Identification of DNA methylation changes associated with human gastric cancer

BMC Medical Genomics

Volumn 4, Issue , 2011, Pages

  Park, Jung Hoon ^a   Park, Jinah ^b   Choi, Jung Kyoon ^c,d   Lyu, Jaemyun ^a   Bae, Min Gyun ^a   Lee, Young Gun ^a   Bae, Jae Bum ^a   Park, Dong Yoon ^a   Yang, Han Kwang ^b   Kim, Tae You ^b   Kim, Young Joon ^a  

^a Yonsei University   (South Korea)

^b Seoul National University College of Medicine   (South Korea)

^c Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^d GENOME INSTITUTE OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; HOX PROTEIN; PROTEIN MDM2; MESSENGER RNA;

ALGORITHM; ARTICLE; CANCER DIAGNOSIS; CANCER TISSUE; CONTROLLED STUDY; CPG ISLAND; DISEASE ASSOCIATION; DNA METHYLATION; DOWN REGULATION; EPIGENETICS; EXON; GENE CONTROL; GENE IDENTIFICATION; GENOME ANALYSIS; HUMAN; HUMAN TISSUE; LYMPH NODE METASTASIS; MULTIGENE FAMILY; PRIORITY JOURNAL; PROMOTER REGION; SHORT INTERSPERSED REPEAT; STOMACH CANCER; BIOASSAY; CLUSTER ANALYSIS; DNA SEQUENCE; GENE SILENCING; GENETICS; HUMAN CHROMOSOME; HUMAN GENOME; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; PATHOLOGY; STOMACH; STOMACH TUMOR;

BIOLOGICAL ASSAY; CHROMOSOMES, HUMAN; CLUSTER ANALYSIS; CPG ISLANDS; DNA METHYLATION; GENE SILENCING; GENOME, HUMAN; HUMANS; LYMPHATIC METASTASIS; MOLECULAR SEQUENCE ANNOTATION; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA; STOMACH; STOMACH NEOPLASMS;

EID: 82455162772     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-4-82     Document Type: Article

References (54)

1. Cancer (Fact sheet N°297). World Health Organization 2009
2. E-cadherin germline mutations in familial gastric cancer. Guilford P, Hopkins J, Harraway J, McLeod M, McLeod N, Harawira P, Taite H, Scoular R, Miller A, Reeve AE, Nature 1998 392 6674 402 405 (Pubitemid 28168738)
3. Ataxia-telangiectasia and stomach cancer. Massad M, Uthman S, Obeid S, Majjar F, Am J Gastroenterol 1990 85 5 630 631 (Pubitemid 20164341)
4. A novel germ line juxtamembrane Met mutation in human gastric cancer. Lee JH, Han SU, Cho H, Jennings B, Gerrard B, Dean M, Schmidt L, Zbar B, Vande Woude GF, Oncogene 2000 19 43 4947 4953
5. Genetic susceptibility and gastric cancer risk. Gonzalez CA, Sala N, Capella G, Int J Cancer 2002 100 3 249 260 (Pubitemid 34728981)
6. A full genome scan for gastric cancer. Aoki M, Yamamoto K, Noshiro H, Sakai K, Yokota J, Kohno T, Tokino T, Ishida S, Ohyama S, Ninomiya I, et al. J Med Genet 2005 42 1 83 87 (Pubitemid 40187127)
7. NF2 expression levels of gastrointestinal stromal tumors: a quantitative real-time PCR study. Taddei A, Castiglione F, Degl'Innocenti DR, Buccoliero AM, Garbini F, Tommasi C, Freschi G, Bechi P, Messerini L, Taddei GL, Tumori 2008 94 4 551 555
8. Integrative approach for differentially overexpressed genes in gastric cancer by combining large-scale gene expression profiling and network analysis. Takeno A, Takemasa I, Doki Y, Yamasaki M, Miyata H, Takiguchi S, Fujiwara Y, Matsubara K, Monden M, Br J Cancer 2008 99 8 1307 1315
9. An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer. Cui J, Chen Y, Chou WC, Sun L, Chen L, Suo J, Ni Z, Zhang M, Kong X, Hoffman LL, et al. Nucleic Acids Res 2011 39 4 1197 1207
10. Microarray analysis identifies versican and CD9 as potent prognostic markers in gastric gastrointestinal stromal tumors. Setoguchi T, Kikuchi H, Yamamoto M, Baba M, Ohta M, Kamiya K, Tanaka T, Baba S, Goto-Inoue N, Setou M, et al. Cancer Sci 2011 102 4 883 889
11. Gene expression profiling of metaplastic lineages identifies CDH17 as a prognostic marker in early stage gastric cancer. Lee HJ, Nam KT, Park HS, Kim MA, Lafleur BJ, Aburatani H, Yang HK, Kim WH, Goldenring JR, Gastroenterology 2010 139 1 213 225 e213
12. Identification of prognostic biomarkers in gastric cancer using endoscopic biopsy samples. Yamada Y, Arao T, Gotoda T, Taniguchi H, Oda I, Shirao K, Shimada Y, Hamaguchi T, Kato K, Hamano T, et al. Cancer Sci 2008 99 11 2193 2199
13. Gene-expression signatures can distinguish gastric cancer grades and stages. Cui J, Li F, Wang G, Fang X, Puett JD, Xu Y, PLoS One 2011 6 3 17819
14. Clinicopathological significance of overexpression of TSPAN1, Ki67 and CD34 in gastric carcinoma. Chen L, Li X, Wang GL, Wang Y, Zhu YY, Zhu J, Tumori 2008 94 4 531 538
15. DNA methylation as a marker for the past and future. Ushijima T, Nakajima T, Maekita T, J Gastroenterol 2006 41 5 401 407 (Pubitemid 43941905)
16. The epigenomics of cancer. Jones PA, Baylin SB, Cell 2007 128 4 683 692 (Pubitemid 46273572)
17. Molecular biology of gastric cancer. El-Rifai W, Powell SM, Semin Radiat Oncol 2002 12 2 128 140 (Pubitemid 34522349)
18. Quantification of epigenetic and genetic 2nd hits in CDH1 during hereditary diffuse gastric cancer syndrome progression. Oliveira C, Sousa S, Pinheiro H, Karam R, Bordeira-Carrico R, Senz J, Kaurah P, Carvalho J, Pereira R, Gusmao L, et al. Gastroenterology 2009 136 7 2137 2148
19. Deciphering the underlying genetic and epigenetic events leading to gastric carcinogenesis. Vogiatzi P, Vindigni C, Roviello F, Renieri A, Giordano A, J Cell Physiol 2007 211 2 287 295 (Pubitemid 46580082)
20. Epidemiology of gastric cancer. Crew KD, Neugut AI, World J Gastroenterol 2006 12 3 354 362 (Pubitemid 43329250)
21. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, et al. Nature 2008 454 7205 766 770
22. Genome-wide DNA methylation profiling. Bibikova M, Fan JB, Wiley Interdiscip Rev Syst Biol Med 2010 2 2 210 223
23. DNA methylation profiling of human chromosomes 6, 20 and 22. Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, et al. Nat Genet 2006 38 12 1378 1385 (Pubitemid 44837559)
24. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Gu H, Bock C, Mikkelsen TS, Jager N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A, Nat Methods 2010 7 2 133 136
25. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Graf S, Johnson N, Herrero J, Tomazou EM, et al. Nat Biotechnol 2008 26 7 779 785 (Pubitemid 351961453)
26. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schubeler D, Nat Genet 2005 37 8 853 862 (Pubitemid 41077111)
27. Whole-genome DNA methylation profiling using MethylCap-seq. Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG, Methods 2010
28. Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Rauch T, Pfeifer GP, Lab Invest 2005 85 9 1172 1180 (Pubitemid 43073989)
29. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Serre D, Lee BH, Ting AH, Nucleic Acids Res 2010 38 2 391 399
30. MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Rauch T, Li H, Wu X, Pfeifer GP, Cancer Res 2006 66 16 7939 7947 (Pubitemid 44299157)
31. DNA methylation profiling using the methylated-CpG island recovery assay (MIRA). Rauch TA, Pfeifer GP, Methods 2010 52 3 213 217
32. Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Rauch T, Wang Z, Zhang X, Zhong X, Wu X, Lau SK, Kernstine KH, Riggs AD, Pfeifer GP, Proceedings of the National Academy of Sciences of the United States of America 2007 104 13 5527 5532 (Pubitemid 47175714)
33. CpG islands in vertebrate genomes. Gardiner-Garden M, Frommer M, J Mol Biol 1987 196 2 261 282 (Pubitemid 17122132)
34. MethPrimer: designing primers for methylation PCRs. Li LC, Dahiya R, Bioinformatics (Oxford, England) 2002 18 11 1427 1431 (Pubitemid 35414532)
35. MBD3L1 is a transcriptional repressor that interacts with methyl-CpG-binding protein 2 (MBD2) and components of the NuRD complex. Jiang CL, Jin SG, Pfeifer GP, J Biol Chem 2004 279 50 52456 52464 (Pubitemid 39656621)
36. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, et al. Nat Methods 2007 4 8 651 657 (Pubitemid 47202477)
37. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, et al. Nature 2007 448 7153 553 560 (Pubitemid 47206934)
38. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D, Nat Genet 2007 39 4 457 466 (Pubitemid 46514772)
39. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, et al. Genome research 2009 19 9 1593 1605
40. DNA methylation patterns in lung carcinomas. Pfeifer GP, Rauch TA, Semin Cancer Biol 2009 19 3 181 187
41. DNA hypomethylation in cancer cells. Ehrlich M, Epigenomics 2009 1 2 239 259
42. Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells. Rodriguez J, Vives L, Jorda M, Morales C, Munoz M, Vendrell E, Peinado MA, Nucleic Acids Res 2008 36 3 770 784 (Pubitemid 351267234)
43. Progress in understanding the biology of the human mutagen LINE-1. Babushok DV, Kazazian HH Jr, Hum Mutat 2007 28 6 527 539 (Pubitemid 46744283)
44. The p53-mdm-2 autoregulatory feedback loop. Wu X, Bayle JH, Olson D, Levine AJ, Genes Dev 1993 7 7A 1126 1132 (Pubitemid 23207405)
45. Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Ordway JM, Bedell JA, Citek RW, Nunberg A, Garrido A, Kendall R, Stevens JR, Cao D, Doerge RW, Korshunova Y, et al. Carcinogenesis 2006 27 12 2409 2423 (Pubitemid 44884098)
46. Inactivation of HOXA genes by hypermethylation in myeloid and lymphoid malignancy is frequent and associated with poor prognosis. Strathdee G, Holyoake TL, Sim A, Parker A, Oscier DG, Melo JV, Meyer S, Eden T, Dickinson AM, Mountford JC, et al. Clin Cancer Res 2007 13 17 5048 5055 (Pubitemid 47502069)
47. Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Scheuermann JC, de Ayala Alonso AG, Oktaba K, Ly-Hartig N, McGinty RK, Fraterman S, Wilm M, Muir TW, Muller J, Nature 2010 465 7295 243 247
48. Cooperation between EZH2, NSPc1-mediated histone H2A ubiquitination and Dnmt1 in HOX gene silencing. Wu X, Gong Y, Yue J, Qiang B, Yuan J, Peng X, Nucleic Acids Res 2008 36 11 3590 3599 (Pubitemid 351917523)
49. Large-scale structure of genomic methylation patterns. Rollins RA, Haghighi F, Edwards JR, Das R, Zhang MQ, Ju J, Bestor TH, Genome research 2006 16 2 157 163 (Pubitemid 43200263)
50. Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis. Bailey JA, Carrel L, Chakravarti A, Eichler EE, Proceedings of the National Academy of Sciences of the United States of America 2000 97 12 6634 6639 (Pubitemid 30412766)
51. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, et al. Cell 2006 126 6 1189 1201 (Pubitemid 44380289)
52. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S, Nat Genet 2007 39 1 61 69 (Pubitemid 46026502)
53. High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. Rauch TA, Zhong X, Wu X, Wang M, Kernstine KH, Wang Z, Riggs AD, Pfeifer GP, Proceedings of the National Academy of Sciences of the United States of America 2008 105 1 252 257
54. Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line. Gal-Yam EN, Egger G, Iniguez L, Holster H, Einarsson S, Zhang X, Lin JC, Liang G, Jones PA, Tanay A, Proceedings of the National Academy of Sciences of the United States of America 2008 105 35 12979 12984