BCG Vaccination in Humans Elicits Trained Immunity via the Hematopoietic Progenitor Compartment
Branko Cirovic, L Charlotte J de Bree, Laszlo Groh, Bas A Blok, Joyce Chan, Walter J F M van der Velden, M E J Bremmers, Reinout van Crevel, Kristian Händler, Simone Picelli, Jonas Schulte-Schrepping, Kathrin Klee, Marije Oosting, Valerie A C M Koeken, Jakko van Ingen, Yang Li, Christine S Benn, Joachim L Schultze, Leo A B Joosten, Nigel Curtis, Mihai G Netea, Andreas Schlitzer, Branko Cirovic, L Charlotte J de Bree, Laszlo Groh, Bas A Blok, Joyce Chan, Walter J F M van der Velden, M E J Bremmers, Reinout van Crevel, Kristian Händler, Simone Picelli, Jonas Schulte-Schrepping, Kathrin Klee, Marije Oosting, Valerie A C M Koeken, Jakko van Ingen, Yang Li, Christine S Benn, Joachim L Schultze, Leo A B Joosten, Nigel Curtis, Mihai G Netea, Andreas Schlitzer
Abstract
Induction of trained immunity by Bacille-Calmette-Guérin (BCG) vaccination mediates beneficial heterologous effects, but the mechanisms underlying its persistence and magnitude remain elusive. In this study, we show that BCG vaccination in healthy human volunteers induces a persistent transcriptional program connected to myeloid cell development and function within the hematopoietic stem and progenitor cell (HSPC) compartment in the bone marrow. We identify hepatic nuclear factor (HNF) family members 1a and b as crucial regulators of this transcriptional shift. These findings are corroborated by higher granulocyte numbers in BCG-vaccinated infants, HNF1 SNP variants that correlate with trained immunity, and elevated serum concentrations of the HNF1 target alpha-1 antitrypsin. Additionally, transcriptomic HSPC remodeling was epigenetically conveyed to peripheral CD14+ monocytes, displaying an activated transcriptional signature three months after BCG vaccination. Taken together, transcriptomic, epigenomic, and functional reprogramming of HSPCs and peripheral monocytes is a hallmark of BCG-induced trained immunity in humans.
Trial registration: ClinicalTrials.gov NCT01906853.
Keywords: BCG; epigenetic imprinting; hematopoietic stem cells; monocyte; myeloid cell; myelopoiesis; trained immunity; vaccination.
Conflict of interest statement
Declaration of Interests M.G.N. and L.A.B.J. are scientific founders of Trained Therapeutics Discovery. All other authors declare no competing interests.
Copyright © 2020 Elsevier Inc. All rights reserved.
Figures
References
- Aaby P., Roth A., Ravn H., Napirna B.M., Rodrigues A., Lisse I.M., Stensballe L., Diness B.R., Lausch K.R., Lund N. Randomized trial of BCG vaccination at birth to low-birth-weight children: beneficial nonspecific effects in the neonatal period? J. Infect. Dis. 2011;204:245–252.
- Armendariz A.D., Krauss R.M. Hepatic nuclear factor 1-alpha: inflammation, genetics, and atherosclerosis. Curr. Opin. Lipidol. 2009;20:106–111.
- Arts R.J.W., Moorlag S.J.C.F.M., Novakovic B., Li Y., Wang S.Y., Oosting M., Kumar V., Xavier R.J., Wijmenga C., Joosten L.A.B. 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.e5.
- Assarsson E., Lundberg M., Holmquist G., Björkesten J., Thorsen S.B., Ekman D., Eriksson A., Rennel Dickens E., Ohlsson S., Edfeldt G. Homogenous 96-plex PEA immunoassay exhibiting high sensitivity, specificity, and excellent scalability. PLoS One. 2014;9:e95192.
- Baldwin A.S. The NF-kappa B and I kappa B proteins: new discoveries and insights. Annu. Rev. Immunol. 1996;14:649–683.
- Bankoti R., Ogawa C., Nguyen T., Emadi L., Couse M., Salehi S., Fan X., Dhall D., Wang Y., Brown J. Differential regulation of effector and regulatory T cell function by Blimp1. Sci. Rep. 2017;7:12078.
- Becht E., McInnes L., Healy J., Dutertre C.-A., Kwok I.W.H., Ng L.G., Ginhoux F., Newell E.W. Dimensionality reduction for visualizing single-cell data using UMAP. Nat Biotechnol. 2019;37:38–44.
- Bekkering S., Blok B.A., Joosten L.A., Riksen N.P., van Crevel R., Netea M.G. In vitro experimental model of trained innate immunity in human primary monocytes. Clin. Vaccine Immunol. 2016;23:926–933.
- Bekkering S., Arts R.J.W., Novakovic B., Kourtzelis I., van der Heijden C.D.C.C., Li Y., Popa C.D., Ter Horst R., van Tuijl J., Netea-Maier R.T. Metabolic induction of trained immunity through the mevalonate pathway. Cell. 2018;172:135–146.e9.
- Benn C.S., Netea M.G., Selin L.K., Aaby P. A small jab - a big effect: nonspecific immunomodulation by vaccines. Trends Immunol. 2013;34:431–439.
- Biering-Sørensen S., Aaby P., Lund N., Monteiro I., Jensen K.J., Eriksen H.B., Schaltz-Buchholzer F., Jørgensen A.S.P., Rodrigues A., Fisker A.B., Benn C.S. Early BCG-Denmark and neonatal mortality among infants weighing <2500 g: a randomized controlled trial. Clin. Infect. Dis. 2017;65:1183–1190’.
- Cheng S.C., Quintin J., Cramer R.A., Shepardson K.M., Saeed S., Kumar V., Giamarellos-Bourboulis E.J., Martens J.H.A., Rao N.A., Aghajanirefah A. mTOR- and HIF-1α-mediated aerobic glycolysis as metabolic basis for trained immunity. Science. 2014;345:1250684.
- Christ A., Günther P., Lauterbach M.A.R., Duewell P., Biswas D., Pelka K., Scholz C.J., Oosting M., Haendler K., Baßler K. Western diet triggers NLRP3-dependent innate immune reprogramming. Cell. 2018;172:162–175.e14.
- Clark I.A., Allison A.C., Cox F.E. Protection of mice against Babesia and Plasmodium with BCG. Nature. 1976;259:309–311.
- Coombes J.L., Siddiqui K.R., Arancibia-Cárcamo C.V., Hall J., Sun C.M., Belkaid Y., Powrie F. A functionally specialized population of mucosal CD103+ DCs induces Foxp3+ regulatory T cells via a TGF-beta and retinoic acid-dependent mechanism. J. Exp. Med. 2007;204:1757–1764.
- Crișan T.O., Netea M.G., Joosten L.A. Innate immune memory: implications for host responses to damage-associated molecular patterns. Eur. J. Immunol. 2016;46:817–828.
- Freyne B., Marchant A., Curtis N. BCG-associated heterologous immunity, a historical perspective: intervention studies in animal models of infectious diseases. Trans. R. Soc. Trop. Med. Hyg. 2015;109:52–61.
- Gong Y., Ma Z., Patel V., Fischer E., Hiesberger T., Pontoglio M., Igarashi P. HNF-1beta regulates transcription of the PKD modifier gene Kif12. J. Am. Soc. Nephrol. 2009;20:41–47.
- Higgins J.P.T., Soares-Weiser K., López-López J.A., Kakourou A., Chaplin K., Christensen H., Martin N.K., Sterne J.A.C., Reingold A.L. Association of BCG, DTP, and measles containing vaccines with childhood mortality: systematic review. BMJ (Clin. Res. Ed.) 2016;355:i5170.
- Jaensson E., Uronen-Hansson H., Pabst O., Eksteen B., Tian J., Coombes J.L., Berg P.L., Davidsson T., Powrie F., Johansson-Lindbom B., Agace W.W. Small intestinal CD103+ dendritic cells display unique functional properties that are conserved between mice and humans. J. Exp. Med. 2008;205:2139–2149.
- Jensen K.J., Larsen N., Biering-Sørensen S., Andersen A., Eriksen H.B., Monteiro I., Hougaard D., Aaby P., Netea M.G., Flanagan K.L., Benn C.S. Heterologous immunological effects of early BCG vaccination in low-birth-weight infants in Guinea-Bissau: a randomized-controlled trial. J. Infect. Dis. 2015;211:956–967.
- Jovic S., Linge H.M., Shikhagaie M.M., Olin A.I., Lannefors L., Erjefält J.S., Mörgelin M., Egesten A. The neutrophil-recruiting chemokine GCP-2/CXCL6 is expressed in cystic fibrosis airways and retains its functional properties after binding to extracellular DNA. Mucosal Immunol. 2016;9:112–123.
- Kaufmann E., Sanz J., Dunn J.L., Khan N., Mendonça L.E., Pacis A., Tzelepis F., Pernet E., Dumaine A., Grenier J.C. BCG educates hematopoietic stem cells to generate protective innate immunity against tuberculosis. Cell. 2018;172:176–190.e19.
- Kleinnijenhuis J., Quintin J., Preijers F., Joosten L.A.B., Ifrim D.C., Saeed S., Jacobs C., van Loenhout J., de Jong D., Stunnenberg H.G. Bacille calmette-guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes. Proc. Natl. Acad. Sci. USA. 2012;109:17537–17542.
- Kleinnijenhuis J., Quintin J., Preijers F., Benn C.S., Joosten L.A.B., Jacobs C., van Loenhout J., Xavier R.J., Aaby P., van der Meer J.W.M. Long-lasting effects of BCG vaccination on both heterologous Th1/Th17 responses and innate trained immunity. J. Innate Immun. 2014;6:152–158.
- Lawrence T. The nuclear factor NF-kappaB pathway in inflammation. Cold Spring Harb. Perspect. Biol. 2009;1:a001651.
- Linge H.M., Collin M., Nordenfelt P., Mörgelin M., Malmsten M., Egesten A. The human CXC chemokine granulocyte chemotactic protein 2 (GCP-2)/CXCL6 possesses membrane-disrupting properties and is antibacterial. Antimicrob. Agents Chemother. 2008;52:2599–2607.
- McInnes L., Healy J. UMAP: uniform manifold approximation and projection for dimension reduction. arXiv. 1802 arXiv:1802.03426v2.
- Merad M., Sathe P., Helft J., Miller J., Mortha A. The dendritic cell lineage: ontogeny and function of dendritic cells and their subsets in the steady state and the inflamed setting. Annu. Rev. Immunol. 2013;31:563–604.
- Mitroulis I., Ruppova K., Wang B., Chen L.S., Grzybek M., Grinenko T., Eugster A., Troullinaki M., Palladini A., Kourtzelis I. Modulation of myelopoiesis progenitors is an integral component of trained immunity. Cell. 2018;172:147–161.e12.
- Moraes-Vieira P.M., Yore M.M., Dwyer P.M., Syed I., Aryal P., Kahn B.B. RBP4 activates antigen-presenting cells, leading to adipose tissue inflammation and systemic insulin resistance. Cell Metab. 2014;19:512–526.
- Murphy J.R. Host defenses in murine malaria: nonspecific resistance to Plasmodium berghei generated in response to Mycobacterium bovis infection or Corynebacterium parvum stimulation. Infect. Immun. 1981;33:199–211.
- Netea M.G., Quintin J., van der Meer J.W.M. Trained immunity: A memory for innate host defense. Cell Host Microbe. 2011;9:355–361.
- Netea M.G., Joosten L.A., Latz E., Mills K.H., Natoli G., Stunnenberg H.G., O’Neill L.A., Xavier R.J. Trained immunity: A program of innate immune memory in health and disease. Science. 2016;352:aaf1098.
- Netea M.G., Joosten L.A.B., van der Meer J.W.M. Hypothesis: stimulation of trained immunity as adjunctive immunotherapy in cancer. J. Leukoc. Biol. 2017;102:1323–1332.
- Picelli S., Faridani O.R., Björklund A.K., Winberg G., Sagasser S., Sandberg R. Full-length RNA-seq from single cells using smart-seq2. Nat Protoc. 2014;9:171–181.
- Rasmussen A.L., Wang I.M., Shuhart M.C., Proll S.C., He Y., Cristescu R., Roberts C., Carter V.S., Williams C.M., Diamond D.L. Chronic immune activation is a distinguishing feature of liver and PBMC gene signatures from HCV/HIV coinfected patients and may contribute to hepatic fibrogenesis. Virology. 2012;430:43–52.
- Rieckmann A., Villumsen M., Sørup S., Haugaard L.K., Ravn H., Roth A., Baker J.L., Benn C.S., Aaby P. Vaccinations against smallpox and tuberculosis are associated with better long-term survival: a Danish case-cohort study 1971-2010. Int. J. Epidemiol. 2017;46:695–705.
- Rollini P., Fournier R.E. The HNF-4/HNF-1alpha transactivation cascade regulates gene activity and chromatin structure of the human serine protease inhibitor gene cluster at 14q32.1. Proc. Natl. Acad. Sci. USA. 1999;96:10308–10313.
- Saeed S., Quintin J., Kerstens H.H.D., Rao N.A., Aghajanirefah A., Matarese F., Cheng S.C., Ratter J., Berentsen K., van der Ent M.A. Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity. Science. 2014;345:1251086.
- Sander J., Schmidt S.V., Cirovic B., McGovern N., Papantonopoulou O., Hardt A.L., Aschenbrenner A.C., Kreer C., Quast T., Xu A.M. Cellular differentiation of human monocytes is regulated by time-dependent interleukin-4 signaling and the transcriptional regulator NCOR2. Immunity. 2017;47:1051–1066.e12.
- Savelkoul P.H., Catsburg A., Mulder S., Oostendorp L., Schirm J., Wilke H., van der Zanden A.G., Noordhoek G.T. Detection of Mycobacterium tuberculosis complex with real time PCR: comparison of different primer-probe sets based on the IS6110 element. J. Microbiol. Methods. 2006;66:177–180.
- Siddiqui K.R.R., Powrie F. CD103+ GALT DCs promote Foxp3+ regulatory T cells. Mucosal Immunol. 2008;1:S34–S38.
- Storgaard L., Rodrigues A., Martins C., Nielsen B.U., Ravn H., Benn C.S., Aaby P., Fisker A.B. Development of BCG scar and subsequent morbidity and mortality in rural Guinea-Bissau. Clin. Infect. Dis. 2015;61:950–959.
- Sun J.C., Lopez-Verges S., Kim C.C., DeRisi J.L., Lanier L.L. NK cells and immune “memory”. J. Immunol. 2011;186:1891–1897.
- Ter Horst R., Jaeger M., Smeekens S.P., Oosting M., Swertz M.A., Li Y., Kumar V., Diavatopoulos D.A., Jansen A.F.M., Lemmers H. Host and environmental factors influencing individual human cytokine responses. Cell. 2016;167:1111–1124.e13.
- Varol C., Mildner A., Jung S. Macrophages: development and tissue specialization. Annu. Rev. Immunol. 2015;33:643–675.
- Villumsen M., Sørup S., Jess T., Ravn H., Relander T., Baker J.L., Benn C.S., Sørensen T.I.A., Aaby P., Roth A. Risk of lymphoma and leukaemia after Bacille Calmette-Guérin and smallpox vaccination: a Danish case-cohort study. Vaccine. 2009;27:6950–6958.
- Walk J., de Bree L.C.J., Graumans W., Stoter R., van Gemert G.J., van de Vegte-Bolmer M., Teelen K., Hermsen C.C., Arts R.J.W., Behet M.C. Outcomes of controlled human malaria infection after BCG vaccination. Nat. Commun. 2019;10:874.
- Zimmermann P., Finn A., Curtis N. Does BCG vaccination protect against nontuberculous mycobacterial infection? A systematic review and meta-analysis. J. Infect. Dis. 2018;218:679–687.
Source: PubMed