The Study of Families with Heritable Crohn's Disease to Support Rational Design of Microbiodata-Based Therapies

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Project Summary/Abstract The cause of Crohn's disease (CD) is believed to be rooted in the interactions between genetic susceptibilities and exposures to environmental factors, such as specific gut microbes. Unfortunately, the complexity of these interactions makes it difficult to understand what portion of CD risk is modifiable, and particularly whether gut microbiome compositions can be altered to overcome one's underlying and fixed genetic predisposition. This proposal will address whether individuals at high genetic risk for CD, but who never develop disease, harbor characteristic gut microbial signatures that signal protection from CD. It will furthermore address whether protective microbiomes can be transferred to diminish, delay, or prevent CD activity in others. Aim 1 will entail the study of multigenerational families with multiplex CD – with the rationale that families, sharing common living environments, meals, and behaviors, will minimize common confounders of human microbiome studies. Individuals will be stratified by a polygenic risk score to better identify those at highest genetic risk but remain disease-free and who are hypothesized as being most likely to harbor intestinal microbiomic and metabolomic signatures that characterize disease protection. In Aim 2, select fecal biospecimens (collected in Aim 1) containing putative protective microbiomes will be transplanted into a germ-free CD mouse model. These mice will then be characterized by their phenotypic, microbial, metabolomic, and immune responses and assessed for alterations in disease onset and severity. These studies will provide insights into microbially-mediated modulators of CD activity; for example, clarifying the yet unknown reason why fecal transplants are very effective for only a small portion of inflammatory bowel disease cases and why outcomes appear to be heavily donor-dependent. Coupling the study of an enriched human population with an animal model, to mechanistically test candidate protective microbiomes, will streamline the scientific approach and expedite the transition of promising study findings into clinical care. The scientific proposal and associated training plan will furthermore prepare the PI, so that she will be well-equipped to lead future studies of host-microbe dynamics in inflammatory bowel disease as an independent translational investigator.