Molecular classification and prediction in gastric cancer

Computational and Structural Biotechnology Journal

Volumn 13, Issue , 2015, Pages 448-458

  Lin, Xiandong ^a,b   Zhao, Yongzhong ^a   Song, Won Min ^a   Zhang, Bin ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b FUJIAN PROVINCIAL CANCER HOSPITAL   (China)

Author keywords

Gastric cancer; Gene expression profiling; Molecular classification; Molecular subtyping

Indexed keywords

ANTINEOPLASTIC AGENT;

BIOLOGICAL FUNCTIONS; CANCER CHEMOTHERAPY; CANCER CLASSIFICATION; CANCER DIAGNOSIS; CANCER PROGNOSIS; HUMAN; MOLECULAR DIAGNOSIS; MOLECULAR TYPING; PREDICTION; PRIORITY JOURNAL; REVIEW; STAGING; STOMACH CANCER; TREATMENT RESPONSE;

EID: 84948747250     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.1016/j.csbj.2015.08.001     Document Type: Review

References (88)

1. Jemal A, Bray F, Center MM et al. Global cancer statistics. CA Cancer J Clin 61: 69-90.
2. R. Siegel, D. Naishadham, and A. Jemal Cancer statistics, 2012 CA Cancer J Clin 62 2012 10 29
3. L. Shen, Y.S. Shan, H.M. Hu, and et al. Management of gastric cancer in Asia: resource-stratified guidelines Lancet Oncol 14 2013 e535 e547
4. J.T. Lin Screening of gastric cancer: who, when, and how Clin Gastroenterol Hepatol 12 1 2014 135 138
5. G.Y. Liu, K.H. Liu, Y. Zhang, and et al. Alterations of tumor-related genes do not exactly match the histopathological grade in gastric adenocarcinomas World J Gastroenterol 16 2010 1129 1137
6. B. Hu, N. El Hajj, S. Sittler, and et al. Gastric cancer: classification, histology and application of molecular pathology J Gastrointest Oncol 3 2012 251 261
7. V.S. Warneke, H.M. Behrens, J.T. Hartmann, and et al. Cohort study based on the seventh edition of the TNM classification for gastric cancer: proposal of a new staging system J Clin Oncol 29 2011 2364 2371
8. K.H. Brettingham-Moore, C.P. Duong, A.G. Heriot, and et al. Using gene expression profiling to predict response and prognosis in gastrointestinal cancers-the promise and the perils Ann Surg Oncol 18 2011 1484 1491
9. F. Chibon Cancer gene expression signatures - the rise and fall? Eur J Cancer 49 2013 2000 2009
10. S.P. Balasubramanian Evaluation of the necessity for gastrectomy with lymph node dissection for patients with submucosal invasive gastric cancer (Br J Surg 2001; 88: 444-9) Br J Surg 88 2001 1133 1134
11. A. Boussioutas, H. Li, J. Liu, and et al. Distinctive patterns of gene expression in premalignant gastric mucosa and gastric cancer Cancer Res 63 2003 2569 2577
12. M. Vecchi, P. Nuciforo, S. Romagnoli, and et al. Gene expression analysis of early and advanced gastric cancers Oncogene 26 2007 4284 4294
13. S. Nam, J. Lee, S.H. Goh, and et al. Differential gene expression pattern in early gastric cancer by an integrative systematic approach Int J Oncol 41 2012 1675 1682
14. Kim H, Eun JW, Lee H et al. Gene expression changes in patient-matched gastric normal mucosa, adenomas, and carcinomas. Exp Mol Pathol 90: 201-209.
15. Z. Lei, I.B. Tan, K. Das, and et al. Identification of molecular subtypes of gastric cancer with different responses to PI3-kinase inhibitors and 5-fluorouracil Gastroenterology 145 2013 554 565
16. N. Pavlidis, and G. Pentheroudakis Cancer of unknown primary site Lancet 379 2012 1428 1435
17. F.A. Monzon, and T.J. Koen Diagnosis of metastatic neoplasms: molecular approaches for identification of tissue of origin Arch Pathol Lab Med 134 2010 216 224
18. F.A. Greco, D.R. Spigel, D.A. Yardley, and et al. Molecular profiling in unknown primary cancer: accuracy of tissue of origin prediction Oncologist 15 2010 500 506
19. J.D. Hainsworth, M.S. Rubin, D.R. Spigel, and et al. Molecular gene expression profiling to predict the tissue of origin and direct site-specific therapy in patients with carcinoma of unknown primary site: a prospective trial of the Sarah Cannon research institute J Clin Oncol 31 2013 217 223
20. P. Lauren The two histological main types of gastric carcinoma: diffuse and so-called intestinal-type carcinoma. An attempt at a histo-clinical classification Acta Pathol Microbiol Scand 64 1965 31 49
21. W. Polkowski, J.W. van Sandick, G.J. Offerhaus, and et al. Prognostic value of Lauren classification and c-erbB-2 oncogene overexpression in adenocarcinoma of the esophagus and gastroesophageal junction Ann Surg Oncol 6 1999 290 297
22. S. Noda, K. Soejima, and K. Inokuchi Clinicopathological analysis of the intestinal type and diffuse type of gastric carcinoma Jpn J Surg 10 1980 277 283
23. M.G. Fontana, M. La Pinta, D. Moneghini, and et al. Prognostic value of Goseki histological classification in adenocarcinoma of the cardia Br J Cancer 88 2003 401 405
24. O.J. Lee, H.J. Kim, J.R. Kim, and H. Watanabe The prognostic significance of the mucin phenotype of gastric adenocarcinoma and its relationship with histologic classifications Oncol Rep 21 2009 387 393
25. M.A. Shah, R. Khanin, L. Tang, and et al. Molecular classification of gastric cancer: a new paradigm Clin Cancer Res 17 2011 2693 2701
26. I.B. Tan, T. Ivanova, K.H. Lim, and et al. Intrinsic subtypes of gastric cancer, based on gene expression pattern, predict survival and respond differently to chemotherapy Gastroenterology 141 2011 476 485 [485 e471-411]
27. K. Teramoto, M. Tada, E. Tamoto, and et al. Prediction of lymphatic invasion/lymph node metastasis, recurrence, and survival in patients with gastric cancer by cDNA array-based expression profiling J Surg Res 124 2005 225 236
28. A. Marchet, S. Mocellin, C. Belluco, and et al. Gene expression profile of primary gastric cancer: towards the prediction of lymph node status Ann Surg Oncol 14 2007 1058 1064
29. Y.Z. Zhang, L.H. Zhang, Y. Gao, and et al. Discovery and validation of prognostic markers in gastric cancer by genome-wide expression profiling World J Gastroenterol 17 2011 1710 1717
30. A. Amini, and H. Sanati Complete pathologic response with combination oxaliplatin and 5-fluorouracil chemotherapy in an older patient with advanced gastric cancer Anticancer Drugs 22 2011 1024 1026
31. Z. Zhao, Y. Liu, H. He, and et al. Candidate genes influencing sensitivity and resistance of human glioblastoma to Semustine Brain Res Bull 86 2011 189 194
32. M. Youns, Y.J. Fu, Y.G. Zu, and et al. Sensitivity and resistance towards isoliquiritigenin, doxorubicin and methotrexate in T cell acute lymphoblastic leukaemia cell lines by pharmacogenomics Naunyn Schmiedebergs Arch Pharmacol 382 2010 221 234
33. T. Tanaka, K. Tanimoto, K. Otani, and et al. Concise prediction models of anticancer efficacy of 8 drugs using expression data from 12 selected genes Int J Cancer 111 2004 617 626
34. N. Nakatsu, Y. Yoshida, K. Yamazaki, and et al. Chemosensitivity profile of cancer cell lines and identification of genes determining chemosensitivity by an integrated bioinformatical approach using cDNA arrays Mol Cancer Ther 4 2005 399 412
35. J.J. Jung, H.C. Jeung, H.C. Chung, and et al. In vitro pharmacogenomic database and chemosensitivity predictive genes in gastric cancer Genomics 93 2009 52 61
36. T. Ivanova, H. Zouridis, Y. Wu, and et al. Integrated epigenomics identifies BMP4 as a modulator of cisplatin sensitivity in gastric cancer Gut 62 2013 22 33
37. J.S. Park, S. Young Yoon, J.M. Kim, and et al. Identification of novel genes associated with the response to 5-FU treatment in gastric cancer cell lines using a cDNA microarray Cancer Lett 214 2004 19 33
38. K. Suganuma, T. Kubota, Y. Saikawa, and et al. Possible chemoresistance-related genes for gastric cancer detected by cDNA microarray Cancer Sci 94 2003 355 359
39. H.K. Kim, I.J. Choi, H.S. Kim, and et al. DNA microarray analysis of the correlation between gene expression patterns and acquired resistance to 5-FU/cisplatin in gastric cancer Biochem Biophys Res Commun 316 2004 781 789
40. H.K. Kim, I.J. Choi, C.G. Kim, and et al. A gene expression signature of acquired chemoresistance to cisplatin and fluorouracil combination chemotherapy in gastric cancer patients PLoS One 6 2011 e16694
41. C.H. Kim, H.K. Kim, R.L. Rettig, and et al. miRNA signature associated with outcome of gastric cancer patients following chemotherapy BMC Med Genomics 4 2011 79
42. J. Wang, J.C. Yu, W.M. Kang, and Z.Q. Ma Prognostic significance of intraoperative chemotherapy and extensive lymphadenectomy in patients with node-negative gastric cancer J Surg Oncol 105 2012 400 404
43. A. Salem, S. Hashem, L.Y. Mula-Hussain, and et al. Management strategies for locoregional recurrence in early-stage gastric cancer: retrospective analysis and comprehensive literature review J Gastrointest Cancer 43 2012 77 82
44. M. Fujiwara, Y. Kodera, K. Misawa, and et al. Longterm outcomes of early-stage gastric carcinoma patients treated with laparoscopy-assisted surgery J Am Coll Surg 206 2008 138 143
45. Y. Yamada, T. Arao, T. Gotoda, and et al. Identification of prognostic biomarkers in gastric cancer using endoscopic biopsy samples Cancer Sci 99 2008 2193 2199
46. C. Lo Nigro, M. Monteverde, M. Riba, and et al. Expression profiling and long lasting responses to chemotherapy in metastatic gastric cancer Int J Oncol 37 2010 1219 1228
47. Z. Wang, Z. Yan, B. Zhang, and et al. Identification of a 5-gene signature for clinical and prognostic prediction in gastric cancer patients upon microarray data Med Oncol 30 2013 678
48. A. Takeno, I. Takemasa, S. Seno, and et al. Gene expression profile prospectively predicts peritoneal relapse after curative surgery of gastric cancer Ann Surg Oncol 17 2010 1033 1042
49. J.Y. Cho, J.Y. Lim, J.H. Cheong, and et al. Gene expression signature-based prognostic risk score in gastric cancer Clin Cancer Res 17 2011 1850 1857
50. M. Kim, and S.Y. Rha Prognostic index reflecting genetic alteration related to disease-free time for gastric cancer patient Oncol Rep 22 2009 421 431
51. V. Stathias, C. Pastori, T.Z. Griffin, and et al. Identifying glioblastoma gene networks based on hypergeometric test analysis PLoS One 9 2014 e115842
52. C.G. Willett, and B.G. Czito Chemoradiotherapy in gastrointestinal malignancies Clin Oncol (R Coll Radiol) 21 2009 543 556
53. H. Kim, J.W. Eun, H. Lee, and et al. Gene expression changes in patient-matched gastric normal mucosa, adenomas, and carcinomas Exp Mol Pathol 90 2011 201 209
54. C. Resende, A. Ristimaki, and J.C. Machado Genetic and epigenetic alteration in gastric carcinogenesis Helicobacter 15 Suppl. 1 2010 34 39
55. J. Zeng, Z. Ge, L. Wang, and et al. The histone demethylase RBP2 Is overexpressed in gastric cancer and its inhibition triggers senescence of cancer cells Gastroenterology 138 2010 981 992
56. K. Asada, T. Ando, T. Niwa, and et al. FHL1 on chromosome X is a single-hit gastrointestinal tumor-suppressor gene and contributes to the formation of an epigenetic field defect Oncogene 32 2013 2140 2149
57. Y. Xu, Z. Liu, and K. Guo Expression of FHL1 in gastric cancer tissue and its correlation with the invasion and metastasis of gastric cancer Mol Cell Biochem 363 2012 93 99
58. Cancer Genome Atlas Research N Comprehensive molecular characterization of gastric adenocarcinoma Nature 513 2014 202 209
59. R. Cristescu, J. Lee, M. Nebozhyn, and et al. Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes Nat Med 21 2015 449 456
60. A. Liberzon, A. Subramanian, R. Pinchback, and et al. Molecular signatures database (MSigDB) 3.0 Bioinformatics 27 2011 1739 1740
61. P. Farmer, H. Bonnefoi, P. Anderle, and et al. A stroma-related gene signature predicts resistance to neoadjuvant chemotherapy in breast cancer Nat Med 15 2009 68 74
62. R. Wesolowski, and B. Ramaswamy Gene expression profiling: changing face of breast cancer classification and management Gene Expr 15 2011 105 115
63. P.E. Colombo, F. Milanezi, B. Weigelt, and J.S. Reis-Filho Microarrays in the 2010s: the contribution of microarray-based gene expression profiling to breast cancer classification, prognostication and prediction Breast Cancer Res 13 2011 212
64. J.J. McCarthy, H.L. McLeod, and G.S. Ginsburg Genomic medicine: a decade of successes, challenges, and opportunities Sci Transl Med 5 2013 189sr184
65. H.C. Kang, I.J. Kim, J.H. Park, and et al. Identification of genes with differential expression in acquired drug-resistant gastric cancer cells using high-density oligonucleotide microarrays Clin Cancer Res 10 2004 272 284
66. M.J. Ahn, Y.D. Yoo, K.H. Lee, and et al. cDNA microarray analysis of differential gene expression in gastric cancer cells sensitive and resistant to 5-fluorouracil and cisplatin Cancer Res Treat 37 2005 54 62
67. D. Szoke, A. Gyorffy, P. Surowiak, and et al. Identification of consensus genes and key regulatory elements in 5-fluorouracil resistance in gastric and colon cancer Onkologie 30 2007 421 426
68. H. Murakami, S. Ito, H. Tanaka, and et al. Establishment of new intraperitoneal paclitaxel-resistant gastric cancer cell lines and comprehensive gene expression analysis Anticancer Res 33 2013 4299 4307
69. B. Gyorffy, P. Surowiak, O. Kiesslich, and et al. Gene expression profiling of 30 cancer cell lines predicts resistance towards 11 anticancer drugs at clinically achieved concentrations Int J Cancer 118 2006 1699 1712
70. H. Liu, N. Li, L. Yao, and et al. Prediction of doxorubicin sensitivity in gastric cancers based on a set of novel markers Oncol Rep 20 2008 963 969
71. Y.H. Zhang, Q. Wu, X.Y. Xiao, and et al. Silencing MRP4 by small interfering RNA reverses acquired DDP resistance of gastric cancer cell Cancer Lett 291 2010 76 82
72. I. Sohma, Y. Fujiwara, Y. Sugita, and et al. Parthenolide, an NF-kappaB inhibitor, suppresses tumor growth and enhances response to chemotherapy in gastric cancer Cancer Genomics Proteomics 8 2011 39 47
73. S. Claerhout, J.Y. Lim, W. Choi, and et al. Gene expression signature analysis identifies vorinostat as a candidate therapy for gastric cancer PLoS One 6 2011 e24662
74. K. Kato, J. Gong, H. Iwama, and et al. The antidiabetic drug metformin inhibits gastric cancer cell proliferation in vitro and in vivo Mol Cancer Ther 11 2012 549 560
75. C.H. Ooi, T. Ivanova, J. Wu, and et al. Oncogenic pathway combinations predict clinical prognosis in gastric cancer PLoS Genet 5 2009 e1000676
76. Z.Y. Xu, J.S. Chen, and Y.Q. Shu Gene expression profile towards the prediction of patient survival of gastric cancer Biomed Pharmacother 64 2010 133 139
77. Z. Yan, Y. Xiong, W. Xu, and et al. Identification of recurrence-related genes by integrating microRNA and gene expression profiling of gastric cancer Int J Oncol 41 2012 2166 2174
78. Z. Yan, Y. Xiong, W. Xu, and et al. Identification of hsa-miR-335 as a prognostic signature in gastric cancer PLoS One 7 2012 e40037
79. B. Brenner, M.B. Hoshen, O. Purim, and et al. MicroRNAs as a potential prognostic factor in gastric cancer World J Gastroenterol 17 2011 3976 3985
80. X. Zhang, Z. Yan, J. Zhang, and et al. Combination of hsa-miR-375 and hsa-miR-142-5p as a predictor for recurrence risk in gastric cancer patients following surgical resection Ann Oncol 22 2011 2257 2266
81. M. Kim, and H.C. Chung Standardized genetic alteration score and predicted score for predicting recurrence status of gastric cancer J Cancer Res Clin Oncol 135 2009 1501 1512
82. U. Yamaguchi, R. Nakayama, K. Honda, and et al. Distinct gene expression-defined classes of gastrointestinal stromal tumor J Clin Oncol 26 2008 4100 4108
83. S.Y. Leung, S.T. Yuen, K.M. Chu, and et al. Expression profiling identifies chemokine (C-C motif) ligand 18 as an independent prognostic indicator in gastric cancer Gastroenterology 127 2004 457 469
84. C.N. Chen, J.J. Lin, J.J. Chen, and et al. Gene expression profile predicts patient survival of gastric cancer after surgical resection J Clin Oncol 23 2005 7286 7295
85. T. Setoguchi, H. Kikuchi, M. Yamamoto, and et al. Microarray analysis identifies versican and CD9 as potent prognostic markers in gastric gastrointestinal stromal tumors Cancer Sci 102 2011 883 889
86. N. Deng, L.K. Goh, H. Wang, and 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 61 2012 673 684
87. S.S. Wong, K.M. Kim, J.C. Ting, and et al. Genomic landscape and genetic heterogeneity in gastric adenocarcinoma revealed by whole-genome sequencing Nat Commun 5 2014 5477
88. M. Kakiuchi, T. Nishizawa, H. Ueda, and et al. Recurrent gain-of-function mutations of RHOA in diffuse-type gastric carcinoma Nat Genet 46 2014 583 587