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Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

Abstract

Intestinal microbes provide multicellular hosts with nutrients and confer resistance to infection. The delicate balance between pro- and anti-inflammatory mechanisms, essential for gut immune homeostasis, is affected by the composition of the commensal microbial community. Regulatory T cells (Treg cells) expressing transcription factor Foxp3 have a key role in limiting inflammatory responses in the intestine1. Although specific members of the commensal microbial community have been found to potentiate the generation of anti-inflammatory Treg or pro-inflammatory T helper 17 (TH17) cells2,3,4,5,6, the molecular cues driving this process remain elusive. Considering the vital metabolic function afforded by commensal microorganisms, we reasoned that their metabolic by-products are sensed by cells of the immune system and affect the balance between pro- and anti-inflammatory cells. We tested this hypothesis by exploring the effect of microbial metabolites on the generation of anti-inflammatory Treg cells. We found that in mice a short-chain fatty acid (SCFA), butyrate, produced by commensal microorganisms during starch fermentation, facilitated extrathymic generation of Treg cells. A boost in Treg-cell numbers after provision of butyrate was due to potentiation of extrathymic differentiation of Treg cells, as the observed phenomenon was dependent on intronic enhancer CNS1 (conserved non-coding sequence 1), essential for extrathymic but dispensable for thymic Treg-cell differentiation1,7. In addition to butyrate, de novo Treg-cell generation in the periphery was potentiated by propionate, another SCFA of microbial origin capable of histone deacetylase (HDAC) inhibition, but not acetate, which lacks this HDAC-inhibitory activity. Our results suggest that bacterial metabolites mediate communication between the commensal microbiota and the immune system, affecting the balance between pro- and anti-inflammatory mechanisms.

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Figure 1: SCFAs produced by commensal bacteria stimulate in vitro generation of Treg cells.
Figure 2: Butyrate provision promotes extrathymic Treg-cell generation in vivo.
Figure 3: Butyrate acts within T cells to enhance acetylation of the Foxp3 locus and Foxp3 protein.
Figure 4: HDAC-inhibitory activity of butyrate decreases pro-inflammatory cytokine expression within dendritic cells to promote Treg induction.

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Gene Expression Omnibus

Data deposits

Microarray data have been deposited in the Gene Expression Omnibus (GEO) under accession number GSE51263.

References

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

    Article  ADS  CAS  Google Scholar 

  2. 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  ADS  CAS  Google Scholar 

  3. Ivanov, I. I. et al. Induction of intestinal TH17 cells by segmented filamentous bacteria. Cell 139, 485–498 (2009)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  6. Atarashi, K. et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 500, 232–236 (2013)

    Article  ADS  CAS  Google Scholar 

  7. Zheng, Y. et al. Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate. Nature 463, 808–812 (2010)

    Article  ADS  CAS  Google Scholar 

  8. Annison, G., Illman, R. J. & Topping, D. L. Acetylated, propionylated or butyrylated starches raise large bowel short-chain fatty acids preferentially when fed to rats. J. Nutr. 133, 3523–3528 (2003)

    Article  CAS  Google Scholar 

  9. Smith, P. M. et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 341, 569–573 (2013)

    Article  ADS  CAS  Google Scholar 

  10. van Loosdregt, J. et al. Rapid temporal control of Foxp3 protein degradation by sirtuin-1. PLoS ONE 6, e19047 (2011)

    Article  ADS  CAS  Google Scholar 

  11. van Loosdregt, J. et al. Regulation of Treg functionality by acetylation-mediated Foxp3 protein stabilization. Blood 115, 965–974 (2010)

    Article  CAS  Google Scholar 

  12. Zhang, H., Xiao, Y., Zhu, Z., Li, B. & Greene, M. I. Immune regulation by histone deacetylases: a focus on the alteration of FOXP3 activity. Immunol. Cell Biol. 90, 95–100 (2012)

    Article  Google Scholar 

  13. Song, X. et al. Structural and biological features of FOXP3 dimerization relevant to regulatory T cell function. Cell Rep. 1, 665–675 (2012)

    Article  CAS  Google Scholar 

  14. Wang, L., de Zoeten, E. F., Greene, M. I. & Hancock, W. W. Immunomodulatory effects of deacetylase inhibitors: therapeutic targeting of FOXP3+ regulatory T cells. Nature Rev. Drug Discov. 8, 969–981 (2009)

    Article  CAS  Google Scholar 

  15. Tao, R. et al. Deacetylase inhibition promotes the generation and function of regulatory T cells. Nature Med. 13, 1299–1307 (2007)

    Article  CAS  Google Scholar 

  16. Maslowski, K. M. et al. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature 461, 1282–1286 (2009)

    Article  ADS  CAS  Google Scholar 

  17. Thangaraju, M. et al. GPR109A is a G-protein-coupled receptor for the bacterial fermentation product butyrate and functions as a tumor suppressor in colon. Cancer Res. 69, 2826–2832 (2009)

    Article  CAS  Google Scholar 

  18. Nilsson, N. E., Kotarsky, K., Owman, C. & Olde, B. Identification of a free fatty acid receptor, FFA2R, expressed on leukocytes and activated by short-chain fatty acids. Biochem. Biophys. Res. Commun. 303, 1047–1052 (2003)

    Article  CAS  Google Scholar 

  19. MacDonald, K. P. et al. Effector and regulatory T-cell function is differentially regulated by RelB within antigen-presenting cells during GVHD. Blood 109, 5049–5057 (2007)

    Article  CAS  Google Scholar 

  20. Zhu, H. C. et al. Tolerogenic dendritic cells generated by RelB silencing using shRNA prevent acute rejection. Cell. Immunol. 274, 12–18 (2012)

    Article  CAS  Google Scholar 

  21. Shih, V. F. et al. Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways. Nature Immunol. 13, 1162–1170 (2012)

    Article  CAS  Google Scholar 

  22. Fontenot, J. D. et al. Regulatory T cell lineage specification by the forkhead transcription factor Foxp3. Immunity 22, 329–341 (2005)

    Article  CAS  Google Scholar 

  23. Kim, J. M., Rasmussen, J. P. & Rudensky, A. Y. Regulatory T cells prevent catastrophic autoimmunity throughout the lifespan of mice. Nature Immunol. 8, 191–197 (2007)

    Article  CAS  Google Scholar 

  24. Torii, T. et al. Measurement of short-chain fatty acids in human faeces using high-performance liquid chromatography: specimen stability. Ann. Clin. Biochem. 47, 447–452 (2010)

    Article  CAS  Google Scholar 

  25. Samstein, R. M. et al. Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification. Cell 151, 153–166 (2012)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the Robert Black Fellowship of the Damon Runyon Cancer Research Foundation DRG-2143-13 (N.A.), Ludwig Center at Memorial Sloan Kettering Cancer Center and the US National Institutes of Health (NIH) grant T32 A1007621 (N.A.) and R37 AI034206 (A.Y.R.). A.Y.R. is an investigator with the Howard Hughes Medical Institute.

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Authors

Contributions

N.A., C.C. and X.F. performed experiments and analysed data, with general assistance from S.D. and assistance from P.d. for HPLC, P.J.C. for immunoprecipitation of acetylated Foxp3 and J.v.d.V. for ChIP–qPCR experiments. H.L. and J.R.C. performed LC–MS. N.A., C.C., X.F. and A.Y.R. designed and interpreted experiments. K.P. provided Gpr109a mice. N.A. and A.Y.R. wrote the paper.

Corresponding author

Correspondence to Alexander Y. Rudensky.

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The authors declare no competing financial interests.

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Arpaia, N., Campbell, C., Fan, X. et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 504, 451–455 (2013). https://doi.org/10.1038/nature12726

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