Alveolar macrophage responses to Mycobacterium tuberculosis reveal human-to-human variation in important immunobiology pathways gleaned from functional genomics study

Abstract

Abstract Human alveolar macrophages (AMs) are the primary target of Mycobacterium tuberculosis (M.tb) in the lung, where M.tb establishes intracellular residence and growth. This study characterizes M.tb-AM interactions and processes driving inter-subject variability. AMs were obtained by bronchoalveolar lavage from 28 healthy donors and cultured in the presence and absence of virulent M.tb strain H37Rv engineered to produce bioluminescence. Luminescence intensity (RLU) was measured at 2, 24, 48, and 72h post infection. At 2, 24, and 72h, we also measured 27 secreted proteins and AM RNA transcriptomes using AmpliSeq, targeting 20,804 genes, including 2,228 non-coding RNAs. RLUs reveal large differences in M.tb uptake at 2h, varying rates of intracellular adaptation between 2 and 24h, and a range of growth rates from 48 to 72h, resulting in discrete donor groups for each type of interaction. We identify 5039 significant differentially expressed RNAs (DE genes), revealing immune-related pathways, gene networks, and hub genes. A sub-group of three AMs with rapid growth rates (72/48h RLU ratios) displays the most significant DE RNA profiles, including TREM1 networks, IL8 and IL1B, CXCL10, and most prominently IDO1 at 72h, recently identified as a key protein characteristic of active TB, in a cluster of 73 tightly co-expressed genes. Large inter-individual differences in secreted proteins are mostly consistent with the RNA results. Our results identify known and novel key genes in the early phase of M.tb infection in a subset of HAMs, potentially relevant to in vivo infection and TB risk. These key genes can guide a search for genetic variants that contribute to TB risk, and potential targets for diagnostics, treatment, and prevention strategies.