Classification of Colorectal Cancer Based on DNA Methylation Array Analysis
Maciej Milewski, Dermot Leahy, Judith Conroy, Tiago Magalhaes, Sean Ennis, Aoife Maguire, Hugh Mulcahy, John Hyland, Diarmuid O'Donoghue, Kieran Sheahan. University College Dublin, Dublin, Ireland; St. Vincent's University Hospital, Dublin, Ireland
Background: Colorectal cancers are usually classified based on a limited number of molecular features. Aberrant DNA methylation of CpG islands is considered to be an important influence on colorectal tumorigenesis. In this study, we present a novel classification scheme based solely on extensive genome-wide methylation analysis.
Design: We analysed a group of 102 samples. This group was composed of 70 colorectal tumors (both sporadic and Lynch syndrome) with 24 adjacent normal tissues. Mucosa from 8 diverticulosis cases was also included. All tumor samples had been tested for microsatellite instability and mutations in BRAF and KRAS and were classified using currently accepted criteria. Genomic DNA was extracted from formalin fixed paraffin embedded tissue and treated with sodium bisulfite. The methylation status of 1505 CpG sites in 807 genes was determined for each sample using the Illumina GoldenGate Methylation Assay methodology.
Results: Following unsupervised hierarchical clustering, four distinct tumor sub-groups emerged. The majority of Lynch syndrome samples were located in one group while a large proportion of sporadic microsatellite stable cases were gathered in another. Most of the sporadic MSI samples combined in a cluster showing a distinctive pattern of DNA methylation, highly correlated with BRAF mutation. All the normal samples clustered into two sub-groups separate from the tumor groups. While some of the methylation based sub-groups paralleled the traditional classification, there were significant differences and their importance remains to be determined.
Conclusions: Refining classification and determining the biological processes which underlie the sub-groups of colorectal cancer is necessary to optimise patient treatment. This study further highlights the importance of DNA methylation in the molecular pathology of colorectal carcinogenesis.
Monday, March 4, 2013 1:00 PM
Poster Session II # 135, Monday Afternoon