Genome-wide DNA methylation profiling of primary colorectal laterally spreading tumors identifies disease-specific epimutations on common pathways

Colorectal laterally spreading tumors (LSTs) are rare but are becoming more prevalent. Unlike many neoplasms in colons, LST grows to extremely large size while rarely invades deeply. Also, there is a low tendency for LSTs to become cancerous. In this study, we used the Illumina Human Methylation 450K array to query the main epigenetic difference between LSTs and para-cancerous samples. We built a discovery cohort with 10 matched cases, and a validation cohort with 9 additional matched cases. Our results suggest that LST displays significant decrease in DNA methylation, highlighted by the discovery of 1,018 hypomethylated intergenic regions (IGR). Comparing to classic differentially methylated positions and regions (DMPs & DMRs) that overlap Transcription Starting Site (TSS) and CpG island (CGI), IGR-regions were associated more closely with genes involved in functional biological processes and correlated with specific histone modifications. Hypomethylated IGR regions were often annotated as tissue-specific regulatory elements for non-colon tissues and were typically epigenetically silenced in normal colon mucosa. By integration of public data, we defined the commonality and specific epigenetic signatures for adenomas, LSTs and colon adenocarcinomas. Only 435 hypermethylated DMPs & DMRs and 517 hypomethylated DMPs & DMRs were shared by the three diseases. However, our pathway-level analysis discovered that genes in four pathways were common target of epi-mutations in LSTs, adenomas and CRCs: insulin secretion, cholinergic synapse, morphine addiction, and circadian entrainment. More interestingly, different diseases seem to employ distinct epigenetic insult to disturb specific pathways. Between LST and adenoma, we found eight pathways including cancer related pathway, Ras signaling and Rap1 signaling pathway were commonly targeted but the epi-mutation patterns were opposite. Comparison between precancerous conditions and invasive states revealed the key pathways governing the progression to malignancy, including CAMs and PI3K-Akt pathways.