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Quantitative DNA Methylation Profiling in Cancer

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Cancer Gene Profiling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1381))

Abstract

Epigenetic mechanisms including DNA methylation are fundamental for the regulation of gene expression. Epigenetic alterations can lead to the development and the evolution of malignant tumors as well as the emergence of phenotypically different cancer cells or metastasis from one single tumor cell. Here we describe bisulfite pyrosequencing, a technology to perform quantitative DNA methylation analyses, to detect aberrant DNA methylation in malignant tumors.

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References

  1. Bestor TH (2000) The DNA methyltransferases of mammals. Hum Mol Genet 9(16):2395–2402

    Article  CAS  PubMed  Google Scholar 

  2. Brenner C, Fuks F (2006) DNA methyltransferases: facts, clues, mysteries. Curr Top Microbiol Immunol 301:45–66

    CAS  PubMed  Google Scholar 

  3. Cheng X, Blumenthal RM (2008) Mammalian DNA methyltransferases: a structural perspective. Structure 16(3):341–350. doi:10.1016/j.str.2008.01.004

    Article  PubMed Central  PubMed  Google Scholar 

  4. Gowher H, Jeltsch A (2004) Mechanism of inhibition of DNA methyltransferases by cytidine analogs in cancer therapy. Cancer Biol Ther 3(11):1062–1068

    Article  CAS  PubMed  Google Scholar 

  5. Wigler MH (1981) The inheritance of methylation patterns in vertebrates. Cell 24(2):285–286

    Article  CAS  PubMed  Google Scholar 

  6. Clark SJ, Harrison J, Frommer M (1995) CpNpG methylation in mammalian cells. Nat Genet 10(1):20–27. doi:10.1038/ng0595-20

    Article  CAS  PubMed  Google Scholar 

  7. Gama-Sosa MA, Wang RY, Kuo KC, Gehrke CW, Ehrlich M (1983) The 5-methylcytosine content of highly repeated sequences in human DNA. Nucleic Acids Res 11(10):3087–3095

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. Hsieh J, Gage FH (2004) Epigenetic control of neural stem cell fate. Curr Opin Genet Dev 14(5):461–469. doi:10.1016/j.gde.2004.07.006

    Article  CAS  PubMed  Google Scholar 

  9. Lopez-Serra L, Esteller M (2008) Proteins that bind methylated DNA and human cancer: reading the wrong words. Br J Cancer 98(12):1881–1885. doi:10.1038/sj.bjc.6604374

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Morgan HD, Santos F, Green K, Dean W, Reik W (2005) Epigenetic reprogramming in mammals. Hum Mol Genet 14 Spec No 1:R47–R58. doi:10.1093/hmg/ddi114

    Article  PubMed  Google Scholar 

  11. Plass C, Smiraglia DJ (2006) Genome-wide analysis of DNA methylation changes in human malignancies. Curr Top Microbiol Immunol 310:179–198

    CAS  PubMed  Google Scholar 

  12. Robertson KD (2001) DNA methylation, methyltransferases, and cancer. Oncogene 20(24):3139–3155. doi:10.1038/sj.onc.1204341

    Article  CAS  PubMed  Google Scholar 

  13. Robertson KD (2005) DNA methylation and human disease. Nat Rev Genet 6(8):597–610. doi:10.1038/nrg1655

    Article  CAS  PubMed  Google Scholar 

  14. Simonsson S, Gurdon JB (2005) Changing cell fate by nuclear reprogramming. Cell Cycle 4(4):513–515

    Article  CAS  PubMed  Google Scholar 

  15. Smith SS (1991) DNA methylation in eukaryotic chromosome stability. Mol Carcinog 4(2):91–92

    Article  CAS  PubMed  Google Scholar 

  16. Smith SS, Crocitto L (1999) DNA methylation in eukaryotic chromosome stability revisited: DNA methyltransferase in the management of DNA conformation space. Mol Carcinog 26(1):1–9

    Article  CAS  PubMed  Google Scholar 

  17. Turek-Plewa J, Jagodzinski PP (2005) The role of mammalian DNA methyltransferases in the regulation of gene expression. Cell Mol Biol Lett 10(4):631–647

    CAS  PubMed  Google Scholar 

  18. Soejima H, Wagstaff J (2005) Imprinting centers, chromatin structure, and disease. J Cell Biochem 95(2):226–233. doi:10.1002/jcb.20443

    Article  CAS  PubMed  Google Scholar 

  19. Brueckner B, Kuck D, Lyko F (2007) DNA methyltransferase inhibitors for cancer therapy. Cancer J 13(1):17–22. doi:10.1097/PPO.0b013e31803c7245

    Article  CAS  PubMed  Google Scholar 

  20. Ghoshal K, Bai S (2007) DNA methyltransferases as targets for cancer therapy. Drugs of Today 43(6):395–422. doi:10.1358/dot.2007.43.6.1062666

    Article  CAS  PubMed  Google Scholar 

  21. Cooper WN, Luharia A, Evans GA, Raza H, Haire AC, Grundy R, Bowdin SC, Riccio A, Sebastio G, Bliek J, Schofield PN, Reik W, Macdonald F, Maher ER (2005) Molecular subtypes and phenotypic expression of Beckwith-Wiedemann syndrome. Eur J Hum Genet 13(9):1025–1032. doi:10.1038/sj.ejhg.5201463

    Article  CAS  PubMed  Google Scholar 

  22. Shuman C, Beckwith JB, Smith AC, Weksberg R (1993) Beckwith-Wiedemann Syndrome. In: Pagon RA, Adam MP, Ardinger HH et al (eds) GeneReviews(R). Seattle (WA),

    Google Scholar 

  23. Hegi ME, Diserens AC, Godard S, Dietrich PY, Regli L, Ostermann S, Otten P, Van Melle G, de Tribolet N, Stupp R (2004) Clinical trial substantiates the predictive value of O-6-methylguanine-DNA methyltransferase promoter methylation in glioblastoma patients treated with temozolomide. Clin Cancer Res 10(6):1871–1874

    Article  CAS  PubMed  Google Scholar 

  24. Parkinson JF, Wheeler HR, Clarkson A, McKenzie CA, Biggs MT, Little NS, Cook RJ, Messina M, Robinson BG, McDonald KL (2008) Variation of O(6)-methylguanine-DNA methyltransferase (MGMT) promoter methylation in serial samples in glioblastoma. J Neurooncol 87(1):71–78. doi:10.1007/s11060-007-9486-0

    Article  CAS  PubMed  Google Scholar 

  25. Yachi K, Watanabe T, Ohta T, Fukushima T, Yoshino A, Ogino A, Katayama Y, Nagase H (2008) Relevance of MSP assay for the detection of MGMT promoter hypermethylation in glioblastomas. Int J Oncol 33(3):469–475

    CAS  PubMed  Google Scholar 

  26. Mund C, Brueckner B, Lyko F (2006) Reactivation of epigenetically silenced genes by DNA methyltransferase inhibitors: basic concepts and clinical applications. Epigenetics 1(1):7–13

    Article  PubMed  Google Scholar 

  27. Ammerpohl O, Martin-Subero JI, Richter J, Vater I, Siebert R (2009) Hunting for the 5th base: techniques for analyzing DNA methylation. Biochim Biophys Acta 1790(9):847–862. doi:10.1016/j.bbagen.2009.02.001

    Article  CAS  PubMed  Google Scholar 

  28. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A 89(5):1827–1831

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  29. Kladde MP, Xu M, Simpson RT (1999) DNA methyltransferases as probes of chromatin structure in vivo. Methods Enzymol 304:431–447

    Article  CAS  PubMed  Google Scholar 

  30. Lutsenko E, Bhagwat AS (1999) Principal causes of hot spots for cytosine to thymine mutations at sites of cytosine methylation in growing cells. a model, its experimental support and implications. Mutat Res 437(1):11–20

    Article  CAS  PubMed  Google Scholar 

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Correspondence to Ole Ammerpohl Ph.D. .

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Ammerpohl, O., Haake, A., Kolarova, J., Siebert, R. (2016). Quantitative DNA Methylation Profiling in Cancer. In: Grützmann, R., Pilarsky, C. (eds) Cancer Gene Profiling. Methods in Molecular Biology, vol 1381. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3204-7_5

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  • DOI: https://doi.org/10.1007/978-1-4939-3204-7_5

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3203-0

  • Online ISBN: 978-1-4939-3204-7

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