Original ResearchFull Report: Basic and Translational—Alimentary TractDifferences in DNA Methylation Signatures Reveal Multiple Pathways of Progression From Adenoma to Colorectal Cancer
Section snippets
Primary Human Tissue Samples
DNA extracted from snap-frozen tissues was used for the studies using the HumanMethylation450 arrays. A detailed description of the samples used is available in the Supplementary Methods.
DNA Isolation and Bisulfite Conversion
Genomic DNA was extracted and bisulfite modified as described previously.24
Molecular Characterization
The CIMP status and MSI status of the CRCs were assessed using methods as described previously.24, 25 Gene mutation status of KRAS, BRAFV600E, APC, TP53, and PIK3CA was determined using the qBiomarker Somatic Mutation PCR System
Identification and Validation of Methylated Probes on the Human Methylation450 Arrays That Are Differentially Methylated Between Normal Colon, Tubular Adenomas, and Colorectal Cancer
We and others have reported previously that results from the HM450 BeadChips are technically robust, but that there is a measurable false discovery rate.26, 27 Therefore, we initially conducted technical validation studies and biological validation studies of a subset of differentially methylated CpGs (n = 4) found on the HM450 arrays (described in detail in the Supplementary Methods and Results). All of the CpG probes (n = 4) that were either aberrantly methylated in cancers or adenomas were
Discussion
In these studies we have found considerable genetic and epigenetic heterogeneity among not only CRCs but also among adenomas.6, 38, 39 The existence of different classes of CRC that differ based on DNA methylation patterns was first proposed by Issa and colleagues in 1999 when they identified a CIMP class of CRCs.8 Our studies provide additional insight into CIMP CRCs by showing that in the high methylation pattern CRCs there is a low frequency of APC mutations, consistent with findings from
Acknowledgments
The authors would like to acknowledge the outstanding service provided by the Genomics Shared Resources (FHCRC) and the Cooperative Human Tissue Network for the tissues they provided. We also thank the ColoCare team (Chris Velicer, Rebecca Holmes, Stephanie Zschäbitz, Kathy Vickers, Rachel Wilbur, Shannon Rush, and Sara Bates and others) for their assistance on these studies. In addition, we would like to thank Toshinori Hinoue and Peter W. Laird for kindly sharing their data. Finally, we would
References (48)
- et al.
Genomic and epigenetic instability in colorectal cancer pathogenesis
Gastroenterology
(2008) - et al.
High prevalence of sessile serrated adenomas with braf mutations: a prospective study of patients undergoing colonoscopy
Gastroenterology
(2006) - et al.
Incidence of advanced adenomas at surveillance colonoscopy in patients with a personal history of colon adenomas: a meta-analysis and systematic review
Gastrointest Endosc
(2006) - et al.
Role of the serrated pathway in colorectal cancer pathogenesis
Gastroenterology
(2010) - et al.
Molecular dissection of premalignant colorectal lesions reveals early onset of the cpg island methylator phenotype
Am J Pathol
(2012) - et al.
Correlation of beta-catenin localization with cyclooxygenase-2 expression and cpg island methylator phenotype (cimp) in colorectal cancer
Neoplasia
(2007) - et al.
Frequent switching of polycomb repressive marks and DNA hypermethylation in the pc3 prostate cancer cell line
Proc Natl Acad Sci U S A
(2008) - et al.
Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions
BMC Bioinformatics
(2008) - et al.
Cancer genome landscapes
Science
(2013) - et al.
The genomic landscapes of human breast and colorectal cancers
Science
(2007)
Comprehensive molecular characterization of human colon and rectal cancer
Nature
Molecular heterogeneity of colorectal cancer: Implications for cancer control
Surg Oncol
Identification of differentially methylated sequences in colorectal cancer by methylated cpg island amplification
Cancer Res
Methylation of the oestrogen receptor cpg island links ageing and neoplasia in human colon
Nat Genet
Colorectal cancer epigenetics: complex simplicity
J Clin Oncol
A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing
Nat Genet
Cpg island methylator phenotype in cancer
Nat Rev Cancer
Genome-scale analysis of aberrant DNA methylation in colorectal cancer
Genome Res
Cpg island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with braf mutation in colorectal cancer
Nat Genet
Genomic aberrations occurring in subsets of serrated colorectal lesions but not conventional adenomas
Cancer Res
Serrated lesions of the colorectum: review and recommendations from an expert panel
Am J Gastroenterol
Distinct CpG island methylation profiles and braf mutation status in serrated and adenomatous colorectal polyps
Int J Cancer
Epigenetics and colorectal cancer
Nat Rev Gastroenterol Hepatol
Mgmt promoter methylation and field defect in sporadic colorectal cancer
J Natl Cancer Inst
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Funding This research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under award number RO1CA115513, P30CA15704, UO1CA152756, U54CA143862, and P01CA077852 (WMG), P50CA95103 (ZW), R01CA121060, P30CA68485, K07CA122451 (MJS). The content is solely the responsibility of the authors, and does not necessarily represent the official views of the National Institutes of Health. Support for these studies was also provided by a Burroughs Wellcome Fund Translational Research Award for Clinician Scientist (WMG), Program of Introducing Talents of Discipline to Universities of China (B12003, JW) and International Science & Technology Cooperation Program of China (2011DFA32570, JW), National Natural Science Foundation of China (81201920, YL); and 5P50CA150964 (SDM).
Author names in bold designate shared co-first authorship.