Identification of Mycobacterium tuberculosis-derived metabolites acting as ligands for MR1-restricted T cells.

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Project Summary Tuberculosis (TB) remains a leading global cause of morbidity and mortality, yet the immune correlates of protection remain elusive. Improved understanding of the initial immune events following Mycobacterium tuberculosis (Mtb) exposure that determine progression to infection and active disease is a critical priority for developing novel immune therapies and vaccines. Our laboratory studies innate lymphocyte biology and utilizes systems immunology approaches to identify targets for immune therapies against TB. In this proposal, we will focus on one of the most abundant innate lymphocytes responding to Mtb, mucosal-associated invariant T (MAIT) cells, that recognize activating/inhibitory microbial metabolites of riboflavin metabolism that act as non-peptide antigens presented by the evolutionarily conserved MHC I-related protein, MR1. While MAIT cells are activated by Mtb in vitro and in vivo, they do not robustly expand after infection. Moreover, MAIT cells are depleted during chronic murine and human TB disease. Our working hypothesis to explain this observation is that Mtb synthesizes an abundance of inhibitory MR1 ligands, which suppress MAIT cell activity and contribute to immune evasion. We have recently developed LC-MS technologies to detect MR1 ligands within biological samples and will couple this platform with our expertise in in mycobacterial genetics and TB immunology to define the MR1 metabolome of Mtb as compared to non-mycobacterial species as well as Mtb riboflavin auxotrophs we will generate by inducible CRISPRi knockdown to transiently perturb specific branchpoints of mycobacterial riboflavin biosynthesis. In parallel, we will quantify Mtb-specific MR1 ligands and MR1 expression/MAIT cell function in vivo during initial Mtb exposure and infection in humans who have been recently exposed to Mtb in their household. In sum, our approach will identify MR1 ligands specific to Mtb metabolism and determine their impact on MR1/MAIT cell activity, informing future targeting of Mtb Vitamin B metabolism in TB immune therapies and mucosal vaccines.