CpG island methylation profiling in human melanoma cell lines

Melanoma Research

Volumn 19, Issue 3, 2009, Pages 146-155

  Tellez, Carmen S ^a,d   Shen, Lanlan ^a   Estécio, Marcos R H ^a   Jelinek, Jaroslav ^a   Gershenwald, Jeffrey E ^b,c   Issa, Jean Pierre J ^a  

^a Departments of Leukemia

^b Surgical Oncology ^*

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

^d LOVELACE RESPIRATORY RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

B RAF KINASE; MASPIN; METHYLATED DNA PROTEIN CYSTEINE METHYLTRANSFERASE; OLIGODENDROCYTE TRANSCRIPTION FACTOR 2; PROTEIN MLH1; PROTEIN P16; RAS ASSOCIATION DOMAIN FAMILY PROTEIN 1A; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR NKX2.3; TRANSCRIPTION FACTOR PAX7; UNCLASSIFIED DRUG;

ARTICLE; CANCER CELL CULTURE; CDH13 GENE; CODON; CPG ISLAND; DNA METHYLATION; ECAD GENE; ER GENE; GENE EXPRESSION PROFILING; GENE MUTATION; GENE SEQUENCE; HUMAN; HUMAN CELL; LINE 1 GENE; MELANOMA; METHYLATION; MGMT GENE; PGRB GENE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PYROSEQUENCING; RARB2 GENE; RIL GENE; TUMOR GENE; GENE EXPRESSION REGULATION; GENE FREQUENCY; GENETIC EPIGENESIS; GENETICS; MUTATION; SKIN TUMOR; TUMOR CELL LINE;

CELL LINE, TUMOR; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE FREQUENCY; HUMANS; MELANOMA; MUTATION; PROMOTER REGIONS, GENETIC; SKIN NEOPLASMS;

EID: 67849109939     PISSN: 09608931     EISSN: None     Source Type: Journal    
DOI: 10.1097/CMR.0b013e32832b274e     Document Type: Article

References (43)

1. Jemal A, Siegel R, Ward E, Hao Y, Xu J, Murray T, et al. Cancer statistics, 2008. CA Cancer J Clin 2008; 58:71-96.
2. Esteller M. Cancer epigenetics: DNA methylation and chromatin alterations in human cancer. Adv Exp Med Biol 2003; 532:39-49. (Pubitemid 37176778)
3. Toyota M, Ahuja N, Ohe-Toyota M, Herman JG, Baylin SB, Issa JP. CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci U S A 1999; 96:8681-8686. (Pubitemid 29354851)
4. Toyota M, Ohe-Toyota M, Ahuja N, Issa JP. Distinct genetic profiles in colorectal tumors with or without the CpG island methylator phenotype. Proc Natl Acad Sci U S A 2000; 97:710-715.
5. Issa JP. CpG island methylator phenotype in cancer. Nat Rev 2004; 4:988-993.
6. Li Q, Jedlicka A, Ahuja N, Gibbons MC, Baylin SB, Burger PC, et al. Concordant methylation of the ER and N33 genes in glioblastoma multiforme. Oncogene 1998; 16:3197-3202.
7. Abe M, Ohira M, Kaneda A, Yagi Y, Yamamoto S, Kitano Y, et al. CpG island methylator phenotype is a strong determinant of poor prognosis in neuroblastomas. Cancer Res 2005; 65:828-834.
8. Toyota M, Ahuja N, Suzuki H, Itoh F, Ohe-Toyota M, Imai K, et al. Aberrant methylation in gastric cancer associated with the CpG island methylator phenotype. Cancer Res 1999; 59:5438-5442.
9. Shen L, Ahuja N, Shen Y, Habib NA, Toyota M, Rashid A, et al. DNA methylation and environmental exposures in human hepatocellular carcinoma. J Natl Cancer Inst 2002; 94:755-761.
10. Roman-Gomez J, Jimenez-Velasco A, Agirre X, Prosper F, Heiniger A, Torres A. Lack of CpG island methylator phenotype defines a clinical subtype of T-cell acute lymphoblastic leukemia associated with good prognosis. J Clin Oncol 2005; 23:7043-7049.
11. Chan AO, Kim SG, Bedeir A, Issa JP, Hamilton SR, Rashid A. CpG island methylation in carcinoid and pancreatic endocrine tumors. Oncogene 2003; 22 :924-934.
12. Strathdee G, Appleton K, Illand M, Millan DW, Sargent J, Paul J, et al. Primary ovarian carcinomas display multiple methylator phenotypes involving known tumor suppressor genes. Am J Pathol 2001; 158:1121-1127.
13. Gama-Sosa MA, Slagel VA, Trewyn RW, Oxenhandler R, Kuo KC, Gehrke CW, et al. The 5-methylcytosine content of DNA from human tumors. Nucleic Acids Res 1983; 11:6883-6894.
14. Ehrlich M. DNA methylation in cancer: too much, but also too little. Oncogene 2002; 21:5400-5413.
15. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature 2001; 409:860-921.
16. Jurgens B, Schmitz-Drager BJ, Schulz WA. Hypomethylation of L1 LINE sequences prevailing in human urothelial carcinoma. Cancer Res 1996; 56 :5698-5703.
17. Takai D, Yagi Y, Habib N, Sugimura T, Ushijima T. Hypomethylation of LINE1 retrotransposon in human hepatocellular carcinomas, but not in surrounding liver cirrhosis. Jpn J Clin Oncol 2000; 30:306-309.
18. Kaneda A, Tsukamoto T, Takamura-Enya T, Watanabe N, Kaminishi M, Sugimura T, et al. Frequent hypomethylation in multiple promoter CpG islands is associated with global hypomethylation, but not with frequent promoter hypermethylation. Cancer Sci 2004; 95:58-64.
19. Weisenberger DJ, Campan M, Long TI, Kim M, Woods C, Fiala E, et al. Analysis of repetitive element DNA methylation by MethyLight. Nucleic Acids Res 2005; 33:6823-6836.
20. Yang AS, Estecio MR, Doshi K, Kondo Y, Tajara EH, Issa JP. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res 2004; 32:e38.
21. Scanlan MJ, Gure AO, Jungbluth AA, Old LJ, Chen YT. Cancer/testis antigens: an expanding family of targets for cancer immunotherapy. Immunol Rev 2002; 188:22-32.
22. Honda T, Tamura G, Waki T, Kawata S, Terashima M, Nishizuka S, et al. Demethylation of MAGE promoters during gastric cancer progression. Br J Cancer 2004; 90:838-843.
23. Jang SJ, Soria JC, Wang L, Hassan KA, Morice RC, Walsh GL, et al. Activation of melanoma antigen tumor antigens occurs early in lung carcinogenesis. Cancer Res 2001; 61:7959-7963.
24. Ongenaert M, Van Neste L, De Meyer T, Menschaert G, Bekaert S, Van Criekinge W. PubMeth: a cancer methylation database combining text-mining and expert annotation. Nucleic Acids Res 2008; 36:D842-D846.
25. Estecio MR, Yan PS, Ibrahim AE, Tellez CS, Shen L, Huang TH, et al. High-throughput methylation profiling by MCA coupled to CpG island microarray. Genome Res 2007; 17:1529-1536.
26. Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res 1994; 22:2990-2997.
27. Colella S, Shen L, Baggerly KA, Issa JP, Krahe R. Sensitive and quantitative universal Pyrosequencing methylation analysis of CpG sites. Biotechniques 2003; 35:146-150.
28. Kozlowski JM, Hart IR, Fidler IJ, Hanna N. A human melanoma line heterogeneous with respect to metastatic capacity in athymic nude mice. J Natl Cancer Inst 1984; 72:913-917.
29. Li L, Price JE, Fan D, Zhang RD, Bucana CD, Fidler IJ. Correlation of growth capacity of human tumor cells in hard agarose with their in vivo proliferative capacity at specific metastatic sites. J Natl Cancer Inst 1989; 81:1406-1412.
30. Satyamoorthy K, DeJesus E, Linnenbach AJ, Kraj B, Kornreich DL, Rendle S, et al. Melanoma cell lines from different stages of progression and their biological and molecular analyses. Melanoma Res 1997; 7 (Suppl 2):S35-S42.
31. Fang D, Nguyen TK, Leishear K, Finko R, Kulp AN, Hotz S, et al. A tumorigenic subpopulation with stem cell properties in melanomas. Cancer Res 2005; 65:9328-9337.
32. Hoon DS, Spugnardi M, Kuo C, Huang SK, Morton DL, Taback B. Profiling epigenetic inactivation of tumor suppressor genes in tumors and plasma from cutaneous melanoma patients. Oncogene 2004; 23:4014-4022.
33. Furuta J, Umebayashi Y, Miyamoto K, Kikuchi K, Otsuka F, Sugimura T, et al. Promoter methylation profiling of 30 genes in human malignant melanoma. Cancer Sci 2004; 95:962-968.
34. Mori T, O'Day SJ, Umetani N, Martinez SR, Kitago M, Koyanagi K, et al. Predictive utility of circulating methylated DNA in serum of melanoma patients receiving biochemotherapy. J Clin Oncol 2005; 23:9351-9358.
35. Bariol C, Suter C, Cheong K, Ku SL, Meagher A, Hawkins N, et al. The relationship between hypomethylation and CpG Island methylation in colorectal neoplasia. Am J Pathol 2003; 162:1361-1371. (Pubitemid 36350680)
36. Ehrlich M, Jiang G, Fiala E, Dome JS, Yu MC, Long TI, et al. Hypomethylation and hypermethylation of DNA in Wilms tumors. Oncogene 2002; 21 :6694-6702.
37. Estecio MR, Gharibyan V, Shen L, Ibrahim AE, Doshi K, He R, et al. LINE-1 hypomethylation in cancer is highly variable and inversely correlated with microsatellite instability. PLoS ONE 2007; 2:e399.
38. Ehrlich M, Woods CB, Yu MC, Dubeau L, Yang F, Campan M, et al. Quantitative analysis of associations between DNA hypermethylation, hypomethylation, and DNMT RNA levels in ovarian tumors. Oncogene 2006; 25 :2636-2645.
39. Cravo M, Pinto R, Fidalgo P, Chaves P, Gloria L, Nobre-Leitao C, et al. Global DNA hypomethylation occurs in the early stages of intestinal type gastric carcinoma. Gut 1996; 39:434-438.
40. Roman-Gomez J, Jimenez-Velasco A, Agirre X, Cervantes F, Sanchez J, Garate L, et al. Promoter hypomethylation of the LINE-1 retrotransposable elements activates sense/antisense transcription and marks the progression of chronic myeloid leukemia. Oncogene 2005; 24:7213-7223.
41. Demunter A, Stas M, Degreef H, De Wolf-Peeters C, van den Oord JJ. Analysis of N- and K-ras mutations in the distinctive tumor progression phases of melanoma. J Invest Dermatol 2001; 117:1483-1489.
42. Ball NJ, Yohn JJ, Morelli JG, Norris DA, Golitz LE, Hoeffler JP. Ras mutations in human melanoma: a marker of malignant progression. J Invest Dermatol 1994; 102:285-290.
43. Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, et al. Mutations of the BRAF gene in human cancer. Nature 2002; 417: 949-954.