Multi-omics characterization of inflammatory bowel disease induced hyperplasia/dysplasia in the Rag2-/- / Il10-/- mouse model [RNA-Seq]

Epigenetic dysregulation is likely to play a role in the observed association between inflammatory bowel disease (IBD) and colon tumor development. In the present work, DNA methylome, hydroxymethylome, and transcriptome analyses were conducted in proximal colon tissues harvested from the Helicobacter hepaticus-infected murine model of IBD. Reduced representation bisulfite sequencing (RRBS) and oxidative RRBS (oxRRBS) analyses identified 1606 differentially methylated regions (DMR) and 3011 differentially hydroxymethylated (DhMR) regions. These DMR/DhMR overlapped with genes that are associated with gastrointestinal disease, inflammatory disease, and cancer. RNA-seq revealed pronounced expression changes of a number of genes associated with inflammation and cancer. Several genes (e.g. Duox2, Tgm2, Cdhr5, Hk2) exhibited both changes in DNA methylation/ hydroxymethylation and altered gene expression levels. Overall, our results suggest that chronic inflammation triggers changes in methylation and hydroxymethylation patterns in the genome, altering the expression of key tumorigenesis genes and potentially contributing to the initiation of colorectal cancer. Overall design: Proximal colon tissues from 3 Rag2-/- / Il10-/- mice and 3 H.hepaticus infected Rag2-/- / Il10-/- mice were used for RNA-seq analysis.