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.

  • Article
  • Published:

Antigen-presenting innate lymphoid cells induced by BCG vaccination promote a respiratory antiviral immune response through the skin‒lung axis

Abstract

The route of vaccine administration is associated with various immune outcomes, and the relationship between the route of administration and broad protection against heterologous pathogens remains unclear. Here, we found that subcutaneous vaccination with Bacillus Calmette-Guérin (BCG) promotes respiratory influenza clearance and T-cell responses. Group 1 innate lymphoid cells (ILC1s) express MHCII molecules and engage in antigen processing and presentation after BCG vaccination. During influenza virus infection, ILC1s in the lungs of BCG-vaccinated mice can present influenza virus antigens and prime Th1 cells. After subcutaneous vaccination with BCG, MHCII+ ILC1s migrate from the skin to the lungs and play an antigen-presenting role in influenza infection. Both the BCG and the BCG component lipomannan can induce MHCII expression and skin-to-lung migration of ILC1s via TLR2 signaling. Our study revealed an important regulatory mechanism by which subcutaneous vaccination with BCG promotes respiratory antiviral immune responses via the skin‒lung axis.

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

Access options

Buy this article

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Data availability

All data, including raw sequencing data, have been deposited at the National Genomics Data Center under accession number: CRA022270 (https://ngdc.cncb.ac.cn/).

References

  1. Lange C, Aaby P, Behr MA, Donald PR, Kaufmann S, Netea MG, et al. 100 years of Mycobacterium bovis bacille Calmette-Guerin. Lancet Infect Dis. 2022;22:e2–e12.

    Article  CAS  PubMed  Google Scholar 

  2. Prentice S, Nassanga B, Webb EL, Akello F, Kiwudhu F, Akurut H, et al. BCG-induced nonspecific effects on heterologous infectious disease in Ugandan neonates: an investigator-blind randomized controlled trial. Lancet Infect Dis. 2021;21:993–1003.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Shann F. Nonspecific effects of vaccines and the reduction of mortality in children. Clin Ther. 2013;35:109–14.

    Article  PubMed  Google Scholar 

  4. Lenis AT, Lec PM, Chamie K, Mshs MD. Bladder cancer: a review. JAMA. 2020;324:1980–91.

    Article  CAS  PubMed  Google Scholar 

  5. O’Neill LAJ, Netea MG. BCG-induced trained immunity: can it offer protection against COVID-19? Nat Rev Immunol. 2020;20:335–7.

    Article  PubMed  PubMed Central  Google Scholar 

  6. Divangahi M, Aaby P, Khader SA, Barreiro LB, Bekkering S, Chavakis T, et al. Trained immunity, tolerance, priming and differentiation: distinct immunological processes. Nat Immunol. 2021;22:2–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Ziogas A, Netea MG. Trained immunity-related vaccines: innate immune memory and heterologous protection against infections. Trends Mol Med. 2022;28:497–512.

    Article  CAS  PubMed  Google Scholar 

  8. Ziogas A, Bruno M, van der Meel R, Mulder WJM, Netea MG. Trained immunity: target for prophylaxis and therapy. Cell Host Microbe. 2023;31:1776–91.

    Article  CAS  PubMed  Google Scholar 

  9. Kleinnijenhuis J, Quintin J, Preijers F, Joosten LA, Ifrim DC, Saeed S, et al. Bacille Calmette-Guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes. Proc Natl Acad Sci USA. 2012;109:17537–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Boraschi D, Tagliabue A. Harnessing the power of inflammation in immunoprevention and immunotherapy. The Innovation Life. 2023;1:100025.

    Article  Google Scholar 

  11. Arts R, Carvalho A, La Rocca C, Palma C, Rodrigues F, Silvestre R, et al. Immunometabolic pathways in BCG-induced trained immunity. Cell Rep. 2016;17:2562–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Kaufmann E, Sanz J, Dunn JL, Khan N, Mendonça LE, Pacis A, et al. BCG educates hematopoietic stem cells to generate protective innate immunity against tuberculosis. Cell. 2018;172:176–90.e119.

    Article  CAS  PubMed  Google Scholar 

  13. Shao F, Yu D, Xia PY, Wang S. Dynamic regulation of innate lymphoid cells in the mucosal immune system. Cellular & Molecular Immunology. 2021;18:1387–94.

    Article  CAS  Google Scholar 

  14. Hepworth MR, Fung TC, Masur SH, Kelsen JR, McConnell FM, Dubrot J, et al. Immune tolerance. Group 3 innate lymphoid cells mediate intestinal selection of commensal bacteria-specific CD4(+) T cells. Science. 2015;348:1031–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Lyu M, Suzuki H, Kang L, Gaspal F, Zhou W, Goc J, et al. ILC3s select microbiota-specific regulatory T cells to establish tolerance in the gut. Nature. 2022;610:744–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Grigg JB, Shanmugavadivu A, Regen T, Parkhurst CN, Ahmed A, Joseph AM, et al. Antigen-presenting innate lymphoid cells orchestrate neuroinflammation. Nature. 2021;600:707–12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Oliphant CJ, Hwang YY, Walker JA, Salimi M, Wong SH, Brewer JM, et al. MHCII-mediated dialog between group 2 innate lymphoid cells and CD4(+) T cells potentiates type 2 immunity and promotes parasitic helminth expulsion. Immunity. 2014;41:283–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Weizman OE, Adams NM, Schuster IS, Krishna C, Pritykin Y, Lau C, et al. ILC1 confer early host protection at initial sites of viral infection. Cell. 2017;171:795–808.e712.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Nabekura T, Riggan L, Hildreth AD, O’Sullivan TE, Shibuya A. Type 1 innate lymphoid cells protect mice from acute liver injury via interferon-gamma secretion for upregulating Bcl-xL expression in hepatocytes. Immunity. 2020;52:96–108.e109.

    Article  CAS  PubMed  Google Scholar 

  20. Kang A, Ye G, Singh R, Afkhami S, Bavananthasivam J, Luo X, et al. Subcutaneous BCG vaccination protects against streptococcal pneumonia by regulating innate immune responses in the lung. EMBO Mol Med. 2023;15:e17084.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Zhang, BZ, Shuai H, Gong HR, Hu JC, Yan B, Yuen TT, et al. Bacillus Calmette-Guerin-induced trained immunity protects against SARS-CoV-2 challenge in K18-hACE2 mice. JCI Insight. 2022;7:e157393.

  22. Darrah PA, Zeppa JJ, Maiello P, Hackney JA, Wadsworth MH, Hughes TK, et al. Prevention of tuberculosis in macaques after intravenous BCG immunization. Nature. 2020;577:95–102.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Larson EC, Ellis-Connell AL, Rodgers MA, Gubernat AK, Gleim JL, Moriarty RV, et al. Intravenous Bacille Calmette-Guerin vaccination protects simian immunodeficiency virus-infected macaques from tuberculosis. Nat Microbiol. 2023;8:2080–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Lobo N, Brooks NA, Zlotta AR, Cirillo JD, Boorjian S, Black PC, et al. 100 years of Bacillus Calmette-Guerin immunotherapy: from cattle to COVID-19. Nat Rev Urol. 2021;18:611–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Gao X, Liu C, Wang S. Mucosal immune responses in the lung during respiratory infection: the organization and regulation of iBALT structure. hLife. 2023;1:71–82.

    Article  Google Scholar 

  26. Ma T, Chen H, Liao YP, Li J, Wang X, Li L, et al. Pulmonary human immune responses in a humanized immune mouse model during influenza virus infection. The Innovation Life. 2023;1:315–23.

    Article  CAS  Google Scholar 

  27. Zhao M, Shao F, Liu Z, Ma J, Yu D, Zhang H, et al. Spatially resolved transcriptomics reveals distinct pulmonary immune responses during influenza virus and SARS-CoV-2 infections. Sci Bull. 2023;68:3137–41.

    Article  Google Scholar 

  28. Zhang X, Gao X, Liu Z, Shao F, Yu D, Zhao M, et al. Microbiota regulates the TET1-mediated DNA hydroxymethylation program in innate lymphoid cell differentiation. Nature Communications. 2024;15:4792.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Kalafati L, Kourtzelis I, Schulte-Schrepping J, Li X, Hatzioannou A, Grinenko T, et al. Innate immune training of granulopoiesis promotes anti-tumor activity. Cell. 2020;183:771–85.e712.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Mitroulis I, Ruppova K, Wang B, Chen LS, Grzybek M, Grinenko T, et al. Modulation of myelopoiesis progenitors is an integral component of trained immunity. Cell. 2018;172:147–61.e112.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Chen T, Ying L, Xiong L, Wang X, Lu P, Wang Y, et al. Understanding carbapenem-resistant hypervirulent Klebsiella pneumoniae: Key virulence factors and evolutionary convergence. hLife. 2024;2:611–24.

    Article  Google Scholar 

  32. Liu Q, Li W, Qian Y, Wang C, Xia P. AA467197 controls the hyperactivation of the NLRP3 inflammasome during infection. The Innovation Life. 2023;1:100012.

    Article  Google Scholar 

  33. Hepworth MR, Monticelli LA, Fung TC, Ziegler CG, Grunberg S, Sinha R, et al. Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria. Nature. 2013;498:113–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Zhao M, Shao F, Yu D, Zhang J, Liu Z, Ma J, et al. Maturation and specialization of group 2 innate lymphoid cells through the lung-gut axis. Nat Commun. 2022;13:7600.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Shand FH, Ueha S, Otsuji M, Koid SS, Shichino S, Tsukui T, et al. Tracking of intertissue migration reveals the origins of tumor-infiltrating monocytes. Proc Natl Acad Sci USA. 2014;111:7771–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Zhang S, Wan D, Zhu M, Wang G, Zhang X, Huang N, et al. CD11b + CD43 hi Ly6C lo splenocyte-derived macrophages exacerbate liver fibrosis via spleen-liver axis. Hepatology. 2023;77:1612–29.

    Article  PubMed  Google Scholar 

  37. Gilleron M, Nigou J, Nicolle D, Quesniaux V, Puzo G. The acylation state of mycobacterial lipomannans modulates innate immunity response through Toll-like receptor 2. Chem Biol. 2006;13:39–47.

    Article  CAS  PubMed  Google Scholar 

  38. Lin Y, Hu Z, Fu Y-X, Peng H. Mucosal vaccine development for respiratory viral infections. hLife. 2024;2:50–63.

    Article  Google Scholar 

  39. Islam SA, Luster AD. T-cell homing to epithelial barriers in allergic disease. Nat Med. 2012;18:705–15.

    Article  CAS  PubMed  Google Scholar 

  40. Yu D, Zhang JQ, Wang S. Trained immunity in the mucosal diseases. Wires Mech Dis. 2022;14:1543.

    Article  Google Scholar 

  41. Aaby P, Roth A, Ravn H, Napirna BM, Rodrigues A, Lisse IM, et al. Randomized trial of BCG vaccination at birth to low-birth-weight children: beneficial nonspecific effects in the neonatal period? J Infect Dis. 2011;204:245–52.

    Article  CAS  PubMed  Google Scholar 

  42. de Castro MJ, Pardo-Seco J, Martinon-Torres F. Nonspecific (heterologous) protection of neonatal BCG vaccination against hospitalization due to respiratory infection and sepsis. Clin Infect Dis. 2015;60:1611–9.

    Article  PubMed  Google Scholar 

  43. Chen J, Gao L, Wu X, Fan Y, Liu M, Peng L, et al. BCG-induced trained immunity: history, mechanisms and potential applications. J Transl Med. 2023;21:106.

    Article  PubMed  PubMed Central  Google Scholar 

  44. Arts R, Moorlag S, Novakovic B, Li Y, Wang SY, Oosting M, et al. BCG vaccination protects against experimental viral infection in humans through the induction of cytokines associated with trained immunity. Cell Host Microbe. 2018;23:89–100.e105.

    Article  CAS  PubMed  Google Scholar 

  45. Cirovic B, de Bree L, Groh L, Blok BA, Chan J, van der Velden W, et al. BCG vaccination in humans elicits trained immunity via the hematopoietic progenitor compartment. Cell Host Microbe. 2020;28:322–334 e325.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Moorlag S, Folkman L, Ter Horst R, Krausgruber T, Barreca D, Schuster LC, et al. Multiomics analysis of innate and adaptive responses to BCG vaccination reveals epigenetic cell states that predict trained immunity. Immunity. 2024;57:171–187 e114.

    Article  CAS  PubMed  Google Scholar 

  47. Pettenati C, Ingersoll MA. Mechanisms of BCG immunotherapy and its outlook for bladder cancer. Nat Rev Urol. 2018;15:615–25.

    Article  CAS  PubMed  Google Scholar 

  48. Soto JA, Gálvez N, Andrade CA, Ramírez MA, Riedel CA, Kalergis AM, et al. BCG vaccination induces cross-protective immunity against pathogenic microorganisms. Trends Immunol. 2022;43:322–35.

    Article  CAS  PubMed  Google Scholar 

  49. Kaufmann E, Khan N, Tran KA, Ulndreaj A, Pernet E, Fontes G, et al. BCG vaccination provides protection against IAV but not SARS-CoV-2. Cell Rep. 2022;38:110502.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Faustman DL, Lee A, Hostetter ER, Aristarkhova A, Ng NC, Shpilsky GF, et al. Multiple BCG vaccinations for the prevention of COVID-19 and other infectious diseases in type 1 diabetes. Cell Rep Med. 2022;3:100728.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Giamarellos-Bourboulis EJ, Tsilika M, Moorlag S, Antonakos N, Kotsaki A, Domínguez-Andrés J, et al. Activate: randomized clinical trial of BCG vaccination against infection in the elderly. Cell. 2020;183:315–23.e319.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Leentjens J, Kox M, Stokman R, Gerretsen J, Diavatopoulos DA, van Crevel R, et al. BCG vaccination enhances the immunogenicity of subsequent influenza vaccination in healthy volunteers: a randomized, placebo-controlled pilot study. J Infect Dis. 2015;212:1930–8.

    Article  CAS  PubMed  Google Scholar 

  53. Rivas, MN, Ebinger JE, Wu M, Sun N, Braun J, Sobhani K, et al. BCG vaccination history associates with decreased SARS-CoV-2 seroprevalence across a diverse cohort of health care workers. J Clin Invest. 2021;131:e145157.

  54. Lee A, Floyd K, Wu S, Fang Z, Tan TK, Froggatt HM, et al. BCG vaccination stimulates integrated organ immunity by feedback of the adaptive immune response to imprint prolonged innate antiviral resistance. Nat Immunol. 2024;25:41–53.

    Article  CAS  PubMed  Google Scholar 

  55. Xia P, Liu J, Wang S, Ye B, Du Y, Xiong Z, et al. WASH maintains NKp46(+) ILC3 cells by promoting AHR expression. Nat Commun. 2017;8:15685.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Bai, L, Vienne M, Tang L, Kerdiles Y, Etiennot M, Escalière B, et al. Liver type 1 innate lymphoid cells develop locally via an interferon-gamma-dependent loop. Science. 2021;371:eaba4177.

  57. Sparks IL, Kado T, Prithviraj M, Nijjer J, Yan J, Morita YS. Lipoarabinomannan mediates localized cell wall integrity during division in mycobacteria. Nature Communications. 2024;15:2191.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Graham DB, Luo C, O'Connell DJ, Lefkovith A, Brown EM, Yassour M, et al. Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes. Nat Med. 2018;24:1762–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Wan X, Vomund AN, Peterson OJ, Chervonsky AV, Lichti CF, Unanue ER. The MHC-II peptidome of pancreatic islets identifies key features of autoimmune peptides. Nat Immunol. 2020;21:455–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Anderson KG, Mayer-Barber K, Sung H, Beura L, James BR, Taylor JJ, et al. Intravascular staining for discrimination of vascular and tissue leukocytes. Nat Protoc. 2014;9:209–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank Prof. George F Gao (Institute of Microbiology, Chinese Academy of Sciences) for providing the influenza A/Puerto Rico/8/34 (H1N1, PR8) virus strain. We thank Prof. Cuihua Liu (Institute of Microbiology, Chinese Academy of Sciences) for providing Bacillus Calmette-Guérin (BCG). We thank Prof. Zongfang Li (Xi’an Jiaotong University, China) for providing KikGR mice. We thank Prof. Pengyan Xia and Qiannv Liu (Peking University, China) for their technical support. We thank Dr. Tong Zhao and Dr. Jingfang Liu (Institute of Microbiology, Chinese Academy of Sciences) for their technical support. We thank Prof. Changyong Tian (Technical Institute of Physics and Chemistry, Chinese Academy of Sciences) for providing the 405 nm laser. This work was supported by the National Key R&D Program of China (2022YFC2302900, 2021YFA1300202, 2023YFC2306204), the Beijing Natural Science Foundation (JQ24043), and the CAS Project for Young Scientists in Basic Research (YSBR-010). The cartoons in Figs. 1a, 3c, f, 4a, 5b, 5f and the supplementary information Fig. S7 were created with BioRender.com.

Author information

Authors and Affiliations

Contributions

DY performed the experiments and analyzed the data; XG, FS, ZL, AL, MZ, ZT, and YG performed the experiments; SW initiated the study and organized, designed, and wrote the paper.

Corresponding author

Correspondence to Shuo Wang.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

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

Supplementary information

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

Yu, D., Gao, X., Shao, F. et al. Antigen-presenting innate lymphoid cells induced by BCG vaccination promote a respiratory antiviral immune response through the skin‒lung axis. Cell Mol Immunol 22, 390–402 (2025). https://doi.org/10.1038/s41423-025-01267-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41423-025-01267-w

Keywords

This article is cited by

Search

Quick links