Specific CD4+ T cell phenotypes associate with bacterial control in people who ‘resist’ infection with Mycobacterium tuberculosis

Meng Sun*, Jolie M. Phan*, Nathan S. Kieswetter, Krystle K.Q. Yu, Malisa T. Smith, Huang Huang, Sanjana Gupta, Gerlinde Obermoser, Holden Terry Maecker, Akshaya Krishnan, Neha Gupta, Mary Rieck, Peter Acs, Mustafa Ghanizada, Shin-Heng Chiou, Purvesh Khatri, W. Henry Boom, Thomas R. Hawn, Catherine M. Stein, Harriet Mayanja-Kizza, Mark M. Davis*, Chetan Seshadri*

Abstract: A subset of individuals with a high probability of exposure to M. tuberculosis (M.tb) appears to ‘resist’ infection, as demonstrated by serially negative tuberculin skin test (TST) or IFN-γ release assay (IGRA) results. Though ‘resisters’ (RSTR) display IFN-γ-independent T cell responses to the M.tb-specific antigens ESAT-6 and CFP-10, it is currently unknown whether specific T cell functional programs are associated with ‘resistance’ to M.tb infection. We used multi-modal single-cell RNA and TCR sequencing to compare the phenotypes and functions of ESAT-6 and CFP-10 (M.tb) specific T cells between RSTRs and matched controls with ‘latent’ TB infection (LTBI). M.tb-specific T cells were clonally expanded in both RSTRs and LTBIs, confirming the priming of adaptive immune responses after M.tb exposure. However, M.tb-specific T cells derived from RSTRs showed an early differentiation phenotype as well as enrichment of Th17-like functional programs compared to LTBIs, which were characterized by Th1-like effector phenotypes. These results were internally validated in an independent set of RSTRs and LTBIs using flow cytometry and multiplex cytokine analysis and externally validated in a cohort of long-term TB non-progressors. Enriched gene programs were also associated with bacterial control in a published study of non-human primates. Together, these data suggest that ‘resisters’ may have cleared M.tb after exposure and immune priming and establish a set of T cell biomarkers to facilitate further study of this important clinical phenotype.