Longitudinal DNA Methylation Profiling of the Rectal Mucosa Identifies Cell-specific Signatures of Disease Status, Severity and Clinical Outcomes in Ulcerative Colitis

Background. Previous work has established that DNA methylation (DNAm) patterns in the blood can robustly distinguish treatment-naive active inflammatory bowel disease (IBD) from controls. Using a treatment-naive pediatric ulcerative colitis (UC) inception cohort, we examine affected rectal tissue longitudinally from diagnosis through follow-up to identify DNAm signatures of disease onset, progression, and outcomes. Methods DNAm of rectal mucosal biopsies of pediatric UC (n=211) and non-IBD control (n=85) patients were profiled to perform epigenome-wide association studies (EWAS) of specific cell types to identify UC specific differences. Longitudinal analysis was performed on follow-up samples (n=73), and comparisons were made among patients with clinical outcomes including those undergoing colectomy versus those who did not. RNA-seq was used to assess the impact of CpG sites on the transcription of nearby genes during the disease course. Results At diagnosis, UC rectal mucosa exhibited a lower proportion of epithelial cells and fibroblasts, and higher proportion of immune cells, in conjunction with variation in the DNAm pattern. While treatment had significant effects on the methylation signature of immune cells, its effects on fibroblasts and epithelial cells were attenuated. Individuals who required colectomy exhibited cell composition and DNAm patterns at follow-up more similar to disease onset than patients who did not require colectomy. Combining these results with gene expression profiles, we identify CpG sites whose methylation patterns are most consistent with a contribution to poor disease outcomes and could thus be potential therapeutic targets. Conclusions Cell-specific epigenetic changes in the rectal mucosa in UC are associated with disease severity and outcome. Current therapeutics may more effectively target the immune than the epithelial and fibroblast compartments. Targeting epithelial genes involved in barrier function, perhaps by attempting to revert methylation patterns to control levels, may improve mucosal healing.