Abstract
Accumulation of epigenetic alteration plays important roles in tumorigenesis. Aberrant DNA hypermethylation in gene promoter regions is a common epigenetic mechanism for silencing tumor suppressor genes in many types of cancer including colorectal cancer (CRC). By using quantitative methylation information, CRC can be classified into three distinct methylation epigenotypes with different genetic features, suggesting existence of at least three molecular pathways in genesis of CRC. We describe in this chapter, the methods for analyses of aberrant DNA methylation to epigenotype CRC.
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References
Feinberg AP, Tycko B (2004) The history of cancer epigenetics. Nat Rev Cancer 4:143–153
Esteller M (2008) Epigenetics in cancer. N Engl J Med 358:1148–1159
Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128:683–692
Grady WM, Carethers JM (2008) Genomic and epigenetic instability in colorectal cancer pathogenesis. Gastroenterology 135:1079–1099
Shen L, Toyota M, Kondo Y, Lin E, Zhang L, Guo Y et al (2007) Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer. Proc Natl Acad Sci U S A 104:18654–18659
Yagi K, Akagi K, Hayashi H, Nagae G, Tsuji S, Isagawa T et al (2010) Three DNA methylation epigenotypes in human colorectal cancer. Clin Cancer Res 16:21–33
Hinoue T, Weisenberger DJ, Lange CP, Shen H, Byun HM, Van Den Berg D et al (2012) Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res 22:271–282
Vogelstein B, Fearon ER, Hamilton SR, Kern SE, Preisinger AC, Leppert M et al (1988) Genetic alterations during colorectal-tumor development. N Engl J Med 319:525–532
Feinberg AP, Ohlsson R, Henikoff S (2006) The epigenetic progenitor origin of human cancer. Nat Rev Genet 7:21–33
Toyota M, Ahuja N, Ohe-Toyota M, Herman JG, Baylin SB, Issa JP (1999) CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci U S A 96:8681–8686
Weisenberger DJ, Siegmund KD, Campan M, Young J, Long TI, Faasse MA et al (2006) CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet 38:787–793
Yagi K, Takahashi H, Akagi K, Matsusaka K, Seto Y, Aburatani H et al (2012) Intermediate methylation epigenotype and its correlation to KRAS mutation in conventional colorectal adenoma. Am J Pathol 180:616–625
Kim YH, Kakar S, Cun L, Deng G, Kim YS (2008) Distinct CpG island methylation profiles and BRAF mutation status in serrated and adenomatous colorectal polyps. Int J Cancer 123:2587–2593
Snover DC (2011) Update on the serrated pathway to colorectal carcinoma. Hum Pathol 42:1–10
Kaneda A, Yagi K (2011) Two groups of DNA methylation markers to classify colorectal cancer into three epigenotypes. Cancer Sci 102:18–24
Nosho K, Irahara N, Shima K, Kure S, Kirkner GJ, Schernhammer ES et al (2008) Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample. PLoS One 3:e3698
Ehrich M, Nelson MR, Stanssens P, Zabeau M, Liloglou T, Xinarianos G et al (2005) Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci U S A 102:15785–15790
Coolen MW, Statham AL, Gardiner-Garden M, Clark SJ (2007) Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements. Nucleic Acids Res 35:e119
Vogel N, Schiebel K, Humeny A (2009) Technologies in the Whole-Genome Age: MALDI-TOF-Based Genotyping. Transfus Med Hemother 36:253–262
Acknowledgement
This work was supported by a grant of Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency, and Grants-in-Aids for Scientific Research from Ministry of Education, Culture, Sports, Science, and Technology of Japan.
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Kaneda, A., Yagi, K. (2015). Quantitative DNA Methylation Analysis for Epigenotyping of Colorectal Cancer. In: Verma, M. (eds) Cancer Epigenetics. Methods in Molecular Biology, vol 1238. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1804-1_15
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DOI: https://doi.org/10.1007/978-1-4939-1804-1_15
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