Hooper, L. V., Littman, D. R. & Macpherson, A. J. Interactions between the microbiota and the immune system. Science 336, 1268–1273 (2012).
Google Scholar
Ansaldo, E., Farley, T. K. & Belkaid, Y. Control of immunity by the microbiota. Annu. Rev. Immunol. 39, 449–479 (2021).
Google Scholar
Xu, M. et al. c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont. Nature 554, 373–377 (2018).
Google Scholar
Chai, J. N. et al. Helicobacter species are potent drivers of colonic T cell responses in homeostasis and inflammation. Sci. Immunol. 2, eaal5068 (2017).
Google Scholar
Wang, J. et al. Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium. Sci. Immunol. 6, eabl5053 (2021).
Google Scholar
Russler-Germain, E. V. et al. Gut Helicobacter presentation by multiple dendritic cell subsets enables context-specific regulatory T cell generation. eLife 10, e54792 (2021).
Google Scholar
Darrasse-Jèze, G. et al. Feedback control of regulatory T cell homeostasis by dendritic cells in vivo. J. Exp. Med. 206, 1853–1862 (2009).
Google Scholar
Durai, V. & Murphy, K. M. Functions of murine dendritic cells. Immunity 45, 719–736 (2016).
Google Scholar
Esterházy, D. et al. Classical dendritic cells are required for dietary antigen-mediated induction of peripheral Treg cells and tolerance. Nat. Immunol. 17, 545–555 (2016).
Google Scholar
Nussenzweig, M. C., Steinman, R. M., Gutchinov, B. & Cohn, Z. A. Dendritic cells are accessory cells for the development of anti-trinitrophenyl cytotoxic T lymphocytes. J. Exp. Med. 152, 1070–1084 (1980).
Google Scholar
Sefik, E. et al. Individual intestinal symbionts induce a distinct population of RORγ+ regulatory T cells. Science 349, 993–997 (2015).
Google Scholar
Esterhazy, D. et al. Compartmentalized gut lymph node drainage dictates adaptive immune responses. Nature 569, 126–130 (2019).
Google Scholar
Worbs, T. et al. Oral tolerance originates in the intestinal immune system and relies on antigen carriage by dendritic cells. J. Exp. Med. 203, 519–527 (2006).
Google Scholar
Koscso, B. et al. Gut-resident CX3CR1hi macrophages induce tertiary lymphoid structures and IgA response in situ. Sci. Immunol. 5, eaax0062 (2020).
Google Scholar
Mildner, A. & Jung, S. Development and function of dendritic cell subsets. Immunity 40, 642–656 (2014).
Google Scholar
Anderson, D. A. 3rd, Dutertre, C. A., Ginhoux, F. & Murphy, K. M. Genetic models of human and mouse dendritic cell development and function. Nat. Rev. Immunol. 21, 101–115 (2021).
Google Scholar
Coombes, J. L. et al. A functionally specialized population of mucosal CD103+ DCs induces Foxp3+ regulatory T cells via a TGF-β and retinoic acid-dependent mechanism. J. Exp. Med. 204, 1757–1764 (2007).
Google Scholar
Persson, E. K. et al. IRF4 transcription-factor-dependent CD103+CD11b+ dendritic cells drive mucosal T helper 17 cell differentiation. Immunity 38, 958–969 (2013).
Google Scholar
Pool, L., Rivollier, A. & Agace, W. W. Deletion of IRF4 in dendritic cells leads to delayed onset of T cell-dependent colitis. J. Immunol. 204, 1047–1055 (2020).
Google Scholar
Wohn, C. et al. Absence of MHC class II on cDC1 dendritic cells triggers fatal autoimmunity to a cross-presented self-antigen. Science Immunol. 5, eaba1896 (2020).
Google Scholar
Yamano, T. et al. Aire-expressing ILC3-like cells in the lymph node display potent APC features. J. Exp. Med. 216, 1027–1037 (2019).
Google Scholar
Hepworth, M. R. et al. Group 3 innate lymphoid cells mediate intestinal selection of commensal bacteria-specific CD4+ T cells. Science 348, 1031–1035 (2015).
Google Scholar
Bartleson, J. M. et al. Strength of tonic T cell receptor signaling instructs T follicular helper cell-fate decisions. Nat. Immunol. 21, 1384–1396 (2020).
Google Scholar
Mackley, E. C. et al. CCR7-dependent trafficking of RORγ+ ILCs creates a unique microenvironment within mucosal draining lymph nodes. Nat. Commun. 6, 5862 (2015).
Google Scholar
Kim, M. H., Taparowsky, E. J. & Kim, C. H. Retinoic acid differentially regulates the migration of innate lymphoid cell subsets to the gut. Immunity 43, 107–119 (2015).
Google Scholar
Wang, R. et al. GARP regulates the bioavailability and activation of TGFβ. Mol. Biol. Cell 23, 1129–1139 (2012).
Google Scholar
Lienart, S. et al. Structural basis of latent TGF-β1 presentation and activation by GARP on human regulatory T cells. Science 362, 952–956 (2018).
Google Scholar
Qin, Y. et al. A milieu molecule for TGF-β required for microglia function in the nervous system. Cell 174, 156–171.e116 (2018).
Google Scholar
Lacy-Hulbert, A. et al. Ulcerative colitis and autoimmunity induced by loss of myeloid alphav integrins. Proc. Natl Acad. Sci. USA 104, 15823–15828 (2007).
Google Scholar
Paidassi, H. et al. Preferential expression of integrin αVβ8 promotes generation of regulatory T cells by mouse CD103+ dendritic cells. Gastroenterology 141, 1813–1820 (2011).
Google Scholar
Travis, M. A. et al. Loss of integrin αVβ8 on dendritic cells causes autoimmunity and colitis in mice. Nature 449, 361–365 (2007).
Google Scholar
Gardner, J. M. et al. Deletional tolerance mediated by extrathymic Aire-expressing cells. Science 321, 843–847 (2008).
Google Scholar
Nakawesi, J. et al. αVβ8 integrin-expression by BATF3-dependent dendritic cells facilitates early IgA responses to Rotavirus. Mucosal Immunol. 14, 53–67 (2021).
Google Scholar
Brown, C. C. et al. Transcriptional basis of mouse and human dendritic cell heterogeneity. Cell 179, 846–863.e824 (2019).
Google Scholar
Barnett, L. G. et al. B cell antigen presentation in the initiation of follicular helper T cell and germinal center differentiation. J. Immunol. 192, 3607–3617 (2014).
Google Scholar
Hepworth, M. R. et al. Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria. Nature 498, 113–117 (2013).
Google Scholar
Goto, Y. et al. Segmented filamentous bacteria antigens presented by intestinal dendritic cells drive mucosal Th17 cell differentiation. Immunity 40, 594–607 (2014).
Google Scholar
Yin, X., Chen, S. & Eisenbarth, S. C. Dendritic cell regulation of T helper cells. Annu. Rev. Immunol. 39, 759–790 (2021).
Google Scholar
Eberl, G. & Littman, D. R. Thymic origin of intestinal αβ T cells revealed by fate mapping of RORγt+ cells. Science 305, 248–251 (2004).
Google Scholar
Lochner, M. et al. In vivo equilibrium of proinflammatory IL-17+ and regulatory IL-10+Foxp3+RORγt+ T cells. J. Exp. Med. 205, 1381–1393 (2008).
Google Scholar
Kaplan, D. H., Jenison, M. C., Saeland, S., Shlomchik, W. D. & Shlomchik, M. J. Epidermal Langerhans cell-deficient mice develop enhanced contact hypersensitivity. Immunity 23, 611–620 (2005).
Google Scholar
Dow, L. E. et al. Conditional reverse Tet-transactivator mouse strains for the efficient induction of TRE-regulated transgenes in mice. PLoS ONE 9, e95236 (2014).
Google Scholar
Metzger, T. C. et al. Lineage tracing and cell ablation identify a post-Aire-expressing thymic epithelial cell population. Cell Rep. 5, 166–179 (2013).
Google Scholar
Stoeckius, M. et al. Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 14, 865–868 (2017).
Google Scholar
Stoeckius, M. et al. Cell hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. Genome Biol. 19, 224 (2018).
Google Scholar
van Buggenum, J. A. et al. A covalent and cleavable antibody–DNA conjugation strategy for sensitive protein detection via immuno-PCR. Sci Rep. 6, 22675 (2016).
Google Scholar
Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).
Google Scholar
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e3529 (2021).
Google Scholar
Waltman, L., & Nees, J. v. E. A smart local moving algorithm for large-scale modularity-based community detection. Eur. Phys. J. B 86, 471 (2013).
Google Scholar
Wolock, S. L., Lopez, R. & Klein, A. M. Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell Syst. 8, 281–291.e289 (2019).
Google Scholar
Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
Google Scholar
Lopez, R., Regier, J., Cole, M. B., Jordan, M. I. & Yosef, N. Deep generative modeling for single-cell transcriptomics. Nat. Methods 15, 1053–1058 (2018).
Google Scholar