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A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells

Nature Immunology volume 13, pages 972–980 (2012)Cite this article

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Abstract

The transcription factor Foxp3 participates dominantly in the specification and function of Foxp3+CD4+ regulatory T cells (Treg cells) but is neither strictly necessary nor sufficient to determine the characteristic Treg cell signature. Here we used computational network inference and experimental testing to assess the contribution of other transcription factors to this. Enforced expression of Helios or Xbp1 elicited distinct signatures, but Eos, IRF4, Satb1, Lef1 and GATA-1 elicited exactly the same outcome, acting in synergy with Foxp3 to activate expression of most of the Treg cell signature, including key transcription factors, and enhancing occupancy by Foxp3 at its genomic targets. Conversely, the Treg cell signature was robust after inactivation of any single cofactor. A redundant genetic switch thus 'locked in' the Treg cell phenotype, a model that would account for several aspects of Treg cell physiology, differentiation and stability.

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Figure 1: Computational prediction of transcription factors in control of the Treg cell signature.
Figure 2: Validity of the predicted Foxp3 targets.
Figure 3: Transcriptional induction of genes of the Treg cell signature by Foxp3 and other transcription factors.
Figure 4: Mechanistic effect of Foxp3 cofactors.
Figure 5: Genome-wide analysis of Foxp3.
Figure 6: Mathematical modeling of a 'self-locking' network.

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Acknowledgements

We thank R. Samstein and A. Rudensky for the unpublished ChIP-seq data; S. Smale (University of California, Los Angeles) for mouse cDNA encoding Helios; M. Calderwood and the Center for Cancer Systems Biology for expression cDNA; P. Rahl for advice on ChIP-Seq; J. Ericson, S. Davis, H. Paik and R. Cruse for genomic data analysis; H. Chen and Q. Cai for experimental support; and J. LaVecchio and G. Buruzala for sorting. This work benefited from public data generated by the Immunological Genome Project consortium. Supported by the US National Institutes of Health (AI051530 to C.B. and D.M.; AI072073 to C.B., D.M. and J.C.; training grant T32 DK7260 for support of M.S.F.; and 3R24AI072073-03S1 for support of A.E.), GlaxoSmithKline, the Damon Runyon Cancer Research Foundation (S.H.), the American Diabetes Association (7-07-BETA-14 to W.F.) and the Canadian Institutes of Health Research (J.H.).

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Author notes

  1. Jonathan A Hill & Sokol Haxhinasto

    Present address: Present addresses: Tempero Pharmaceuticals, Cambridge, Massachusetts, USA (J.A.H.), and Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut, USA (S.H.).,

  2. Ayla Ergun and Ting Lu: These authors contributed equally to this work.

Authors and Affiliations

  1. Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA

    Wenxian Fu, Ayla Ergun, Jonathan A Hill, Sokol Haxhinasto, Marlys S Fassett, Diane Mathis & Christophe Benoist

  2. Department of Biomedical Engineering, Howard Hughes Medical Institute, and Center for BioDynamics, Boston University, Boston, Massachusetts, USA

    Ayla Ergun, Ting Lu & James J Collins

  3. Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

    Ting Lu

  4. Immune Disease Institute, Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, Massachusetts, USA

    Roi Gazit & Derrick Rossi

  5. Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA

    Stanley Adoro & Laurie Glimcher

  6. Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France

    Susan Chan & Philippe Kastner

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Contributions

W.F., A.E., T.L., M.S.F., J.A.H., S.A., J.J.C., D.M. and C.B. designed experiments; W.F., J.A.H., S.H., M.S.F. and R.G. did experiments; A.E. and T.L. did computation; L.G., S.C., P.K. and D.R. provided mice and advice; and W.F., A.E., T.L., J.A.H., R.G., M.S.F., J.J.C., D.M. and C.B. analyzed data and wrote manuscript.

Corresponding authors

Correspondence to Diane Mathis or Christophe Benoist.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8 and Note (PDF 2747 kb)

Supplementary Table 1

Cell samples use for CLR prediction. (XLSX 16 kb)

Supplementary Table 2

CLR predicted TFs and the number of genes they influence in the Treg signature. (XLSX 13 kb)

Supplementary Table 3

Expression of Treg signature genes in Tconv cells transduced with different retroviruses, as indicated. (XLSX 70 kb)

Supplementary Table 4

Expression of endogenous TFs in transduced cells (FoldChange from control). (XLSX 11 kb)

Supplementary Table 5

Summary and primary data for ChIP-seq. (XLSX 9 kb)

Supplementary Table 6

Genome-wide FoxP3 binding in Tconv cells transduced with FoxP3, or FoxP3+GATA1. (XLSX 1187 kb)

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Fu, W., Ergun, A., Lu, T. et al. A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells. Nat Immunol 13, 972–980 (2012). https://doi.org/10.1038/ni.2420

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