Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Thymus-derived regulatory T cells contribute to tolerance to commensal microbiota

Nature volume 497, pages 258–262 (2013)Cite this article

Subjects

Abstract

Peripheral mechanisms preventing autoimmunity and maintaining tolerance to commensal microbiota involve CD4+Foxp3+ regulatory T (Treg) cells1,2 generated in the thymus or extrathymically by induction of naive CD4+Foxp3− T cells. Previous studies suggested that the T-cell receptor repertoires of thymic Treg cells and induced Treg cells are biased towards self and non-self antigens, respectively3,4,5,6, but their relative contribution in controlling immunopathology, such as colitis and other untoward inflammatory responses triggered by different types of antigens, remains unresolved7. The intestine, and especially the colon, is a particularly suitable organ to study this question, given the variety of self-, microbiota- and food-derived antigens to which Treg cells and other T-cell populations are exposed. Intestinal environments can enhance conversion to a regulatory lineage8,9 and favour tolerogenic presentation of antigens to naive CD4+ T cells10,11, suggesting that intestinal homeostasis depends on microbiota-specific induced Treg cells12,13,14,15. Here, to identify the origin and antigen-specificity of intestinal Treg cells, we performed single-cell and high-throughput sequencing of the T-cell receptor repertoires of CD4+Foxp3+ and CD4+Foxp3− T cells, and analysed their reactivity against specific commensal species. We show that thymus-derived Treg cells constitute most Treg cells in all lymphoid and intestinal organs, including the colon, where their repertoire is heavily influenced by the composition of the microbiota. Our results suggest that thymic Treg cells, and not induced Treg cells, dominantly mediate tolerance to antigens produced by intestinal commensals.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: TCR repertoires of intestinal Treg cells are similar to the TCR repertoire of CD4+ Foxp3+ thymocytes.
Figure 2: In TCR-β Foxp3GFP transgenic mice most colonic CD4+ Foxp3+ T cells share TCRs with CD4+ Foxp3+ thymocytes.
Figure 3: Antibiotic-induced changes in colonic flora have profound influence on the TCR repertoire of colonic thymic Treg cells.
Figure 4: TCRs from colonic thymic Treg cells recognize microbial antigens.

Similar content being viewed by others

References

  1. Belkaid, Y. & Rouse, B. T. Natural regulatory T cells in infectious disease. Nature Immunol. 6, 353–360 (2005)

    Article  CAS  Google Scholar 

  2. Sakaguchi, S., Powrie, F. & Ransohoff, R. M. Re-establishing immunological self-tolerance in autoimmune disease. Nature Med. 18, 54–58 (2012)

    Article  CAS  Google Scholar 

  3. Jordan, M. S. et al. Thymic selection of CD4+CD25+ regulatory T cells induced by an agonist self-peptide. Nature Immunol. 2, 301–306 (2001)

    Article  CAS  Google Scholar 

  4. Ribot, J., Romagnoli, P. & van Meerwijk, J. P. Agonist ligands expressed by thymic epithelium enhance positive selection of regulatory T lymphocytes from precursors with a normally diverse TCR repertoire. J. Immunol. 177, 1101–1107 (2006)

    Article  CAS  Google Scholar 

  5. Coutinho, A. et al. Thymic commitment of regulatory T cells is a pathway of TCR-dependent selection that isolates repertoires undergoing positive or negative selection. Curr. Top. Microbiol. Immunol. 293, 43–71 (2005)

    CAS  PubMed  Google Scholar 

  6. Hsieh, C. S. et al. An intersection between the self-reactive regulatory and nonregulatory T cell receptor repertoires. Nature Immunol. 7, 401–410 (2006)

    Article  CAS  Google Scholar 

  7. Curotto de Lafaille, M. A. & Lafaille, J. J. Natural and adaptive Foxp3+ regulatory T cells: more of the same or a division of labor? Immunity 30, 626–635 (2009)

    Article  CAS  Google Scholar 

  8. Barnes, M. J. & Powrie, F. Regulatory T cells reinforce intestinal homeostasis. Immunity 31, 401–411 (2009)

    Article  CAS  Google Scholar 

  9. Mucida, D. et al. Reciprocal TH17 and regulatory T cell differentiation mediated by retinoic acid. Science 317, 256–260 (2007)

    Article  CAS  ADS  Google Scholar 

  10. 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)

    Article  CAS  Google Scholar 

  11. Denning, T. L. et al. Lamina propria macrophages and dendritic cells differentially induce regulatory and interleukin 17-producing T cell responses. Nature Immunol. 8, 1086–1094 (2007)

    Article  CAS  Google Scholar 

  12. Round, J. L. & Mazmanian, S. K. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc. Natl Acad. Sci. USA 107, 12204–12209 (2010)

    Article  CAS  ADS  Google Scholar 

  13. Atarashi, K. et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331, 337–341 (2011)

    Article  CAS  ADS  Google Scholar 

  14. Lathrop, S. K. et al. Peripheral education of the immune system by colonic commensal microbiota. Nature 478, 250–254 (2011)

    Article  CAS  ADS  Google Scholar 

  15. Haribhai, D. et al. A requisite role for induced regulatory T cells in tolerance based on expanding antigen receptor diversity. Immunity 35, 109–122 (2011)

    Article  CAS  Google Scholar 

  16. Pacholczyk, R. et al. Origin and T cell receptor diversity of Foxp3+CD4+CD25+ T cells. Immunity 25, 249–259 (2006)

    Article  CAS  Google Scholar 

  17. Kuczma, M. et al. Foxp3-deficient regulatory T cells do not revert into conventional effector CD4+ T cells but constitute a unique cell subset. J. Immunol. 183, 3731–3741 (2009)

    Article  CAS  Google Scholar 

  18. Hsieh, C. S. et al. Recognition of the peripheral self by naturally arising CD25+ CD4+ T cell receptors. Immunity 21, 267–277 (2004)

    Article  CAS  Google Scholar 

  19. Wong, J., Mathis, D. & Benoist, C. TCR-based lineage tracing: no evidence for conversion of conventional into regulatory T cells in response to a natural self-antigen in pancreatic islets. J. Exp. Med. 204, 2039–2045 (2007)

    Article  CAS  Google Scholar 

  20. Lathrop, S. K. et al. Antigen-specific peripheral shaping of the natural regulatory T cell population. J. Exp. Med. 205, 3105–3117 (2008)

    Article  CAS  Google Scholar 

  21. Kuczma, M. et al. Intratumoral convergence of the TCR repertoires of effector and Foxp3+ CD4+ T cells. PLoS ONE 5, e13623 (2010)

    Article  ADS  Google Scholar 

  22. Pacholczyk, R. et al. Nonself-antigens are the cognate specificities of Foxp3+ regulatory T cells. Immunity 27, 493–504 (2007)

    Article  CAS  Google Scholar 

  23. Bautista, J. L. et al. Intraclonal competition limits the fate determination of regulatory T cells in the thymus. Nature Immunol. 10, 610–617 (2009)

    Article  CAS  Google Scholar 

  24. Suffia, I. J. et al. Infected site-restricted Foxp3+ natural regulatory T cells are specific for microbial antigens. J. Exp. Med. 203, 777–788 (2006)

    Article  CAS  Google Scholar 

  25. Geuking, M. B. et al. Intestinal bacterial colonization induces mutualistic regulatory T cell responses. Immunity 34, 794–806 (2011)

    Article  CAS  Google Scholar 

  26. Josefowicz, S. Z. et al. Extrathymically generated regulatory T cells control mucosal TH2 inflammation. Nature 482, 395–399 (2012)

    Article  CAS  ADS  Google Scholar 

  27. Fahlén, L. et al. T cells that cannot respond to TGF-β escape control by CD4+CD25+ regulatory T cells. J. Exp. Med. 201, 737–746 (2005)

    Article  Google Scholar 

  28. Rempala, G. A. & Seweryn, M. Methods for diversity and overlap analysis in T-cell receptor populations. J. Math. Biol. . http://dx.doi.org/10.1007/s00285-012-0589-7 (25 September 2012)

  29. Singh, N. et al. Generation of T cell hybridomas from naturally occurring FoxP3+ regulatory T cells. Methods Mol. Biol. 707, 39–44 (2011)

    Article  CAS  Google Scholar 

  30. Renyi, A. On measures of information and entropy. Proc. 4th Berkley Symp. Math. Stat. Prob. 1, 547–561 (1961)

    MATH  Google Scholar 

Download references

Acknowledgements

This work was supported by basic research grants from the National Institutes of Health (NIH; AI 5R01AI079277 to L.I., and DMS1106485 and R01CA152158 to G.A.R.). The Harvard Digestive Disease Center (HDDC) Microbiome Core facility is supported by P30-DK034854 and Brigham and Women’s Hospital in Boston, Massachusetts. Microbiological analyses were performed by M. Delaney, A. Dubois and Q. Liu in the HDDC Microbiome Core, with additional review of findings by A. B. Onderdonk. We thank J. Pihkala and H. Ignatowicz for technical assistance, M. Kuczma, L. Wojciech, E. Szurek, A. Miazek and P. Muranski for discussion and R. Markowitz for editing the manuscript.

Author information

Authors and Affiliations

  1. Center for Biotechnology and Genomic Medicine, Georgia Regents University, Augusta, 30912, Gerogia, USA

    Anna Cebula, Simarjot Singh Pabla, Richard A. McIndoe, Piotr Kraj & Leszek Ignatowicz

  2. Mathematical Biosciences Institute, College of Public Health, Ohio State University, Columbus, 43210, Ohio, USA

    Michal Seweryn & Grzegorz A. Rempala

  3. Faculty of Mathematics and Computer Science, University of Lodz, Lodz, 90-238, Poland

    Michal Seweryn

  4. Department of Pediatrics, Emory University, Atlanta, 30329, Georgia, USA

    Timothy L. Denning

  5. Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Lynn Bry

  6. Department of Tumor Immunology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Wroclaw, 53-114, Poland

    Pawel Kisielow

Authors
  1. Anna Cebula
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Michal Seweryn
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Grzegorz A. Rempala
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Simarjot Singh Pabla
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Richard A. McIndoe
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Timothy L. Denning
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Lynn Bry
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Piotr Kraj
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Pawel Kisielow
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Leszek Ignatowicz
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

A.C. performed most experiments and analysed the data; M.S. and G.A.R. performed statistical analyses; S.S.P. and R.A.M. designed the PACE program; T.L.D. provided expertise in colonic T-cell isolation; L.B. performed the microbiological study; P.Kr. established TCRmini and Foxp3GFP mice models; P.Ki. and L.I. designed the study, analysed the data and wrote the paper.

Corresponding author

Correspondence to Leszek Ignatowicz.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-7 and Supplementary Tables 1-6. (PDF 641 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cebula, A., Seweryn, M., Rempala, G. et al. Thymus-derived regulatory T cells contribute to tolerance to commensal microbiota. Nature 497, 258–262 (2013). https://doi.org/10.1038/nature12079

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature12079

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing