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Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria

Abstract

Innate lymphoid cells (ILCs) are a recently characterized family of immune cells that have critical roles in cytokine-mediated regulation of intestinal epithelial cell barrier integrity1,2,3,4,5,6,7,8,9,10. Alterations in ILC responses are associated with multiple chronic human diseases, including inflammatory bowel disease, implicating a role for ILCs in disease pathogenesis3,8,11,12,13. Owing to an inability to target ILCs selectively, experimental studies assessing ILC function have predominantly used mice lacking adaptive immune cells1,2,3,4,5,6,7,8,9,10. However, in lymphocyte-sufficient hosts ILCs are vastly outnumbered by CD4+ T cells, which express similar profiles of effector cytokines. Therefore, the function of ILCs in the presence of adaptive immunity and their potential to influence adaptive immune cell responses remain unknown. To test this, we used genetic or antibody-mediated depletion strategies to target murine ILCs in the presence of an adaptive immune system. We show that loss of retinoic-acid-receptor-related orphan receptor-γt-positive (RORγt+) ILCs was associated with dysregulated adaptive immune cell responses against commensal bacteria and low-grade systemic inflammation. Remarkably, ILC-mediated regulation of adaptive immune cells occurred independently of interleukin (IL)-17A, IL-22 or IL-23. Genome-wide transcriptional profiling and functional analyses revealed that RORγt+ ILCs express major histocompatibility complex class II (MHCII) and can process and present antigen. However, rather than inducing T-cell proliferation, ILCs acted to limit commensal bacteria-specific CD4+ T-cell responses. Consistent with this, selective deletion of MHCII in murine RORγt+ ILCs resulted in dysregulated commensal bacteria-dependent CD4+ T-cell responses that promoted spontaneous intestinal inflammation. These data identify that ILCs maintain intestinal homeostasis through MHCII-dependent interactions with CD4+ T cells that limit pathological adaptive immune cell responses to commensal bacteria.

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Figure 1: RORγt+ ILCs regulate adaptive immune cell responses to commensal bacteria and are enriched in MHCII-associated genes.
Figure 2: T-betNKp46RORγt+ ILCs express MHCII and process and present antigen, but do not induce T-cell proliferation.
Figure 3: Loss of RORγt+ ILC-intrinsic MHCII expression results in commensal bacteria-dependent intestinal inflammation.
Figure 4: RORγt+ ILC-intrinsic MHCII regulates pathological CD4+ T-cell responses to commensal bacteria.

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Acknowledgements

We thank members of the Sonnenberg and Artis laboratories for discussions and critical reading of the manuscript. We also thank H. L. Ma, L. A. Fouser, S. Olland, R. Zollner, K. Lam and A. Root at Pfizer for critical discussions, valuable advice and the preparation of IL-22 antibodies; M. M. Elloso at Janssen Research and Development for critical discussions, valuable advice and the preparation of IL-17 and IL-23 antibodies; and M.S. Marks for providing the E-alpha protein and Y-Ae antibody. The research is supported by the National Institutes of Health (AI061570, AI087990, AI074878, AI095776, AI102942, AI095466, AI095608 and AI097333 to D.A.; T32-AI055428 to L.A.M.; DK071176 to C.O.E.; and DP5OD012116 to G.F.S.), the Crohn’s and Colitis Foundation of America (to D.A.) and the Burroughs Wellcome Fund Investigator in Pathogenesis of Infectious Disease Award (to D.A.). We also thank the Matthew J. Ryan Veterinary Hospital Pathology Lab, the National Institute of Diabetes and Digestive and Kidney Disease Center for the Molecular Studies in Digestive and Liver Disease Molecular Pathology and Imaging Core (P30DK50306), the Penn Microarray Facility and the Abramson Cancer Center Flow Cytometry and Cell Sorting Resource Laboratory (partially supported by NCI Comprehensive Cancer Center Support Grant (2-P30 CA016520)) for technical advice and support. Human tissue samples were provided by the Cooperative Human Tissue Network, which is funded by the National Cancer Institute.

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M.R.H., L.A.M., T.C.F., D.A. and G.F.S. designed and performed the research. C.G.K.Z. performed analyses of microarray data. A.C., J.M.A. and E.J.W. performed the microarray of naive CD4+ T cells. S.G., R.S. and F.D.B. provided advice, performed and analysed 454 pyrosequencing of intestinal commensal bacteria. A.R.M. assisted with reagents and advice for antigen presentation assays. H.-L.M., P.A.K., C.O.E. and G.E. provided essential mouse strains, valuable advice and technical expertise for these studies. M.R.H., L.A.M., T.C.F., D.A. and G.F.S. analysed the data. M.R.H., D.A. and G.F.S. wrote the manuscript.

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Correspondence to Gregory F. Sonnenberg.

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Hepworth, M., Monticelli, L., Fung, T. et al. Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria. Nature 498, 113–117 (2013). https://doi.org/10.1038/nature12240

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