Project Summary Bacteria in the human microbiome produce a complex pool of bioactive small molecules that have been associated with effects on human biology in health and disease, but the mechanisms of action of these molecules remain largely undefined. This proposal builds on preliminary data that a microbiome-derived small molecule, the secondary bile acid lithocholic acid (LCA), induces the Unfolded Protein Response (UPR), a signaling pathway that responds to endoplasmic reticulum (ER) stress. This observation links a microbiome-derived small molecule to a basic aspect of host cell biology. In this proposal, the applicant seeks to bring this observation to the mechanistic level using three complementary aims. In Aim 1, the consequences of LCA-mediated UPR activation will be defined in physiological models of liver homeostasis and injury. In Aim 2, the molecular mechanism by which LCA induces the UPR will be dissected using a combination of in-depth monitoring of ER function and chemical and genetic perturbations to probe the roles of putative signaling pathways and receptors. In Aim 3, the broader scope of UPR induction by bile acids, both individually and in combinations, will be assessed using high-throughput assays and animal models. Together, this work will establish the molecular basis of UPR induction by microbiome-derived small molecules. Dysregulation of the UPR is implicated in metabolic disorders, neurodegenerative disease, and multiple forms of cancer. Thus, this work may inform the development of biomarkers and therapeutic strategies for such diseases. More broadly, this work will provide a blueprint to define how small molecules from the microbiome shape host biology by impacting fundamental cell biological processes. Harvard Medical School houses world leaders in biomedical research in a collaborative and multidisciplinary environment and contains cutting-edge facilities for microscopy, genomics, and proteomics that will support the proposed research. The co-sponsors Dr. Marco Jost and Dr. Wade Harper are experts in studying host- microbiome interactions and regulation proteostasis, respectively, and provide complementary technical expertise and mentoring viewpoints. Completion of the proposed research will directly support the applicant’s training goals, including training in microbiome biology, systematic genetics, and animal models of disease and growth of skills to support an academic career.

Project Narrative The human microbiota produce a rich diversity of small molecules that fundamentally shape human physiology and have been linked to diseases including metabolic disease, neurodegenerative disorders, and cancer. This project will define a causal link between a class of prominent microbiome-derived molecules and the unfolded protein response, a stress response pathway that is important for protein homeostasis. Understanding how these small molecules influence health and disease may enable the development of novel biomarkers and microbiome- derived therapeutics to improve human health.