Genome-wide CpG island methylation analyses in non-small cell lung cancer patients

Carcinogenesis

Volumn 34, Issue 3, 2013, Pages 513-521

  Heller, Gerwin ^a   Babinsky, Valerie N ^a   Ziegler, Barbara ^a   Weinzierl, Marlene ^a   Noll, Christian ^a   Altenberger, Corinna ^a   Müllauer, Leonhard ^a   Dekan, Gerhard ^a   Grin, Yuliya ^a   Lang, György ^a   End pfützenreuter, Adelheid ^a   Steiner, Irene ^a   Zehetmayer, Sonja ^a   Döme, Balazs ^a,b   Arns, Britt Madeleine ^c   Fong, Kwun M ^d   Wright, Casey M ^d   Yang, Ian A ^d   Klepetko, Walter ^a   Posch, Martin ^a   Zielinski, Christoph C ^a   Zöchbauer Müller, Sabine ^a   more..

^a MEDICAL UNIVERSITY OF VIENNA   (Austria)

^b NATIONAL KORANYI INSTITUTE OF PULMONOLOGY   (Hungary)

^c Landesklinikum Thermenregion Hochegg   (Austria)

^d UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR HOXA10; TRANSCRIPTION FACTOR HOXA2; UNCLASSIFIED DRUG;

ADULT; ARTICLE; CANCER CELL; CANCER PROGNOSIS; CANCER STAGING; CANCER TISSUE; CELL ADHESION; CLINICAL ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; EPIGENETICS; FEMALE; GENE EXPRESSION; GENE SILENCING; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; IMMUNOPRECIPITATION; LUNG NON SMALL CELL CANCER; LUNG PARENCHYMA; LUNG SQUAMOUS CELL CARCINOMA; MALE; MOLECULAR GENETICS; PRIORITY JOURNAL; PROTEIN EXPRESSION; TRANSCRIPTION REGULATION; UPREGULATION;

ADENOCARCINOMA; BASE SEQUENCE; CADHERINS; CARCINOMA, NON-SMALL-CELL LUNG; CARCINOMA, SQUAMOUS CELL; CHROMOSOME MAPPING; CPG ISLANDS; DNA METHYLATION; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; GENOME-WIDE ASSOCIATION STUDY; HOMEODOMAIN PROTEINS; HUMANS; LUNG NEOPLASMS; MALE; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ROC CURVE; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME;

EID: 84874764694     PISSN: 01433334     EISSN: 14602180     Source Type: Journal    
DOI: 10.1093/carcin/bgs363     Document Type: Article

References (42)

1. Heller, G. et al. (2010) Lung cancer: from single-gene methylation to methylome profiling. Cancer Metastasis Rev., 29, 95-107.
2. Sato, M. et al. (2007) A translational view of the molecular pathogenesis of lung cancer. J. Thorac. Oncol., 2, 327-343.
3. Shogren-Knaak, M. et al. (2006) Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science, 311, 844-847.
4. Vettese-Dadey, M. et al. (1996) Acetylation of histone H4 plays a primary role in enhancing transcription factor binding to nucleosomal DNA in vitro. EMBO J., 15, 2508-2518.
5. Esteller, M. (2008) Epigenetics in cancer. N. Engl. J. Med., 358, 1148-1159.
6. Esteller, M. (2007) Cancer epigenomics: DNA methylomes and histonemodification maps. Nat. Rev. Genet., 8, 286-298.
7. Illingworth, R.S. et al. (2009) CpG islands-'a rough guide'. FEBS Lett., 583, 1713-1720.
8. Herman, J.G. et al. (2003) Gene silencing in cancer in association with promoter hypermethylation. N. Engl. J. Med., 349, 2042-2054.
9. Baylin, S.B. et al. (2001) Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Hum. Mol. Genet., 10, 687-692.
10. Jones, P.A. et al. (2007) The epigenomics of cancer. Cell, 128, 683-692.
11. Costello, J.F. et al. (2000) Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat. Genet., 24, 132-138.
12. Cameron, E.E. et al. (1999) Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nat. Genet., 21, 103-107.
13. Zöhbauer-Müller, S. et al. (2001) Aberrant promoter methylation of multiple genes in non-small cell lung cancers. Cancer Res., 61, 249-255.
14. Toyooka, S. et al. (2003) Epigenetic down-regulation of death-associated protein kinase in lung cancers. Clin. Cancer Res., 9, 3034-3041.
15. Burbee, D.G. et al. (2001) Epigenetic inactivation of RASSF1A in lung and breast cancers and malignant phenotype suppression. J. Natl. Cancer Inst., 93, 691-699.
16. Cooper, W.N. et al. (2008) Epigenetic regulation of the ras effector/ tumour suppressor RASSF2 in breast and lung cancer. Oncogene, 27, 1805-1811.
17. Tessema, M. et al. (2009) Concomitant promoter methylation of multiple genes in lung adenocarcinomas from current, former and never smokers. Carcinogenesis, 30, 1132-1138.
18. Ehrich, M. et al. (2006) Cytosine methylation profiles as a molecular marker in non-small cell lung cancer. Cancer Res., 66, 10911-10918.
19. Weber, M. et al. (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet., 37, 853-862.
20. Heller, G. et al. (2006) Expression and methylation pattern of TSLC1 cascade genes in lung carcinomas. Oncogene, 25, 959-968.
21. Heller, G. et al. (2012) Genome-wide microRNA expression profiling identifies miR-9-3 and miR-193a as targets for DNA methylation in non-small cell lung cancers. Clin Cancer Res., 18, 1619-1629.
22. Stanzer, S. et al. (2010) Rapid and reliable detection of LINE-1 hypomethylation using high-resolution melting analysis. Clin. Biochem., 43, 1443-1448.
23. Balic, M. et al. (2009) High quality assessment of DNA methylation in archival tissues from colorectal cancer patients using quantitative highresolution melting analysis. J. Mol. Diagn., 11, 102-108.
24. Hsia, D.A. et al. (2010) KDM8, a H3K36me2 histone demethylase that acts in the cyclin A1 coding region to regulate cancer cell proliferation. Proc. Natl. Acad. Sci. U.S.A., 107, 9671-9676.
25. Pollard, K.S. et al. (2010) multtest: Resampling-based Multiple Hypothesis Testing. R Package Version 2.5.14. http://CRAN.R-project.org/package= multtest
26. Westfall, P.H. et al. (1993) Resampling-based multiple testing. Examples and methods for p-value adjustment. Wiley Series in Probability and Mathematical Statistics. Wiley, New York.
27. Wu, X. et al. (2010) CpG island hypermethylation in human astrocytomas. Cancer Res., 70, 2718-2727.
28. Bauer, S. et al. (2008) Ontologizer 2.0: a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics, 24, 1650-1651.
29. Pascal, L.E. et al. (2008) Correlation of mRNA and protein levels: cell typespecific gene expression of cluster designation antigens in the prostate. BMC Genomics, 9, 246.
30. Blazejczyk, M. et al. (2007) FlexArray: A Statistical Data Analysis Software for Gene Expression Microarrays. Génome Québec, Montreal, Canada. http://genomequebec.mcgill.ca/FlexArray.
31. Li, Y. et al. (2011) Evaluation of EML4-ALK fusion proteins in non-small cell lung cancer using small molecule inhibitors. Neoplasia, 13, 1-11.
32. Walter, K., et al. (2012) DNA methylation profiling defines clinically relevant biological subsets of non-small cell lung cancer. Clin Cancer Res., 18, 2360-2373.
33. Shames, D.S. et al. (2006) A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies. PLoS Med., 3, e486.
34. Nelson, H.H. et al. (2012) Key epigenetic changes associated with lung cancer development: results from dense methylation array profiling. Epigenetics, 7, 559-566.
35. Zhong, S. et al. (2007) Pharmacologic inhibition of epigenetic modifications, coupled with gene expression profiling, reveals novel targets of aberrant DNA methylation and histone deacetylation in lung cancer. Oncogene, 26, 2621-2634.
36. Rauch, T.A. et al. (2008) High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. Proc. Natl. Acad. Sci. U.S.A., 105, 252-257.
37. Lokk, K. et al. (2012) Methylation markers of early-stage non-small cell lung cancer. PLoS ONE, 7, e39813.
38. Rauch, T. et al. (2007) Homeobox gene methylation in lung cancer studied by genome-wide analysis with a microarray-based methylated CpG island recovery assay. Proc. Natl. Acad. Sci. U.S.A., 104, 5527-5532.
39. Kim, J.H. et al. (2011) Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Res., 21, 1028-1041.
40. Morris, M.R. et al. (2011) Genome-wide methylation analysis identifies epigenetically inactivated candidate tumour suppressor genes in renal cell carcinoma. Oncogene, 30, 1390-1401.
41. Brock, M.V. et al. (2008) DNA methylation markers and early recurrence in stage I lung cancer. N. Engl. J. Med., 358, 1118-1128.
42. Brabender, J. et al. (2003) Quantitative O(6)-methylguanine DNA methyltransferase methylation analysis in curatively resected non-small cell lung cancer: associations with clinical outcome. Clin. Cancer Res., 9, 223-227.