Human macrophage variation & TB pathogenesis

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Variation in clinical outcomes after Mtb exposure ranges from resistance to infection to disseminated disease. Human genetic and cellular mechanisms of resistance and dissemination are largely unknown and may provide insight into novel therapeutic strategies. In Vietnam, we enrolled and examined large cohorts of PTB and TBM subjects with detailed immunogenetic studies of both the host and pathogen to discover determinants of disease progression. In Uganda in a large TB household contact study over the past 20 years, we found that ~9% of close adult household contacts remained persistently TST and Interferon- Release Assay (IGRA) negative during extended follow-up and appear to be resistant to traditionally defined LTBI (RSTR). With transcriptional and proteomic profiling of Mtb-infected monocytes, we discovered genes and pathways that are enriched in RSTR compared to LTBI. Some genes were differentially enriched in both datasets, including RAB11B, a gene involved in vesicle trafficking, which was increased in RSTR macrophages and also identified in the human-M. tuberculosis protein-protein interaction (PPI) network. Furthermore, with a cellular GWAS approach in Mtb-infected macrophages, we discovered human polymorphisms associated with IL-1β expression that are in genes not previously known to regulate IL-1. These findings suggest new genes and variants that globally regulate human Mtb induced IL-1β, a key cytokine that promotes control of Mtb in macrophages and in murine in vivo models. In genetic association studies in RSTRs & LTBI (Uganda) and TBM & PTB (Vietnam), we found polymorphisms in several candidate genes (associated with RSTR or TB disease or macrophage IL-1 regulation) that were strongly associated with clinical outcomes. Together, these data support our hypothesis that Mtb-induced macrophage responses are genetically regulated and associated with different clinical outcomes. However, there are many gaps in our knowledge. First, the Mtb-induced post- translational modification (PTM) profiles of macrophages from RSTR, LTBI, and TB disease individuals are unknown. Second, the global human genetic regulators (genes and variants) of Mtb-induced macrophage anti- microbial pathways are mostly unknown. Third, molecular and cellular mechanisms of human Mtb resistance and dissemination are almost completely unknown, including the role of Mtb strain variation in pathogenesis. To address these gaps, we will use genomic, genetic, and proteomic methods to profile human macrophages and discover differentially abundant PTMs that are associated with clinical outcomes and/or are Mtb strain dependent. We will then use genetic and cellular strategies to discover the global regulators of anti-microbial macrophage responses to Mtb infection and examine how these genes and their variants regulate macrophage function in the context of Mtb strain variation. Our primary goal is to discover new vulnerabilities between Mtb and macrophages, and thus inform mechanisms of disease heterogeneity, insights into risk stratification for clinical management, and development of effective host directed therapies and vaccines.