Using human intestinal organoids to model IBD pathogenesis

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ABSTRACT Inflammatory bowel disease (IBD) is a chronic disease characterized by intermittent episodes of intestinal inflammation and disruption of the intestinal epithelial barrier. The IBD Genetics Consortium has intensively studied the genetic architecture of this complex disease. Assigning molecular mechanisms to IBD risk variants is critical to understanding disease etiology and for identification of new drug targets. Human genetics has the potential to provide an unbiased view of the causative disease mechanisms. IBD already has been the subject of intensive genetic investigations, including genome-wide association studies (GWAS) that have uncovered dozens of risk loci. However, mechanistic understanding of these risk loci has been a challenge, and in this exploratory R21 proposal, we will employ two functional models – patient-derived enteroids and human intestinal organoids (HIOs) – to study the role of several important genes in epithelial restitution during IBD. This project depends on close collaboration with the NIDDK IBD Genetics Consortium (IBDGC) for two reasons. First, we will benefit from early access to IBDGC data to ensure that we deploy our pipeline for functional characterization of the highest priority IBD risk variants. Second, we will access patient-derived enteroids as a collaboration with the IBDGC. Our central goal is functional characterization of the biological pathways disrupted by IBD risk variants, which we will accomplish with two specific aims. In Aim 1, we will use gene editing to delete genetic loci, produce HIOs, and study developmental role of genes of interest. In Aim 2, we will investigate the contribution of specific genetic loci to intestinal dysfunction in proliferation, epithelial barrier integrity, autophagy, cellular stress, and regenerative ability using patient-derived enteroids and gene-edited HIOs.