Multimodal profiling of lung granulomas reveals cellular correlates of tuberculosis control

Abstract

In humans and nonhuman primates, Mycobacterium tuberculosis lung infection yields a complex multicellular structure: the tuberculosis granuloma. All granulomas are not equivalent, however, even within the same host: in some, local immune activity promotes bacterial clearance, while in others, it allows persistence or outgrowth. Here, we used single-cell RNA-sequencing to define holistically cellular responses associated with control in cynomolgus macaques. Granulomas that facilitated bacterial killing contained significantly higher proportions of CD4+ and CD8+ T cells expressing hybrid Type1-Type17 immune responses or stem-like features and CD8-enriched T cells with specific cytotoxic functions; failure to control correlated with mast cell, plasma cell and fibroblast abundance. Co-registering these data with serial PET-CT imaging suggests that a degree of early immune control can be achieved through cytotoxic activity, but that more robust restriction only arises after the priming of specific adaptive immune responses, defining new targets for vaccination and treatment.

Classical CD4 T cells as the cornerstone of antimycobacterial immunity

“…T cells expressing a "hybrid Th1/Th17 immune response", 75 thus further strengthening the hypothesis that Th1* have a role in containment of Mtb infection. This may be mediated in part by their expression of CCR6, which mediates cell homing to inflamed tissues, 76 and thus allows peripheral localization.…”

“…A recent study that used single‐cell RNA sequencing to define cellular responses associated with control of Mtb infection (ie, bacterial killing in granulomas), identified higher proportions of CD4 T cells expressing a “hybrid Th1/Th17 immune response”, 75 thus further strengthening the hypothesis that Th1* have a role in containment of Mtb infection. This may be mediated in part by their expression of CCR6, which mediates cell homing to inflamed tissues, 76 and thus allows peripheral localization.…”

“…↑ CD4 T cells expressing a “hybrid Th1/Th17 immune response” detected using single‐cell RNA‐sequencing in TB granulomas of NHPs infected with Mtb 75 …”

Dissemination and progression of pulmonaryMycobacterium aviuminfection in mouse model is associated with type 2 macrophage activation

“…Another limitation is a narrow focus on macrophage M1/M2 markers. The integration of T cell markers in our spatial analysis will prove informative in linking local macrophage phenotypes with T cell responses within distinct granuloma compartments, as described by Gideon et al (61). Technical limitations also include an impeded accuracy of segmentation of histiocytes due to their occasional multinucleation, as well as heterogeneity in cytoplasmic area and shape.…”

Sterilizing immunity: New opportunities for rational TB vaccine design

“…triggers a sterilizing immunity to Mtb challenge, and interestingly, a prominent airway CD8 T lymphocyte response was observed in i.v.-vaccinated monkeys but not in animals immunized with BCG by the less-protective intradermal and aerosol routes ( Darrah et al, 2020 ). In related work, single-cell RNAseq has revealed that within individual macaques, granulomas that control infection, in comparison with those that do not, are characterized by the presence of a diverse set of cytotoxic lymphocytes ( Gideon, 2021 Preprint ). Systems serology has also revealed IgM antibody responses that correlate with sterilizing protection in vaccinated NHPs ( Irvine, 2021 Preprint ), suggesting the possible involvement of humoral immunity.…”