A Systems Biology Approach for Identification of Host and Microbial Mechanisms and Druggable Targets for the Treatment of PSC-IBD

Primary sclerosing cholangitis (PSC) is the classical hepatobiliary manifestation of inflammatory bowel disease (IBD). Although rare, PSC is associated with significant and disproportionate unmet needs; with heightened risks of colorectal cancer and colectomy, and greater all-cause mortality rates compared to age- and sex-matched IBD controls. Unfortunately, no medical therapy has been proven to slow disease progression in PSC-IBD, and liver transplantation is the only lifesaving intervention for patients. The strong association between PSC and IBD has led to several pathogenic hypotheses, in which dysregulated mucosal immune responses are proposed to contribute. Of note, the investigators of this study recently identified distinct mucosal transcriptomic profiles in PSC-IBD; with regards bile acid metabolism, bile acid signalling, and a central role of enteric dysbiosis. In parallel, pilot data from other groups have shown that treatment with oral vancomycin (a non-absorbable, gut-specific antibiotic) attenuates colonic inflammation and improves biochemical markers of cholestasis in PSC. However, there is no mechanistic data exploring the host-microbial alterations under vancomycin treatment in PSC-IBD, neither the impact of vancomycin on bile acid circulation. In this study, fifteen PSC-IBD patients will be recruited through a large tertiary referral centre, who are undergoing lower gastrointestinal examination as per routine standard of care. Participants will be offered 4 weeks of treatment with oral vancomycin, and stool samples collected at different timepoints to evaluate changes in metagenomic, metatranscriptomic, and bile acid profiles. Colonic biopsies will be collected at baseline and at week 4 (flexible sigmoidoscopy) and subjected to FACS sorted RNA sequencing to identify changes in colonic epithelial cell pathways. Multi-omics data integration will be performed to uncover combinations of predictive profiles, model microbial networks, and host transcriptomic changes implicated in the response to oral vancomycin. This study will inform the downstream identification of specific host molecular and microbial pathways that has a potential for development of therapeutic targets for PSC-IBD in clinical practice.