Advances in flow cytometry and other single-cell technologies have enabled high-dimensional, high-throughput measurements of individual cells and allowed interrogation of cell population heterogeneity. Computational tools to take full advantage of these technologies are lacking. Here, we present COMPASS, a computational framework for unbiased polyfunctionality analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed functional cell subsets and select those most likely to exhibit antigen-specific responses. Cell-subset responses are quantified by posterior probabilities, while subject-level responses are quantified by two novel summary statistics that can be correlated directly with clinical outcome, and describe the quality of an individual’s (poly)functional response. Using three clinical datasets of cytokine production we demonstrate how COMPASS improves characterization of antigen-specific T cells and reveals novel cellular correlates of protection in the RV144 HIV vaccine efficacy trial that are missed by other methods. COMPASS is available as open-source software.

Mycobacterium tuberculosis is a leading cause of mortality worldwide and establishes a long-lived latent infection in a substantial proportion of the human population. Multiple lines of evidence suggest that some individuals are resistant to latent M. tuberculosis infection despite long-term and intense exposure, and we term these individuals 'resisters'. In this Review, we discuss the epidemiological and genetic data that support the existence of resisters and propose criteria to optimally define and characterize the resister phenotype. We review recent insights into the immune mechanisms of M. tuberculosis clearance, including responses mediated by macrophages, T cells and B cells. Understanding the cellular mechanisms that underlie resistance to M. tuberculosis infection may reveal immune correlates of protection that could be utilized for improved diagnostics, vaccine development and novel host-directed therapeutic strategies.

SUMMARY Exposure to Mycobacterium tuberculosis (Mtb) results in heterogeneous clinical outcomes including primary progressive tuberculosis (TB) and latent Mtb infection (LTBI). Mtb infection is identified using the tuberculin skin test (TST) and IFN-γ release assay (IGRA), and a positive result may prompt chemoprophylaxis to prevent progression to TB. Here, we report a cohort of Ugandan household contacts, highly exposed to Mtb yet IGRA and TST negative, “resisting” development of classical LTBI. We show that “resisters” possess IgM, class-switched IgG antibody responses and non IFN-γ T-cell responses to Mtb-specific proteins ESAT6 and CFP10, immunologic evidence of exposure to Mtb. Compared to subjects with classical LTBI, “resisters” display enhanced antibody avidity and distinct Mtb-specific IgG Fc profiles. These data reveal a distinct adaptive immune profile among Mtb exposed subjects, supporting an expanded definition of the host response to Mtb exposure with implications for public health and the design of clinical trials.

Knockout of lprG results in decreased virulence of Mycobacterium tuberculosis (Mtb) in mice. Mtb lipoprotein LprG has TLR2 agonist activity, thought to be dependent on its N-terminal triacylation. Surprisingly, here we find that non-acylated LprG retains TLR2 activity. Moreover, we show LprG association with triacylated glycolipid TLR2 agonists lipoarabinomannan, lipomannan and phosphatidylinositol mannosides (which share core structures). Binding of triacylated species was specific to LprG (not LprA) and increased LprG TLR2 agonist activity; conversely, association of glycolipids with LprG enhanced their recognition by TLR2. The crystal structure of LprG in complex with phosphatidylinositol mannoside revealed a hydrophobic pocket that accommodates the three alkyl chains of the ligand. In conclusion, we demonstrate a glycolipid binding function of LprG that enhances recognition of triacylated Mtb glycolipids by TLR2 and may affect glycolipid assembly or transport for bacterial cell wall biogenesis.