Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Finding and filling the knowledge gaps in mechanisms of T cell-mediated TB immunity to inform vaccine design

Nature Reviews Immunology (2025)Cite this article

Subjects

Abstract

Mycobacterium tuberculosis, the bacterium that causes tuberculosis (TB), results in more human mortality than any other single pathogen, in part because of the lack of an effective vaccine. Although T cells are essential for immunity to TB, the mechanisms that provide protective immunity are poorly understood. In this Review, we describe current gaps in our knowledge about T cell-mediated immune responses to M. tuberculosis and discuss how recent technologies, including multiphoton intravital microscopy, spatial multiomics and high-resolution in vivo analyses of cell–cell interactions, may be used to gain insights that can inform the design of T cell-targeted TB vaccines.

Access through your institution
Buy or subscribe

This is a preview of subscription content, access via your institution

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: T cell responses to Mtb.
Fig. 2: Spatial segregation of T cells and myeloid cells in Mtb granulomas.
Fig. 3: Interactions of CD4+ and CD8+ T cells with Mtb-infected myeloid cells in granulomas.

Similar content being viewed by others

References

  1. Darrah, P. A. et al. Prevention of tuberculosis in macaques after intravenous BCG immunization. Nature 577, 95–102 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Dijkman, K. et al. Prevention of tuberculosis infection and disease by local BCG in repeatedly exposed rhesus macaques. Nat. Med. 25, 255–262 (2019).

    Article  CAS  PubMed  Google Scholar 

  3. Hansen, S. G. et al. Prevention of tuberculosis in rhesus macaques by a cytomegalovirus-based vaccine. Nat. Med. 24, 130–143 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Dijkman, K. et al. A protective, single-visit TB vaccination regimen by co-administration of a subunit vaccine with BCG. NPJ Vaccines 8, 66 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Woodworth, J. S. et al. A Mycobacterium tuberculosis-specific subunit vaccine that provides synergistic immunity upon co-administration with Bacillus Calmette-Guérin. Nat. Commun. 12, 6658 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Nemeth, J. et al. Contained Mycobacterium tuberculosis infection induces concomitant and heterologous protection. PLoS Pathog. 16, e1008655 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Coussens, A. K. et al. Classification of early tuberculosis states to guide research for improved care and prevention: an international Delphi consensus exercise. Lancet Respir. Med. 12, 484–498 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  8. Garcia-Basteiro, A. L. et al. A global tuberculosis dictionary: unified terms and definitions for the field of tuberculosis. Lancet Glob. Health 12, e737–e739 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Cohen, S. B. et al. Alveolar macrophages provide an early Mycobacterium tuberculosis niche and initiate dissemination. Cell Host Microbe 24, 439–446.e434 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Pisu, D. et al. Single cell analysis of M. tuberculosis phenotype and macrophage lineages in the infected lung. J. Exp. Med. 218, e20210615 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Wolf, A. J. et al. Mycobacterium tuberculosis infects dendritic cells with high frequency and impairs their function in vivo. J. Immunol. 179, 2509–2519 (2007). Myeloid DCs are key reservoirs for M. tuberculosis in the lungs and lymph nodes, while strategically impairing antigen presentation to CD4+ T cells, thereby promoting persistent infection.

    Article  CAS  PubMed  Google Scholar 

  12. Lee, J. et al. CD11cHi monocyte-derived macrophages are a major cellular compartment infected by Mycobacterium tuberculosis. PLoS Pathog. 16, e1008621 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Zheng, W. et al. Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection. PLoS Pathog. 20, e1012205 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Lai, R., Williams, T., Rakib, T., Lee, J. & Behar, S. M. Heterogeneity in lung macrophage control of Mycobacterium tuberculosis is modulated by T cells. Nat. Commun. 15, 5710 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Kwan, C. K. & Ernst, J. D. HIV and tuberculosis: a deadly human syndemic. Clin. Microbiol. Rev. 24, 351–376 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Jasenosky, L. D., Scriba, T. J., Hanekom, W. A. & Goldfeld, A. E. T cells and adaptive immunity to Mycobacterium tuberculosis in humans. Immunol. Rev. 264, 74–87 (2015).

    Article  CAS  PubMed  Google Scholar 

  17. Flynn, J. L. & Chan, J. Immune cell interactions in tuberculosis. Cell 185, 4682–4702 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Nathan, A. et al. Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment and disease. Nat. Immunol. 22, 781–793 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Gideon, H. P. et al. Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control. Immunity 55, 827–846.e810 (2022). Advanced single-cell analyses, coupled with detailed in vivo measurements of Mtb granulomas, identified the cellular and transcriptional characteristics associated with an effective host immune response to TB in NHPs.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Bromley, J. D. et al. CD4+ T cells re-wire granuloma cellularity and regulatory networks to promote immunomodulation following Mtb reinfection. Immunity 57, 2380–2398 e2386 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Chackerian, A. A., Alt, J. M., Perera, T. V., Dascher, C. C. & Behar, S. M. Dissemination of Mycobacterium tuberculosis is influenced by host factors and precedes the initiation of T-cell immunity. Infect. Immun. 70, 4501–4509 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Wolf, A. J. et al. Initiation of the adaptive immune response to Mycobacterium tuberculosis depends on antigen production in the local lymph node, not the lungs. J. Exp. Med. 205, 105–115 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Miller, E. A. & Ernst, J. D. Anti-TNF immunotherapy and tuberculosis reactivation: another mechanism revealed. J. Clin. Invest. 119, 1079–1082 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Mathe, G. et al. Intravenous B.C.G. in monkeys and man. Lancet 1, 92 (1976).

    Article  CAS  PubMed  Google Scholar 

  25. Crispen, R. G. Immunotherapy with intravenous B.C.G. Lancet 2, 56 (1974).

    Article  CAS  PubMed  Google Scholar 

  26. Davis, J. M. & Ramakrishnan, L. The role of the granuloma in expansion and dissemination of early tuberculous infection. Cell 136, 37–49 (2009). Prompted reconsideration of the dogma that granulomas simply contain mycobacterial infection by demonstrating the role of ongoing cell recruitment in enabling cell-to-cell spread and progression of infection.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Cronan, M. R. et al. A non-canonical type 2 immune response coordinates tuberculous granuloma formation and epithelialization. Cell 184, 1757–1774 e1714 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Cohen, S. B., Gern, B. H. & Urdahl, K. B. The tuberculous granuloma and preexisting immunity. Annu. Rev. Immunol. 40, 589–614 (2022).

    Article  CAS  PubMed  Google Scholar 

  29. Sawyer, A. J. et al. Spatial mapping reveals granuloma diversity and histopathological superstructure in human tuberculosis. J. Exp. Med. 220, e20221392 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Kauffman, K. D. et al. Defective positioning in granulomas but not lung-homing limits CD4 T-cell interactions with Mycobacterium tuberculosis-infected macrophages in rhesus macaques. Mucosal Immunol. 11, 462–473 (2018).

    Article  CAS  PubMed  Google Scholar 

  31. Carow, B. et al. Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma. Nat. Commun. 10, 1823 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  32. McCaffrey, E. F. et al. The immunoregulatory landscape of human tuberculosis granulomas. Nat. Immunol. 23, 318–329 (2022). TB granulomas of individuals with active TB were mapped using multiplexed ion beam imaging by time of flight, identifying three spatial modules including the myeloid core enriched with IDO1 and PD-L1, lymphocytic cuff and stromal compartment revealing novel functional–spatial relationships.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Esaulova, E. et al. The immune landscape in tuberculosis reveals populations linked to disease and latency. Cell Host Microbe 29, 165–178.e168 (2021).

    Article  CAS  PubMed  Google Scholar 

  34. Magoulopoulou, A. et al. Spatial resolution of Mycobacterium tuberculosis bacteria and their surrounding immune environments based on selected key transcripts in mouse lungs. Front. Immunol. 13, 876321 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Ernst, J. D., Cornelius, A., Desvignes, L., Tavs, J. & Norris, B. A. Limited antimycobacterial efficacy of epitope peptide administration despite enhanced antigen-specific CD4 T cell activation. J. Infect. Dis. https://doi.org/10.1093/infdis/jiy142 (2018).

  36. Szabo, P. A., Miron, M. & Farber, D. L. Location, location, location: tissue resident memory T cells in mice and humans. Sci. Immunol. 4, eaas9673 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Srivastava, S. & Ernst, J. D. Cutting edge: direct recognition of infected cells by CD4 T cells is required for control of intracellular Mycobacterium tuberculosis in vivo. J. Immunol. 191, 1016–1020 (2013). Direct recognition of infected cells by CD4+ T cells is essential for controlling intracellular Mtb, as long-range cytokine diffusion alone is insufficient to reduce bacterial burden, highlighting a critical mechanism of host defence against TB.

    Article  CAS  PubMed  Google Scholar 

  38. Muller, A. J. et al. CD4+ T cells rely on a cytokine gradient to control intracellular pathogens beyond sites of antigen presentation. Immunity 37, 147–157 (2012).

    Article  CAS  PubMed  Google Scholar 

  39. Lin, K. Y. et al. Ectopic expression of vascular cell adhesion molecule-1 as a new mechanism for tumor immune evasion. Cancer Res. 67, 1832–1841 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Tian, C. et al. Motility and tumor infiltration are key aspects of invariant natural killer T cell anti-tumor function. Nat. Commun. 15, 1213 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Nunes-Alves, C. et al. In search of a new paradigm for protective immunity to TB. Nat. Rev. Microbiol. 12, 289–299 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Winchell, C. G. et al. CD8+ lymphocytes are critical for early control of tuberculosis in macaques. J. Exp. Med. 220, e20230707 (2023). The study investigates the role of innate and conventional CD8 immunity in TB, revealing that CD8αα+ lymphocytes have a key role in the early suppression of Mtb growth in macaque lungs.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Cai, Y. et al. Single-cell immune profiling reveals functional diversity of T cells in tuberculous pleural effusion. J. Exp. Med. 219, e20211777 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Schurr, E. et al. Mycobacterium tuberculosis resisters despite HIV exhibit activated T cells and macrophages in their pulmonary alveoli. J. Clin. Invest. 135, e188016 (2025). Poly-cytotoxic T cells and alveolar macrophages contribute to natural resistance to Mtb infection in individuals with HIV.

    Article  PubMed  PubMed Central  Google Scholar 

  45. Simonson, A. W. et al. CD4 T cells and CD8α+ lymphocytes are necessary for intravenous BCG-induced protection against tuberculosis in macaques. J. Exp. Med. 222, e20241571 (2025). This article presents evidence that CD8+ and CD4+ T cells have a crucial role in mediating protection in NHPs vaccinated with intravenous BCG.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Patankar, Y. R. et al. Limited recognition of Mycobacterium tuberculosis-infected macrophages by polyclonal CD4 and CD8 T cells from the lungs of infected mice. Mucosal Immunol. 13, 140–148 (2020).

    Article  CAS  PubMed  Google Scholar 

  47. Carpenter, S. M., Nunes-Alves, C., Booty, M. G., Way, S. S. & Behar, S. M. A higher activation threshold of memory CD8+ T cells has a fitness cost that is modified by TCR affinity during tuberculosis. PLoS Pathog. 12, e1005380 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Billeskov, R., Vingsbo-Lundberg, C., Andersen, P. & Dietrich, J. Induction of CD8 T cells against a novel epitope in TB10.4: correlation with mycobacterial virulence and the presence of a functional region of difference-1. J. Immunol. 179, 3973–3981 (2007).

    Article  CAS  PubMed  Google Scholar 

  49. Yang, J. D. et al. Mycobacterium tuberculosis-specific CD4+ and CD8+ T cells differ in their capacity to recognize infected macrophages. PLoS Pathog. 14, e1007060 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  50. Sutiwisesak, R. et al. A natural polymorphism of Mycobacterium tuberculosis in the esxH gene disrupts immunodomination by the TB10.4-specific CD8 T cell response. PLoS Pathog. 16, e1009000 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Nyendak, M. et al. Adenovirally-induced polyfunctional T cells do not necessarily recognize the infected target: lessons from a phase I trial of the AERAS-402 vaccine. Sci. Rep. 6, 36355 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Behar, S. M., Martin, C. J., Nunes-Alves, C., Divangahi, M. & Remold, H. G. Lipids, apoptosis, and cross-presentation: links in the chain of host defense against Mycobacterium tuberculosis. Microbes Infect. 13, 749–756 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Athman, J. J. et al. Mycobacterium tuberculosis membrane vesicles inhibit T cell activation. J. Immunol. 198, 2028–2037 (2017).

    Article  CAS  PubMed  Google Scholar 

  54. Caouaille, M., Hudrisier, D. & Neyrolles, O. Mycobacterial d-serine impairs TB control. Nat. Immunol. 25, 1129–1130 (2024).

    Article  CAS  PubMed  Google Scholar 

  55. Cheng, H. et al. Mycobacterium tuberculosis produces d-serine under hypoxia to limit CD8+ T cell-dependent immunity in mice. Nat. Microbiol. 9, 1856–1872 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Mahon, R. N. et al. Mycobacterium tuberculosis cell wall glycolipids directly inhibit CD4+ T-cell activation by interfering with proximal T-cell-receptor signaling. Infect. Immun. 77, 4574–4583 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Mahon, R. N. et al. Mycobacterium tuberculosis ManLAM inhibits T-cell-receptor signaling by interference with ZAP-70, Lck and LAT phosphorylation. Cell Immunol. 275, 98–105 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Mwebaza, I. et al. Impact of Mycobacterium tuberculosis glycolipids on the CD4+ T cell-macrophage immunological synapse. J. Immunol. 211, 1385–1396 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Sande, O. J. et al. Mannose-capped lipoarabinomannan from Mycobacterium tuberculosis induces CD4+ T cell anergy via GRAIL. J. Immunol. 196, 691–702 (2016).

    Article  CAS  PubMed  Google Scholar 

  60. Collins, J. M. et al. Tryptophan catabolism reflects disease activity in human tuberculosis. JCI Insight 5, e137131 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  61. Gautam, U. S. et al. In vivo inhibition of tryptophan catabolism reorganizes the tuberculoma and augments immune-mediated control of Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA 115, E62–E71 (2018). Inhibiting IDO activity in tuberculomas in macaques induces the reorganization of the granulomata, with T cells otherwise present in the peripheral region of lesions being able to gain greater access to the core region. This can potentially improve TB control by enhancing immune-mediated control and reducing bacterial burden and pathology.

    Article  CAS  PubMed  Google Scholar 

  62. Desvignes, L. & Ernst, J. D. Interferon-gamma-responsive nonhematopoietic cells regulate the immune response to Mycobacterium tuberculosis. Immunity 31, 974–985 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Ahmed, A. & Vyakarnam, A. Emerging patterns of regulatory T cell function in tuberculosis. Clin. Exp. Immunol. 202, 273–287 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Kotov, D. I. et al. Early cellular mechanisms of type I interferon-driven susceptibility to tuberculosis. Cell 186, 5536–53.e22 (2023). Plasmacytoid DCs drive Mtb pathogenesis by producing type I interferons that impair interstitial macrophage responses to IFNγ, promoting bacterial replication, neutrophil recruitment and active tuberculosis disease.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Ji, D. X. et al. Type I interferon-driven susceptibility to Mycobacterium tuberculosis is mediated by IL-1Ra. Nat. Microbiol. 4, 2128–2135 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Berry, M. P. et al. An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 466, 973–977 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Moreira-Teixeira, L., Mayer-Barber, K., Sher, A. & O’Garra, A. Type I interferons in tuberculosis: foe and occasionally friend. J. Exp. Med. 215, 1273–1285 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Lazar-Molnar, E. et al. Programmed death-1 (PD-1)-deficient mice are extraordinarily sensitive to tuberculosis. Proc. Natl Acad. Sci. USA 107, 13402–13407 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Kauffman, K. D. et al. PD-1 blockade exacerbates Mycobacterium tuberculosis infection in rhesus macaques. Sci. Immunol. 6, eabf3861 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Jayaraman, P. et al. TIM3 mediates T cell exhaustion during Mycobacterium tuberculosis infection. PLoS Pathog. 12, e1005490 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  71. Zhu, C. et al. An IL-27/NFIL3 signalling axis drives Tim-3 and IL-10 expression and T-cell dysfunction. Nat. Commun. 6, 6072 (2015).

    Article  CAS  PubMed  Google Scholar 

  72. Torrado, E. et al. Interleukin 27R regulates CD4+ T cell phenotype and impacts protective immunity during Mycobacterium tuberculosis infection. J. Exp. Med. 212, 1449–1463 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Panda, S. et al. Identification of differentially recognized T cell epitopes in the spectrum of tuberculosis infection. Nat. Commun. 15, 765 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Lindestam Arlehamn, C. S. et al. A quantitative analysis of complexity of human pathogen-specific CD4 T cell responses in healthy M. tuberculosis infected South Africans. PLoS Pathog. 12, e1005760 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  75. Lewinsohn, D. M. et al. Human Mycobacterium tuberculosis CD8 T cell antigens/epitopes identified by a proteomic peptide library. PLoS ONE 8, e67016 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Samstein, M. et al. Essential yet limited role for CCR2+ inflammatory monocytes during Mycobacterium tuberculosis-specific T cell priming. eLife 2, e01086 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  77. Srivastava, S. & Ernst, J. D. Cell-to-cell transfer of M. tuberculosis antigens optimizes CD4 T cell priming. Cell Host Microbe 15, 741–752 (2014). During Mtb infection, inefficient antigen presentation by infected migratory DCs is bypassed through the release and transfer of bacterial antigens to uninfected resident lymph node DCs, enabling optimal CD4+ T cell priming and enhancing immune control of TB.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Delamarre, L., Pack, M., Chang, H., Mellman, I. & Trombetta, E. S. Differential lysosomal proteolysis in antigen-presenting cells determines antigen fate. Science 307, 1630–1634 (2005).

    Article  CAS  PubMed  Google Scholar 

  79. Commandeur, S. et al. An unbiased genome-wide Mycobacterium tuberculosis gene expression approach to discover antigens targeted by human T cells expressed during pulmonary infection. J. Immunol. 190, 1659–1671 (2013).

    Article  CAS  PubMed  Google Scholar 

  80. Bold, T. D., Banaei, N., Wolf, A. J. & Ernst, J. D. Suboptimal activation of antigen-specific CD4+ effector cells enables persistence of M. tuberculosis in vivo. PLoS Pathog. 7, e1002063 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Rogerson, B. J. et al. Expression levels of Mycobacterium tuberculosis antigen-encoding genes versus production levels of antigen-specific T cells during stationary level lung infection in mice. Immunology 118, 195–201 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Banchereau, J. & Steinman, R. M. Dendritic cells and the control of immunity. Nature 392, 245–252 (1998).

    Article  CAS  PubMed  Google Scholar 

  83. Rothchild, A. C. et al. Alveolar macrophages generate a noncanonical NRF2-driven transcriptional response to Mycobacterium tuberculosis in vivo. Sci. Immunol. 4, eaaw6693 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Eisenbarth, S. C. Dendritic cell subsets in T cell programming: location dictates function. Nat. Rev. Immunol. 19, 89–103 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Shah, J. A., Lindestam Arlehamn, C. S., Horne, D. J., Sette, A. & Hawn, T. R. Nontuberculous mycobacteria and heterologous immunity to tuberculosis. J. Infect. Dis. 220, 1091–1098 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Simeone, R. et al. Cytosolic access of Mycobacterium tuberculosis: critical impact of phagosomal acidification control and demonstration of occurrence in vivo. PLoS Pathog. 11, e1004650 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  87. Divangahi, M. et al. Mycobacterium tuberculosis evades macrophage defenses by inhibiting plasma membrane repair. Nat. Immunol. 10, 899–906 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Woodworth, J. S., Fortune, S. M. & Behar, S. M. Bacterial protein secretion is required for priming of CD8+ T cells specific for the Mycobacterium tuberculosis antigen CFP10. Infect. Immun. 76, 4199–4205 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Woodworth, J. S. & Behar, S. M. Mycobacterium tuberculosis-specific CD8+ T cells and their role in immunity. Crit. Rev. Immunol. 26, 317–352 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Lewinsohn, D. A. et al. Immunodominant tuberculosis CD8 antigens preferentially restricted by HLA-B. PLoS Pathog. 3, 1240–1249 (2007).

    Article  CAS  PubMed  Google Scholar 

  91. Lewinsohn, D. M. et al. Secreted proteins from Mycobacterium tuberculosis gain access to the cytosolic MHC class-I antigen-processing pathway. J. Immunol. 177, 437–442 (2006).

    Article  CAS  PubMed  Google Scholar 

  92. Tobian, A. A., Canaday, D. H., Boom, W. H. & Harding, C. V. Bacterial heat shock proteins promote CD91-dependent class I MHC cross-presentation of chaperoned peptide to CD8+ T cells by cytosolic mechanisms in dendritic cells versus vacuolar mechanisms in macrophages. J. Immunol. 172, 5277–5286 (2004).

    Article  CAS  PubMed  Google Scholar 

  93. Grotzke, J. E., Siler, A. C., Lewinsohn, D. A. & Lewinsohn, D. M. Secreted immunodominant Mycobacterium tuberculosis antigens are processed by the cytosolic pathway. J. Immunol. 185, 4336–4343 (2010).

    Article  CAS  PubMed  Google Scholar 

  94. Grotzke, J. E. et al. The Mycobacterium tuberculosis phagosome is a HLA-I processing competent organelle. PLoS Pathog. 5, e1000374 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  95. Mazzaccaro, R. J. et al. Major histocompatibility class I presentation of soluble antigen facilitated by Mycobacterium tuberculosis infection. Proc. Natl Acad. Sci. USA 93, 11786–11791 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Mott, D. et al. High bacillary burden and the ESX-1 type VII secretion system promote MHC class I presentation by Mycobacterium tuberculosis-infected macrophages to CD8 T cells. J. Immunol. 210, 1531–1542 (2023).

    Article  CAS  PubMed  Google Scholar 

  97. Schaible, U. E. et al. Apoptosis facilitates antigen presentation to T lymphocytes through MHC-I and CD1 in tuberculosis. Nat. Med. 9, 1039–1046 (2003).

    Article  CAS  PubMed  Google Scholar 

  98. Tzelepis, F. et al. Annexin1 regulates DC efferocytosis and cross-presentation during Mycobacterium tuberculosis infection. J. Clin. Invest. 125, 752–768 (2015).

    Article  PubMed  Google Scholar 

  99. Smith, V. L., Cheng, Y., Bryant, B. R. & Schorey, J. S. Exosomes function in antigen presentation during an in vivo Mycobacterium tuberculosis infection. Sci. Rep. 7, 43578 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  100. Baptista, A. P. et al. The chemoattractant receptor Ebi2 drives intranodal naive CD4+ T cell peripheralization to promote effective adaptive immunity. Immunity 50, 1188–1201 e1186 (2019).

    Article  CAS  PubMed  Google Scholar 

  101. Kapoor, V. N. et al. Gremlin 1+ fibroblastic niche maintains dendritic cell homeostasis in lymphoid tissues. Nat. Immunol. 22, 571–585 (2021).

    Article  CAS  PubMed  Google Scholar 

  102. Leal, J. M. et al. Innate cell microenvironments in lymph nodes shape the generation of T cell responses during type I inflammation. Sci. Immunol. 6, eabb9435 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Daniel, L. et al. Stromal structure remodeling by B lymphocytes limits T cell activation in lymph nodes of Mycobacterium tuberculosis-infected mice. J. Clin. Invest. 132, e157873 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Musvosvi, M. et al. T cell receptor repertoires associated with control and disease progression following Mycobacterium tuberculosis infection. Nat. Med. 29, 258–269 (2023). Using both deep TCR sequencing and genome-wide antigen screen, the authors identified peptides targeted by T cell similarity groups enriched either in controllers or in progressors.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Chugh, S., Bahal, R. K., Dhiman, R. & Singh, R. Antigen identification strategies and preclinical evaluation models for advancing tuberculosis vaccine development. NPJ Vaccines 9, 57 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  106. Comas, I. et al. Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat. Genet. 42, 498–503 (2010). The hyperconservation of human T cell epitopes in Mtb suggests strong purifying selection, indicating that immune recognition may have a role in the persistence and evolutionary success of the pathogen.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Ogongo, P. et al. Rare variable M. tuberculosis antigens induce predominant Th17 responses in human infection. Preprint at bioRxiv https://doi.org/10.1101/2024.03.05.583634 (2024). Rare variable Mtb antigens preferentially induce IL-17-producing TH17 cells, suggesting their potential as vaccine targets to enhance protective immunity in individuals already exposed to TB.

  108. Lindestam Arlehamn, C. S., Lewinsohn, D., Sette, A. & Lewinsohn, D. Antigens for CD4 and CD8 T cells in tuberculosis. Cold Spring Harb. Perspect. Med. 4, a018465 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  109. Sakai, S. et al. CD4 T cell-derived IFN-gamma plays a minimal role in control of pulmonary Mycobacterium tuberculosis infection and must be actively repressed by PD-1 to prevent lethal disease. PLoS Pathog. 12, e1005667 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  110. Coppola, M. et al. New genome-wide algorithm identifies novel in-vivo expressed Mycobacterium Tuberculosis antigens inducing human T-cell responses with classical and unconventional cytokine profiles. Sci. Rep. 6, 37793 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Khader, S. A. et al. IL-23 and IL-17 in the establishment of protective pulmonary CD4+ T cell responses after vaccination and during Mycobacterium tuberculosis challenge. Nat. Immunol. 8, 369–377 (2007). Vaccination induces IL-17-producing CD4+ T cells that, upon Mtb infection, drive chemokine-mediated recruitment of IFNγ-producing CD4+ T cells to the lung, accelerating bacterial control and highlighting IL-23 as a key regulator of protective immunity.

    Article  CAS  PubMed  Google Scholar 

  112. Scriba, T. J. et al. Sequential inflammatory processes define human progression from M. tuberculosis infection to tuberculosis disease. PLoS Pathog. 13, e1006687 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  113. Moguche, A. O. et al. Antigen availability shapes T cell differentiation and function during tuberculosis. Cell Host Microbe 21, 695–706.e695 (2017). Effective Mtb vaccine design requires tailored strategies, as Ag85B-specific CD4+ T cells are limited by reduced antigen expression during persistent infection, and ESAT-6-specific T cells become functionally exhausted due to chronic stimulation, restricting their ability to control TB.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Coscolla, M. et al. M. tuberculosis T cell epitope analysis reveals paucity of antigenic variation and identifies rare variable TB antigens. Cell Host Microbe https://doi.org/10.1016/j.chom.2015.10.008 (2015).

  115. Coppola, M. et al. In-vivo expressed Mycobacterium tuberculosis antigens recognised in three mouse strains after infection and BCG vaccination. NPJ Vaccines 6, 81 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Nunes-Alves, C. et al. Human and murine clonal CD8+ T cell expansions arise during tuberculosis because of TCR selection. PLoS Pathog. 11, e1004849 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  117. Carpenter, S. M., Yang, J. D., Lee, J., Barreira-Silva, P. & Behar, S. M. Vaccine-elicited memory CD4+ T cell expansion is impaired in the lungs during tuberculosis. PLoS Pathog. 13, e1006704 (2017). The transient protection of TB vaccines is driven by the inability of memory CD4+ T cells to sustain expansion in the lung, as their initial proliferation and recruitment curb early Mtb growth but fail to maintain long-term immunity.

    Article  PubMed  PubMed Central  Google Scholar 

  118. Bhattacharyya, N. D. et al. TCR affinity controls the dynamics but not the functional specification of the antimycobacterial CD4+ T cell response. J. Immunol. 206, 2875–2887 (2021).

    Article  CAS  PubMed  Google Scholar 

  119. Ogongo, P. & Ernst, J. D. Finding antigens for TB vaccines: the good, the bad and the useless. Nat. Med. 29, 35–36 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Alon, R. et al. Leukocyte trafficking to the lungs and beyond: lessons from influenza for COVID-19. Nat. Rev. Immunol. 21, 49–64 (2021).

    Article  CAS  PubMed  Google Scholar 

  121. Hoft, S. G. et al. The rate of CD4 T cell entry into the lungs during Mycobacterium tuberculosis infection is determined by partial and opposing effects of multiple chemokine receptors. Infect. Immun. 87, e00841–18 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  122. Santiago-Carvalho, I. et al. T cell-specific P2RX7 favors lung parenchymal CD4+ T cell accumulation in response to severe lung infections. Cell Rep. 42, 113448 (2023). Extracellular ATP released by damaged cells is sensed by CD4+ T cells expressing P2RX7 receptor and critical to induce tissue CD4+ T cell accumulation through upregulation of the chemokine receptor CXCR3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Egen, J. G. et al. Intravital imaging reveals limited antigen presentation and T cell effector function in mycobacterial granulomas. Immunity 34, 807–819 (2011). Intravital imaging in BCG-infected liver show that few T cells are arrested within the granuloma and stably interact with APC, indicating that limited antigen presentation in mycobacterial granulomas leads to a muted T cell response, using only a fraction of the host’s potential effector capacity during chronic infection.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Stark, R. et al. TRM maintenance is regulated by tissue damage via P2RX7. Sci. Immunol. 3, eaau1022 (2018). Extracellular ATP and NAD+ enhanced TRM cell death via P2RX7, whereas TCR activation downregulated P2RX7, making TRM cells resistant to NAD-induced death. Tissue damage regulates TRM cells through P2RX7, favouring antigen-specific TRM cell persistence.

    Article  PubMed  Google Scholar 

  125. Gern, B. H. et al. TGFβ restricts expansion, survival, and function of T cells within the tuberculous granuloma. Cell Host Microbe 29, 594–606.e596 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Kang, T. G. et al. Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx. Nat. Commun. 13, 3155 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Potter, E. L. et al. Measurement of leukocyte trafficking kinetics in macaques by serial intravascular staining. Sci. Transl. Med. 13, eabb4582 (2021).

    Article  CAS  PubMed  Google Scholar 

  128. Takamura, S. et al. Specific niches for lung-resident memory CD8+ T cells at the site of tissue regeneration enable CD69-independent maintenance. J. Exp. Med. 213, 3057–3073 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Asrir, A. et al. Tumor-associated high endothelial venules mediate lymphocyte entry into tumors and predict response to PD-1 plus CTLA-4 combination immunotherapy. Cancer Cell 40, 318–334.e319 (2022). Tumour-associated HEVs serve as key entry points for lymphocytes into tumours, enhancing immune checkpoint blockade efficacy by promoting infiltration of stem-like CD8+ T cells, with their presence correlating with better responses and survival in patients with metastatic melanoma.

    Article  CAS  PubMed  Google Scholar 

  130. Blanchard, L. & Girard, J. P. High endothelial venules (HEVs) in immunity, inflammation and cancer. Angiogenesis 24, 719–753 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Carow, B. et al. Immune mapping of human tuberculosis and sarcoidosis lung granulomas. Front. Immunol. 14, 1332733 (2023).

    Article  CAS  PubMed  Google Scholar 

  132. Kahnert, A. et al. Mycobacterium tuberculosis triggers formation of lymphoid structure in murine lungs. J. Infect. Dis. 195, 46–54 (2007).

    Article  CAS  PubMed  Google Scholar 

  133. Pally, D. & Naba, A. Extracellular matrix dynamics: a key regulator of cell migration across length-scales and systems. Curr. Opin. Cell Biol. 86, 102309 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Overstreet, M. G. et al. Inflammation-induced interstitial migration of effector CD4+ T cells is dependent on integrin alphaV. Nat. Immunol. 14, 949–958 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Wilson, E. H. et al. Behavior of parasite-specific effector CD8+ T cells in the brain and visualization of a kinesis-associated system of reticular fibers. Immunity 30, 300–311 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Salmon, H. et al. Matrix architecture defines the preferential localization and migration of T cells into the stroma of human lung tumors. J. Clin. Invest. 122, 899–910 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Al Shammari, B. et al. The extracellular matrix regulates granuloma necrosis in tuberculosis. J. Infect. Dis. 212, 463–473 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Bromley, S. K., Peterson, D. A., Gunn, M. D. & Dustin, M. L. Cutting edge: hierarchy of chemokine receptor and TCR signals regulating T cell migration and proliferation. J. Immunol. 165, 15–19 (2000). This study provided insight into the relationships between chemokine receptor and TCR signalling in determining trafficking and positioning of T cells in immunity.

    Article  CAS  PubMed  Google Scholar 

  139. Li, J. et al. Mycobacterium tuberculosis-specific memory T cells in bronchoalveolar lavage of patients with pulmonary tuberculosis. Cytokine 171, 156374 (2023).

    Article  CAS  PubMed  Google Scholar 

  140. Yang, Q. et al. Cutting edge: characterization of human tissue-resident memory T cells at different infection sites in patients with tuberculosis. J. Immunol. 204, 2331–2336 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Morrison, H. & McShane, H. Local pulmonary immunological biomarkers in tuberculosis. Front. Immunol. 12, 640916 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Hunter, R. L. Tuberculosis as a three-act play: a new paradigm for the pathogenesis of pulmonary tuberculosis. Tuberculosis 97, 8–17 (2016).

    Article  PubMed  Google Scholar 

  143. Jameson, S. C. The naming of memory T-cell subsets. Cold Spring Harb. Perspect. Biol. 13, a037788 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Christo, S. N., Park, S. L., Mueller, S. N. & Mackay, L. K. The multifaceted role of tissue-resident memory T cells. Annu. Rev. Immunol. 42, 317–345 (2024).

    Article  CAS  PubMed  Google Scholar 

  145. Mueller, S. N., Gebhardt, T., Carbone, F. R. & Heath, W. R. Memory T cell subsets, migration patterns, and tissue residence. Annu. Rev. Immunol. 31, 137–161 (2013).

    Article  CAS  PubMed  Google Scholar 

  146. Amezcua Vesely, M. C. et al. Effector TH17 cells give rise to long-lived TRM cells that are essential for an immediate response against bacterial infection. Cell 178, 1176–1188.e1115 (2019).

    Article  CAS  PubMed  Google Scholar 

  147. Haddadi, S. et al. Expression and role of VLA-1 in resident memory CD8 T cell responses to respiratory mucosal viral-vectored immunization against tuberculosis. Sci. Rep. 7, 9525 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  148. Perdomo, C. et al. Mucosal BCG vaccination induces protective lung-resident memory T cell populations against tuberculosis. MBio 7, e01686–16 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Hu, Z. et al. Sendai virus mucosal vaccination establishes lung-resident memory CD8 T cell immunity and boosts BCG-primed protection against TB in mice. Mol. Ther. 25, 1222–1233 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Dijkman, K. et al. Pulmonary MTBVAC vaccination induces immune signatures previously correlated with prevention of tuberculosis infection. Cell Rep. Med. 2, 100187 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Palendira, U., Bean, A. G., Feng, C. G. & Britton, W. J. Lymphocyte recruitment and protective efficacy against pulmonary mycobacterial infection are independent of the route of prior Mycobacterium bovis BCG immunization. Infect. Immun. 70, 1410–1416 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Ganchua, S. K. et al. Antibiotic treatment modestly reduces protection against Mycobacterium tuberculosis reinfection in macaques. Infect. Immun. 92, e0053523 (2024).

    Article  PubMed  Google Scholar 

  153. Stolley, J. M. et al. Depleting CD103+ resident memory T cells in vivo reveals immunostimulatory functions in oral mucosa. J. Exp. Med. 220, e20221853 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Behr, F. M. et al. Tissue-resident memory CD8+ T cells shape local and systemic secondary T cell responses. Nat. Immunol. 21, 1070–1081 (2020).

    Article  CAS  PubMed  Google Scholar 

  155. Florido, M. et al. Pulmonary immunization with a recombinant influenza A virus vaccine induces lung-resident CD4+ memory T cells that are associated with protection against tuberculosis. Mucosal Immunol. 11, 1743–1752 (2018).

    Article  CAS  PubMed  Google Scholar 

  156. Turner, D. L. et al. Lung niches for the generation and maintenance of tissue-resident memory T cells. Mucosal Immunol. 7, 501–510 (2014).

    Article  CAS  PubMed  Google Scholar 

  157. Ogongo, P. et al. Tissue-resident-like CD4+ T cells secreting IL-17 control Mycobacterium tuberculosis in the human lung. J. Clin. Invest. 131, e142014 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  158. Alexandrov, T., Saez-Rodriguez, J. & Saka, S. K. Enablers and challenges of spatial omics, a melting pot of technologies. Mol. Syst. Biol. 19, e10571 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Breart, B., Lemaitre, F., Celli, S. & Bousso, P. Two-photon imaging of intratumoral CD8+ T cell cytotoxic activity during adoptive T cell therapy in mice. J. Clin. Invest. 118, 1390–1397 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Filipe-Santos, O. et al. A dynamic map of antigen recognition by CD4 T cells at the site of Leishmania major infection. Cell Host Microbe 6, 23–33 (2009).

    Article  CAS  PubMed  Google Scholar 

  161. Ashouri, J. F. & Weiss, A. Endogenous Nur77 is a specific indicator of antigen receptor signaling in human T and B cells. J. Immunol. 198, 657–668 (2017).

    Article  CAS  PubMed  Google Scholar 

  162. Moran, A. E. et al. T cell receptor signal strength in Treg and iNKT cell development demonstrated by a novel fluorescent reporter mouse. J. Exp. Med. 208, 1279–1289 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Formaglio, P. et al. Nitric oxide controls proliferation of Leishmania major by inhibiting the recruitment of permissive host cells. Immunity 54, 2724–2739 e2710 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  164. Halle, S. et al. In vivo killing capacity of cytotoxic T cells is limited and involves dynamic interactions and T cell cooperativity. Immunity 44, 233–245 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  165. Looney, M. R. & Headley, M. B. Live imaging of the pulmonary immune environment. Cell Immunol. 350, 103862 (2020). The review summarizes how advances in intravital microscopy have enhanced our understanding of lung function and immunity in steady state and diseases by visualizing immune dynamics in real-time.

    Article  CAS  PubMed  Google Scholar 

  166. Ueki, H., Wang, I. H., Zhao, D., Gunzer, M. & Kawaoka, Y. Multicolor two-photon imaging of in vivo cellular pathophysiology upon influenza virus infection using the two-photon IMPRESS. Nat. Protoc. 15, 1041–1065 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. Barlerin, D. et al. Biosafety level 3 setup for multiphoton microscopy in vivo. Sci. Rep. 7, 571 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Gazit, R. et al. Lethal influenza infection in the absence of the natural killer cell receptor gene Ncr1. Nat. Immunol. 7, 517–523 (2006).

    Article  CAS  PubMed  Google Scholar 

  169. Ovchinnikov, D. A. et al. Expression of Gal4-dependent transgenes in cells of the mononuclear phagocyte system labeled with enhanced cyan fluorescent protein using Csf1r-Gal4VP16/UAS-ECFP double-transgenic mice. J. Leukoc. Biol. 83, 430–433 (2008).

    Article  CAS  PubMed  Google Scholar 

  170. Lindquist, R. L. et al. Visualizing dendritic cell networks in vivo. Nat. Immunol. 5, 1243–1250 (2004).

    Article  CAS  PubMed  Google Scholar 

  171. Boulch, M. et al. A cross-talk between CAR T cell subsets and the tumor microenvironment is essential for sustained cytotoxic activity. Sci. Immunol. 6, eabd4344 (2021).

    Article  CAS  PubMed  Google Scholar 

  172. Boulch, M., Grandjean, C. L., Cazaux, M. & Bousso, P. Tumor immunosurveillance and immunotherapies: a fresh look from intravital imaging. Trends Immunol. 40, 1022–1034 (2019).

    Article  CAS  PubMed  Google Scholar 

  173. Grandjean, C. L., Garcia, Z., Lemaitre, F., Breart, B. & Bousso, P. Imaging the mechanisms of anti-CD20 therapy in vivo uncovers spatiotemporal bottlenecks in antibody-dependent phagocytosis. Sci. Adv. 7, eabd6167 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  174. Wu, J. et al. A highly polarized TH2 bladder response to infection promotes epithelial repair at the expense of preventing new infections. Nat. Immunol. 21, 671–683 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. Hoekstra, M. E., Dijkgraaf, F. E., Schumacher, T. N. & Rohr, J. C. Assessing T lymphocyte function and differentiation by genetically encoded reporter systems. Trends Immunol. 36, 392–400 (2015).

    Article  CAS  PubMed  Google Scholar 

  176. Chitirala, P. et al. Studying the biology of cytotoxic T lymphocytes in vivo with a fluorescent granzyme B-mTFP knock-in mouse. eLife 9, e58065 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Vorobjev, I. A. & Barteneva, N. S. Multi-parametric imaging of cell heterogeneity in apoptosis analysis. Methods 112, 105–123 (2017).

    Article  CAS  PubMed  Google Scholar 

  178. Fukumura, D., Duda, D. G., Munn, L. L. & Jain, R. K. Tumor microvasculature and microenvironment: novel insights through intravital imaging in pre-clinical models. Microcirculation 17, 206–225 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  179. McCarthy, C. E., White, J. M., Viola, N. T. & Gibson, H. M. In vivo imaging technologies to monitor the immune system. Front. Immunol. 11, 1067 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. MacGilvary, N. J. & Tan, S. Fluorescent Mycobacterium tuberculosis reporters: illuminating host-pathogen interactions. Pathog. Dis. 76, fty017 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  181. Huang, L., Nazarova, E. V., Tan, S., Liu, Y. & Russell, D. G. Growth of Mycobacterium tuberculosis in vivo segregates with host macrophage metabolism and ontogeny. J. Exp. Med. https://doi.org/10.1084/jem.20172020 (2018).

  182. Tan, S., Sukumar, N., Abramovitch, R. B., Parish, T. & Russell, D. G. Mycobacterium tuberculosis responds to chloride and pH as synergistic cues to the immune status of its host cell. PLoS Pathog. 9, e1003282 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  183. Liu, Z. et al. Detecting tumor antigen-specific T cells via interaction-dependent fucosyl-biotinylation. Cell 183, 1117–1133.e19 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  184. Qiu, S. et al. Use of intercellular proximity labeling to quantify and decipher cell-cell interactions directed by diversified molecular pairs. Sci. Adv. 8, eadd2337 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  185. Pasqual, G. et al. Monitoring T cell-dendritic cell interactions in vivo by intercellular enzymatic labelling. Nature 553, 496–500 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. Nakandakari-Higa, S. et al. Universal recording of immune cell interactions in vivo. Nature 627, 399–406 (2024). A new genetically encoded method for proximity labelling to identify cell–cell interactions in vivo, such as T cell–APC interactions.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  187. Kiepiela, P. et al. CD8+ T-cell responses to different HIV proteins have discordant associations with viral load. Nat. Med. 13, 46–53 (2007).

    Article  CAS  PubMed  Google Scholar 

  188. Ranasinghe, S. et al. HIV-specific CD4 T cell responses to different viral proteins have discordant associations with viral load and clinical outcome. J. Virol. 86, 277–283 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Coppola, M. & Ottenhoff, T. H. Genome wide approaches discover novel Mycobacterium tuberculosis antigens as correlates of infection, disease, immunity and targets for vaccination. Semin. Immunol. 39, 88–101 (2018).

    Article  CAS  PubMed  Google Scholar 

  190. Nair, S. K. et al. High-throughput identification and dendritic cell-based functional validation of MHC class I-restricted Mycobacterium tuberculosis epitopes. Sci. Rep. 4, 4632 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  191. Lichti, C. F., Vigneron, N., Clauser, K. R., Van den Eynde, B. J. & Bassani-Sternberg, M. Navigating critical challenges associated with immunopeptidomics-based detection of proteasomal spliced peptide candidates. Cancer Immunol. Res. 10, 275–284 (2022).

    Article  CAS  PubMed  Google Scholar 

  192. Gulden, P. H. et al. A listeria monocytogenes pentapeptide is presented to cytolytic T lymphocytes by the H2-M3 MHC class Ib molecule. Immunity 5, 73–79 (1996).

    Article  CAS  PubMed  Google Scholar 

  193. Purcell, A. W., Ramarathinam, S. H. & Ternette, N. Mass spectrometry-based identification of MHC-bound peptides for immunopeptidomics. Nat. Protoc. 14, 1687–1707 (2019).

    Article  CAS  PubMed  Google Scholar 

  194. Shao, W. et al. The SysteMHC atlas project. Nucleic Acids Res. 46, D1237–D1247 (2018).

    Article  CAS  PubMed  Google Scholar 

  195. Bettencourt, P. et al. Identification of antigens presented by MHC for vaccines against tuberculosis. NPJ Vaccines 5, 2 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  196. Leddy, O., White, F. M. & Bryson, B. D. Immunopeptidomics reveals determinants of Mycobacterium tuberculosis antigen presentation on MHC class I. eLife 12, e84070 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Cayabyab, M. J., Qin, L., Kashino, S. S., Izzo, A. & Campos-Neto, A. An unbiased peptide-wide discovery approach to select Mycobacterium tuberculosis antigens that target CD8+ T cell response during infection. Vaccine 31, 4834–4840 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  198. Baert, L. et al. Induced pluripotent stem cell-derived human macrophages as an infection model for Leishmania donovani. PLoS Negl. Trop. Dis. 18, e0011559 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  199. Higaki, K. et al. Generation of HIV-resistant macrophages from IPSCs by using transcriptional gene silencing and promoter-targeted RNA. Mol. Ther. Nucleic Acids 12, 793–804 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  200. Hong, D. et al. Human-induced pluripotent stem cell-derived macrophages and their immunological function in response to tuberculosis infection. Stem Cell Res. Ther. 9, 49 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  201. Nielsen, M., Ternette, N. & Barra, C. The interdependence of machine learning and LC–MS approaches for an unbiased understanding of the cellular immunopeptidome. Expert. Rev. Proteom. 19, 77–88 (2022).

    Article  CAS  Google Scholar 

  202. Huang, S. et al. CD1 lipidomes reveal lipid-binding motifs and size-based antigen-display mechanisms. Cell 186, 4583–4596 e4513 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  203. Beckman, E. M. et al. Recognition of a lipid antigen by CD1-restricted αβ+ T cells. Nature 372, 691–694 (1994).

    Article  CAS  PubMed  Google Scholar 

  204. Moody, D. B. et al. CD1c-mediated T-cell recognition of isoprenoid glycolipids in Mycobacterium tuberculosis infection. Nature 404, 884–888 (2000).

    Article  CAS  PubMed  Google Scholar 

  205. Huang, H., Wang, C., Rubelt, F., Scriba, T. J. & Davis, M. M. Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening. Nat. Biotechnol. 38, 1194–1202 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  207. Mead, H. L. et al. Integrated, high-dimensional analysis of CD4 T cell epitope specificities and phenotypes reveals unexpected diversity in the response to Mycobacterium tuberculosis. Preprint at bioRxiv https://doi.org/10.1101/2024.11.05.622086 (2024).

  208. Ogongo, P. et al. Differential skewing of donor-unrestricted and γδ T cell repertoires in tuberculosis-infected human lungs. J. Clin. Investig. 130, 214–230 (2020).

    Article  CAS  PubMed  Google Scholar 

  209. Kramnik, I., Dietrich, W. F., Demant, P. & Bloom, B. R. Genetic control of resistance to experimental infection with virulent Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA 97, 8560–8565 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  210. Churchill, G. A. et al. The collaborative cross, a community resource for the genetic analysis of complex traits. Nat. Genet. 36, 1133–1137 (2004).

    Article  CAS  PubMed  Google Scholar 

  211. Churchill, G. A., Gatti, D. M., Munger, S. C. & Svenson, K. L. The diversity outbred mouse population. Mamm. Genome 23, 713–718 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  212. Niazi, M. K. et al. Lung necrosis and neutrophils reflect common pathways of susceptibility to Mycobacterium tuberculosis in genetically diverse, immune-competent mice. Dis. Model. Mech. 8, 1141–1153 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  213. Smith, C. M. et al. Host–pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice. eLife 11, e74419 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  214. Lai, R. et al. Host genetic background is a barrier to broadly effective vaccine-mediated protection against tuberculosis. J. Clin. Invest. 133, e167762 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  215. Wu, R., Velickovic, M. & Burnum-Johnson, K. E. From single cell to spatial multi-omics: unveiling molecular mechanisms in dynamic and heterogeneous systems. Curr. Opin. Biotechnol. 89, 103174 (2024).

    Article  CAS  PubMed  Google Scholar 

  216. Larenas-Munoz, F. et al. Proteomic analysis of granulomas from cattle and pigs naturally infected with Mycobacterium tuberculosis complex by MALDI imaging. Front. Immunol. 15, 1369278 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  217. Greco, F. et al. Lipids associated with atherosclerotic plaque instability revealed by mass spectrometry imaging of human carotid arteries. Atherosclerosis 397, 118555 (2024).

    Article  CAS  PubMed  Google Scholar 

  218. Shariatgorji, R. et al. Spatial visualization of comprehensive brain neurotransmitter systems and neuroactive substances by selective in situ chemical derivatization mass spectrometry imaging. Nat. Protoc. 16, 3298–3321 (2021).

    Article  CAS  PubMed  Google Scholar 

  219. Rajbhandari, P., Neelakantan, T. V., Hosny, N. & Stockwell, B. R. Spatial pharmacology using mass spectrometry imaging. Trends Pharmacol. Sci. 45, 67–80 (2024).

    Article  CAS  PubMed  Google Scholar 

  220. Blanc, L. et al. High-resolution mapping of fluoroquinolones in TB rabbit lesions reveals specific distribution in immune cell types. eLife 7, e41115 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  221. Moore, M. J. et al. Humanization of T cell-mediated immunity in mice. Sci. Immunol. 6, eabj4026 (2021).

    Article  CAS  PubMed  Google Scholar 

  222. Patel, S., Liu, W., K, R., McCormick, C. & Fan, Y. Engineering immune organoids to regenerate host immune system. Curr. Opin. Genet. Dev. 89, 102276 (2024).

    Article  CAS  PubMed  Google Scholar 

  223. Wagar, L. E. et al. Modeling human adaptive immune responses with tonsil organoids. Nat. Med. 27, 125–135 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  224. Ramachandra, L., Noss, E., Boom, W. H. & Harding, C. V. Processing of Mycobacterium tuberculosis antigen 85B involves intraphagosomal formation of peptide-major histocompatibility complex II complexes and is inhibited by live bacilli that decrease phagosome maturation. J. Exp. Med. 194, 1421–1432 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  225. Mehra, A. et al. Mycobacterium tuberculosis type VII secreted effector EsxH targets host ESCRT to impair trafficking. PLoS Pathog. 9, e1003734 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  226. Portal-Celhay, C. et al. Mycobacterium tuberculosis EsxH inhibits ESCRT-dependent CD4+ T-cell activation. Nat. Microbiol. 2, 16232 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  227. Madan-Lala, R. et al. Mycobacterium tuberculosis impairs dendritic cell functions through the serine hydrolase Hip1. J. Immunol. 192, 4263–4272 (2014).

    Article  CAS  PubMed  Google Scholar 

  228. Dolasia, K., Nazar, F. & Mukhopadhyay, S. Mycobacterium tuberculosis PPE18 protein inhibits MHC class II antigen presentation and B cell response in mice. Eur. J. Immunol. 51, 603–619 (2021).

    Article  CAS  PubMed  Google Scholar 

  229. Saini, N. K. et al. Suppression of autophagy and antigen presentation by Mycobacterium tuberculosis PE_PGRS47. Nat. Microbiol. 1, 16133 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  230. Fulton, S. A. et al. Inhibition of major histocompatibility complex II expression and antigen processing in murine alveolar macrophages by Mycobacterium bovis BCG and the 19-kilodalton mycobacterial lipoprotein. Infect. Immun. 72, 2101–2110 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  231. Gehring, A. J. et al. The Mycobacterium tuberculosis 19-kilodalton lipoprotein inhibits gamma interferon-regulated HLA-DR and Fc gamma R1 on human macrophages through toll-like receptor 2. Infect. Immun. 71, 4487–4497 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  232. Pai, R. K., Convery, M., Hamilton, T. A., Boom, W. H. & Harding, C. V. Inhibition of IFN-gamma-induced class II transactivator expression by a 19-kDa lipoprotein from Mycobacterium tuberculosis: a potential mechanism for immune evasion. J. Immunol. 171, 175–184 (2003).

    Article  CAS  PubMed  Google Scholar 

  233. Su, H. et al. Recombinant lipoprotein Rv1016c derived from Mycobacterium tuberculosis is a TLR-2 ligand that induces macrophages apoptosis and inhibits MHC II antigen processing. Front. Cell Infect. Microbiol. 6, 147 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  234. Pecora, N. D., Gehring, A. J., Canaday, D. H., Boom, W. H. & Harding, C. V. Mycobacterium tuberculosis LprA is a lipoprotein agonist of TLR2 that regulates innate immunity and APC function. J. Immunol. 177, 422–429 (2006).

    Article  CAS  PubMed  Google Scholar 

  235. Gehring, A. J., Dobos, K. M., Belisle, J. T., Harding, C. V. & Boom, W. H. Mycobacterium tuberculosis LprG (Rv1411c): a novel TLR-2 ligand that inhibits human macrophage class II MHC antigen processing. J. Immunol. 173, 2660–2668 (2004).

    Article  CAS  PubMed  Google Scholar 

  236. Huber, A. et al. Mycobacterial cord factor reprograms the macrophage response to IFN-gamma towards enhanced inflammation yet impaired antigen presentation and expression of GBP1. J. Immunol. 205, 1580–1592 (2020).

    Article  CAS  PubMed  Google Scholar 

  237. Srivastava, S., Grace, P. S. & Ernst, J. D. Antigen export reduces antigen presentation and limits T cell control of M. tuberculosis. Cell Host Microbe 19, 44–54 (2016).Mtb evades CD4+ T cell immunity by exporting antigens from infected DCs, diverting them from the antigen presentation pathway, a process dependent on kinesin-2, whose depletion enhances T cell activation and intracellular bacterial control.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  238. Grace, P. S. & Ernst, J. D. Suboptimal antigen presentation contributes to virulence of Mycobacterium tuberculosis in vivo. J. Immunol. 196, 357–364 (2016).

    Article  CAS  PubMed  Google Scholar 

  239. Sreejit, G. et al. The ESAT-6 protein of Mycobacterium tuberculosis interacts with beta-2-microglobulin (β2M) affecting antigen presentation function of macrophage. PLoS Pathog. 10, e1004446 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  240. Velmurugan, K. et al. Mycobacterium tuberculosis nuoG is a virulence gene that inhibits apoptosis of infected host cells. PLoS Pathog. 3, e110 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  241. Winau, F. et al. Apoptotic vesicles crossprime CD8 T cells and protect against tuberculosis. Immunity 24, 105–117 (2006).

    Article  CAS  PubMed  Google Scholar 

  242. Singh, B. et al. Inhibition of indoleamine dioxygenase leads to better control of tuberculosis adjunctive to chemotherapy. JCI Insight 8, e163101 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  243. Barber, D. L., Mayer-Barber, K. D., Feng, C. G., Sharpe, A. H. & Sher, A. CD4 T cells promote rather than control tuberculosis in the absence of PD-1-mediated inhibition. J. Immunol. 186, 1598–1607 (2011).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This study was supported by the French National Research Agency: JCJC (grant ANR-20-CE14-0045-01) and TBVAC Horizon Europe programme (E.L.); Agence Nationale de le Recherche sur le SIDA — Maladies Infectieuses Emergentes KILL-TB ECTZ206385 (D.H.); TBVAC-HORIZON (EU), Immunotherapies for Tuberculosis and Other Mycobacterial Diseases (EU) and EXPLORE-TB (Fondation Bettencourt Schueller) (O.N.); National Institutes of Health, National Institute of Allergy and Infectious Diseases (grants R01AI172905 to S.M.B., U01AI166309, R21AI156407 and R21AI176234 to J.D.E. and contracts 75N93019C00071 to S.M.B. and 75N93024C0054 to J.D.E.).

Author information

Author notes

  1. These authors contributed equally: Emma Lefrançais, Denis Hudrisier.

  2. These authors jointly supervised this work: Olivier Neyrolles, Samuel M. Behar, Joel D. Ernst.

Authors and Affiliations

  1. Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France

    Emma Lefrançais, Denis Hudrisier & Olivier Neyrolles

  2. Department of Microbiology, University of Massachusetts Chan Medical School, Worcester, MA, USA

    Samuel M. Behar

  3. Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA

    Joel D. Ernst

Authors
  1. Emma Lefrançais
    View author publications

    Search author on:PubMed Google Scholar

  2. Denis Hudrisier
    View author publications

    Search author on:PubMed Google Scholar

  3. Olivier Neyrolles
    View author publications

    Search author on:PubMed Google Scholar

  4. Samuel M. Behar
    View author publications

    Search author on:PubMed Google Scholar

  5. Joel D. Ernst
    View author publications

    Search author on:PubMed Google Scholar

Contributions

All authors researched data for the article. All authors contributed substantially to discussion of the content. All authors wrote the article. All authors reviewed and/or edited the manuscript before submission.

Corresponding author

Correspondence to Joel D. Ernst.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Reviews Immunology thanks Stefan Kaufmann, Thomas Scriba, Cecilia Lindestam Arlehamn and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lefrançais, E., Hudrisier, D., Neyrolles, O. et al. Finding and filling the knowledge gaps in mechanisms of T cell-mediated TB immunity to inform vaccine design. Nat Rev Immunol (2025). https://doi.org/10.1038/s41577-025-01192-z

Download citation

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1038/s41577-025-01192-z

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology