Investigation of epithelial key disease-driver genes (KDGs) in inflammatory bowel disease

Inflammatory bowel diseases (IBD) comprise two main diseases, Crohn’s disease (CD) and ulcerative colitis (UC). Recent studies have reported a significant rise in prevalence of IBD in many regions impacting around 7 million IBD cases globally (1). IBD involves a relapsing and remitting clinical course of chronic inflammation in the digestive tract followed by the need for lifelong medication frequently resulting in intestinal surgical resection and impaired quality of life. Current therapies primarily target immune cells and inflammation and there is a lack of effective therapeutic strategies targeting mucosal healing, improving epithelial barrier integrity and barrier repair in IBD, which are needed in order to maintain long term clinical remission. Therapies targeting the mucosal healing and the epithelial barrier integrity have been identified as one of the strongest unmet clinical needs in IBD (2). It remains unknown whether the hallmark features of epithelial dysregulation in IBD pathology, such as aberrant crypt proliferation/apoptosis, loss of goblet cells and mucin depletion, increased barrier permeability, and delayed epithelial barrier repair are programmed into epithelial stem cells intrinsically or completely controlled by the constant influence of an inflammatory microenvironment. Using colon organoids (colonoids) derived from non-IBD and UC patients we show that some of these pathologic epithelial features are perpetuated in vitro in daughter epithelial cells and thus are programmed intrinsically into stem cells. We then sought to identify which genes may contribute to this epithelial intrinsic process. Using data generated with collaborators from a comprehensive multi-omics approach to characterise epithelial Key Driver Genes (KDGs) in IBD using Bayesian networks, we identified a top 10 ranked epithelial-specific KDG candidates. Leveraging these findings, we conducted in silico studies to refine these 10 KDGs to our top 5 for potential functional and therapeutic targeting. The top 5 epithelial KDGs were studied using a functional genomic pipeline (short hairpin RNA [shRNA]) in human colonoids followed by our 2-dimensional and 3-dimentional in vitro functional assays that reflect features of IBD epithelial barrier pathology. Through this analysis, KDGs associated with IBD were identified and our research revealed that STARD10 demonstrated functional effects on the disease including regulating colon stem cell proliferation and mucous/goblet cell differentiation. This study contributes to a better understanding of IBD epithelial barrier pathogenesis and highlights how multi-omic approaches combined with in vitro studies can identify key genes that play roles in a complex disease such as IBD.