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Oral presentations: Scientific Session 9: Basic Science: Big Data research (2020)

OP31 Meta–omics reveals microbiome-driven proteolysis as a contributing factor to the severity of ulcerative colitis disease activity

R. Mills1, P. Dulai2, Y. Vázquez-Baeza3, Q. Zhu3, G. Humphrey3, L. DeRight Goldasich3, R. Quinn4, A. Gewirtz5, B. Chassaing5, H. Chu6, W. Sandborn2, P. Dorrestein1, R. Knight3, D. Gonzalez1

1Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California - San Diego, San Diego, USA, 2Department of Gastroenterology, University of California - San Diego, San Diego, USA, 3Computer Science and Engineering, University of California - San Diego, San Diego, USA, 4Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA, 5Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, USA, 6University of California San Diego, Pathology, San Diego, USA

Background

Ulcerative colitis (UC) is characterised by an aberrant immune response directed towards the gut microbiota. It remains poorly understood which mechanisms govern pathogenic roles of the microbiome in UC.

Methods

A prospective cohort of 40 UC patients were phenotyped with clinical (partial Mayo), biochemical (faecal calprotectin), endoscopic (Mayo endoscopic sub-score and ulcerative colitis Endoscopic Index of Severity) and histologic (Geboes) disease activity indices. Individual patient-matched faecal samples collected within 24 h prior to the lower endoscopy underwent 16S, shotgut metagenomic, metabolomic, metaproteomic, and metapeptidomic sequencing in addition to proteomic sequencing of paired serum samples. Sequencing datasets were integrated and analysed for microbial determinants of UC disease severity. Confirmatory in-vivo and in-vitro experiments were performed in Caco-2 epithelial monolayers and IL10 knockout mice.

Results

All meta-omics displayed large-scale shifts related to disease severity, with the metabolome and metaproteome best predicting disease severity and the metapeptidome demonstrating an increase of peptide fragments in UC patients with high severity. Broad-scale analyses and taxonomic inferences identified Bacteroides proteases as a distinguishing feature of disease severity, with the Bacteroides association being driven by changes in protease protein expression. Using a Caco-2 model we confirmed that epithelial disruption by Bacteroides vulgatus was prevented by protease inhibition, without influencing growth rates. Guided by the metagenome and metaproteome we transplanted a high-severity UC faecal sample with an increased abundance of proteases related to Bacteroides vulgatus into an IL10−/− gnotobiotic mouse model, and observed that colitis induced by transplant of faeces was attenuated by oral administration of protease inhibitors.

Conclusion

Through an integrated multi-omics data analysis we demonstrate that certain members of the microbiome, such as Bacteroides vulgatus, may contribute to exacerbating disease activity in UC through protease activity. In-vivo and in-vitro experiments provide evidence that bacterial protease inhibition may be a novel therapeutic approach in UC.