Commensal viruses maintain intestinal intraepithelial lymphocytes via noncanonical RIG-I signaling

Abstract

Much attention has focused on commensal bacteria in health and disease, but the role of commensal viruses is understudied. Although metagenomic analysis shows that the intestine of healthy humans and animals harbors various commensal viruses and the dysbiosis of these viruses can be associated with inflammatory diseases, there is still a lack of causal data and underlying mechanisms to understand the physiological role of commensal viruses in intestinal homeostasis. In the present study, we show that commensal viruses are essential for the homeostasis of intestinal intraepithelial lymphocytes (IELs). Mechanistically, the cytosolic viral RNA-sensing receptor RIG-I in antigen-presenting cells can recognize commensal viruses and maintain IELs via a type I interferon–independent, but MAVS-IRF1-IL-15 axis-dependent, manner. The recovery of IELs by interleukin-15 administration reverses the susceptibility of commensal virus-depleted mice to dextran sulfate sodium–induced colitis. Collectively, our results indicate that commensal viruses maintain the IELs and consequently sustain intestinal homeostasis via noncanonical RIG-I signaling.

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Fig. 1: Commensal viruses maintain IELs.
Fig. 2: RIG-I recognizes commensal viruses to maintain IELs.
Fig. 3: RIG-I signaling in APCs maintains IELs.
Fig. 4: RIG-I signaling maintains IELs independently of microbiota dysbiosis.
Fig. 5: RIG-I signaling supports IEL proliferation and survival.
Fig. 6: Commensal viruses and RIG-I-MAVS signaling maintain IELs via IL-15.
Fig. 7: Commensal viruses and RIG-I signaling promote IL-15 production via IRF-1.
Fig. 8: Recovery of IELs reverses the colitis susceptibility of commensal virus-depleted mice.

Data availability

The EMBL-EBL accession number for viral metagenomics sequences and the 16S ribosomal RNA bacterial sequences is PRJEB27933. The data that support the other findings of this study are available from the corresponding author upon reasonable request.

References

  1. 1.

    Honda, K. & Littman, D. R. The microbiome in infectious disease and inflammation. Annu. Rev. Immunol. 30, 759–795 (2012).

  2. 2.

    Reyes, A. et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334–338 (2010).

  3. 3.

    Virgin, H. W. The virome in mammalian physiology and disease. Cell 157, 142–150 (2014).

  4. 4.

    Zhang, T. et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 4, e3 (2006).

  5. 5.

    Shi, Y. & Mu, L. An expanding stage for commensal microbes in host immune regulation. Cell Mol. Immunol. 14, 339–348 (2017).

  6. 6.

    Lopetuso, L. R., Ianiro, G., Scaldaferri, F., Cammarota, G. & Gasbarrini, A. Gut virome and inflammatory bowel disease. Inflamm. Bowel Dis. 22, 1708–1712 (2016).

  7. 7.

    Yang, J. Y. et al. Enteric viruses ameliorate gut inflammation via Toll-like receptor 3 and Toll-like receptor 7-mediated interferon-β production. Immunity 44, 889–900 (2016).

  8. 8.

    Broggi, A., Tan, Y., Granucci, F. & Zanoni, I. IFN-λ suppresses intestinal inflammation by non-translational regulation of neutrophil function. Nat. Immunol. 18, 1084–1093 (2017).

  9. 9.

    Kernbauer, E., Ding, Y. & Cadwell, K. An enteric virus can replace the beneficial function of commensal bacteria. Nature 516, 94–98 (2014).

  10. 10.

    Cheroutre, H., Lambolez, F. & Mucida, D. The light and dark sides of intestinal intraepithelial lymphocytes. Nat. Rev. Immunol. 11, 445–456 (2011).

  11. 11.

    Cheroutre, H. & Madakamutil, L. Acquired and natural memory T cells join forces at the mucosal front line. Nat. Rev. Immunol. 4, 290–300 (2004).

  12. 12.

    Cheroutre, H. Starting at the beginning: new perspectives on the biology of mucosal T cells. Annu. Rev. Immunol. 22, 217–246 (2004).

  13. 13.

    Mowat, A. M. & Agace, W. W. Regional specialization within the intestinal immune system. Nat. Rev. Immunol. 14, 667–685 (2014).

  14. 14.

    Denning, T. L. et al. Mouse TCRαβ+CD8αα intraepithelial lymphocytes express genes that down-regulate their antigen reactivity and suppress immune responses. J. Immunol. 178, 4230–4239 (2007).

  15. 15.

    Olivares-Villagomez, D. et al. Thymus leukemia antigen controls intraepithelial lymphocyte function and inflammatory bowel disease. Proc. Natl Acad. Sci. USA 105, 17931–17936 (2008).

  16. 16.

    Jiang, W. et al. Recognition of gut microbiota by NOD2 is essential for the homeostasis of intestinal intraepithelial lymphocytes. J. Exp. Med. 210, 2465–2476 (2013).

  17. 17.

    Yu, Q. et al. MyD88-dependent signaling for IL-15 production plays an important role in maintenance of CD8αα TCRαβ and TCRγδ intestinal intraepithelial lymphocytes. J. Immunol. 176, 6180–6185 (2006).

  18. 18.

    Qiu, Y. et al. TLR2-dependent signaling for IL-15 production is essential for the homeostasis of intestinal intraepithelial lymphocytes. Mediators Inflamm. 2016, 4281865 (2016).

  19. 19.

    Konkel, J. E. et al. Control of the development of CD8αα+ intestinal intraepithelial lymphocytes by TGF-β. Nat. Immunol. 12, 312–319 (2011).

  20. 20.

    Cervantes-Barragan, L. et al. Lactobacillus reuteri induces gut intraepithelial CD4+CD8αα+ T cells. Science 357, 806–810 (2017).

  21. 21.

    Karst, S. M., Wobus, C. E., Lay, M. & Davidson, J. Virgin HWt. STAT1-dependent innate immunity to a Norwalk-like virus. Science 299, 1575–1578 (2003).

  22. 22.

    Ma, H., Tao, W. & Zhu, S. T lymphocytes in the intestinal mucosa: defense and tolerance. Cell Mol. Immunol. 16, 216–224 (2019).

  23. 23.

    Ramanan, D., Tang, M. S., Bowcutt, R., Loke, P. & Cadwell, K. Bacterial sensor Nod2 prevents inflammation of the small intestine by restricting the expansion of the commensal Bacteroides vulgatus. Immunity 41, 311–324 (2014).

  24. 24.

    Mueller, S. N. & Mackay, L. K. Tissue-resident memory T cells: local specialists in immune defence. Nat. Rev. Immunol. 16, 79–89 (2016).

  25. 25.

    Cao, X. Self-regulation and cross-regulation of pattern-recognition receptor signalling in health and disease. Nat. Rev. Immunol. 16, 35–50 (2016).

  26. 26.

    Kawai, T. & Akira, S. Innate immune recognition of viral infection. Nat. Immunol. 7, 131–137 (2006).

  27. 27.

    Gross, M., Salame, T. M. & Jung, S. Guardians of the gut—murine intestinal macrophages and dendritic cells. Front Immunol. 6, 254 (2015).

  28. 28.

    Zhu, H. et al. RNA virus receptor Rig-I monitors gut microbiota and inhibits colitis-associated colorectal cancer. J. Exp. Clin. Cancer Res. 36, 2 (2017).

  29. 29.

    Cheroutre, H. & Lambolez, F. The thymus chapter in the life of gut-specific intraepithelial lymphocytes. Curr. Opin. Immunol. 20, 185–191 (2008).

  30. 30.

    Gangadharan, D. et al. Identification of pre- and postselection TCRαβ+ intraepithelial lymphocyte precursors in the thymus. Immunity 25, 631–641 (2006).

  31. 31.

    Fischer, J. C. et al. RIG-I/MAVS and STING signaling promote gut integrity during irradiation- and immune-mediated tissue injury. Sci. Transl. Med. 9, eaag2513 (2017).

  32. 32.

    Fujihashi, K., McGhee, J. R., Yamamoto, M., Peschon, J. J. & Kiyono, H. An interleukin-7 internet for intestinal intraepithelial T cell development: knockout of ligand or receptor reveal differences in the immunodeficient state. Eur. J. Immunol. 27, 2133–2138 (1997).

  33. 33.

    Cao, X. et al. Defective lymphoid development in mice lacking expression of the common cytokine receptor γ chain. Immunity 2, 223–238 (1995).

  34. 34.

    Odendall, C. et al. Diverse intracellular pathogens activate type III interferon expression from peroxisomes. Nat. Immunol. 15, 717–726 (2014).

  35. 35.

    Ohteki, T. et al. The transcription factor interferon regulatory factor 1 (IRF-1) is important during the maturation of natural killer 1.1 +T cell receptor-α/β+ (NK1+ T) cells, natural killer cells, and intestinal intraepithelial T cells. J. Exp. Med. 187, 967–972 (1998).

  36. 36.

    Ogasawara, K. et al. Requirement for IRF-1 in the microenvironment supporting development of natural killer cells. Nature 391, 700–703 (1998).

  37. 37.

    Kamanaka, M. et al. Expression of interleukin-10 in intestinal lymphocytes detected by an interleukin-10 reporter knockin tiger mouse. Immunity 25, 941–952 (2006).

  38. 38.

    Das, G. et al. An important regulatory role for CD4+CD8αα T cells in the intestinal epithelial layer in the prevention of inflammatory bowel disease. Proc. Natl Acad. Sci. USA 100, 5324–5329 (2003).

  39. 39.

    Li, Y. et al. Exogenous stimuli maintain intraepithelial lymphocytes via aryl hydrocarbon receptor activation. Cell 147, 629–640 (2011).

  40. 40.

    Luda, K. M. et al. IRF8 Transcription-factor-dependent classical dendritic cells are essential for intestinal T cell homeostasis. Immunity 44, 860–874 (2016).

  41. 41.

    Li, X. D. et al. Mitochondrial antiviral signaling protein (MAVS) monitors commensal bacteria and induces an immune response that prevents experimental colitis. Proc. Natl Acad. Sci. USA 108, 17390–17395 (2011).

  42. 42.

    Bandeira, A. et al. Localization of γ/δ T cells to the intestinal epithelium is independent of normal microbial colonization. J. Exp. Med. 172, 239–244 (1990).

  43. 43.

    Hoytema van Konijnenburg, D. P. et al. Intestinal epithelial and intraepithelial T cell crosstalk mediates a dynamic response to infection. Cell 171, 783–794 e713 (2017).

  44. 44.

    Sujino, T. et al. Tissue adaptation of regulatory and intraepithelial CD4+ T cells controls gut inflammation. Science 352, 1581–1586 (2016).

  45. 45.

    Zeng, M. et al. MAVS, cGAS, and endogenous retroviruses in T-independent B cell responses. Science 346, 1486–1492 (2014).

  46. 46.

    Manso, C. F., Bibby, D. F. & Mbisa, J. L. Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples. Sci. Rep. 7, 4173 (2017).

  47. 47.

    Chiu, Y. H., Macmillan, J. B. & Chen, Z. J. RNA polymerase III detects cytosolic DNA and induces type I interferons through the RIG-I pathway. Cell 138, 576–591 (2009).

  48. 48.

    Sweere, J. M. et al. Bacteriophage trigger antiviral immunity and prevent clearance of bacterial infection. Science 363, eaat9691 (2019).

  49. 49.

    Kato, H. et al. Cell type-specific involvement of RIG-I in antiviral response. Immunity 23, 19–28 (2005).

  50. 50.

    Yamamoto, M. et al. Role of adaptor TRIF in the MyD88-independent toll-like receptor signaling pathway. Science 301, 640–643 (2003).

  51. 51.

    Michallet, M. C. et al. TRADD protein is an essential component of the RIG-like helicase antiviral pathway. Immunity 28, 651–661 (2008).

  52. 52.

    Gitlin, L. et al. Essential role of mda-5 in type I IFN responses to polyriboinosinic:polyribocytidylic acid and encephalomyocarditis picornavirus. Proc. Natl Acad. Sci. USA 103, 8459–8464 (2006).

  53. 53.

    Baldridge, M. T. et al. Commensal microbes and interferon-λ determine persistence of enteric murine norovirus infection. Science 347, 266–269 (2015).

  54. 54.

    Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S. & Medzhitov, R. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 118, 229–241 (2004).

  55. 55.

    Thurber, R. V., Haynes, M., Breitbart, M., Wegley, L. & Rohwer, F. Laboratory procedures to generate viral metagenomes. Nat. Protoc. 4, 470–483 (2009).

  56. 56.

    Wang, D. et al. Microarray-based detection and genotyping of viral pathogens. Proc. Natl Acad. Sci. USA 99, 15687–15692 (2002).

  57. 57.

    Wood, D. E. & Salzberg, S. L. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46 (2014).

  58. 58.

    Menzel, P., Ng, K. L. & Krogh, A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7, 11257 (2016).

  59. 59.

    Dieleman, L. A. et al. Chronic experimental colitis induced by dextran sulphate sodium (DSS) is characterized by Th1 and Th2 cytokines. Clin. Exp. Immunol. 114, 385–391 (1998).

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Acknowledgements

We thank S. Akria, J. Tschopp, M. Colonna, Z. Yi and Z. Jiang for providing mice lines. We thank T. Xue for providing AAV plasmids. This work was supported by the National Key R&D program of China (grant no. 2018YFA0507403 to R.Z.), the Strategic Priority Research Program of the Chinese Academy of Sciences (grant no. XDB29030102 to R.Z. and S.Z.), the National Natural Science Foundation of China (grant nos. 31770991 to W.J., 91742202 to R.Z., 81525013 to R.Z., 81722022 to W.J., 81821001 to R.Z., W.J. and S.Z., 81788101 to R.Z.) and the Young Talent Support Program and the Fundamental Research Funds for the Central Universities.

Author information

L.L., T.G., W.T., B.L., X.Z. and C.L. performed the experiments for this work. L.L., S.Z., W.J. and R.Z. designed the research. L.L., T.G., W.J. and R.Z. wrote the manuscript. W.J. and R.Z. supervised the project.

Correspondence to Shu Zhu or Wei Jiang or Rongbin Zhou.

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Liu, L., Gong, T., Tao, W. et al. Commensal viruses maintain intestinal intraepithelial lymphocytes via noncanonical RIG-I signaling. Nat Immunol 20, 1681–1691 (2019) doi:10.1038/s41590-019-0513-z

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