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.

  • Resource
  • Published:

Epigenetic and transcriptional signatures of stable versus plastic differentiation of proinflammatory γδ T cell subsets

Nature Immunology volume 14, pages 1093–1100 (2013)Cite this article

Subjects

Abstract

Two distinct subsets of γδ T cells that produce interleukin 17 (IL-17) (CD27− γδ T cells) or interferon-γ (IFN-γ) (CD27+ γδ T cells) develop in the mouse thymus, but the molecular determinants of their functional potential in the periphery remain unknown. Here we conducted a genome-wide characterization of the methylation patterns of histone H3, along with analysis of mRNA encoding transcription factors, to identify the regulatory networks of peripheral IFN-γ-producing or IL-17-producing γδ T cell subsets in vivo. We found that CD27+ γδ T cells were committed to the expression of Ifng but not Il17, whereas CD27− γδ T cells displayed permissive chromatin configurations at loci encoding both cytokines and their regulatory transcription factors and differentiated into cells that produced both IL-17 and IFN-γ in a tumor microenvironment.

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: Genome-wide histone H3 methylation in subsets of γδ T cells and CD4+ helper T cells.
Figure 2: Peripheral γδ27+ and γδ27− T cells display distinct genome-wide histone H3 methylation patterns.
Figure 3: DKK3 and SLAMF1 are molecular determinants of γδ27− T cells.
Figure 4: Epigenetic and transcriptional patterning of Ifng and Il17a in γδ T cell subsets.
Figure 5: Permissive histone H3 methylation patterns associate with transcription of TH1- and TH17-related factors in γδ T cell subsets.
Figure 6: Differentiation of IL-17+IFN-γ+ γδ27− cells in vitro and in vivo.

Similar content being viewed by others

Accession codes

Primary accessions

Gene Expression Omnibus

References

  1. Sutton, C.E. et al. Interleukin-1 and IL-23 induce innate IL-17 production from γδ T cells, amplifying Th17 responses and autoimmunity. Immunity 31, 331–341 (2009).

    CAS  PubMed  Google Scholar 

  2. Petermann, F. et al. γδ T cells enhance autoimmunity by restraining regulatory T cell responses via an interleukin-23-dependent mechanism. Immunity 33, 351–363 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Pantelyushin, S. et al. Rorγt+ innate lymphocytes and γδ T cells initiate psoriasiform plaque formation in mice. J. Clin. Invest. 122, 2252–2256 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Shichita, T. et al. Pivotal role of cerebral interleukin-17-producing γδ T cells in the delayed phase of ischemic brain injury. Nat. Med. 15, 946–950 (2009).

    CAS  PubMed  Google Scholar 

  5. Cai, Y. et al. Pivotal role of dermal IL-17-producing γδ T cells in skin inflammation. Immunity 35, 596–610 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Lockhart, E., Green, A.M. & Flynn, J.L. IL-17 production is dominated by γδ T cells rather than CD4 T cells during Mycobacterium tuberculosis infection. J. Immunol. 177, 4662–4669 (2006).

    CAS  PubMed  Google Scholar 

  7. Bonneville, M., O'Brien, R.L. & Born, W.K. γδ T cell effector functions: a blend of innate programming and acquired plasticity. Nat. Rev. Immunol. 10, 467–478 (2010).

    CAS  PubMed  Google Scholar 

  8. Yin, Z. et al. T-Bet expression and failure of GATA-3 cross-regulation lead to default production of IFN-γ by γδ T cells. J. Immunol. 168, 1566–1571 (2002).

    CAS  PubMed  Google Scholar 

  9. Gomes, A.Q., Martins, D.S. & Silva-Santos, B. Targeting γδ T lymphocytes for cancer immunotherapy: from novel mechanistic insight to clinical application. Cancer Res. 70, 10024–10027 (2010).

    CAS  PubMed  Google Scholar 

  10. Ribot, J.C. et al. CD27 is a thymic determinant of the balance between interferon-γ- and interleukin 17-producing γδ T cell subsets. Nat. Immunol. 10, 427–436 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Jensen, K.D. et al. Thymic selection determines γδ T cell effector fate: antigen-naive cells make interleukin-17 and antigen-experienced cells make interferon γ. Immunity 29, 90–100 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Shibata, K. et al. Identification of CD25+ γδ T cells as fetal thymus-derived naturally occurring IL-17 producers. J. Immunol. 181, 5940–5947 (2008).

    CAS  PubMed  Google Scholar 

  13. Haas, J.D. et al. CCR6 and NK1.1 distinguish between IL-17A and IFN-γ-producing γδ effector T cells. Eur. J. Immunol. 39, 3488–3497 (2009).

    CAS  PubMed  Google Scholar 

  14. Martin, B., Hirota, K., Cua, D.J., Stockinger, B. & Veldhoen, M. Interleukin-17-producing γδ T cells selectively expand in response to pathogen products and environmental signals. Immunity 31, 321–330 (2009).

    CAS  PubMed  Google Scholar 

  15. Zhu, J., Yamane, H. & Paul, W.E. Differentiation of effector CD4 T cell populations. Annu. Rev. Immunol. 28, 445–489 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Haas, J.D. et al. IL-17-mediated negative feedback restricts development of IL-17-producing γδ T cells to an embryonic wave. Immunity 37, 48–59 (2012).

    CAS  PubMed  Google Scholar 

  17. Narayan, K. et al. Intrathymic programming of effector fates in three molecularly distinct γδ T cell subtypes. Nat. Immunol. 13, 511–518 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Wei, G. et al. Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity 30, 155–167 (2009).

    PubMed  PubMed Central  Google Scholar 

  19. Hirahara, K. et al. Helper T-cell differentiation and plasticity: insights from epigenetics. Immunology 134, 235–245 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Ribot, J.C. et al. Cutting edge: adaptive versus innate receptor signals selectively control the pool sizes of murine IFN-γ- or IL-17-producing γδ T cells upon infection. J. Immunol. 185, 6421–6425 (2010).

    CAS  PubMed  Google Scholar 

  21. Randall, K.L. et al. DOCK8 deficiency impairs CD8 T cell survival and function in humans and mice. J. Exp. Med. 208, 2305–2320 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Jabara, H.H. et al. DOCK8 functions as an adaptor that links TLR-MyD88 signaling to B cell activation. Nat. Immunol. 13, 612–620 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Papatriantafyllou, M. et al. Dickkopf-3, an immune modulator in peripheral CD8 T-cell tolerance. Proc. Natl. Acad. Sci. USA 109, 1631–1636 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Griewank, K. et al. Homotypic interactions mediated by Slamf1 and Slamf6 receptors control NKT cell lineage development. Immunity 27, 751–762 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. van Driel, B. et al. Signaling lymphocyte activation molecule regulates development of colitis in mice. Gastroenterology 143, 1544–1554 (2012).

    CAS  PubMed  Google Scholar 

  26. Means, T.K. et al. Evolutionarily conserved recognition and innate immunity to fungal pathogens by the scavenger receptors SCARF1 and CD36. J. Exp. Med. 206, 637–653 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Alfaro, D. et al. EphrinB1-EphB signaling regulates thymocyte-epithelium interactions involved in functional T cell development. Eur. J. Immunol. 37, 2596–2605 (2007).

    CAS  PubMed  Google Scholar 

  28. Basu, A. et al. Cutting edge: Vascular endothelial growth factor-mediated signaling in human CD45RO+CD4+ T cells promotes Akt and ERK activation and costimulates IFN-γ production. J. Immunol. 184, 545–549 (2010).

    CAS  PubMed  Google Scholar 

  29. Croft, M. Control of immunity by the TNFR-related molecule OX40 (CD134). Annu. Rev. Immunol. 28, 57–78 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Furuichi, K. et al. Chemokine receptor CCR1 regulates inflammatory cell infiltration after renal ischemia-reperfusion injury. J. Immunol. 181, 8670–8676 (2008).

    CAS  PubMed  Google Scholar 

  31. Akimzhanov, A.M., Yang, X.O. & Dong, C. Chromatin remodeling of interleukin-17 (IL-17)-IL-17F cytokine gene locus during inflammatory helper T cell differentiation. J. Biol. Chem. 282, 5969–5972 (2007).

    CAS  PubMed  Google Scholar 

  32. Mukasa, R. et al. Epigenetic instability of cytokine and transcription factor gene loci underlies plasticity of the T helper 17 cell lineage. Immunity 32, 616–627 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Schoenborn, J.R. et al. Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing transcription of the gene encoding interferon-γ. Nat. Immunol. 8, 732–742 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Wang, X. et al. Transcription of il17 and il17f is controlled by conserved noncoding sequence 2. Immunity 36, 23–31 (2012).

    PubMed  PubMed Central  Google Scholar 

  35. Turchinovich, G. & Hayday, A.C. Skint-1 identifies a common molecular mechanism for the development of interferon-γ-secreting versus interleukin-17-secreting γδ T cells. Immunity 35, 59–68 (2011).

    CAS  PubMed  Google Scholar 

  36. Laird, R.M., Laky, K. & Hayes, S.M. Unexpected role for the B cell-specific Src family kinase B lymphoid kinase in the development of IL-17-producing γδ T cells. J. Immunol. 185, 6518–6527 (2010).

    CAS  PubMed  Google Scholar 

  37. de Almeida, S.F. et al. Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nat. Struct. Mol. Biol. 18, 977–983 (2011).

    PubMed  Google Scholar 

  38. Charles, K.A. et al. The tumor-promoting actions of TNF-α involve TNFR1 and IL-17 in ovarian cancer in mice and humans. J. Clin. Invest. 119, 3011–3023 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Lee, Y.K. et al. Late developmental plasticity in the T helper 17 lineage. Immunity 30, 92–107 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Veeck, J. & Dahl, E. Targeting the Wnt pathway in cancer: the emerging role of Dickkopf-3. Biochim. Biophys. Acta 1825, 18–28 (2012).

    CAS  PubMed  Google Scholar 

  41. Kaech, S.M., Hemby, S., Kersh, E. & Ahmed, R. Molecular and functional profiling of memory CD8 T cell differentiation. Cell 111, 837–851 (2002).

    CAS  PubMed  Google Scholar 

  42. Malhotra, N. et al. A network of high-mobility group box transcription factors programs innate interleukin-17 production. Immunity 38, 681–693 (2013).

    CAS  PubMed  Google Scholar 

  43. Vahedi, G. et al. STATs shape the active enhancer landscape of T cell populations. Cell 151, 981–993 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Durant, L. et al. Diverse targets of the transcription factor STAT3 contribute to T cell pathogenicity and homeostasis. Immunity 32, 605–615 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Shibata, K. et al. Notch-Hes1 pathway is required for the development of IL-17-producing γδ T cells. Blood 118, 586–593 (2011).

    CAS  PubMed  Google Scholar 

  46. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Carmi, Y. et al. Microenvironment-derived IL-1 and IL-17 interact in the control of lung metastasis. J. Immunol. 186, 3462–3471 (2011).

    CAS  PubMed  Google Scholar 

  48. Hirota, K. et al. Fate mapping of IL-17-producing T cells in inflammatory responses. Nat. Immunol. 12, 255–263 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Sheridan, B.S. et al. γδ T cells exhibit multifunctional and protective memory in intestinal tissues. Immunity 39, 184–195 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Reynolds, J.M., Martinez, G.J., Chung, Y. & Dong, C. Toll-like receptor 4 signaling in T cells promotes autoimmune inflammation. Proc. Natl. Acad. Sci. USA 109, 13064–13069 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Schnekenburger, M., Talaska, G. & Puga, A. Chromium cross-links histone deacetylase 1-DNA methyltransferase 1 complexes to chromatin, inhibiting histone-remodeling marks critical for transcriptional activation. Mol. Cell. Biol. 27, 7089–7101 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25–R35 (2009).

    PubMed  PubMed Central  Google Scholar 

  53. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    PubMed  PubMed Central  Google Scholar 

  54. Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137–R146 (2008).

    PubMed  PubMed Central  Google Scholar 

  56. Feng, J., Liu, T. & Zhang, Y. Using MACS to identify peaks from ChIP-Seq data. Curr Protoc Bioinformatics 34, 2.14.1–2.14.14 (2011).

    Google Scholar 

  57. Zang, C. et al. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25, 1952–1958 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Song, Q. & Smith, A.D. Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics 27, 870–871 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Rhead, B. et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 38, D613–D619 (2010).

    CAS  PubMed  Google Scholar 

  60. Althammer, S., Gonzalez-Vallinas, J., Ballare, C., Beato, M. & Eyras, E. Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data. Bioinformatics 27, 3333–3340 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, 2013).

Download references

Acknowledgements

We thank V. Benes for technical assistance with the ChIP-seq experiments; J. Ribot, S. de Almeida and N. Gonçalves-Sousa for technical advice; H. Kulbe, F. Balkwill and R. Thompson for help with the ID8 tumor model; M.J. Nunes and E. Rodrigues for help with ChIP procedures; and M. Soares, A. Vieira and S. Marques for help with cell sorting; A. Hayday, L. Lefrançois and M. Saraiva for discussions; B. Arnold and C. Niehrs (Deutsches Krebsforschungszentrum, Heidelberg) for Dkk3-deficient mice; C. Terhorst and B. van Driel (Harvard Medical School) for Slamf1-deficient mice; K. Roby (University of Kansas) for ID8 ovarian cancer cells; A. Pamplona (Instituto de Medicina Molecular) for Plasmodium berghei ANKA with transgenic expression of GFP; P. Simas (Instituto de Medicina Molecular) for murid herpes virus 4; M. Correia-Neves (Universidade do Minho) for Mycobacterium avium strain 244.; C. Reis e Sousa (The London Research Institute) for Candida albicans yeast strain WT-SC 3314; and the staff of the animal and flow cytometry facilities of our institutes for experimental assistance. Supported by the European Research Council (StG_260352 to B.S.-S.), the Wellcome Trust (D.J.P.), the European Molecular Biology Organization (B.S.-S.), Fundação para a Ciência e Tecnologia (K.S., A.R.G. and M.R.) and the Graduate Program in Areas of Basic and Applied Biology of Universidade do Porto (M.R.).

Author information

Author notes

  1. Nina Schmolka and Karine Serre: These authors contributed equally to this work.

Authors and Affiliations

  1. Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal

    Nina Schmolka, Karine Serre, Ana R Grosso, Margarida Rei, Anita Q Gomes & Bruno Silva-Santos

  2. Blizard Institute, Barts and The London School of Medicine, Queen Mary University of London, London, UK

    Margarida Rei & Daniel J Pennington

  3. Escola Superior de Tecnologia da Saúde de Lisboa, Lisbon, Portugal

    Anita Q Gomes

  4. Instituto Gulbenkian de Ciência, Oeiras, Portugal

    Bruno Silva-Santos

Authors
  1. Nina Schmolka
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Karine Serre
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ana R Grosso
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Margarida Rei
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Daniel J Pennington
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Anita Q Gomes
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Bruno Silva-Santos
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

N.S. planned and did experiments in Figures 1, 2, 4 and 5; K.S. planned and did experiments in Figures 3,4,5,6; A.R.G. planned and did experiments in Figures 1 and 2; M.R. planned and did experiments in Figure 6; A.Q.G. planned and did experiments in Figures 4 and 5; D.J.P. contributed to designing the study and writing the manuscript; A.Q.G. helped to design and supervise the study; and B.S.-S. designed and supervised the study and wrote the manuscript.

Corresponding authors

Correspondence to Anita Q Gomes or Bruno Silva-Santos.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–9 and Supplementary Tables 2 and 3 (PDF 1458 kb)

Supplementary Table 1

Supplementary Table 1 (XLS 17112 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Schmolka, N., Serre, K., Grosso, A. et al. Epigenetic and transcriptional signatures of stable versus plastic differentiation of proinflammatory γδ T cell subsets. Nat Immunol 14, 1093–1100 (2013). https://doi.org/10.1038/ni.2702

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ni.2702

This article is cited by

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