Analyzing aberrantly methylated collagen genes in colorectal adenocarcinoma.

Abstract

e15721 Background: Abnormal methylation, a hallmark of colorectal cancer, interferes with the normal function of genes. By examining methylation patterns across the entire genome in large patient populations, we can identify novel biomarkers for diagnosis, prognosis, and potentially new therapeutic targets. Playing an essential role in extracellular matrix remodelling, regulation of collagen family genes can contribute to tumor progression. This study explores the methylation changes of collagen genes on a sizable dataset of genom-wide methylation data. Methods: Raw files of a collection of 19 GEO (Gene Expression Omnibus) database series and GDC (Genomic Data Commons) data were processed and combined in R using the minfi and the watermelon libraries. The data originated from Illumina HumanMethylation450K and EPIC microarrray platforms. Based on a matrix of β-values, methylated regions and CpG loci were identified using Kruskal-Wallis-test complemented with ROC analysis. For data visualization we employed epigenplot.com web platform. Results: A database containing data from two microarray platforms (Illumina HM450K and EPIC) of 2,356 tumor and normal samples was created. Of the collagen family genes, eight contained regions with a Δβ > = 0.2 in case of both technological platforms and a cross-validated AUC > = 0.9 in HM450K data. When comparing tumor to normal samples, the genes COL25A1, COL4A1, COL4A2, COL23A1, COL5A1 and COL15A1 were hypermethylated in proximal promoter region. On a CpG level, hypermethylation was constricted to CpG islands in the proximal promoter region. Significantly hypomethylated regions included the TSS1500 regions of COL29A1 and COL6A6. These genes were less enriched in CpG sites than the hypermethylated ones. While COL29A1 contained CpG island chr3:130064574-130064840 with two sites and five shore or shelf sites, COL6A6 only contained open sea CpGs. Conclusions: Multiple collagen family genes were regulated through DNA methylation in colorectal adenocarcinoma. Further exploitation of these genes might lead to discovery of novel biomarkers and a better understanding of the changes of the extracellular matrix during tumor progression driven by epigenetic regulation of gene paralogs.