Mycobacterium tuberculosis resisters despite HIV exhibit activated T cells and macrophages in their pulmonary alveoli [scRNA-seq]

Natural resistance to Mycobacterium tuberculosis (Mtb) infection in some people living with HIV (PLWH) is unexplained. We performed single cell RNA-sequencing of bronchoalveolar lavage cells, unstimulated or ex vivo stimulated with Mtb, for 7 PLWH who were Tuberculin skin test (TST) & Interferon Gamma Release Assay (IGRA) positive (called LTBI) and 6 who were persistently TST & IGRA negative (called resisters). Alveolar macrophages (AM) from resisters displayed a stronger baseline M1 phenotype than LTBI AM. Resisters displayed alveolar lymphocytosis (10%-60%), with enrichment of all T cell subpopulations including CD4+ and CD8+ IFNG-expressing cells. Alveolar lymphocytosis was strongly associated with most of the AM transcriptomic features of resisters. In both groups, mycobactericidal granulysin was expressed almost exclusively by a CD8+ T cell subtype that co-expressed granzyme B, perforin and NK cell receptors. These poly-cytotoxic T lymphocytes (CTL) over-expressed activating NK cell receptors and were increased in resisters. Following challenge with Mtb, only a subpopulation of Intraepithelial Lymphocytes (IEL)-like cells in LTBI participants responded with increased transcription of IFNG. AM from resisters responded with stronger TNF signature at 6h post-infection (p.i.) while at 24h p.i. AM from LTBI displayed stronger IFN-γ signature. Conversely, at 24h p.i. only AM from resisters displayed a significant upregulation of MICA transcripts which encode an activating ligand for the CD8+ poly-CTL. These results suggest that CD8+ CTL and AM mediate the resister phenotype in PLWH.