High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 1, 2008, Pages 252-257

  Rauch, Tibor A ^a   Zhong, Xueyan ^a   Wu, Xiwei ^a   Wang, Melody ^a   Kernstine, Kemp H ^a   Wang, Zunde ^a   Riggs, Arthur D ^a   Pfeifer, Gerd P ^a  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

Author keywords

CpG islands; DNA methylation; Tiling arrays

Indexed keywords

ARTICLE; CANCER DIAGNOSIS; CPG ISLAND; DEMETHYLATION; DNA DETERMINATION; DNA METHYLATION; DNA MICROARRAY; DNA SEQUENCE; HUMAN; HUMAN TISSUE; LUNG CANCER; PRIORITY JOURNAL; SQUAMOUS CELL CARCINOMA;

CARCINOMA, SQUAMOUS CELL; CHROMOSOME MAPPING; CPG ISLANDS; DNA; DNA METHYLATION; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LUNG NEOPLASMS; MODELS, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; TUMOR MARKERS, BIOLOGICAL;

EID: 38349135680     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0710735105     Document Type: Article

References (49)

1. Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128:683-692.
2. Lapeyre JN, Becker FF (1979) 5-Methylcytosine content of nuclear DNA during chemical hepatocarcinogenesis and in carcinomas which result. Biochem Biophys Res Commun 87:698-705.
3. Romanov GA, Vanyushin BF (1981) Methylation of reiterated sequences in mammalian DNAs. Effects of the tissue type, age, malignancy and hormonal induction. Biochim Biophys Acta 653:204-218.
4. Feinberg AP, Vogelstein B (1983) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301:89-92.
5. Gama-Sosa MA, et al. (1983) Tissue-specific differences in DNA methylation in various mammals. Biochim Biophys Acta 740:212-219.
6. Riggs AD, Jones PA (1983) 5-Methylcytosine, gene regulation, and cancer. Adv Cancer Res 40:1-30.
7. Gaudet F, et al. (2003) Induction of tumors in mice by genomic hypomethylation. Science 300:489-492.
8. Gonzalez-Zulueta M, et al. (1995) Methylation of the 5′ CpG island of the p16/CDKN2 tumor suppressor gene in normal and transformed human tissues correlates with gene silencing. Cancer Res 55:4531-4535.
9. Herman JG, et al. (1995) Inactivation of the CDKN2/p16/MTS1 gene is frequently associated with aberrant DNA methylation in all common human cancers. Cancer Res 55:4525-4530.
10. Merlo A, et al. (1995) 5′ CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers. Nat Med 1:686-692.
11. Kane MF, et al. (1997) Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines. Cancer Res 57:808-811.
12. Esteller M, Corn PG, Baylin SB, Herman JG (2001) A gene hypermethylation profile of human cancer. Cancer Res 61:3225-3229.
13. Dammann R, et al. (2000) Epigenetic inactivation of a RAS association domain family protein from the lung tumour suppressor locus 3p21.3. Nat Genet 25:315-319.
14. Zochbauer-Muller S, et al. (2001) Aberrant promoter methylation of multiple genes in non-small cell lung cancers. Cancer Res 61:249-255.
15. Yanagawa N, et al. (2003) Promoter hypermethylation of tumor suppressor and tumor-related genes in non-small cell lung cancers. Cancer Sci 94:589-592.
16. Topaloglu O, et al. (2004) Detection of promoter hypermethylation of multiple genes in the tumor and bronchoalveolar lavage of patients with lung cancer. Clin Cancer Res 10:2284-2288.
17. Dammann R, et al. (2005) CpG island methylation and expression of tumour-associated genes in lung carcinoma. Eur J Cancer 41:1223-1236.
18. Laird PW (2003) The power and the promise of DNA methylation markers. Nat Rev Cancer 3:253-266.
19. Belinsky SA (2004) Gene-promoter hypermethylation as a biomarker in lung cancer. Nat Rev Cancer 4:707-717.
20. Ushijima T (2005) Detection and interpretation of altered methylation patterns in cancer cells. Nat Rev Cancer 5:223-231.
21. Ehrlich M (2002) DNA methylation in cancer: too much, but also too little. Oncogene 21:5400-5413.
22. Weisenberger DJ, et al. (2005) Analysis of repetitive element DNA methylation by MethyLight. Nucleic Acids Res 33:6823-6836.
23. Cadieux B, Ching TT, Vandenberg SR, Costello JF (2006) Genome-wide hypomethylation in human glioblastomas associated with specific copy number alteration, methylenetetrahydrofolate reductase allele status, and increased proliferation. Cancer Res 66:8469-8476.
24. Rodriguez J, et al. (2006) Chromosomal instability correlates with genome-wide DNA demethylation in human primary colorectal cancers. Cancer Res 66:8462-9468.
25. Estecio MR, et al. (2007) LINE-1 hypomethylation in cancer is highly variable and inversely correlated with microsatellite instability. PLoS ONE 2:e399.
26. Wilson AS, Power BE, Molloy PL (2007) DNA hypomethylation and human diseases. Biochim Biophys Acta 1775:138-162.
27. Esteller M (2007) Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 8:286-298.
28. Rauch T, Pfeifer GP (2005) Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab Invest 85:1172-1180.
29. Rauch T, Li H, Wu X, Pfeifer GP (2006) 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. Cancer Res 66:7939-7947.
30. Lander ES, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921.
31. Yoder JA, Walsh CP, Bestor TH (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13:335-340.
32. Koed K, et al. (2005) High-density single nucleotide polymorphism array defines novel stage and location-dependent allelic imbalances in human bladder tumors. Cancer Res 65:34-45.
33. Yang AS, et al. (2004) A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res 32:e38.
34. Brock GJ, Charlton J, Bird A (1999) Densely methylated sequences that are preferentially localized at telomere-proximal regions of human chromosomes. Gene 240:269-277.
35. Blasco MA (2007) The epigenetic regulation of mammalian telomeres. Nat Rev Genet 8:299-309.
36. De Smet C, Loriot A, Boon T (2004) Promoter-dependent mechanism leading to selective hypomethylation within the 5′ region of gene MAGE-A1 in tumor cells. Mol Cell Biol 24:4781-4790.
37. Ogasawara S, et al. (2004) Disruption of cell-type-specific methylation at the Maspin gene promoter is frequently involved in undifferentiated thyroid cancers. Oncogene 23:1117-1124.
38. Sato N, Fukushima N, Matsubayashi H, Goggins M (2004) Identification of maspin and S100P as novel hypomethylation targets in pancreatic cancer using global gene expression profiling. Oncogene 23:1531-1538.
39. Chen ZX, Riggs AD (2005) Maintenance and regulation of DNA methylation patterns in mammals. Biochem Cell Biol 83:438-448.
40. Chen ZX, Mann JR, Hsieh CL, Riggs AD, Chedin F (2005) Physical and functional interactions between the human DNMT3L protein and members of the de novo methyltransferase family. J Cell Biochem 95:902-917.
41. Bourc'his D, Bestor TH (2004) Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431:96-99.
42. Gibbons RJ, et al. (2000) Mutations in ATRX, encoding a SWI/SNF-like protein, cause diverse changes in the pattern of DNA methylation. Nat Genet 24:368-371.
43. Dennis K, Fan T, Geiman T, Yan Q, Muegge K (2001) Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev 15:2940-2944.
44. Huang J, et al. (2004) Lsh, an epigenetic guardian of repetitive elements. Nucleic Acids Res 32:5019-5028.
45. Lee DW, et al. (2000) Proliferation-associated SNF2-like gene (PASG): a SNF2 family member altered in leukemia. Cancer Res 60:3612-3622.
46. Yano M, et al. (2004) Tumor-specific exon creation of the HELLS/SMARCA6 gene in non-small cell lung cancer. Int J Cancer 112:8-13.
47. Costello JF, et al. (2000) Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet 24:132-138.
48. Rauch T, et al. (2007) Homeobox gene methylation in lung cancer studied by genomewide analysis with a microarray-based methylated CpG island recovery assay. Proc Natl Acad Sci USA 104:5527-5532.
49. Xiong Z, Laird PW (1997) COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res 25:2532-2534.