Increased methylation variation in epigenetic domains across cancer types

Nature Genetics

Volumn 43, Issue 8, 2011, Pages 768-775

  Hansen, Kasper Daniel ^a,b   Timp, Winston ^b,c   Bravo, Héctor Corrada ^b,d   Sabunciyan, Sarven ^b   Langmead, Benjamin ^a,b   McDonald, Oliver G ^b   Wen, Bo ^b   Wu, Hao ^e   Liu, Yun ^b   Diep, Dinh ^f   Briem, Eirikur ^b   Zhang, Kun ^f   Irizarry, Rafael A ^a,b   Feinberg, Andrew P ^b  

^a JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c Johns Hopkins University   (United States)

^d University of Maryland ^*  (United States)

^e EMORY UNIVERSITY   (United States)

^f UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MESSENGER RNA;

ARTICLE; BREAST CANCER; CANCER DIAGNOSIS; CELL CYCLE; COLON CANCER; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; EPIGENETICS; GENE EXPRESSION; GENOME; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; LUNG CANCER; NEOPLASM; PRIORITY JOURNAL; THYROID CANCER;

CPG ISLANDS; DNA METHYLATION; DNA, NEOPLASM; EPIGENOMICS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENETIC VARIATION; HUMANS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; SULFITES; TUMOR MARKERS, BIOLOGICAL;

EID: 79960927422     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.865     Document Type: Article

References (42)

1. Jones, P.A. & Baylin, S.B. The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3, 415-428 (2002). (Pubitemid 34587077)
2. Feinberg, A.P. & Tycko, B. The history of cancer epigenetics. Nat. Rev. Cancer 4, 143-153 (2004). (Pubitemid 38198742)
3. Esteller, M. Epigenetics in cancer. N. Engl. J. Med. 358, 1148-1159 (2008).
4. Irizarry, R.A. et al. The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet. 41, 178-186 (2009).
5. Doi, A. et al. Differential methylation of tissue-and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat. Genet. 41, 1350-1353 (2009).
6. Irizarry, R.A. et al. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 18, 780-790 (2008). (Pubitemid 351645068)
7. Bibikova, M. et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 16, 383-393 (2006). (Pubitemid 43327509)
8. Feinberg, A.P., Gehrke, C.W., Kuo, K.C. & Ehrlich, M. Reduced genomic 5-methylcytosine content in human colonic neoplasia. Cancer Res. 48, 1159-1161 (1988). (Pubitemid 18075525)
9. Ehrlich, M. DNA methylation in cancer: too much, but also too little. Oncogene 21, 5400-5413 (2002). (Pubitemid 34983477)
10. Ogino, S. et al. A cohort study of tumoral LINE-1 hypomethylation and prognosis in colon cancer. J. Natl. Cancer Inst. 100, 1734-1738 (2008).
11. Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315-322 (2009).
12. Wen, B., Wu, H., Shinkai, Y., Irizarry, R.A. & Feinberg, A.P. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat. Genet. 41, 246-250 (2009).
13. Hesselberth, J.R. et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat. Methods 6, 283-289 (2009).
14. Li, Y. et al. The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol. 8, e1000533 (2010).
15. Falcon, S. & Gentleman, R. Using GOstats to test gene lists for GO term association. Bioinformatics 23, 257-258 (2007). (Pubitemid 46189622)
16. Frigola, J. et al. Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat. Genet. 38, 540-549 (2006).
17. Gal-Yam, E.N., Saito, Y., Egger, G. & Jones, P.A. Cancer epigenetics: modifications, screening, and therapy. Annu. Rev. Med. 59, 267-280 (2008). (Pubitemid 351287937)
18. Yu, A.E., Hewitt, R.E., Connor, E.W. & Stetler-Stevenson, W.G. Matrix metalloproteinases. Novel targets for directed cancer therapy. Drugs Aging 11, 229-244 (1997). (Pubitemid 27421320)
19. Aleman, M.J. et al. Inhibition of Single Minded 2 gene expression mediates tumor-selective apoptosis and differentiation in human colon cancer cells. Proc. Natl. Acad. Sci. USA 102, 12765-12770 (2005). (Pubitemid 41279440)
20. Yeung, H.Y. et al. Hypoxia-inducible factor-1-mediated activation of stanniocalcin-1 in human cancer cells. Endocrinology 146, 4951-4960 (2005). (Pubitemid 41446634)
21. Eurich, K., Segawa, M., Toei-Shimizu, S. & Mizoguchi, E. Potential role of chitinase 3-like-1 in inflammation-associated carcinogenic changes of epithelial cells. World J. Gastroenterol. 15, 5249-5259 (2009).
22. Fischer, H. et al. COL11A1 in FAP polyps and in sporadic colorectal tumors. BMC Cancer 1, 17 (2001).
23. Clark, S.J. Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis. Hum. Mol. Genet. 16, R88-R95 (2007). (Pubitemid 47241847)
24. Feber, A. et al. Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors. Genome Res. 21, 515-524 (2011).
25. Feinberg, A.P. & Irizarry, R. Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc. Natl. Acad. Sci. USA 107, 1757-1764 (2010).
26. Zilliox, M.J. & Irizarry, R.A. A gene expression bar code for microarray data. Nat. Methods 4, 911-913 (2007). (Pubitemid 350042377)
27. Bolstad, B.M., Irizarry, R.A., Astrand, M. & Speed, T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193 (2003). (Pubitemid 36181903)
28. Leek, J.T. et al. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat. Rev. Genet. 11, 733-739 (2010).
29. Aryee, M.J. et al. Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics 12, 197-210 (2011).
30. Bormann Chung, C.A. et al. Whole methylome analysis by ultra-deep sequencing using two-base encoding. PLoS ONE 5, e9320 (2010).
31. Deng, J. et al. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat. Biotechnol. 27, 353-360 (2009).
32. Xi, Y. & Li, W. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10, 232 (2009).
33. Loader, C. Local Regression and Likelihood (Springer Verlag, New York, New York, USA, 1999).
34. Eckhardt, F. et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38, 1378-1385 (2006). (Pubitemid 44837559)
35. Jurka, J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 16, 418-420 (2000). (Pubitemid 30665376)
36. Olshen, A.B., Venkatraman, E.S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557-572 (2004). (Pubitemid 41180205)
37. Sabates-Bellver, J. et al. Transcriptome profile of human colorectal adenomas. Mol. Cancer Res. 5, 1263-1275 (2007).
38. Gyorffy, B., Molnar, B., Lage, H., Szallasi, Z. & Eklund, A.C. Evaluation of microarray preprocessing algorithms based on concordance with RT-PCR in clinical samples. PLoS ONE 4, e5645 (2009).
39. Galamb, O. et al. Reversal of gene expression changes in the colorectal normal-adenoma pathway by NS398 selective COX2 inhibitor. Br. J. Cancer 102, 765-773 (2010).
40. Smith, J.C., Boone, B.E., Opalenik, S.R., Williams, S.M. & Russell, S.B. Gene profiling of keloid fibroblasts shows altered expression in multiple fibrosis-associated pathways. J. Invest. Dermatol. 128, 1298-1310 (2008). (Pubitemid 351543197)
41. Chen, Y. et al. Developing and applying a gene functional association network for anti-angiogenic kinase inhibitor activity assessment in an angiogenesis co-culture model. BMC Genomics 9, 264 (2008).
42. Duarte, T.L., Cooke, M.S. & Jones, G.D. Gene expression profiling reveals new protective roles for vitamin C in human skin cells. Free Radic. Biol. Med. 46, 78-87 (2009).