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How stem cells respond to infection, inflammation and ageing

Abstract

Stem cells maintain tissue architecture by replacing differentiated cells at steady state and upon injury. Implementing this cornerstone role requires protection of stem cells from pathogens and from the toxic effects of immune system activation. However, the pro-inflammatory innate immune mechanisms that protect differentiated cells from infection are poorly functional in stem cells. Instead, stem cells employ other specific defence mechanisms, such as antiviral RNA interference. At steady state, the proliferation and differentiation of tissue stem cells is regulated by multiple cell types, including immune cells. Following sterile tissue injury or during infection, the immune response — in addition to controlling pathogens and clearing cell debris — orchestrates tissue repair by fine-tuning stem cell activity, through direct cell–cell contacts and via inflammatory mediators such as cytokines. There is thus stem–immune cross-talk that is fundamental to the maintenance of tissue homeostasis. Inflammageing, which is defined as the age-driven elevation of inflammation and is associated with an altered immune cell composition, profoundly affects this stem–immune cross-talk, impacting the ability to repair tissues and participating in ageing of the whole organism.

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Fig. 1: Stem cell-specific immune mechanisms.
Fig. 2: Cross-talk between hair follicle stem cells and immune cells at steady state.
Fig. 3: Cross-talk between muscle stem cells and immune cells during repair.

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References

  1. Swartzendruber, D. E. & Lehman, J. M. Neoplastic differentiation: interaction of simian virus 40 and polyoma virus with murine teratocarcinoma cells in vitro. J. Cell. Physiol. 85, 179–187 (1975). This early work documents how differentiation renders cells permissive to viral infection.

    Article  CAS  PubMed  Google Scholar 

  2. Teich, N. M., Weiss, R. A., Martin, G. R. & Lowy, D. R. Virus infection of murine teratocarcinoma stem cell lines. Cell 12, 973–982 (1977).

    Article  CAS  PubMed  Google Scholar 

  3. Wu, X., Kwong, A. C. & Rice, C. M. Antiviral resistance of stem cells. Curr. Opin. Immunol. 56, 50–59 (2019).

    Article  CAS  PubMed  Google Scholar 

  4. Gonczol, E., Andrews, P. W. & Plotkin, S. A. Cytomegalovirus replicates in differentiated but not in undifferentiated human embryonal carcinoma cells. Science 224, 159–161 (1984).

    Article  CAS  PubMed  Google Scholar 

  5. Davis, B. R. et al. Absent or rare human immunodeficiency virus infection of bone marrow stem/progenitor cells in vivo. J. Virol. 65, 1985–1990 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Weichold, F. F. et al. Neither human immunodeficiency virus-1 (HIV-1) nor HIV-2 infects most-primitive human hematopoietic stem cells as assessed in long-term bone marrow cultures. Blood 91, 907–915 (1998).

    Article  CAS  PubMed  Google Scholar 

  7. Shen, H. et al. Intrinsic human immunodeficiency virus type 1 resistance of hematopoietic stem cells despite coreceptor expression. J. Virol. 73, 728–737 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Belzile, J.-P., Stark, T. J., Yeo, G. W. & Spector, D. H. Human cytomegalovirus infection of human embryonic stem cell-derived primitive neural stem cells is restricted at several steps but leads to the persistence of viral DNA. J. Virol. 88, 4021–4039 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  9. Villa, N. Y. et al. Ex vivo virotherapy with myxoma virus does not impair hematopoietic stem and progenitor cells. Cytotherapy 18, 465–480 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  10. Tang, H. et al. Zika virus infects human cortical neural progenitors and attenuates their growth. Cell Stem Cell 18, 587–590 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Zhang, B. et al. Differential antiviral immunity to Japanese encephalitis virus in developing cortical organoids. Cell Death Dis. 9, 719 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  12. Dang, J. et al. Zika virus depletes neural progenitors in human cerebral organoids through activation of the innate immune receptor TLR3. Cell Stem Cell 19, 258–265 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Sindre, H. et al. Human cytomegalovirus suppression of and latency in early hematopoietic progenitor cells. Blood 88, 4526–4533 (1996).

    Article  CAS  PubMed  Google Scholar 

  14. Mirandola, P. et al. Infection of CD34+ hematopoietic progenitor cells by human herpesvirus 7 (HHV-7). Blood 96, 126–131 (2000).

    Article  CAS  PubMed  Google Scholar 

  15. Feuer, G. et al. Human T-cell leukemia virus infection of human hematopoietic progenitor cells: maintenance of virus infection during differentiation in vitro and in vivo. J. Virol. 70, 7 (1996).

    Article  Google Scholar 

  16. Parsons, C. H., Szomju, B. & Kedes, D. H. Susceptibility of human fetal mesencyhmal stem cells to Kaposi sarcoma-associated herpesvirus. Blood 104, 2736–2738 (2004).

    Article  CAS  PubMed  Google Scholar 

  17. Zhu, D. et al. Human cytomegalovirus reprogrammes haematopoietic progenitor cells into immunosuppressive monocytes to achieve latency. Nat. Microbiol. 3, 503–513 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Tsueng, G. et al. Coxsackievirus preferentially replicates and induces cytopathic effects in undifferentiated neural progenitor cells. J. Virol. 85, 5718–5732 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Yang, K. et al. Mesenchymal stem cells detect and defend against gammaherpesvirus infection via the cGAS–STING pathway. Sci. Rep. 5, 7820 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Ruangrung, K. et al. Analysis of influenza A virus infection in human induced pluripotent stem cells (hiPSCs) and their derivatives. Virus Res. 323, 199009 (2023).

    Article  CAS  PubMed  Google Scholar 

  21. Zaikos, T. D. et al. Hematopoietic stem and progenitor cells are a distinct HIV reservoir that contributes to persistent viremia in suppressed patients. Cell Rep. 25, 3759–3773.e9 (2018).

    Article  CAS  PubMed  Google Scholar 

  22. Triana, S. et al. Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection. Mol. Syst. Biol. 17, e9833 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Kolb-Mäurer, A., Wilhelm, M., Weissinger, F., Bröcker, E.-B. & Goebel, W. Interaction of human hematopoietic stem cells with bacterial pathogens. Blood 100, 3703–3709 (2002).

    Article  PubMed  Google Scholar 

  24. Mändle, T. et al. Infection of human CD34+ progenitor cells with Bartonella henselae results in intraerythrocytic presence of B. henselae. Blood 106, 1215–1222 (2005).

    Article  PubMed  Google Scholar 

  25. Kaufmann, E. et al. BCG educates hematopoietic stem cells to generate protective innate immunity against tuberculosis. Cell 172, 176–190.e19 (2018).

    Article  CAS  PubMed  Google Scholar 

  26. Allahverdiyev, A. M. et al. Adipose tissue-derived mesenchymal stem cells as a new host cell in latent leishmaniasis. Am. Soc. Trop. Med. Hyg. 85, 535–539 (2011).

    Article  CAS  Google Scholar 

  27. Dirkx, L. et al. Long-term hematopoietic stem cells as a parasite niche during treatment failure in visceral leishmaniasis. Commun. Biol. 5, 626 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Dirkx, L. et al. Long-term hematopoietic stem cells trigger quiescence in Leishmania parasites. PLoS Pathog. 20, e1012181 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Bonhomme, D. & Poirier, E. Z. Early signaling pathways in virus-infected cells. Curr. Opin. Virol. 66, 101411 (2024).

    Article  CAS  PubMed  Google Scholar 

  30. Tan, X., Sun, L., Chen, J. & Chen, Z. J. Detection of microbial infections through innate immune sensing of nucleic acids. Annu. Rev. Microbiol. 72, 447–478 (2018).

    Article  CAS  PubMed  Google Scholar 

  31. Schoggins, J. W. Interferon-stimulated genes: what do they all do? Annu. Rev. Virol. 6, 567–584 (2019).

    Article  CAS  PubMed  Google Scholar 

  32. Pevsner-Fischer, M. et al. Toll-like receptors and their ligands control mesenchymal stem cell functions. Blood 109, 1422–1432 (2007).

    Article  CAS  PubMed  Google Scholar 

  33. Xia, P. et al. A circular RNA protects dormant hematopoietic stem cells from DNA sensor cGAS-mediated exhaustion. Immunity https://doi.org/10.1016/j.immuni.2018.03.016 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  34. Burke, D. C., Graham, C. F. & Lehman, J. M. Appearance of interferon inducibility and sensitivity during differentiation of murine teratocarcinoma cells in vitro. Cell 13, 243–248 (1978).

    Article  CAS  PubMed  Google Scholar 

  35. Chen, L.-L., Yang, L. & Carmichael, G. Molecular basis for an attenuated cytoplasmic dsRNA response in human embryonic stem cells. Cell Cycle 9, 3552–3564 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Hong, X.-X. & Carmichael, G. G. Innate immunity in pluripotent human cells: attenuated response to interferon-β. J. Biol. Chem. 288, 16196–16205 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. D’Angelo, W. et al. The molecular basis for the lack of inflammatory responses in mouse embryonic stem cells and their differentiated cells. J. Immunol. 198, 2147–2155 (2017).

    Article  PubMed  Google Scholar 

  38. Witteveldt, J., Knol, L. I. & Macias, S. MicroRNA-deficient mouse embryonic stem cells acquire a functional interferon response. eLife 8, e44171 (2019). This work provides the molecular basis of interferon attenuation in ES cells, which downregulate MAVS, a pivotal actor of the immune signalling cascade.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Wang, R. et al. Mouse embryonic stem cells are deficient in type I interferon expression in response to viral infections and double-stranded RNA. J. Biol. Chem. 288, 15926–15936 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Farshchian, M. et al. Suppression of dsRNA response genes and innate immunity following Oct4, Stella, and Nanos2 overexpression in mouse embryonic fibroblasts. Cytokine 106, 1–11 (2018).

    Article  CAS  PubMed  Google Scholar 

  41. Eggenberger, J., Blanco-Melo, D., Panis, M., Brennand, K. J. & tenOever, B. R. Type I interferon response impairs differentiation potential of pluripotent stem cells. Proc. Natl Acad. Sci. USA https://doi.org/10.1073/pnas.1812449116 (2019). This paper shows how artificially inducing an innate immune signature is detrimental to induced pluripotent stem cells, providing a reason for the attenuated interferon pathway in stem cells.

  42. Minamide, K. et al. IRF2 maintains the stemness of colonic stem cells by limiting physiological stress from interferon. Sci. Rep. 10, 14639 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Sato, T. Regulated IFN signalling preserves the stemness of intestinal stem cells by restricting differentiation into secretory-cell lineages. Nat. Cell Biol. 22, 31 (2020).

    Article  Google Scholar 

  44. Hertzog, P. J., Hwang, S. Y. & Kola, I. Role of interferons in the regulation of cell proliferation, differentiation, and development. Mol. Reprod. Dev. 39, 226–232 (1994).

    Article  CAS  PubMed  Google Scholar 

  45. Sato, T. et al. Characterization of radioresistant epithelial stem cell heterogeneity in the damaged mouse intestine. Sci. Rep. 10, 8308 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Carvajal Ibañez, D. et al. Interferon regulates neural stem cell function at all ages by orchestrating mTOR and cell cycle. EMBO Mol. Med. 15, e16434 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  47. Essers, M. A. G. et al. IFNα activates dormant haematopoietic stem cells in vivo. Nature 458, 904–908 (2009).

    Article  CAS  PubMed  Google Scholar 

  48. Baldridge, M. T., King, K. Y., Boles, N. C., Weksberg, D. C. & Goodell, M. A. Quiescent haematopoietic stem cells are activated by IFN-γ in response to chronic infection. Nature 465, 793–797 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Matatall, K. A. et al. Chronic infection depletes hematopoietic stem cells through stress-induced terminal differentiation. Cell Rep. 17, 2584–2595 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Sato, T. et al. Interferon regulatory factor-2 protects quiescent hematopoietic stem cells from type I interferon-dependent exhaustion. Nat. Med. 15, 6 (2009).

    Article  Google Scholar 

  51. Grow, E. J. et al. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature 522, 221–225 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Altshuler, A. et al. Discrete limbal epithelial stem cell populations mediate corneal homeostasis and wound healing. Cell Stem Cell 28, 1248–1261.e8 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Wu, X. et al. Intrinsic immunity shapes viral resistance of stem cells. Cell https://doi.org/10.1016/j.cell.2017.11.018 (2017). This work identifies an important stem cell-specific mechanism of defence relying on the expression of ISGs at steady state, independently of canonical interferon signalling.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Wakim, L. M., Gupta, N., Mintern, J. D. & Villadangos, J. A. Enhanced survival of lung tissue-resident memory CD8+ T cells during infection with influenza virus due to selective expression of IFITM3. Nat. Immunol. 14, 238–245 (2013).

    Article  CAS  PubMed  Google Scholar 

  55. Gattinoni, L., Speiser, D. E., Lichterfeld, M. & Bonini, C. T memory stem cells in health and disease. Nat. Med. 23, 18–27 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Poirier, E. Z. et al. An isoform of Dicer protects mammalian stem cells against multiple RNA viruses. Science 373, 231–236 (2021). This work identifies a stem cell-specific mechanism of defence relying on the expression of aviD, an isoform of Dicer that implements antiviral RNAi and protects against RNA viruses.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Anobile, D. P. & Poirier, E. Z. RNA interference, an emerging component of antiviral immunity in mammals. Biochem. Soc. Trans. https://doi.org/10.1042/BST20220385 (2023).

  58. Maillard, P. V. et al. Antiviral RNA interference in mammalian cells. Science 342, 235–238 (2013).

    Article  CAS  PubMed  Google Scholar 

  59. Li, Y., Lu, J., Han, Y., Xiaoxu, F. & Ding, S.-W. RNA interference functions as an antiviral immunity mechanism in mammals. Science 1241911, 342 (2013).

    Google Scholar 

  60. Martens, E. C., Neumann, M. & Desai, M. S. Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier. Nat. Rev. Microbiol. 16, 457–470 (2018).

    Article  CAS  PubMed  Google Scholar 

  61. Cha, J., Kim, T.-G. & Ryu, J.-H. Conversation between skin microbiota and the host: from early life to adulthood. Exp. Mol. Med. https://doi.org/10.1038/s12276-025-01427-y (2025).

  62. Nigro, G., Rossi, R., Commere, P.-H., Jay, P. & Sansonetti, P. J. The cytosolic bacterial peptidoglycan sensor Nod2 affords stem cell protection and links microbes to gut epithelial regeneration. Cell Host Microbe 15, 792–798 (2014).

    Article  CAS  PubMed  Google Scholar 

  63. Levy, A. et al. Innate immune receptor NOD2 mediates LGR5+ intestinal stem cell protection against ROS cytotoxicity via mitophagy stimulation. Proc. Natl Acad. Sci. USA 117, 1994–2003 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Zhang, S. et al. Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid. Nat. Microbiol. 10, 765–783 (2025).

    Article  CAS  PubMed  Google Scholar 

  65. Wang, G. et al. Bacteria induce skin regeneration via IL-1β signaling. Cell Host Microbe 29, 777–791.e6 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Kaiko, G. E. et al. The colonic crypt protects stem cells from microbiota-derived metabolites. Cell 167, 1137 (2016).

    Article  CAS  PubMed  Google Scholar 

  67. Naik, S., Larsen, S. B., Cowley, C. J. & Fuchs, E. Two to tango: dialog between immunity and stem cells in health and disease. Cell 175, 908–920 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Blanpain, C. & Fuchs, E. Epidermal stem cells of the skin. Annu. Rev. Cell Dev. Biol. 22, 339–373 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Greco, V. et al. A two-step mechanism for stem cell activation during hair regeneration. Cell Stem Cell 4, 155–169 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Oshimori, N. & Fuchs, E. Paracrine TGF-β signaling counterbalances BMP-mediated repression in hair follicle stem cell activation. Cell Stem Cell 10, 63–75 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Park, M. D., Silvin, A., Ginhoux, F. & Merad, M. Macrophages in health and disease. Cell 185, 4259–4279 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Sakaguchi, S. et al. Regulatory T cells and human disease. Annu. Rev. Immunol. 38, 541–566 (2020).

    Article  CAS  PubMed  Google Scholar 

  73. Castellana, D., Paus, R. & Perez-Moreno, M. Macrophages contribute to the cyclic activation of adult hair follicle stem cells. PLoS Biol. 12, e1002002 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  74. Wang, E. C. E., Dai, Z., Ferrante, A. W., Drake, C. G. & Christiano, A. M. A subset of TREM2+ dermal macrophages secretes oncostatin M to maintain hair follicle stem cell quiescence and inhibit hair growth. Cell Stem Cell 24, 654–669.e6 (2019).

    Article  CAS  PubMed  Google Scholar 

  75. Ali, N. et al. Regulatory T cells in skin facilitate epithelial stem cell differentiation. Cell 169, 1119–1129.e11 (2017). This work documents how Treg cells of adaptive immunity fine-tune the activity of HFS cells through direct modulation of the Notch pathway.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Liu, Z. et al. Glucocorticoid signaling and regulatory T cells cooperate to maintain the hair-follicle stem-cell niche. Nat. Immunol. 23, 1086–1097 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Biton, M. et al. T helper cell cytokines modulate intestinal stem cell renewal and differentiation. Cell 175, 1307–1320.e22 (2018). This work shows that IS cell proliferation and renewal is modulated by different cytokines produced by subpopulations of T cells.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Kim, J.-E. et al. Gut microbiota promotes stem cell differentiation through macrophage and mesenchymal niches in early postnatal development. Immunity 55, 2300–2317.e6 (2022).

    Article  CAS  PubMed  Google Scholar 

  79. Zhu, P. et al. Gut microbiota drives macrophage-dependent self-renewal of intestinal stem cells via niche enteric serotonergic neurons. Cell Res. 32, 555–569 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Chow, A. et al. Bone marrow CD169+ macrophages promote the retention of hematopoietic stem and progenitor cells in the mesenchymal stem cell niche. J. Exp. Med. 208, 261–271 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Hirata, Y. et al. CD150high bone marrow tregs maintain hematopoietic stem cell quiescence and immune privilege via adenosine. Cell Stem Cell 22, 445–453.e5 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Miron, V. E. et al. M2 microglia and macrophages drive oligodendrocyte differentiation during CNS remyelination. Nat. Neurosci. 16, 1211–1218 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Dombrowski, Y. et al. Regulatory T cells promote myelin regeneration in the central nervous system. Nat. Neurosci. 20, 674–680 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Gyorki, D. E., Asselin-Labat, M.-L., Van Rooijen, N., Lindeman, G. J. & Visvader, J. E. Resident macrophages influence stem cell activity in the mammary gland. Breast Cancer Res. 11, R62 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  85. Chakrabarti, R. et al. Notch ligand Dll1 mediates cross-talk between mammary stem cells and the macrophageal niche. Science 360, eaan4153 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  86. Liu, C. et al. Niche inflammatory signals control oscillating mammary regeneration and protect stem cells from cytotoxic stress. Cell Stem Cell 31, 89–105.e6 (2024).

    Article  CAS  PubMed  Google Scholar 

  87. Agudo, J. et al. Quiescent tissue stem cells evade immune surveillance. Immunity 48, 271–285.e5 (2018). This work shows that cycling, but not quiescent, tissue stem cells can be targeted by CD8+ T cells through MHC class I–TCR interaction, suggesting that stem cells can be surveilled by the immune system.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Hernández-Malmierca, P. et al. Antigen presentation safeguards the integrity of the hematopoietic stem cell pool. Cell Stem Cell 29, 760–775.e10 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  89. Medzhitov, R. Origin and physiological roles of inflammation. Nature 454, 428–435 (2008).

    Article  CAS  PubMed  Google Scholar 

  90. Swann, J. W., Olson, O. C. & Passegué, E. Made to order: emergency myelopoiesis and demand-adapted innate immune cell production. Nat. Rev. Immunol. 24, 596–613 (2024).

    Article  CAS  PubMed  Google Scholar 

  91. Du, H. et al. Macrophage-released ADAMTS1 promotes muscle stem cell activation. Nat. Commun. 8, 669 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  92. He, Y. et al. Intravital microscopy of satellite cell dynamics and their interaction with myeloid cells during skeletal muscle regeneration. Sci. Adv. 9, eadi1891 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Baht, G. S. et al. Meteorin-like facilitates skeletal muscle repair through a Stat3/IGF-1 mechanism. Nat. Metab. 2, 278–289 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Lee, D. E. et al. Meteorin-like is an injectable peptide that can enhance regeneration in aged muscle through immune-driven fibro/adipogenic progenitor signaling. Nat. Commun. 13, 7613 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Burzyn, D. et al. A special population of regulatory T cells potentiates muscle repair. Cell 155, 1282–1295 (2013). This work documents how Treg cells home to wounded muscles and secrete amphiregulin to promote repair.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Heredia, J. E. et al. Type 2 innate signals stimulate fibro/adipogenic progenitors to facilitate muscle regeneration. Cell 153, 376–388 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Ito, M. et al. Stem cells in the hair follicle bulge contribute to wound repair but not to homeostasis of the epidermis. Nat. Med. 11, 1351–1354 (2005).

    Article  CAS  PubMed  Google Scholar 

  98. Mathur, A. N. et al. Treg-cell control of a CXCL5–IL-17 inflammatory axis promotes hair-follicle-stem-cell differentiation during skin-barrier repair. Immunity 50, 655–667.e4 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Konieczny, P. et al. Interleukin-17 governs hypoxic adaptation of injured epithelium. Science 377, eabg9302 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Subudhi, I. et al. Metabolic coordination between skin epithelium and type 17 immunity sustains chronic skin inflammation. Immunity 57, 1665–1680.e7 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Choi, J. et al. Inflammatory signals induce AT2 cell-derived damage-associated transient progenitors that mediate alveolar regeneration. Cell Stem Cell 27, 366–382.e7 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Katsura, H., Kobayashi, Y., Tata, P. R. & Hogan, B. L. M. IL-1 and TNFα contribute to the inflammatory niche to enhance alveolar regeneration. Stem Cell Rep. 12, 657–666 (2019).

    Article  CAS  Google Scholar 

  103. Ruscitti, C. et al. Recruited atypical Ly6G+ macrophages license alveolar regeneration after lung injury. Sci. Immunol. 9, eado1227 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Kaiser, K. A., Loffredo, L. F., Santos-Alexis, K. D. L., Ringham, O. R. & Arpaia, N. Regulation of the alveolar regenerative niche by amphiregulin-producing regulatory T cells. J. Exp. Med. 220, e20221462 (2023).

    Article  CAS  PubMed  Google Scholar 

  105. Luan, J. et al. CD80 on skin stem cells promotes local expansion of regulatory T cells upon injury to orchestrate repair within an inflammatory environment. Immunity 57, 1071–1086.e7 (2024). This work shows that upon wounding of the skin, HFS cells regulate the repair process by communicating with Treg cells and neutrophils, through CD80 and Cxcl5 expression, respectively.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Keyes, B. E. et al. Impaired epidermal to dendritic T cell signaling slows wound repair in aged skin. Cell 167, 1323–1338.e14 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Liu, S. et al. A tissue injury sensing and repair pathway distinct from host pathogen defense. Cell 186, 2127–2143.e22 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Stewart, K. S. et al. Stem cells tightly regulate dead cell clearance to maintain tissue fitness. Nature 633, 407–416 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Chen, M., Reed, R. R. & Lane, A. P. Chronic inflammation directs an olfactory stem cell functional switch from neuroregeneration to immune defense. Cell Stem Cell 25, 501–513.e5 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Mosher, K. I. et al. Neural progenitor cells regulate microglia functions and activity. Nat. Neurosci. 15, 1485–1487 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Halper-Stromberg, A. & Jabri, B. Maladaptive consequences of inflammatory events shape individual immune identity. Nat. Immunol. 23, 1675–1686 (2022).

    Article  CAS  PubMed  Google Scholar 

  112. Netea, M. G. et al. Defining trained immunity and its role in health and disease. Nat. Rev. Immunol. 20, 375–388 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Naik, S. et al. Inflammatory memory sensitizes skin epithelial stem cells to tissue damage. Nature 550, 475–480 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Larsen, S. B. et al. Establishment, maintenance, and recall of inflammatory memory. Cell Stem Cell 28, 1758–1774.e8 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Mitroulis, I. et al. Modulation of myelopoiesis progenitors is an integral component of trained immunity. Cell 172, 147–161.e12 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. De Laval, B. et al. C/EBPβ-dependent epigenetic memory induces trained immunity in hematopoietic stem cells. Cell Stem Cell 26, 657–674.e8 (2020).

    Article  PubMed  Google Scholar 

  117. Kain, B. N. et al. Hematopoietic stem and progenitor cells confer cross-protective trained immunity in mouse models. iScience 26, 107596 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Lim, A. I. et al. Prenatal maternal infection promotes tissue-specific immunity and inflammation in offspring. Science 373, eabf3002 (2021).

    Article  CAS  PubMed  Google Scholar 

  119. Ordovas-Montanes, J. et al. Allergic inflammatory memory in human respiratory epithelial progenitor cells. Nature 560, 649–654 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Gonzales, K. A. U. et al. Stem cells expand potency and alter tissue fitness by accumulating diverse epigenetic memories. Science 374, eabh2444 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. López-Otín, C., Blasco, M. A., Partridge, L., Serrano, M. & Kroemer, G. Hallmarks of aging: an expanding universe. Cell 186, 243–278 (2023).

    Article  PubMed  Google Scholar 

  122. Al Zouabi, L. & Bardin, A. J. Stem cell DNA damage and genome mutation in the context of aging and cancer initiation. Cold Spring Harb. Perspect. Biol. 12, a036210 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Blokzijl, F. et al. Tissue-specific mutation accumulation in human adult stem cells during life. Nature 538, 260–264 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Carlson, M. E., Hsu, M. & Conboy, I. M. Imbalance between pSmad3 and Notch induces CDK inhibitors in old muscle stem cells. Nature 454, 528–532 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Conboy, I. M., Conboy, M. J., Smythe, G. M. & Rando, T. A. Notch-mediated restoration of regenerative potential to aged muscle. Science 302, 1575–1577 (2003).

    Article  CAS  PubMed  Google Scholar 

  126. Yousefzadeh, M. J. et al. An aged immune system drives senescence and ageing of solid organs. Nature 594, 100–105 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Mogilenko, D. A. et al. Comprehensive profiling of an aging immune system reveals clonal GZMK+CD8+ T cells as conserved hallmark of inflammaging. Immunity 54, 99–115.e12 (2021).

    Article  CAS  PubMed  Google Scholar 

  128. Doles, J., Storer, M., Cozzuto, L., Roma, G. & Keyes, W. M. Age-associated inflammation inhibits epidermal stem cell function. Genes. Dev. 26, 2144–2153 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Ge, Y. et al. The aging skin microenvironment dictates stem cell behavior. Proc. Natl Acad. Sci. USA 117, 5339–5350 (2020). This work utilizes transplantation assays of HFS cells, comparing young and old animals, to demonstrate that the regenerative defects of aged HFS cells originate primarily from cell-extrinsic inflammageing.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Jurk, D. et al. Chronic inflammation induces telomere dysfunction and accelerates ageing in mice. Nat. Commun. 5, 4172 (2014).

    Article  CAS  Google Scholar 

  131. Ergen, A. V., Boles, N. C. & Goodell, M. A. Rantes/Ccl5 influences hematopoietic stem cell subtypes and causes myeloid skewing. Blood 119, 2500–2509 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Kovtonyuk, L. V. et al. IL-1 mediates microbiome-induced inflammaging of hematopoietic stem cells in mice. Blood 139, 44–58 (2022).

    Article  CAS  PubMed  Google Scholar 

  133. Mitchell, C. A. et al. Stromal niche inflammation mediated by IL-1 signalling is a targetable driver of haematopoietic ageing. Nat. Cell Biol. 25, 30–41 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Kundu, P., Blacher, E., Elinav, E. & Pettersson, S. Our gut microbiome: the evolving inner self. Cell 171, 1481–1493 (2017).

    Article  CAS  PubMed  Google Scholar 

  135. Zeng, X. et al. Fecal microbiota transplantation from young mice rejuvenates aged hematopoietic stem cells by suppressing inflammation. Blood 141, 1691–1707 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Kalamakis, G. et al. Quiescence modulates stem cell maintenance and regenerative capacity in the aging brain. Cell 176, 1407–1419.e14 (2019). This work shows that during brain ageing, inflammation safeguards the NS cell pool by favouring quiescence.

    Article  CAS  PubMed  Google Scholar 

  137. Dulken, B. W. et al. Single-cell analysis reveals T cell infiltration in old neurogenic niches. Nature 571, 205–210 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Omrani, O. et al. IFNγ–Stat1 axis drives aging-associated loss of intestinal tissue homeostasis and regeneration. Nat. Commun. 14, 6109 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Bogeska, R. et al. Inflammatory exposure drives long-lived impairment of hematopoietic stem cell self-renewal activity and accelerated aging. Cell Stem Cell 29, 1273–1284.e8 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Price, F. D. et al. Inhibition of JAK–STAT signaling stimulates adult satellite cell function. Nat. Med. 20, 1174–1181 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Oh, J. et al. Age-associated NF-κB signaling in myofibers alters the satellite cell niche and re-strains muscle stem cell function. Aging 8, 2871–2896 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Tobin, S. W. et al. Delineating the relationship between immune system aging and myogenesis in muscle repair. Aging Cell 20, e13312 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Cui, C. et al. Skewed macrophage polarization in aging skeletal muscle. Aging Cell 18, e13032 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Krasniewski, L. K. et al. Single-cell analysis of skeletal muscle macrophages reveals age-associated functional subpopulations. eLife 11, e77974 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. McKay, B. R. et al. Elevated SOCS3 and altered IL-6 signaling is associated with age-related human muscle stem cell dysfunction. Am. J. Physiol. Cell Physiol. 304, C717–C728 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Wang, Y. et al. Aging of the immune system causes reductions in muscle stem cell populations, promotes their shift to a fibrogenic phenotype, and modulates sarcopenia. FASEB J. 33, 1415–1427 (2019).

    Article  CAS  PubMed  Google Scholar 

  147. Paliwal, P., Pishesha, N., Wijaya, D. & Conboy, I. M. Age dependent increase in the levels of osteopontin inhibits skeletal muscle regeneration. Aging 4, 553–566 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Liang, J. et al. Reciprocal interactions between alveolar progenitor dysfunction and aging promote lung fibrosis. eLife 12, e85415 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Vennekens, A. et al. Interleukin-6 is an activator of pituitary stem cells upon local damage, a competence quenched in the aging gland. Proc. Natl Acad. Sci. USA 118, e2100052118 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. De La Fuente, A. G. et al. Ageing impairs the regenerative capacity of regulatory T cells in mouse central nervous system remyelination. Nat. Commun. 15, 1870 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  151. Funk, M. C. et al. Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice. Dev. Cell 58, 2914–2929.e7 (2023). This work shows that during ageing, the cross-talk between IS cells and CD4+ T cells takes a wrong turn and participates in propagating inflammageing in the gut.

    Article  CAS  PubMed  Google Scholar 

  152. Duneton, C., Winterberg, P. D. & Ford, M. L. Activation and regulation of alloreactive T cell immunity in solid organ transplantation. Nat. Rev. Nephrol. 18, 663–676 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Simpson, E. A historical perspective on immunological privilege. Immunol. Rev. 213, 12–22 (2006).

    Article  PubMed  Google Scholar 

  154. Agudo, J. Immune privilege of skin stem cells: what do we know and what can we learn? Exp. Dermatol. 30, 522–528 (2021).

    Article  CAS  PubMed  Google Scholar 

  155. Fujisaki, J. et al. In vivo imaging of Treg cells providing immune privilege to the haematopoietic stem-cell niche. Nature 474, 216–219 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Cohen, J. N. et al. Regulatory T cells in skin mediate immune privilege of the hair follicle stem cell niche. Sci. Immunol. 9, eadh0152 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Batlle, E. & Clevers, H. Cancer stem cells revisited. Nat. Med. 23, 1124–1134 (2017).

    Article  CAS  PubMed  Google Scholar 

  158. Bayik, D. & Lathia, J. D. Cancer stem cell–immune cell crosstalk in tumour progression. Nat. Rev. Cancer 21, 526–536 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Miranda, A. et al. Cancer stemness, intratumoral heterogeneity, and immune response across cancers. Proc. Natl Acad. Sci. USA 116, 9020–9029 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Baldominos, P. et al. Quiescent cancer cells resist T cell attack by forming an immunosuppressive niche. Cell https://doi.org/10.1016/j.cell.2022.03.033 (2022).

  161. Alvarado, A. G. et al. Glioblastoma cancer stem cells evade innate immune suppression of self-renewal through reduced TLR4 expression. Cell Stem Cell 20, 450–461.e4 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Lu, H. et al. A breast cancer stem cell niche supported by juxtacrine signalling from monocytes and macrophages. Nat. Cell Biol. 16, 1105–1117 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Wang, R. et al. TH17 cell-derived IL-17A promoted tumor progression via STAT3/NF-κB/Notch1 signaling in non-small cell lung cancer. OncoImmunology 7, e1461303 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  164. He, W. et al. IL22RA1/STAT3 signaling promotes stemness and tumorigenicity in pancreatic cancer. Cancer Res. 78, 3293–3305 (2018).

    Article  CAS  PubMed  Google Scholar 

  165. Gao, J. et al. Infiltrating plasma cells maintain glioblastoma stem cells through IgG-tumor binding. Cancer Cell https://doi.org/10.1016/j.ccell.2024.12.006 (2025).

  166. Miao, Y. et al. Adaptive immune resistance emerges from tumor-initiating stem cells. Cell 177, 1172–1186.e14 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. Fu, Y.-Y. et al. T cell recruitment to the intestinal stem cell compartment drives immune-mediated intestinal damage after allogeneic transplantation. Immunity 51, 90–103.e3 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Takashima, S. et al. T cell-derived interferon-γ programs stem cell death in immune-mediated intestinal damage. Sci. Immunol. 4, eaay8556 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  169. Espín-Palazón, R. et al. Proinflammatory signaling regulates hematopoietic stem cell emergence. Cell 159, 1070–1085 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  170. Sawamiphak, S., Kontarakis, Z. & Stainier, D. Y. R. Interferon γ signaling positively regulates hematopoietic stem cell emergence. Dev. Cell 31, 640–653 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Li, Y. et al. Inflammatory signaling regulates embryonic hematopoietic stem and progenitor cell production. Genes. Dev. 28, 2597–2612 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  172. Wattrus, S. J. et al. Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality. Science 377, 1413–1419 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  173. Pessoa Rodrigues, C. et al. Transcripts of repetitive DNA elements signal to block phagocytosis of hematopoietic stem cells. Science 385, eadn1629 (2024).

    Article  CAS  PubMed  Google Scholar 

  174. Kyritsis, N. et al. Acute inflammation initiates the regenerative response in the adult zebrafish brain. Science 338, 1353–1356 (2012). This work shows that in zebrafish inflammation is pivotal to regenerate the brain after injury. Stem–immune cross-talk is thus conserved beyond mammals.

    Article  CAS  PubMed  Google Scholar 

  175. Benayoun, B. A. et al. Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses. Genome Res. 29, 697–709 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  176. Aurora, A. B. & Olson, E. N. Immune modulation of stem cells and regeneration. Cell Stem Cell 15, 14–25 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Hui, S. P. et al. Zebrafish regulatory T cells mediate organ-specific regenerative programs. Dev. Cell 43, 659–672.e5 (2017).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The author apologizes to colleagues whose work was omitted due to space constraints. The author thanks members of his team, scientists of the Immunity and Cancer Unit of Institut Curie and the Reis e Sousa laboratory of the Crick Institute for fruitful discussions and critical reading of the manuscript. This work is supported by a European Research Council (ERC) Starting Grant (STEMGUARD 101075865), by the grant ‘Impact Santé’ supported by Agence Nationale de la Recherche (ANR) under France 2030 (ANR-24-RRII-0005) on funds administered by Inserm, by funding from the programme France 2030 launched by the French Government (ANR 11 LBX 0043, part of IDEX PSL ANR-10-IDEX-0001-02), by the Major Research Program of PSL Research University ‘DEVINE’ launched by PSL Research University and implemented by ANR (ANR-10-IDEX-0001), by a Jeune Équipe grant from the Fondation pour la Recherche Médicale (ConvAJE202110014409) and by funding from Institut Curie.

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Glossary

Adult stem cells

Cells, located in specific niches within adult tissues, that are undifferentiated cells that generate tissue-specific differentiated cells upon division. Contrary to embryonic stem cells (ES cells), adult stem cells can give rise to a limited number of differentiated cell types. Depending on the tissue, adult stem cells are constantly cycling (intestinal stem cells (IS cells)), alternating between periods of cycling and quiescence (hair follicle stem cells (HFS cells) of the skin) or quiescent without the activation of tissue repair (muscle stem cells (MuS cells)).

Embryonic stem cells

(ES cells). Pluripotent cells isolated from the inner cell mass of blastocysts (early-stage embryos), which can be differentiated in cells of the three primary germ layers. These cells have been widely used as a stem cell model, including in infection studies, due to their relative simplicity of isolation and culture. One disadvantage of using ES cells for pathogen infection relates to a poor physiological relevance, as such cells are rarely in contact with pathogens in natural settings. Nevertheless, ES cells have been an invaluable tool for the stem cell immunity research field, and enabled the discovery of biological mechanisms whose existence was later confirmed in adult stem cells.

Inflammageing

This umbrella term refers to increased inflammation gradually occurring with advanced age, in the absence of infection. There are increased levels of pro-inflammatory cytokines (interferons, interleukins) in the blood and tissues of aged individuals, as well as changes in the composition of immune cells, with a bias towards the myeloid lineage to the detriment of the lymphoid lineage.

Stem–immune cross-talk

The interactions between stem cells and immune cells that modulate their respective activity. Stem–immune cross-talk can be mediated by direct cell–cell contact, or via the secretion of soluble mediators such as cytokines. If research has largely focused on immune cells regulating stem cells, more recent data document that stem cells can also influence immune cells.

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Poirier, E.Z. How stem cells respond to infection, inflammation and ageing. Nat Rev Immunol (2025). https://doi.org/10.1038/s41577-025-01203-z

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