Epithelial-derived mini gut organoid model as a tool to model the interaction between epithelial cells and the gut microbiome in inflammatory Bowel Disease

Inflammatory bowel diseases (IBD) are chronic diseases that affect approximately 6 million people worldwide. The disease is characterized by gut inflammation and is caused by abnormal interaction between the gut bacteria, the immune system and the epithelial cells among people with a genetic predisposition. The disease has no cure, requires life-long therapy, and is highly heterogeneous in disease phenotype, behavior, and most importantly in response to therapy. Animal models do not adequately mimic human IBD physiology, and unable to capture personalized host-microbial interaction and potential response to therapy. Using patients derived epithelial crypts we were able to establish an organoids culture. We were able to show proliferation of the organoid culture up to 10 days, and differentiation was notable after 72h by induction of Sucrase Isomaltose (SI), a transmembrane protein known to metabolize sugars, and a robust reduction of the LGR5 genes known to mark epithelial stemness. Triggering those gut organoids with LPS and TNFɑ or INFγ resulted in the expected induction if IL8. In addition, similarly to the pathogenesis detected in the patients’ biopsy, we detected induction of DUOX2 and reduction of APOA1 in our system, emphasizing the ability of the model to represent IBD pathogenesis. In addition, using anaerobic chamber, we successfully cultured isolated gut bacteria and microbial communities from fecal material obtained from IBD and controls subjects, with an ultimate goal to combine those in co-culturing conditions. This model will be used to elucidate the cross-talk mechanisms between the microbiome and epithelial cells of the gut in IBD.