Genome-wide DNA methylation profiling and gut flora analysis in intestinal polyps patients

The intestinal polyp is the precancerous lesion of colorectal cancer. DNA methylation and intestinal microbiota may play an important role in the development of intestinal polyp.

In this study, we included 10 patients with intestinal polyps who received the colonoscopy examination. We applied the Illumina Human Methylation 850K array to investigate the epigenome-wide DNA methylation patterns. Then, we filtered out the hub genes in the protein-protein interaction networks using functional epigenetic modules analysis. We also analyzed the colonizing bacteria on the surface of polyps compared with those in normal colonic mucosal epithelium with 16S ribosomal DNA sequencing.

We identified 323 hypermethylated sites and 7992 hypomethylated sites between intestinal polyps and normal samples. Five hub genes, including CREB1, LPA, SVIL and KRT18, were identified in five modules. Hypomethylation of CREB1 is a candidate marker of colorectal adenoma. Gut microbiota analysis showed that Butyricicoccus was significantly decreased in the intestinal polyp groups.

In conclusion, we identified DNA methylation disparities in intestinal polyps compared with normal tissue, of which methylation of CREB1 may hold clinical significance in colorectal cancer progress. Colonizing bacteria in the colonic epithelium might be related to the formation of intestinal polyps.