Novel antigen-presenting cell imparts Treg-dependent tolerance to gut microbiota
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Abstract
Establishing and maintaining tolerance to self-antigens or innocuous foreign antigens is vital for the preservation of organismal health. Within the thymus, medullary thymic epithelial cells (mTECs) expressing autoimmune regulator (AIRE) have a critical role in self-tolerance through deletion of autoreactive T cells and promotion of thymic regulatory T (T reg ) cell development 1–4 . Within weeks of birth, a separate wave of T reg cell differentiation occurs in the periphery upon exposure to antigens derived from the diet and commensal microbiota 5–8 , yet the cell types responsible for the generation of peripheral T reg (pT reg ) cells have not been identified. Here we describe the identification of a class of RORγt + antigen-presenting cells called Thetis cells, with transcriptional features of both mTECs and dendritic cells, comprising four major sub-groups (TC I–TC IV). We uncover a developmental wave of Thetis cells within intestinal lymph nodes during a critical window in early life, coinciding with the wave of pT reg cell differentiation. Whereas TC I and TC III expressed the signature mTEC nuclear factor AIRE, TC IV lacked AIRE expression and was enriched for molecules required for pT reg generation, including the TGF-β-activating integrin αvβ8. Loss of either major histocompatibility complex class II (MHCII) or ITGB8 by Thetis cells led to a profound impairment in intestinal pT reg differentiation, with ensuing colitis. By contrast, MHCII expression by RORγt + group 3 innate lymphoid cells (ILC3) and classical dendritic cells was neither sufficient nor required for pT reg generation, further implicating TC IV as the tolerogenic RORγt + antigen-presenting cell with an essential function in early life. Our studies reveal parallel pathways for the establishment of tolerance to self and foreign antigens in the thymus and periphery, respectively, marked by the involvement of shared cellular and transcriptional programmes.
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Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219 · see citing works
Comprehensive Integration of Single-Cell Data
Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453 · see citing works
Twelve years of SAMtools and BCFtools
Danecek, P., Bonfield, J., Liddle, J., Marshall, J., Ohan, V., Pollard, M., Whitwham, A., Keane, T., McCarthy, S., Davies, R. M., et al. (2021) · GigaScience · doi:10.1093/gigascience/giab008 · Cited by 15,314 · see citing works
Mootha, V. K., Lindgren, C. M., Eriksson, K.-F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstråle, M., Laurila, E., et al. (2003) · Nature Genetics · doi:10.1038/ng1180 · Cited by 10,197 · see citing works
UMAP: Uniform Manifold Approximation and Projection
McInnes, L., Healy, J., Saul, N., & Großberger, L. (2018) · Journal of Open Source Software · doi:10.21105/joss.00861 · Cited by 9,826 · see citing works
SCANPY: large-scale single-cell gene expression data analysis
Wolf, F. A., Angerer, P., & Theis, F. J. (2018) · Genome Biology · doi:10.1186/s13059-017-1382-0 · Cited by 8,881 · see citing works
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016) · Science · doi:10.1126/science.aad0501 · Cited by 4,944 · see citing works
La Manno, G., Soldatov, R., Zeisel, A., Braun, E., Hochgerner, H., Petukhov, V., Lidschreiber, K., Kastriti, M. E., Lönnerberg, P., Furlan, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0414-6 · Cited by 4,118 · see citing works
Finak, G., McDavid, A., Yajima, M., Deng, J., Gersuk, V., Shalek, A. K., Slichter, C. K., Miller, H. W., McElrath, M. J., Prlic, M., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0844-5 · Cited by 3,159 · see citing works
‘Actively Acquired Tolerance’ of Foreign Cells
Billingham, R. E., Brent, L., & Medawar, P. B. (1953) · Nature · doi:10.1038/172603a0 · Cited by 3,149 · see citing works
Generalizing RNA velocity to transient cell states through dynamical modeling
Bergen, V., Lange, M., Peidli, S., Wolf, F. A., & Theis, F. J. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0591-3 · Cited by 2,951 · see citing works
GENCODE reference annotation for the human and mouse genomes
Frankish, A., Diekhans, M., Ferreira, A.-M., Johnson, R., Jungreis, I., Loveland, J. E., Mudge, J. M., Sisu, C., Wright, J. C., Armstrong, J. C., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky955 · Cited by 2,929 · see citing works
Projection of an Immunological Self Shadow Within the Thymus by the Aire Protein
Anderson, M. S., Venanzi, E. S., Klein, L., Chen, Z., Berzins, S. P., Turley, S. J., von Boehmer, H., Bronson, R. T., Dierich, A., Benoist, C. O., et al. (2002) · Science · doi:10.1126/science.1075958 · Cited by 2,474 · see citing works
Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis
Levine, J. H., Simonds, E. F., Bendall, S. C., Davis, K. L., Amir, E.-A. D., Tadmor, M. D., Litvin, O., Fienberg, H. G., Jager, A., Zunder, E. R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.047 · Cited by 2,303 · see citing works
p63 is essential for regenerative proliferation in limb, craniofacial and epithelial development
Yang, A., Schweitzer, R., Sun, D., Kaghad, M., Walker, N., Bronson, R. T., Tabin, C. J., Sharpe, A. H., Caput, D., Crum, C. P., et al. (1999) · Nature · doi:10.1038/19539 · Cited by 2,224 · see citing works
Perineuronal nets stabilize the grid cell network
Christensen, A. C., Lensjø, K. K., Lepperød, M. E., Dragly, S.-A., Sutterud, H., Blackstad, J. S., Fyhn, M., & Hafting, T. (2021) · Nature Communications · doi:10.1038/s41467-020-20241-w · Cited by 1,865 · see citing works
Recovering Gene Interactions from Single-Cell Data Using Data Diffusion
van Dijk, D., Sharma, R., Nainys, J., Yim, K., Kathail, P., Carr, A. J., Burdziak, C., Moon, K. R., Chaffer, C. L., Pattabiraman, D., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.061 · Cited by 1,829 · see citing works
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
Weirauch, M. T., Yang, A. W. H., Albu, M., Coté, A. G., Montenegro‐Montero, A., Drewe, P., Najafabadi, H. S., Lambert, S. A., Mann, I. K., Cook, K. B., et al. (2014) · Cell · doi:10.1016/j.cell.2014.08.009 · Cited by 1,705 · see citing works
chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
Schep, A. N., Wu, B., Buenrostro, J. D., & Greenleaf, W. J. (2017) · Nature Methods · doi:10.1038/nmeth.4401 · Cited by 1,680 · see citing works
Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function
Olszak, T., An, D., Zeissig, S., Vera, M. P., Richter, J., Franke, A., Glickman, J. N., Siebert, R., Baron, R. M., Kasper, D. L., et al. (2012) · Science · doi:10.1126/science.1219328 · Cited by 1,661 · see citing works
RNA virus interference via CRISPR/Cas13a system in plants
Aman, R., Ali, Z., Butt, H., Mahas, A., Aljedaani, F., Khan, M. Z., Ding, S., & Mahfouz, M. (2018) · Genome Biology · doi:10.1186/s13059-017-1381-1 · Cited by 1,497 · see citing works
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
Granja, J. M., Corces, M. R., Pierce, S. E., Bagdatli, S. T., Choudhry, H., Chang, H. Y., & Greenleaf, W. J. (2021) · Nature Genetics · doi:10.1038/s41588-021-00790-6 · Cited by 1,392 · see citing works
p63 identifies keratinocyte stem cells
Pellegrini, G., Dellambra, E., Golisano, O., Martinelli, E., Fantozzi, I., Bondanza, S., Ponzin, D., McKeon, F., & Luca, M. D. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061032098 · Cited by 1,359 · see citing works
A Critical Role for Dnmt1 and DNA Methylation in T Cell Development, Function, and Survival
Lee, P. P., Fitzpatrick, D. R., Beard, C., Jessup, H. K., Lehar, S. M., Makar, K. W., Pérez‐Melgosa, M., Sweetser, M. T., Schlissel, M. S., Nguyen, S. P., et al. (2001) · Immunity · doi:10.1016/s1074-7613(01)00227-8 · Cited by 1,280 · see citing works
A conserved dendritic-cell regulatory program limits antitumour immunity
Maier, B. B., Leader, A. M., Chen, S. T., Tung, N., Chang, C., Bérichel, J. L., Chudnovskiy, A., Maskey, S., Walker, L. A., Finnigan, J. P., et al. (2020) · Nature · doi:10.1038/s41586-020-2134-y · Cited by 950 · see citing works
Individual intestinal symbionts induce a distinct population of RORγ <sup>+</sup> regulatory T cells
Sefik, E., Geva-Zatorsky, N., Oh, S., Konnikova, L., Zemmour, D., McGuire, A. M., Burzyn, D., Ortiz-Lopez, A., Lobera, M., Yang, J., et al. (2015) · Science · doi:10.1126/science.aaa9420 · Cited by 879 · see citing works
The microbiota regulates type 2 immunity through RORγt <sup>+</sup> T cells
Ohnmacht, C., Park, J.-H., Cording, S., Wing, J. B., Atarashi, K., Obata, Y., Gaboriau-Routhiau, V., Marques, R., Dulauroy, S., Fedoseeva, M., et al. (2015) · Science · doi:10.1126/science.aac4263 · Cited by 863 · see citing works
Tissue residency of innate lymphoid cells in lymphoid and nonlymphoid organs
Gasteiger, G., Fan, X., Dikiy, S., Lee, S. Y., & Rudensky, A. Y. (2015) · Science · doi:10.1126/science.aac9593 · Cited by 813 · see citing works
Self-citationInnate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria
Hepworth, M. R., Monticelli, L. A., Fung, T. C., Ziegler, C. G. K., Grunberg, S., Sinha, R., Mantegazza, A. R., Ma, H., Crawford, A., Angelosanto, J., et al. (2013) · Nature · doi:10.1038/nature12240 · Cited by 780 · see citing works
A guide to histomorphological evaluation of intestinal inflammation in mouse models.
Erben, U., Loddenkemper, C., Doerfel, K., Spieckermann, S., Haller, D., Heimesaat, M. M., Zeitz, M., Siegmund, B., & Kühl, A. A. (2014) · Europe PMC (PubMed Central) · Cited by 768 · see citing works
A cell atlas of human thymic development defines T cell repertoire formation
Park, J.-E., Botting, R. A., Conde, C. D., Popescu, D.-M., Lavaert, M., Kunz, D. J., Goh, I., Stephenson, E., Ragazzini, R., Tuck, E. J., et al. (2020) · Science · doi:10.1126/science.aay3224 · Cited by 725 · see citing works
Quantitative Studies on Tissue Transplantation Immunity. III. Actively Acquired Tolerance
Billingham, R. E., Brent, L., & Medawar, P. B. (1956) · Philosophical transactions of the Royal Society of London. Series B, Biological sciences · doi:10.1098/rstb.1956.0006 · Cited by 689 · see citing works
A weaning reaction to microbiota is required for resistance to immunopathologies in the adult
Al Nabhani, Z., Dulauroy, S., Marques, R., Cousu, C., Al Bounny, S., Déjardin, F., Sparwasser, T., Bérard, M., Cerf-Bensussan, N., & Eberl, G. (2019) · Immunity · doi:10.1016/j.immuni.2019.02.014 · Cited by 679 · see citing works
Cells of the human intestinal tract mapped across space and time
Elmentaite, R., Kumasaka, N., Roberts, K., Fleming, A., Dann, E., King, H. W., Kleshchevnikov, V., Dabrowska, M. H., Pritchard, S., Bolt, L., et al. (2021) · Nature · doi:10.1038/s41586-021-03852-1 · Cited by 677 · see citing works
Self-citationTranscriptional Basis of Mouse and Human Dendritic Cell Heterogeneity
Brown, C. C., Gudjonson, H., Pritykin, Y., Deep, D., Lavallée, V., Mendoza, A., Fromme, R. M., Mažutis, L., Ariyan, C. E., Leslie, C. S., et al. (2019) · Cell · doi:10.1016/j.cell.2019.09.035 · Cited by 582 · see citing works
Self-citationDietary antigens limit mucosal immunity by inducing regulatory T cells in the small intestine
Kim, K. S., Hong, S., Han, D., Yi, J., Jung, J., Yang, B., Lee, J. Y., Lee, M., & Surh, C. D. (2016) · Science · doi:10.1126/science.aac5560 · Cited by 541 · see citing works
Hepworth, M. R., Fung, T. C., Masur, S. H., Kelsen, J. R., McConnell, F. M., Dubrot, J., Withers, D. R., Hugues, S., Farrar, M. A., Reith, W., et al. (2015) · Science · doi:10.1126/science.aaa4812 · Cited by 515 · see citing works
Loss of integrin αvβ8 on dendritic cells causes autoimmunity and colitis in mice
Travis, M. A., Reizis, B., Melton, A. C., Masteller, E., Tang, Q., Proctor, J. M., Wang, Y., Bernstein, X., Huang, X., Reichardt, L. F., et al. (2007) · Nature · doi:10.1038/nature06110 · Cited by 503 · see citing works
c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont
Xu, M., Pokrovskii, M., Ding, Y., Yi, R., Au, C., Harrison, O. J., Galan, C., Belkaid, Y., Bonneau, R., & Littman, D. R. (2018) · Nature · doi:10.1038/nature25500 · Cited by 498 · see citing works
Deletional Tolerance Mediated by Extrathymic Aire-Expressing Cells
Gardner, J. M., DeVoss, J., Friedman, R. S., Wong, D. J., Tan, Y. X., Zhou, X., Johannes, K., Su, M. A., Chang, H. Y., Krummel, M. F., et al. (2008) · Science · doi:10.1126/science.1159407 · Cited by 492 · see citing works
Regulatory T cells generated early in life play a distinct role in maintaining self-tolerance
Yang, S., Fujikado, N., Kolodin, D., Benoist, C. O., & Mathis, D. J. (2015) · Science · doi:10.1126/science.aaa7017 · Cited by 444 · see citing works
Sansom, S. N., Shikama‐Dorn, N., Zhanybekova, S., Nusspaumer, G., Macaulay, I. C., Deadman, M. E., Heger, A., Ponting, C. P., & Holländer, G. A. (2014) · Genome Research · doi:10.1101/gr.171645.113 · Cited by 335 · see citing works
Martin, W. D., Hicks, G. G., Mendiratta, S. K., Leva, H. I., Ruley, H. E., & Kaer, L. V. (1996) · Cell · doi:10.1016/s0092-8674(00)81030-2 · Cited by 324 · see citing works
Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells
Bornstein, C., Nevo, S., Giladi, A., Kadouri, N., Pouzolles, M., Gerbe, F., David, E., Machado, A., Chuprin, A., Tóth, B., et al. (2018) · Nature · doi:10.1038/s41586-018-0346-1 · Cited by 317 · see citing works
Mapping the developing human immune system across organs
Suo, C., Dann, E., Goh, I., Jardine, L., Kleshchevnikov, V., Park, J.-E., Botting, R. A., Stephenson, E., Engelbert, J., Tuong, Z. K., et al. (2022) · Science · doi:10.1126/science.abo0510 · Cited by 315 · see citing works
Self-citationGenetic Tracing via DNGR-1 Expression History Defines Dendritic Cells as a Hematopoietic Lineage
Schraml, B. U., van Blijswijk, J., Zelenay, S., Whitney, P. G., Filby, A. J., Acton, S. E., Rogers, N. C., Moncaut, N., Carvajal, J. J., & Sousa, C. R. E. (2013) · Cell · doi:10.1016/j.cell.2013.07.014 · Cited by 312 · see citing works
ILC3s select microbiota-specific regulatory T cells to establish tolerance in the gut
Lyu, M., Suzuki, H., Kang, L., Gaspal, F., Zhou, W., Goc, J., Zhou, L., Zhou, J., Zhang, W., Bank, J. L. C., et al. (2022) · Nature · doi:10.1038/s41586-022-05141-x · Cited by 295 · see citing works
Perry, J. S. A., Lio, C. J., Kau, A. L., Nutsch, K., Yang, Z., Gordon, J. I., MURPHY, K. M. M., & Hsieh, C. (2014) · Immunity · doi:10.1016/j.immuni.2014.08.007 · Cited by 281 · see citing works
A RORγt+ cell instructs gut microbiota-specific Treg cell differentiation
Kedmi, R., Najar, T. A., Mesa, K. R., Grayson, A., Kroehling, L., Hao, Y., Hao, S., Pokrovskii, M. V., Xu, M., Talbot, J., et al. (2022) · Nature · doi:10.1038/s41586-022-05089-y · Cited by 261 · see citing works
Ulcerative colitis and autoimmunity induced by loss of myeloid αv integrins
Lacy‐Hulbert, A., Smith, A. M., Tissire, H., Barry, M., Crowley, D. G., Bronson, R. T., Roes, J., Savill, J., & Hynes, R. O. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707421104 · Cited by 225 · see citing works
Michelson, D. A., Hase, K., Kaisho, T., Benoist, C. O., & Mathis, D. J. (2022) · Cell · doi:10.1016/j.cell.2022.05.018 · Cited by 208 · see citing works
Aire Enforces Immune Tolerance by Directing Autoreactive T Cells into the Regulatory T Cell Lineage
Malchow, S., Leventhal, D. S., Lee, V., Nishi, S., Socci, N. D., & Savage, P. A. (2016) · Immunity · doi:10.1016/j.immuni.2016.02.009 · Cited by 207 · see citing works
Delayed protection by ESAT-6–specific effector CD4+ T cells after airborne M. tuberculosis infection
Gallegos, A. M., Pamer, E. G., & Glickman, M. S. (2008) · The Journal of Experimental Medicine · doi:10.1084/jem.20080353 · Cited by 194 · see citing works
A cell atlas of human thymic development defines T cell repertoire formationPreprint
Park, J.-E., Botting, R. A., Conde, C. D., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.28.911115 · Cited by 187 · see citing works
IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment
Nirschl, C. J., Suárez‐Fariñas, M., Izar, B., Prakadan, S. M., Dannenfelser, R., Tirosh, I., Liu, Y., Zhu, Q., Devi, K. S. P., Carroll, S. L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.06.016 · Cited by 182 · see citing works
Vascular Development of the Brain Requires β8 Integrin Expression in the Neuroepithelium
Proctor, J. M., Zang, K., Wang, D., Wang, R., & Reichardt, L. F. (2005) · Journal of Neuroscience · doi:10.1523/jneurosci.3467-05.2005 · Cited by 176 · see citing works
An Immunologic Mode of Multigenerational Transmission Governs a Gut Treg Setpoint
Ramanan, D., Sefik, E., Galván-Peña, S., Wu, M., Yang, L., Yang, Z., Kostic, A. D., Golovkina, T. V., Kasper, D. L., Mathis, D. J., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.030 · Cited by 173 · see citing works
Visualizing the structure of RNA-seq expression data using grade of membership models
Dey, K. K., Hsiao, C. J., & Stephens, M. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006599 · Cited by 161 · see citing works
Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans
Choi, J., Baldwin, T., Wong, M., Bolden, J. E., Fairfax, K., Lucas, E. C., Cole, R., Biben, C., Morgan, C., Ramsay, K., et al. (2018) · Nucleic Acids Res. · doi:10.1093/nar/gky1020 · Cited by 151 · see citing works
Absence of MHC class II on cDCs results in microbial-dependent intestinal inflammation
Loschko, J., Schreiber, H. A., Rieke, G. J., Esterházy, D., Meredith, M. M., Pedicord, V. A., Yao, K.-H., Caballero, S., Pamer, E. G., Mucida, D., et al. (2016) · The Journal of Experimental Medicine · doi:10.1084/jem.20160062 · Cited by 139 · see citing works
The transcription factor TCF-1 enforces commitment to the innate lymphoid cell lineage
Harly, C., Kenney, D., Ren, G., Lai, B., Raabe, T. D., Yang, Q., Cam, M. C., Xue, H., Zhao, K., & Bhandoola, A. (2019) · Nature Immunology · doi:10.1038/s41590-019-0445-7 · Cited by 124 · see citing works
Wang, J., Lareau, C. A., Bautista, J. L., Gupta, A. R., Sandor, K. D., Germino, J., Yin, Y., Arvedson, M. P., Reeder, G. C., Cramer, N. T., et al. (2021) · Science Immunology · doi:10.1126/sciimmunol.abl5053 · Cited by 85 · see citing works
Reciprocal transcription factor networks govern tissue-resident ILC3 subset function and identity
Fiancette, R., Finlay, C. M., Willis, C., Bevington, S. L., Soley, J. K., Ng, S. T. H., Baker, S. M., Andrews, S., Hepworth, M. R., & Withers, D. R. (2021) · Nature Immunology · doi:10.1038/s41590-021-01024-x · Cited by 75 · see citing works
Sensory cortex limits cortical maps and drives top-down plasticity in thalamocortical circuits
Zembrzycki, A., Chou, S.-J., Ashery-Padan, R., Stoykova, A., & O'Leary, D. (2013) · Nature Neuroscience · doi:10.1038/nn.3454 · Cited by 73 · see citing works
Aire-expressing ILC3-like cells in the lymph node display potent APC features
Yamano, T., Dobeš, J., Vobořil, M., Steinert, M., Brabec, T., Ziętara, N., Dobešová, M., Ohnmacht, C., Laan, M., Peterson, P., et al. (2019) · The Journal of Experimental Medicine · doi:10.1084/jem.20181430 · Cited by 70 · see citing works
ZBTB46 defines and regulates ILC3s that protect the intestine
Zhou, W., Zhou, L., Zhou, J., Bank, J. L. C., Artis, D., Longman, R., Sonnenberg, G. F., Scherl, E., Sockolow, R., Lukin, D. J., et al. (2022) · Nature · doi:10.1038/s41586-022-04934-4 · Cited by 66 · see citing works
Dobeš, J., Ben‐Nun, O., Binyamin, A., Stoler‐Barak, L., Oftedal, B. E., Goldfarb, Y., Kadouri, N., Gruper, Y., Givony, T., Zalayat, I., et al. (2022) · Nature Immunology · doi:10.1038/s41590-022-01247-6 · Cited by 61 · see citing works
Transcriptional programs that control expression of the autoimmune regulator gene Aire
Herzig, Y., Nevo, S., Bornstein, C., Brezis, M. R., Ben‐Hur, S., Shkedy, A., Eisenberg‐Bord, M., Levi, B. Z., Delacher, M., Goldfarb, Y., et al. (2016) · Nature Immunology · doi:10.1038/ni.3638 · Cited by 57 · see citing works
Papaioannou, N. E., Salei, N., Rambichler, S., Rengarajan, K. R., Popović, J., Küntzel, V., Lehmann, C. H. K., Fiancette, R., Salvermoser, J., Gajdasik, D. W., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20659-2 · Cited by 48 · see citing works
Fergusson, J., Morgan, M., Bruchard, M., Huitema, L., Heesters, B., van Unen, V., van Hamburg, J. P., van der Wel, N. N., Picavet, D. I., Koning, F., et al. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2018.02902 · Cited by 44 · see citing works
Nakawesi, J., This, S., Hütter, J., Boucard-Jourdin, M., Barateau, V., Muleta, K. G., Gooday, L. J., Thomsen, K., López, A. G., Ulmert, I., et al. (2020) · Mucosal Immunology · doi:10.1038/s41385-020-0276-8 · Cited by 44 · see citing works
Stehle, C., Rückert, T., Fiancette, R., Gajdasik, D. W., Willis, C., Ulbricht, C., Durek, P., Mashreghi, M., Finke, D., Hauser, A. E., et al. (2021) · Nature Immunology · doi:10.1038/s41590-021-01029-6 · Cited by 44 · see citing works
Mapping the developing human immune system across organsPreprint
Suo, C., Dann, E., Goh, I., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.17.476665 · Cited by 40 · see citing works
Salvermoser, J., van Blijswijk, J., Papaioannou, N. E., Rambichler, S., Pásztói, M., Pakalniškytė, D., Rogers, N. C., Keppler, S. J., Straub, T., Sousa, C. R. E., et al. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.00699 · Cited by 36 · see citing works
Positive selection of self-MHC-reactive T cells by individual peptide–MHC class II complexes
Barton, G. M., Beers, C., DeRoos, P. C., Eastman, S., Gomez, M. E., Forbush, K. A., & Rudensky, A. Y. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.102645699 · Cited by 19 · see citing works
Self-citationKedmi, R., Najar, T. A., Mesa, K. R., Grayson, A., Kroehling, L., Hao, Y., Hao, S., Pokrovskii, M. V., Xu, M., Talbot, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.19.469318 · Cited by 3 · see citing works
Core skin DC signatures control immune tolerance to skin cancer and limit anti-tumor immunity
Nirschl, C. J., Liu, Y., Sarin, K. Y., Suárez‐Fariñas, M., Chau, D., Sage, P. T., Sharpe, A. H., & Anandasabapathy, N. (2015) · Journal for ImmunoTherapy of Cancer · doi:10.1186/2051-1426-3-s2-p205 · Cited by 1 · see citing works
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TGF-β signaling in health and disease
Massagué, J., & Sheppard, D. (2023) · Cell · doi:10.1016/j.cell.2023.07.036 · Cited by 890 · see citing works
Kim, C. H. (2023) · Cellular & Molecular Immunology · doi:10.1038/s41423-023-00987-1 · Cited by 420 · see citing works
Principles and therapeutic applications of adaptive immunity
Chi, H., Pepper, M., & Thomas, P. G. (2024) · Cell · doi:10.1016/j.cell.2024.03.037 · Cited by 363 · see citing works
TH17 cell heterogeneity and its role in tissue inflammation
Schnell, A., Littman, D. R., & Kuchroo, V. K. (2023) · Nature Immunology · doi:10.1038/s41590-022-01387-9 · Cited by 286 · see citing works
Nutritional regulation of microbiota-derived metabolites: Implications for immunity and inflammation
Arifuzzaman, M., Collins, N., Guo, C., & Artis, D. (2024) · Immunity · doi:10.1016/j.immuni.2023.12.009 · Cited by 155 · see citing works
Therapeutic induction of antigen-specific immune tolerance
Kenison, J. E., Stevens, N. A., & Quintana, F. J. (2023) · Nature reviews. Immunology · doi:10.1038/s41577-023-00970-x · Cited by 154 · see citing works
The role of transcription factors in shaping regulatory T cell identity
Trujillo-Ochoa, J. L., Kazemian, M., & Afzali, B. (2023) · Nature reviews. Immunology · doi:10.1038/s41577-023-00893-7 · Cited by 136 · see citing works
Regulatory T cells in the face of the intestinal microbiota
Ramanan, D., Pratama, A., Zhu, Y., Venezia, O., Sassone-Corsi, M., Chowdhary, K., Galván-Peña, S., Sefik, E., Brown, C., Gélineau, A., et al. (2023) · Nature Reviews Immunology · doi:10.1038/s41577-023-00890-w · Cited by 126 · see citing works
Self-citationThe gut microbiota promotes distal tissue regeneration via RORγ+ regulatory T cell emissaries
Hanna, B. S., Wang, G., Galván-Peña, S., Mann, A. O., Ramirez, R. N., Muñoz-Rojas, A. R., Smith, K., Wan, M., Benoist, C., & Mathis, D. (2023) · Immunity · doi:10.1016/j.immuni.2023.01.033 · Cited by 126 · see citing works
Ruf, B., Greten, T. F., & Korangy, F. (2023) · Nature reviews. Cancer · doi:10.1038/s41568-023-00562-w · Cited by 116 · see citing works
A chemogenetic screen reveals that Trpv1-expressing neurons control regulatory T cells in the gut
Zhu, Y., Meerschaert, K. A., Galván-Peña, S., Bin, N., Yang, D., Basu, H., Kawamoto, R., Shalaby, A., Liberles, S. D., Mathis, D. J., et al. (2024) · Science · doi:10.1126/science.adk1679 · Cited by 120 · see citing works
Programmed and environmental determinants driving neonatal mucosal immune development
Torow, N., Hand, T. W., & Hornef, M. W. (2023) · Immunity · doi:10.1016/j.immuni.2023.02.013 · Cited by 105 · see citing works
Lo, B. C., Kryczek, I., Yu, J., Vatan, L., Caruso, R., Matsumoto, M., Sato, Y., Shaw, M. H., Inohara, N., Xie, Y., et al. (2024) · Science · doi:10.1126/science.adh8342 · Cited by 108 · see citing works
Trivedi, P. J., Hirschfield, G. M., Adams, D., & Vierling, J. M. (2024) · Gastroenterology · doi:10.1053/j.gastro.2024.01.049 · Cited by 98 · see citing works
Distinct ontogenetic lineages dictate cDC2 heterogeneity
Minutti, C. M., Piot, C., da Costa, M. P., Chakravarty, P., Rogers, N. C., Encabo, H. H., Cardoso, A., Loong, J. H. C., Bessou, G., Mionnet, C., et al. (2024) · Nature Immunology · doi:10.1038/s41590-024-01745-9 · Cited by 90 · see citing works
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de Casas, P. C., Knöpper, K., Sarkar, R. D., & Kastenmüller, W. (2023) · Nature reviews. Immunology · doi:10.1038/s41577-023-00965-8 · Cited by 94 · see citing works
Cui, H., Wang, N., Li, H., Bian, Y., Wen, W., Kong, X., & Wang, F. (2024) · Cell Communication and Signaling · doi:10.1186/s12964-024-01505-0 · Cited by 92 · see citing works
Rodrigues, P. F., Wu, S., Tršan, T., Panda, S. K., Fachi, J. L., Liu, Y. A., Du, S., de Oliveira, S., Antonova, A. U., Khantakova, D., et al. (2025) · Cell · doi:10.1016/j.cell.2025.03.020 · Cited by 84 · see citing works
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Gu, Y., Bartolomé-Casado, R., Xu, C., Bertocchi, A., Janney, A., Heuberger, C., Pearson, C. F., Teichmann, S. A., Thornton, E. E., & Powrie, F. M. (2024) · Nature · doi:10.1038/s41586-024-07251-0 · Cited by 86 · see citing works
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Mutsaers, S. E., Miles, T., Prêle, C. M., & Hoyne, G. F. (2023) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2023.108562 · Cited by 83 · see citing works
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Bosteels, V., & Janssens, S. (2024) · Nature reviews. Immunology · doi:10.1038/s41577-024-01079-5 · Cited by 81 · see citing works
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Abramson, J., Dobeš, J., Lyu, M., & Sonnenberg, G. F. (2023) · Nature reviews. Immunology · doi:10.1038/s41577-023-00906-5 · Cited by 81 · see citing works
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Wardell, C. M., Boardman, D. A., & Levings, M. K. (2024) · Nature Reviews Drug Discovery · doi:10.1038/s41573-024-01089-x · Cited by 90 · see citing works
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Rodrigues, P. F., Tršan, T., Cvijetic, G., Khantakova, D., Panda, S. K., Liu, Z., Ginhoux, F., Cella, M., & Colonna, M. (2024) · Immunity · doi:10.1016/j.immuni.2024.05.007 · Cited by 79 · see citing works
Sequential immunotherapy: towards cures for autoimmunity
Ramírez‐Valle, F., Maranville, J., Roy, S., & Plenge, R. M. (2024) · Nature Reviews Drug Discovery · doi:10.1038/s41573-024-00959-8 · Cited by 80 · see citing works
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Molofsky, A. B., & Locksley, R. M. (2023) · Immunity · doi:10.1016/j.immuni.2023.03.014 · Cited by 72 · see citing works
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Fu, L., Upadhyay, R., Pokrovskii, M. V., Chen, F. M., Romero‐Meza, G., Griesemer, A. D., & Littman, D. R. (2025) · Nature · doi:10.1038/s41586-025-08982-4 · Cited by 70 · see citing works
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Canesso, M. C. C., Castro, T. B. R., Nakandakari-Higa, S., Lockhart, A. A. K., Luehr, J. B. W., Bortolatto, J., Parsa, R., Esterházy, D., Lyu, M., Liu, T., et al. (2024) · Science · doi:10.1126/science.ado5088 · Cited by 69 · see citing works
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Cheru, N. T., Hafler, D. A., & Sumida, T. S. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1154575 · Cited by 64 · see citing works
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Kedmi, R., & Littman, D. R. (2024) · Immunity · doi:10.1016/j.immuni.2024.09.011 · Cited by 60 · see citing works
Weckel, A., Dhariwala, M. O., Ly, K., Tran, V. M., Ojewumi, O. T., Riggs, J. B., Gonzalez, J. R., Dwyer, L. R., Okoro, J. N., Leech, J. M., et al. (2023) · Immunity · doi:10.1016/j.immuni.2023.03.008 · Cited by 56 · see citing works
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Eshleman, E. M., Shao, T., Woo, V., Rice, T., Engleman, L., Didriksen, B. J., Whitt, J., Haslam, D. B., Way, S. S., & Alenghat, T. (2023) · Journal of Clinical Investigation · doi:10.1172/jci162190 · Cited by 58 · see citing works
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Cabric, V., Cabric, V., Park, T., Akagbosu, B., Zhao, Z., Lo, Y., Shibu, G., Fisher, L., Iza, Y. A. P., Leslie, C. S., et al. (2025) · Science · doi:10.1126/science.adp0535 · Cited by 71 · see citing works
Self-citationTorow, N., Li, R., Hitch, T. C. A., Mingels, C., Bounny, S. A., van Best, N., Stange, E.-L., Simons, B., Maié, T., Rüttger, L., et al. (2023) · Immunity · doi:10.1016/j.immuni.2023.04.002 · Cited by 55 · see citing works
Gut microbiota in regulatory T cell generation and function: mechanisms and health implications
Sharma, A., Sharma, G., & Im, S. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2516702 · Cited by 65 · see citing works
Wang, A., Huang, H., Shi, J., Yu, X., Ding, R., Zhang, Y., Han, Q., Ni, Z.-Y., Li, X., Zhao, R., et al. (2023) · Journal of Clinical Investigation · doi:10.1172/jci169365 · Cited by 54 · see citing works
Spatiotemporal regulation of peripheral T cell tolerance
Brown, C. C., & Rudensky, A. Y. (2023) · Science · doi:10.1126/science.adg6425 · Cited by 53 · see citing works
Self-citationThe renaissance of oral tolerance: merging tradition and new insights
Cerovic, V., Pabst, O., & Mowat, A. M. (2024) · Nature reviews. Immunology · doi:10.1038/s41577-024-01077-7 · Cited by 50 · see citing works
Early life microbiome influences on development of the mucosal innate immune system
Ignácio, A., Czyz, S., & McCoy, K. D. (2024) · Seminars in Immunology · doi:10.1016/j.smim.2024.101885 · Cited by 52 · see citing works
Gut Microbiota and Microbial Metabolism in Early Risk of Cardiometabolic Disease
Gabriel, C. L., & Ferguson, J. F. (2023) · Circulation Research · doi:10.1161/circresaha.123.322055 · Cited by 46 · see citing works
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Conrad, M. L., Barrientos, G., Cai, X., Mukherjee, S., Das, M., Victor, E. S., & Harb, H. (2024) · Allergy · doi:10.1111/all.16326 · Cited by 47 · see citing works
Regulatory T cells in dominant immunologic tolerance
Georgiev, P., Benamar, M., Han, S., Haigis, M. C., Sharpe, A. H., & Chatila, T. A. (2023) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2023.09.025 · Cited by 46 · see citing works
Narasimhan, H., Richter, M. L., Shakiba, R., Papaioannou, N. E., Stehle, C., Rengarajan, K. R., Ulmert, I., Kendirli, A., del Val, C. D. L. R., Kuo, P., et al. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2417308122 · Cited by 44 · see citing works
Mi, Z., Chen, J., Zhang, Z., Liu, J., Lei, Y., Tan, H., Li, W., Chen, X. S., & Rong, P. (2025) · Science Translational Medicine · doi:10.1126/scitranslmed.ado8395 · Cited by 44 · see citing works
Antonova, A. U., Lonardi, S., Monti, M., Missale, F., Fan, C., Coates, M. L., Bugatti, M., Jaeger, N., Rodrigues, P. F., Brioschi, S., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2318710120 · Cited by 43 · see citing works
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Bao, H., Wang, Y., Xiong, H., Xia, Y., Cui, Z., & Liu, L. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25020727 · Cited by 47 · see citing works
Miller, C. N., Waterfield, M. R., Gardner, J. M., & Anderson, M. S. (2024) · Annual Review of Immunology · doi:10.1146/annurev-immunol-090222-101050 · Cited by 40 · see citing works
RORγt eTACs mediate oral tolerance and Treg induction
Sun, I., Qualls, A., Yin, H., Wang, J., Arvedson, M. P., Germino, J., Horner, N. K., Zhong, S., Du, J., Valdearcos, M., et al. (2025) · The Journal of Experimental Medicine · doi:10.1084/jem.20250573 · Cited by 37 · see citing works
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Zhou, H., Tang, L., Fenton, K. A., & Song, X. (2025) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiaf046 · Cited by 37 · see citing works
Interferon-γ orchestrates leptomeningeal anti-tumour response
Remšík, J., Tong, X., Kunes, R., Li, M., Estrera, R., Snyder, J., Thomson, C., Osman, A. M., Chabot, K., Sener, U. T., et al. (2025) · Nature · doi:10.1038/s41586-025-09012-z · Cited by 40 · see citing works
Self-citationMicrobiota-mediated mechanisms of mucosal immunity across the lifespan
Iliev, I. D., Blander, J. M., Collins, N., Guo, C., Longman, R., Sonnenberg, G. F., Zeng, M. Y., & Artis, D. (2025) · Nature Immunology · doi:10.1038/s41590-025-02281-w · Cited by 43 · see citing works
Role of microbiome in autoimmune liver diseases
Schneider, K. M., Kummen, M., Trivedi, P. J., & Hov, J. R. (2023) · Hepatology · doi:10.1097/hep.0000000000000506 · Cited by 35 · see citing works
Central and peripheral innate and adaptive immunity in Parkinson’s disease
Harms, A. S., Yang, Y., & Tansey, M. G. (2023) · Science Translational Medicine · doi:10.1126/scitranslmed.adk3225 · Cited by 35 · see citing works
Gut microbiota promotes immune tolerance at the maternal-fetal interface
Brown, J. A., Amir, M., Yu, S., Wong, D. S. H., Gu, J., Balaji, U., Parkhurst, C. N., Hong, S., Hart, L. R., Carrow, H. C., et al. (2025) · Cell · doi:10.1016/j.cell.2025.11.022 · Cited by 35 · see citing works
Tizard, I. R. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-23681-5.00013-5 · Cited by 34 · see citing works
Homeostatic, repertoire and transcriptional relationships between colon T regulatory cell subsets
Ramanan, D., Chowdhary, K., Candéias, S. M., Sassone‐Corsi, M., Gélineau, A., Mathis, D. J., & Benoist, C. O. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2311566120 · Cited by 32 · see citing works
Wu, R., Wang, D., Cheng, L., Su, R. J., Li, B., Fan, C., Gao, C., & Wang, C. (2024) · Arthritis Research & Therapy · doi:10.1186/s13075-023-03260-y · Cited by 32 · see citing works
Regulation of systemic metabolism by tissue-resident immune cell circuits
Li, J. H., Hepworth, M. R., & O’Sullivan, T. E. (2023) · Immunity · doi:10.1016/j.immuni.2023.05.001 · Cited by 34 · see citing works
Early-life microbiota-immune homeostasis
Reynolds, H. M., & Bettini, M. L. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1266876 · Cited by 30 · see citing works
Early life imprinting of intestinal immune tolerance and tissue homeostasis
Iza, Y. A. P., & Brown, C. C. (2024) · Immunological Reviews · doi:10.1111/imr.13321 · Cited by 30 · see citing works
Self-citationA coordinated cellular network regulates tolerance to food
Rudnitsky, A., Oh, H., Margolin, M., Dassa, B., Shteinberg, I., Stoler‐Barak, L., Shulman, Z., & Kedmi, R. (2025) · Nature · doi:10.1038/s41586-025-09173-x · Cited by 37 · see citing works
Oral tolerance to dietary antigens and Foxp3 + regulatory T cells
Miranda, M. C. G., & de Lafaille, M. A. C. (2024) · Immunological Reviews · doi:10.1111/imr.13370 · Cited by 28 · see citing works
Regulatory T cells in allergic inflammation
Benamar, M., Chen, Q., Martínez‐Blanco, M., & Chatila, T. A. (2023) · Seminars in Immunology · doi:10.1016/j.smim.2023.101847 · Cited by 27 · see citing works
Neuroimmune interactions: The bridge between inflammatory bowel disease and the gut microbiota
Zhai, J., Li, Y., Liu, J., & Dai, C. (2025) · Clinical and Translational Medicine · doi:10.1002/ctm2.70329 · Cited by 30 · see citing works
ILC3s sense gut microbiota through STING to initiate immune tolerance
Zhou, W., Zhou, J., Ahmed, A., Kim, M. J., Guo, C., & Sonnenberg, G. F. (2025) · Immunity · doi:10.1016/j.immuni.2025.05.016 · Cited by 27 · see citing works
Eomes expression identifies the early bone marrow precursor to classical NK cells
Liang, Z., Anderson, H. D., Locher, V., O’Leary, C. Y., Riesenfeld, S. J., Jabrì, B., McDonald, B. D., & Bendelac, A. S. (2024) · Nature Immunology · doi:10.1038/s41590-024-01861-6 · Cited by 27 · see citing works
Life and death of tolerogenic dendritic cells
Bourque, J., & Hawiger, D. (2023) · Trends in Immunology · doi:10.1016/j.it.2022.12.006 · Cited by 26 · see citing works
Bile acids and their receptors: Potential therapeutic targets in inflammatory bowel disease
Long, X.-Q., Liu, M., Liu, Z.-H., Xia, L.-Z., Lu, S.-P., Xu, X.-P., & Wu, M. (2023) · World Journal of Gastroenterology · doi:10.3748/wjg.v29.i27.4252 · Cited by 28 · see citing works
Functionally diverse thymic medullary epithelial cells interplay to direct central tolerance
Ushio, A., Matsuda‐Lennikov, M., Kalle-Youngoue, F., Shimizu, A., Abdelmaksoud, A. A., Kelly, M. C., Ishimaru, N., & Takahama, Y. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114072 · Cited by 24 · see citing works
Microbiota and urinary tumor immunity: Mechanisms, therapeutic implications, and future perspectives
Li, D., Wu, R., Yu, Q., Tuo, Z., Wang, J., Yoo, K. H., Wei, W., Yang, Y., Ye, L., Guo, Y., et al. (2024) · Chinese Journal of Cancer Research · doi:10.21147/j.issn.1000-9604.2024.06.03 · Cited by 22 · see citing works
Thymic Mimetic Cells: Ontogeny as Immunology
Michelson, D. A., & Mathis, D. J. (2024) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-112122-023316 · Cited by 22 · see citing works
León, B. (2025) · Trends in Immunology · doi:10.1016/j.it.2024.12.005 · Cited by 21 · see citing works
Gélineau, A., Marcelin, G., Ouhachi, M., Dussaud, S., Voland, L., Manuel, R., Baba, I., Rouault, C., Yvan‐Charvet, L., Clément, K., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49820-x · Cited by 21 · see citing works
All roads lead to IgA : Mapping the many pathways of IgA induction in the gut
Siniscalco, E. R., Williams, A., & Eisenbarth, S. C. (2024) · Immunological Reviews · doi:10.1111/imr.13369 · Cited by 20 · see citing works
Microbiota as key factors in inflammatory bowel disease
White, Z., Cabrera, I., Kapustka, I., & Sano, T. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1155388 · Cited by 21 · see citing works
Revisiting Aire and tissue-restricted antigens at single-cell resolution
Matsumoto, M., Yoshida, H., Tsuneyama, K., Oya, T., & Matsumoto, M. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1176450 · Cited by 19 · see citing works
Intestinal Microbiota and Its Effect on Vaccine-Induced Immune Amplification and Tolerance
Liu, Y., Zhou, J., Yang, Y., Chen, X., Chen, L., & Wu, Y. (2024) · Vaccines · doi:10.3390/vaccines12080868 · Cited by 19 · see citing works
Context-dependent role of group 3 innate lymphoid cells in mucosal protection
Araujo, L. P., Edwards, M., Irie, K., Huang, Y.-M., Kawano, Y., Tran, A., Michele, S. D., Bhagat, G., Wang, H. H., & Ivanov, I. (2024) · Science immunology · doi:10.1126/sciimmunol.ade7530 · Cited by 20 · see citing works
Dendritic cells in food allergy, treatment, and tolerance
Liu, E. G., Yin, X., Siniscalco, E. R., & Eisenbarth, S. C. (2024) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2024.06.017 · Cited by 19 · see citing works
Regulation of immune responses to food by commensal microbes
Light, S. H., & Nagler‐Anderson, C. (2024) · Immunological Reviews · doi:10.1111/imr.13396 · Cited by 18 · see citing works
Microbiota-dependent modulation of intestinal anti-inflammatory CD4+ T cell responses
Edwards, M., & Brockmann, L. (2025) · Seminars in Immunopathology · doi:10.1007/s00281-025-01049-6 · Cited by 18 · see citing works
Antigen-presenting cells as arbiters of mucosal tolerance and immunity
Hölting, T. L. B., Park, T., & Brown, C. C. (2025) · Nature Immunology · doi:10.1038/s41590-025-02320-6 · Cited by 18 · see citing works
Self-citationThe thymoproteasome in shaping the CD8+ T-cell repertoire
Takahama, Y. (2023) · Current Opinion in Immunology · doi:10.1016/j.coi.2023.102336 · Cited by 18 · see citing works
Contribution of T cell subsets to different food allergic diseases
Hung, L., Zientara, B., & Berin, M. C. (2024) · Immunological Reviews · doi:10.1111/imr.13368 · Cited by 18 · see citing works
Comparative Analysis of Fecal Microbiota in Vegetarians and Omnivores
Sun, C., Li, A., Xu, C., Ma, J., Wang, H., Jiang, Z., & Hou, J. (2023) · Nutrients · doi:10.3390/nu15102358 · Cited by 17 · see citing works
Kabil, A., Nayyar, N., Xu, C., Brassard, J., Hill, L. A., Shin, S. B., Chopra, S., Lo, B. C., Li, Y., Bal, M., et al. (2025) · The Journal of Experimental Medicine · doi:10.1084/jem.20241671 · Cited by 16 · see citing works
Innate immune cells link dietary cues to normal and abnormal metabolic regulation
Zhang, P., Watari, K., & Karin, M. (2025) · Nature Immunology · doi:10.1038/s41590-024-02037-y · Cited by 16 · see citing works
Preclinical Atopic Dermatitis Skin in Infants: An Emerging Research Area
Paller, A. S., Scharschmidt, T. C., Kežić, S., & Irvine, A. D. (2024) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2024.02.021 · Cited by 14 · see citing works
Intestinal cDC1s provide cues required for CD4+ T cell–mediated resistance to Cryptosporidium
Cohn, I. S., Wallbank, B. A., Haskins, B. E., O’Dea, K. M., Pardy, R. D., Shaw, S., Merolle, M. I., Gullicksrud, J. A., Christian, D. A., Striepen, B., et al. (2024) · The Journal of Experimental Medicine · doi:10.1084/jem.20232067 · Cited by 14 · see citing works
Tang, M. H., Ligthart, I., Varga, S., Lebeer, S., van Overveld, F. J., & Rijkers, G. T. (2025) · Biology · doi:10.3390/biology14030299 · Cited by 14 · see citing works
Structure of gut microbial glycolipid modulates host inflammatory response
Cho, H., Yoo, J., Song, X., Goh, B., Diallo, A., Lee, J., Son, S., Hwang, Y. S., Park, S. B., Oh, S. F., et al. (2025) · Cell · doi:10.1016/j.cell.2025.05.016 · Cited by 13 · see citing works
Can fecal microbiota transplantations modulate autoimmune responses in type 1 diabetes?
Snethlage, C. M. F., de Wit, D. F., Wortelboer, K., Rampanelli, E., Hanssen, N., & Nieuwdorp, M. (2024) · Immunological Reviews · doi:10.1111/imr.13345 · Cited by 12 · see citing works
Pathogenic mechanisms in the evolution of food allergy
Martínez‐Blanco, M., Mukhatayev, Z., & Chatila, T. A. (2024) · Immunological Reviews · doi:10.1111/imr.13398 · Cited by 13 · see citing works
An embarrassment of riches: RORγt+ antigen-presenting cells in peripheral tolerance
Victor, E. S., & Chatila, T. A. (2022) · Immunity · doi:10.1016/j.immuni.2022.10.009 · Cited by 13 · see citing works
Thetis cells induce food-specific Treg cell differentiation and oral tolerancePreprint
Parisotto, Y. F., Cabric, V., Park, T., Akagbosu, B., Zhao, Z., Lo, Y., Fisher, L., Shibu, G., Iza, Y. A. P., Leslie, C., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.08.592952 · Cited by 13 · see citing works
Self-citationEarly-Life Gut Microbiota: Education of the Immune System and Links to Autoimmune Diseases
de Groen, P., Gouw, S. C., Hanssen, N. M. J., Nieuwdorp, M., & Rampanelli, E. (2026) · Microorganisms · doi:10.3390/microorganisms14010210 · Cited by 18 · see citing works
Microbiome modulation of antigen presentation in tolerance and inflammation
He, Y., Mohapatra, G., Asokan, S., Nobs, S. P., & Elinav, E. (2024) · Current Opinion in Immunology · doi:10.1016/j.coi.2024.102471 · Cited by 12 · see citing works
Roberts, L. B., Kelly, A. M., & Hepworth, M. R. (2025) · Mucosal Immunology · doi:10.1016/j.mucimm.2025.01.012 · Cited by 12 · see citing works
IL-18-induced HIF-1α in ILC3s ameliorates the inflammation of C. rodentium-induced colitis
Valle-Noguera, A., Sancho-Temiño, L., Castillo‐González, R., Villa-Gómez, C., Gómez-Sánchez, M. J., Ochoa-Ramos, A., Yagüe-Fernández, P., Palacios, B. S., Zorita, V., Raposo-Ponce, B., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113508 · Cited by 12 · see citing works
Dendritic Cell Migration: An Essential Step in Initiating Adaptive Immunity Across Tissues
Olson, E. C., Williams, A., & Eisenbarth, S. C. (2025) · Immunological Reviews · doi:10.1111/imr.70080 · Cited by 11 · see citing works
- Authors
- Akagbosu, B., Tayyebi, Z., Shibu, G., Paucar Iza, Y. A., Deep, D., Parisotto, Y. F., Fisher, L., Pasolli, H. A., Thevin, V., Elmentaite, R., Knott, M., Hemmers, S., Jahn, L., Friedrich, C., Verter, J., Wang, Z.-M., van den Brink, M., Gasteiger, G., Grünewald, T. G. P., Marie, J. C., Leslie, C., Rudensky, A. Y., & Brown, C. C.
- Affiliations
- Memorial Sloan Kettering Cancer Center (US)
- Rockefeller University (US)
- Centre National de la Recherche Scientifique (FR)
- Wellcome Sanger Institute (GB)
- Ludwig-Maximilians-Universität München (DE)
- University of Würzburg (DE)
- German Cancer Research Center (DE)
- Corresponding author
- Rudensky, Alexander Y.
- Brown, Chrysothemis C.
- ORCID
- Tayyebi, Zakieh
- Shibu, Gayathri
- Deep, Deeksha
- Fisher, Logan
- Pasolli, H. Amalia
- Thevin, Valentin
- Elmentaite, Rasa
- Knott, Maximilian
- Hemmers, Saskia
- Jahn, Lorenz
- Friedrich, Christin
- Verter, Jacob
- Wang, Zhong-Min
- van den Brink, Marcel
- Gasteiger, Georg
- Grünewald, Thomas G. P.
- Marie, Julien C.
- Leslie, Christina
- Rudensky, Alexander Y.
- Brown, Chrysothemis C.
- Venue
- Nature
- Published
- 2022-09-07
- Volume
- 610
- Issue
- 7933
- Pages
- 752-760
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC9605865
- OpenAlex
- W4294904731
- Cited by
- 273
- References
- 77
- Citations by year
- 2026: 61 · 2025: 72 · 2024: 75 · 2023: 57 · 2022: 8
- FWCI
- 20.20
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Howard Hughes Medical Institute (P30 CA08748)
- Conrad N. Hilton Foundation
- Memorial Sloan-Kettering Cancer Center (P30-CA08748)
- Ludwig Institute for Cancer Research
- Wellcome Trust (WT201483/Z/16/Z, 201483/Z/16/Z)
- Parker Institute for Cancer Immunotherapy
- Cycle for Survival
- National Institutes of Health (CA08748, CCSG, P30 CA08748)
- Weill Cornell Medical College (T32GM007739)
- Ludwig Center at Harvard
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology
- National Cancer Institute (CA08748, U54CA209975, CA209975, P30CA008748, CCSG P30 CA08748)
- National Institute of General Medical Sciences (T32GM007739)
- National Institute of Allergy and Infectious Diseases (F30AI154660, DP2AI171116, R01AI034206)
- Topics
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
- Life Sciences › Immunology and Microbiology › Immunology › Immunotherapy and Immune Responses
- Life Sciences › Immunology and Microbiology › Immunology › Psoriasis: Treatment and Pathogenesis
- Keywords
- peripheral regulatory T cells, antigen-presenting cells, gut microbiota, self-tolerance, AIRE, RORγt, MHC class II, integrin αvβ8, TGF-beta, intestinal lymph nodes, colitis, ILC3, dendritic cells, medullary thymic epithelial cells, early life development
- MeSH terms
- Gastrointestinal Microbiome, Antigen-Presenting Cells, Cell Differentiation, Dendritic Cells, Epithelial Cells, Immune Tolerance, Immunity, Innate, Lymph Nodes, Thymus Gland, Integrins, Transforming Growth Factor beta, T-Lymphocytes, Regulatory, Nuclear Receptor Subfamily 1, Group F, Member 3
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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