Ovarian Cancer pp 67-74

Part of the Methods in Molecular Biology book series (MIMB, volume 1049) | Cite as

Main Principles and Outcomes of DNA Methylation Analysis

  • Susan K. Murphy
  • Christopher F. Bassil
  • Zhiqing Huang
Protocol

Abstract

Epigenetic modifications, including DNA methylation, are critically important mediators of normal cell function over the course of our lives. These modifications therefore also can play prominent roles in the development of disorders and diseases, including ovarian cancer. Genome-wide studies are now beginning to comprehensively decipher the methylome in normal and diseased tissues and cells, providing new insights into the distribution, specificity, and magnitude of modifications that occur and raising questions about these changes at specific loci. Further study of these alterations in specific tissues usually involves targeted approaches, of which there are a number available, all with distinct advantages and disadvantages. Here we provide a brief overview of DNA methylation and some of the methylation alterations that have been identified in ovarian cancer, as well as some of the technical approaches used to study these modifications.

Key words

DNA methylation Ovarian cancer Bisulfite conversion Methylation-specific PCR Bisulfite sequencing Pyrosequencing 

References

  1. 1.
    Li E, Bestor TH, Jaenisch R (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69:915–926PubMedCrossRefGoogle Scholar
  2. 2.
    Okano M, Bell DW, Haber DA, Li E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99:247–257PubMedCrossRefGoogle Scholar
  3. 3.
    Robertson KD (2005) DNA methylation and human disease. Nat Rev Genet 6:597–610PubMedCrossRefGoogle Scholar
  4. 4.
    Doi A, Park IH, Wen B, Murakami P, Aryee MJ et al (2009) Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet 41(12):1350–1353PubMedCrossRefGoogle Scholar
  5. 5.
    Esteller M (2008) Epigenetics in cancer. N Engl J Med 358:1148–1159PubMedCrossRefGoogle Scholar
  6. 6.
    Duncan BK, Miller JH (1980) Mutagenic deamination of cytosine residues in DNA. Nature 287:560–561PubMedCrossRefGoogle Scholar
  7. 7.
    Glass JL, Thompson RF, Khulan B, Figueroa ME, Olivier EN et al (2007) CG dinucleotide clustering is a species-specific property of the genome. Nucleic Acids Res 35:6798–6807PubMedCrossRefGoogle Scholar
  8. 8.
    Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M et al (2010) Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A 107:8689–8694PubMedCrossRefGoogle Scholar
  9. 9.
    Ross JP, Rand KN, Molloy PL (2010) Hypomethylation of repeated DNA sequences in cancer. Epigenomics 2:245–269PubMedCrossRefGoogle Scholar
  10. 10.
    Sharma S, Kelly TK, Jones PA (2010) Epigenetics in cancer. Carcinogenesis 31:27–36PubMedCrossRefGoogle Scholar
  11. 11.
    Ibanez de Caceres I, Battagli C, Esteller M, Herman JG, Dulaimi E et al (2004) Tumor cell-specific BRCA1 and RASSF1A hypermethylation in serum, plasma, and peritoneal fluid from ovarian cancer patients. Cancer Res 64:6476–6481PubMedCrossRefGoogle Scholar
  12. 12.
    Murphy SK (2012) Targeting the epigenome in ovarian cancer. Future Oncol 8:151–164PubMedCrossRefGoogle Scholar
  13. 13.
    Bondurant AE, Huang Z, Whitaker RS, Simel LR, Berchuck A et al (2011) Quantitative detection of RASSF1A DNA promoter methylation in tumors and serum of patients with serous epithelial ovarian cancer. Gynecol Oncol 123:581–587PubMedCrossRefGoogle Scholar
  14. 14.
    Baldwin RL, Nemeth E, Tran H, Shvartsman H, Cass I et al (2000) BRCA1 promoter region hypermethylation in ovarian carcinoma: a population-based study. Cancer Res 60:5329–5333PubMedGoogle Scholar
  15. 15.
    Catteau A, Harris WH, Xu CF, Solomon E (1999) Methylation of the BRCA1 promoter region in sporadic breast and ovarian cancer: correlation with disease characteristics. Oncogene 18:1957–1965PubMedCrossRefGoogle Scholar
  16. 16.
    McCluskey LL, Chen C, Delgadillo E, Felix JC, Muderspach LI et al (1999) Differences in p16 gene methylation and expression in benign and malignant ovarian tumors. Gynecol Oncol 72:87–92PubMedCrossRefGoogle Scholar
  17. 17.
    Strathdee G, Appleton K, Illand M, Millan DW, Sargent J et al (2001) Primary ovarian carcinomas display multiple methylator phenotypes involving known tumor suppressor genes. Am J Pathol 158:1121–1127PubMedCrossRefGoogle Scholar
  18. 18.
    Rathi A, Virmani AK, Schorge JO, Elias KJ, Maruyama R et al (2002) Methylation profiles of sporadic ovarian tumors and nonmalignant ovaries from high-risk women. Clin Cancer Res 8:3324–3331PubMedGoogle Scholar
  19. 19.
    Bianco T, Chenevix-Trench G, Walsh DC, Cooper JE, Dobrovic A (2000) Tumour-specific distribution of BRCA1 promoter region methylation supports a pathogenetic role in breast and ovarian cancer. Carcinogenesis 21:147–151PubMedCrossRefGoogle Scholar
  20. 20.
    Wiley A, Katsaros D, Fracchioli S, Yu H (2006) Methylation of the insulin-like growth factor binding protein-3 gene and prognosis of epithelial ovarian cancer. Int J Gynecol Cancer 16:210–218PubMedCrossRefGoogle Scholar
  21. 21.
    Katsaros D, Cho W, Singal R, Fracchioli S, Rigault De La Longrais IA et al (2004) Methylation of tumor suppressor gene p16 and prognosis of epithelial ovarian cancer. Gynecol Oncol 94:685–692PubMedCrossRefGoogle Scholar
  22. 22.
    Wiley A, Katsaros D, Chen H, Rigault de la Longrais IA, Beeghly A et al (2006) Aberrant promoter methylation of multiple genes in malignant ovarian tumors and in ovarian tumors with low malignant potential. Cancer 107:299–308PubMedCrossRefGoogle Scholar
  23. 23.
    Gifford G, Paul J, Vasey PA, Kaye SB, Brown R (2004) The acquisition of hMLH1 methylation in plasma DNA after chemotherapy predicts poor survival for ovarian cancer patients. Clin Cancer Res 10:4420–4426PubMedCrossRefGoogle Scholar
  24. 24.
    Turner N, Tutt A, Ashworth A (2004) Hallmarks of “BRCAness” in sporadic cancers. Nat Rev Cancer 4:814–819PubMedCrossRefGoogle Scholar
  25. 25.
    Chaudhry P, Srinivasan R, Patel FD (2009) Utility of gene promoter methylation in prediction of response to platinum-based chemotherapy in epithelial ovarian cancer (EOC). Cancer Invest 27:877–884PubMedCrossRefGoogle Scholar
  26. 26.
    Warnecke PM, Stirzaker C, Song J, Grunau C, Melki JR et al (2002) Identification and resolution of artifacts in bisulfite sequencing. Methods 27:101–107PubMedCrossRefGoogle Scholar
  27. 27.
    Thirlwell C, Eymard M, Feber A, Teschendorff A, Pearce K et al (2010) Genome-wide DNA methylation analysis of archival formalin-fixed paraffin-embedded tissue using the Illumina Infinium HumanMethylation27 BeadChip. Methods 52:248–254PubMedCrossRefGoogle Scholar
  28. 28.
    Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB (1996) Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci U S A 93:9821–9826PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, New York 2013

Authors and Affiliations

  • Susan K. Murphy
    • 1
  • Christopher F. Bassil
    • 1
  • Zhiqing Huang
    • 1
  1. 1.Division of Gynecologic OncologyDuke University Medical CenterDurhamUSA

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