Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips

Abstract

Illumina's Infinium HumanMethylation450 BeadChip arrays were used to examine genome-wide DNA methylation profiles in 22 sample pairs from colorectal cancer (CRC) and adjacent tissues and 19 colon tissue samples from cancer-free donors. We show that the methylation profiles of tumors and healthy tissue samples can be clearly distinguished from one another and that the main source of methylation variability is associated with disease status. We used different statistical approaches to evaluate the methylation data. In general, at the CpG-site level, we found that common CRC-specific methylation patterns consist of at least 15,667 CpG sites that were significantly different from either adjacent healthy tissue or tissue from cancer-free subjects. Of these sites, 10,342 were hypermethylated in CRC, and 5,325 were hypomethylated. Hypermethylated sites were common in the maximum number of sample pairs and were mostly located in CpG islands, where they were significantly enriched for differentially methylated regions known to be cancer-specific. In contrast, hypomethylated sites were mostly located in CpG shores and were generally sample-specific. Despite the considerable variability in methylation data, we selected a panel of 14 highly robust candidates showing methylation marks in genes SND1, ADHFE1, OPLAH, TLX2, C1orf70, ZFP64, NR5A2, and COL4A. This set was successfully cross-validated using methylation data from 209 CRC samples and 38 healthy tissue samples from The Cancer Genome Atlas consortium (AUC = 0.981 [95% CI: 0.9677-0.9939], sensitivity = 100% and specificity = 82%). In summary, this study reports a large number of loci with novel differential methylation statuses, some of which may serve as candidate markers for diagnostic purposes.

Runx3 at the interface of immunity, inflammation and cancer

“…Yet, MSP is not a quantitative technique, and a subsequent analysis of GC samples using a quantitative method, a methyl-specific DNA microarray, revealed that merely 23% of GC samples showed RUNX3 P2 hypermethylation as compared to 46% with the conventional MSP technique [78]. Moreover, several more recent studies employing high-density DNA methylation microarrays of gastric, colorectal and breast cancer biopsies all gave the RUNX3 P2 methylation ratio a low ranking among the DNA hypermethylated genes [79][80][81][82][83][84]. Therefore, the low frequency of RUNX3 P2 hypermethylation and low methylation ratio in GC patients indicate that the role of RUNX3 hypermethylation in cancer has been greatly overrated.…”

Aberrant DNA methylation of WNT pathway genes in the development and progression of CIMP-negative colorectal cancer

“…Serrated adenoma samples-representing another neoplastic pathway of CRC development-were also profiled in several previous methylation projects. 23,[25][26][27] Illumina BeadChip technology is a frequently used method in global methylation studies 22,28,29 and allows the determination of the methylation status of >485,000 CpG sites at singlenucleotide resolution. Next generation sequencing of the methylated DNA regions, such as methyl capture sequencing (MethylCap-seq), is another option for genome-wide methylation analysis for revealing novel differentially methylated regions (DMRs).…”

936 Quantitative genome-wide methylation analysis of high-grade non-muscle invasive bladder cancer

“…As our study represents the first 450 K analysis of high-grade bladder cancer a direct 'like-for-like' comparisons of our findings with those of other groups was not possible; however, the number of differentially methylated sites we identified appeared to be lower than those previously reported in other tumor types. 42,43 Potential explanations for these findings are the tumor type per se and/or the stringency of our inclusion-exclusion criteria and definition of differential methylation. 44 For the genes identified, we performed gene ontology and KEGG pathway analyses.…”