Dietary Regulation of Intestinal Inflammation and Repair

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PROJECT SUMMARY Inflammatory bowel diseases (IBD), which include both ulcerative colitis and Crohn's disease, are estimated to affect three million individuals in the United States, and the number of people living with IBD continues to rise. Currently available medications are costly, ineffective for some patients, and associated with serious risks including opportunistic infections, hepatic inflammation, pancreatitis, and cancer. Thus, there is an urgent need to improve our understanding of the modulators of intestinal inflammation and repair in order to identify novel therapeutic targets to treat and prevent IBD. The microbiota is the source of various metabolites which can exert their effects at the site of absorption (intestine), and at distant sites such as brain via bloodstream. In this regard, the microbiota mimics an endocrine organ, and its output has only begun to be understood. Since various dietary components, such as dietary fiber, influence the levels of microbiota-derived metabolites, many of the effects of diets on immune cells could be mediated via the microbiota. Although dietary fiber has some anti-inflammatory effects, IBD patients are often instructed to limit their fiber consumption to reduce the frequency and severity of disease flares. However, the mechanism behind dietary fiber-induced exacerbation of IBD-associated symptoms is poorly understood. In new preliminary studies, we identified that a fiber-rich diet activates ILC2s in the colon and significantly increases the levels of eosinophils, a type 2 inflammatory immune cell regulated by ILC2s. The effects of dietary fiber on the eosinophil responses are dependent on the microbiota and are associated with remarkable changes in microbiota-derived metabolites. Furthermore, the high fiber diet increased disease severity in a murine model of intestinal damage and inflammation. Despite these observations, the mechanisms through which dietary fiber regulates the ILC2-eosinophil axis and colonic inflammation remain unknown. Based on our new preliminary data, we hypothesize that microbial metabolites regulate colonic ILC2s and that alterations of these metabolites by a high fiber diet induce pathologic activation of ILC2s and severe intestinal inflammation. We propose to generate a detailed understanding of how microbial metabolites influence inflammatory pathologies in murine models of intestinal inflammation and examine these pathways in human IBD patient samples. In Aim 1, we will determine what microbial metabolites and host metabolite receptors are involved in the high fiber diet-induced type 2 inflammation and their role in intestinal damage and inflammation. In Aim 2, we will employ a novel CRISPR-based microbial gene-editing technique to directly test the microbial metabolic pathways through which a high fiber diet mediates intestinal inflammation. In Aim 3, we will translate these findings to human disease and determine how alterations in microbial metabolites and the ILC2-eosinphil axis correlate with clinical and endoscopic measures of IBD disease activity. In addition to uncovering novel immunoregulatory mechanisms of diet and microbiota and their unique roles in IBD, these studies will provide preclinical justification for development of novel therapeutics to target this pathway.