Abstract
AbstractBackground and aimsInflammatory Bowel Diseases (IBD) are chronic inflammatory conditions influenced heavily by environmental factors. DNA methylation is a form of epigenetic regulation linking environmental stimuli to gene expression changes and inflammation. Here, we investigated how DNA methylation of theTNFpromoter differs between inflamed and uninflamed mucosa of IBD patients, including anti-TNF responders and non-responders.MethodsWe obtained mucosal biopsies from 200 participants (133 IBD and 67 controls) and analyzedTNFpromoter methylation using bisulfite sequencing, comparing inflamed with uninflamed segments, in addition to paired inflamed/uninflamed samples from individual patients. We conducted similar analyses on purified intestinal epithelial cells from bowel resections. We also comparedTNFmethylation levels of inflamed and uninflamed mucosa from a separate cohort of 15 anti-TNF responders and 17 non-responders. Finally, we sequenced DNA methyltransferase genes to identify rare variants in IBD patients and functionally tested them using rescue experiments in a zebrafish genetic model of DNA methylation deficiency.ResultsTNFpromoter methylation levels were decreased in inflamed mucosa of IBD patients and correlated with disease severity. Isolated IECs from inflamed tissue showed proportional decreases inTNFmethylation. Anti-TNF non-responders showed lower levels ofTNFmethylation than responders in uninflamed mucosa. Our sequencing analysis revealed two missense variants inDNMT1, one of which had reduced functionin vivo.ConclusionsOur study reveals an association ofTNFpromoter hypomethylation with mucosal inflammation, suggesting that IBD patients may be particularly sensitive to inflammatory environmental insults affecting DNA methylation. Together, our analyses indicate thatTNFpromoter methylation analysis may aid in the characterization of IBD status and evaluation of anti-TNF therapy response.
Publisher
Cold Spring Harbor Laboratory