Aberrant DNA methylation of CpG islands has been widely observed in human colorectal tumors and is associated with gene silencing when it occurs in promoter areas. A subset of colorectal tumors has an exceptionally high frequency of methylation of some CpG islands, leading to the suggestion of a distinct trait referred to as 'CpG island methylator phenotype', or 'CIMP'1,2. However, the existence of CIMP has been challenged3,4. To resolve this continuing controversy, we conducted a systematic, stepwise screen of 195 CpG island methylation markers using MethyLight technology, involving 295 primary human colorectal tumors and 16,785 separate quantitative analyses. We found that CIMP-positive (CIMP+) tumors convincingly represent a distinct subset, encompassing almost all cases of tumors with BRAFmutation (odds ratio = 203). Sporadic cases of mismatch repair deficiency occur almost exclusively as a consequence of CIMP-associated methylation of MLH1. We propose a robust new marker panel to classify CIMP+ tumors.
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Toyota, M. et al. CpG island methylator phenotype in colorectal cancer. Proc. Natl. Acad. Sci. USA 96, 8681–8686 (1999).
Issa, J.P. CpG island methylator phenotype in cancer. Nat. Rev. Cancer 4, 988–993 (2004).
Yamashita, K., Dai, T., Dai, Y., Yamamoto, F. & Perucho, M. Genetics supersedes epigenetics in colon cancer phenotype. Cancer Cell 4, 121–131 (2003).
Anacleto, C. et al. Colorectal cancer “methylator phenotype”: fact or artifact? Neoplasia 7, 331–335 (2005).
Samowitz, W.S. et al. Evaluation of a large, population-based sample supports a CpG island methylator phenotype in colon cancer. Gastroenterology 129, 837–845 (2005).
Laird, P.W. Cancer epigenetics. Hum. Mol. Genet. 14 Spec No 1, R65–76 (2005).
Kaufman, L. & Rousseeuw, P.J. Finding Groups in Data: an Introduction to Cluster Analysis (Wiley Interscience, New York, 1990).
McLachlan, G. & Peel, D. Finite Mixture Models (John Wiley & Sons, New York, 2000).
Kambara, T. et al. BRAF mutation is associated with DNA methylation in serrated polyps and cancers of the colorectum. Gut 53, 1137–1144 (2004).
Toyota, M., Ohe-Toyota, M., Ahuja, N. & Issa, J.P. Distinct genetic profiles in colorectal tumors with or without the CpG island methylator phenotype. Proc. Natl. Acad. Sci. USA 97, 710–715 (2000).
Bakin, A.V. & Curran, T. Role of DNA 5-methylcytosine transferase in cell transformation by fos. Science 283, 387–390 (1999).
Ordway, J.M., Williams, K. & Curran, T. Transcription repression in oncogenic transformation: common targets of epigenetic repression in cells transformed by Fos, Ras or Dnmt1. Oncogene 23, 3737–3748 (2004).
Miller, S.A., Dykes, D.D. & Polesky, H.F. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16, 1215 (1988).
Whitehall, V.L. et al. Morphological and molecular heterogeneity within nonmicrosatellite instability-high colorectal cancer. Cancer Res. 62, 6011–6014 (2002).
Wellbrock, C., Karasarides, M. & Marais, R. The RAF proteins take centre stage. Nat. Rev. Mol. Cell Biol. 5, 875–885 (2004).
Young, J. et al. Evidence for BRAF mutation and variable levels of microsatellite instability in a syndrome of familial colorectal cancer. Clin. Gastroenterol. Hepatol. 3, 254–263 (2005).
Young, J. et al. Features of colorectal cancers with high-level microsatellite instability occurring in familial and sporadic settings: parallel pathways of tumorigenesis. Am. J. Pathol. 159, 2107–2116 (2001).
Weisenberger, D.J. et al. Analysis of repetitive element DNA methylation by MethyLight. Nucleic Acids Res. 33, 6823–6836 (2005).
Eads, C.A. et al. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res. 28, E32 (2000).
Eads, C.A. et al. Epigenetic patterns in the progression of esophageal adenocarcinoma. Cancer Res. 61, 3410–3418 (2001).
Widschwendter, M. et al. Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifen. Cancer Res. 64, 3807–3813 (2004).
Breiman, L., Friedman, J.H., Olshen, R.A. & Stone, C.J. Classification and Regression Trees 1st edn. (Wadsworth, Belmont, California, 1984).
Hastie, T. et al. 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Genome Biol. 1, RESEARCH0003.1–RESEARCH0003.21 (2000).
Herman, J.G., Graff, J.R., Myohanen, S., Nelkin, B.D. & Baylin, S.B. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA 93, 9821–9826 (1996).
The work described in this manuscript was supported by US National Institutes of Health grant R01 CA075090 awarded to P.W.L.
The authors declare no competing financial interests.
Methylation-specific PCR of the New CIMP Panel on CIMP+ and CIMP− colon tumor DNA samples. (PDF 318 kb)
MethyLight reaction details. (PDF 265 kb)
New CIMP Classification Panel. (PDF 46 kb)
Cross-panel classification error rates among various CIMP classification panels, expressed as percentages. (PDF 35 kb)
Methylation frequency by KRAS and BRAF status. (PDF 44 kb)
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Weisenberger, D., Siegmund, K., Campan, M. et al. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet 38, 787–793 (2006). https://doi.org/10.1038/ng1834
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