operative in human cancer. Cell Rep 2013;3:246-59.
35. Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, et al. The cBio cancer genomics portal: An open platform for exploring multidimensional cancer genomics data. Cancer Discov 2012;2:401-4.
36. Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 2013;6:p1.
37. Dulak AM, Stojanov P, Peng S, Lawrence MS, Fox C, Stewart C, et al. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nat Genet 2013;45: 478-86.
38. Stirzaker C, Zotenko E, Song JZ, Qu W, Nair SS, Locke WJ, et al. Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value. Nat Commun 2015;6: 1-11.
39. Ni X, Zhuo M, Su Z, Duan J, Gao Y, Wang Z, et al. Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients. Proc Natl Acad Sci USA 2013;110:21083-8.
40. Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA, Kinzler KW. Cancer genome landscapes. Science 2013;339:1546-58.
41. Smith HC, Bennett RP, Kizilyer A, McDougall WM, Prohaska KM. Functions and regulation of the APOBEC family of proteins. Semin Cell Dev Biol 2012;23:258-68.
42. Zhang L, Zhou Y, Cheng C, Cui H, Cheng L, Kong P, et al. Genomic analyses reveal mutational signatures and frequently altered genes in esophageal squamous cell carcinoma. Am J Hum Genet 2015;96:597-611.
43. Breiman L. Random Forests. Mach Lean 2001;45:5-32.
44. Liaw A, Wiener M. Classification and regression by random forest. R News 2002;2:18-22.
45. Wong SS, Kim KM, Ting JC, Yu K, Fu J, Liu S, et al. Genomic landscape and genetic heterogeneity in gastric adenocarcinoma revealed by wholegenome sequencing. Nat Commun 2014;5:5477.
46. Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, et al. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell 2014;158:1-16.
47. Gross AM, Orosco RK, Shen JP, Egloff AM, Carter H, Choueiri M, et al. Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nat Genet 2014;46:939-43.
48. Akbani R, Akdemir KC, Aksoy BA, Albert M, Ally A, Amin SB, et al. Genomic classification of cutaneous melanoma. Cell 2015;161:1681-96.