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c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4+ T cells

A Publisher Correction to this article was published on 08 February 2019

This article has been updated

Abstract

The transcription factor c-Maf induces the anti-inflammatory cytokine IL-10 in CD4+ T cells in vitro. However, the global effects of c-Maf on diverse immune responses in vivo are unknown. Here we found that c-Maf regulated IL-10 production in CD4+ T cells in disease models involving the TH1 subset of helper T cells (malaria), TH2 cells (allergy) and TH17 cells (autoimmunity) in vivo. Although mice with c-Maf deficiency targeted to T cells showed greater pathology in TH1 and TH2 responses, TH17 cell–mediated pathology was reduced in this context, with an accompanying decrease in TH17 cells and increase in Foxp3+ regulatory T cells. Bivariate genomic footprinting elucidated the c-Maf transcription-factor network, including enhanced activity of NFAT; this led to the identification and validation of c-Maf as a negative regulator of IL-2. The decreased expression of the gene encoding the transcription factor RORγt (Rorc) that resulted from c-Maf deficiency was dependent on IL-2, which explained the in vivo observations. Thus, c-Maf is a positive and negative regulator of the expression of cytokine-encoding genes, with context-specific effects that allow each immune response to occur in a controlled yet effective manner.

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Fig. 1: Expression of Maf and that of Il10 correlate in all helper T cell and Treg cell subsets.
Fig. 2: c-Maf deficiency in CD4+ T cells affects susceptibility to disease in a context-specific manner.
Fig. 3: Deciphering c-Maf-driven transcriptional programs within dominant disease-associated immune responses.
Fig. 4: c-Maf regulates Il10 expression in CD4+ T cells in vivo with wider disease-specific effects.
Fig. 5: c-Maf deficiency results in the loss of IL-10-secreting effector TH1 and TH2 cells in the malaria and HDM allergy models, while in the EAE model, c-Maf has a dominant role in controlling the balance of TH17 cells and Treg cells.
Fig. 6: The context specificity of c-Maf in the immune response is driven by both direct mechanisms and indirect mechanisms.
Fig. 7: Identification and validation of IL-2 as a c-Maf target from inferred c-Maf regulated TF networks.

Change history

  • 08 February 2019

    In the version of this article initially published, the Supplementary Data file was an incorrect version. The correct version is now provided. The error has been corrected in the HTML and PDF version of the article.

References

  1. 1.

    Sher, A. & Coffman, R. L. Regulation of immunity to parasites by T cells and T cell-derived cytokines. Annu. Rev. Immunol. 10, 385–409 (1992).

    CAS  Article  Google Scholar 

  2. 2.

    Littman, D. R. & Rudensky, A. Y. Th17 and regulatory T cells in mediating and restraining inflammation. Cell 140, 845–858 (2010).

    CAS  Article  Google Scholar 

  3. 3.

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

    CAS  Article  Google Scholar 

  4. 4.

    Gabrysova, L., Howes, A., Saraiva, M. & O’Garra, A. The regulation of IL-10 expression. Curr. Top. Microbiol. Immunol. 380, 157–190 (2014).

    CAS  PubMed  Google Scholar 

  5. 5.

    Josefowicz, S. Z., Lu, L. F. & Rudensky, A. Y. Regulatory T cells: mechanisms of differentiation and function. Annu. Rev. Immunol. 30, 531–564 (2012).

    CAS  Article  Google Scholar 

  6. 6.

    Apetoh, L. et al. The aryl hydrocarbon receptor interacts with c-Maf to promote the differentiation of type 1 regulatory T cells induced by IL-27. Nat. Immunol. 11, 854–861 (2010).

    CAS  Article  Google Scholar 

  7. 7.

    Ciofani, M. et al. A validated regulatory network for Th17 cell specification. Cell 151, 289–303 (2012).

    CAS  Article  Google Scholar 

  8. 8.

    Cipolletta, D. et al. PPAR-gamma is a major driver of the accumulation and phenotype of adipose tissue Treg cells. Nature 486, 549–553 (2012).

    CAS  Article  Google Scholar 

  9. 9.

    Jones, E. A. & Flavell, R. A. Distal enhancer elements transcribe intergenic RNA in the IL-10 family gene cluster. J. Immunol. 175, 7437–7446 (2005).

    CAS  Article  Google Scholar 

  10. 10.

    Li, P. et al. BATF-JUN is critical for IRF4-mediated transcription in T cells. Nature 490, 543–546 (2012).

    CAS  Article  Google Scholar 

  11. 11.

    Li, W. et al. MiR-568 inhibits the activation and function of CD4+ T cells and Treg cells by targeting NFAT5. Int. Immunol. 26, 269–281 (2014).

    CAS  Article  Google Scholar 

  12. 12.

    Mascanfroni, I. D. et al. Metabolic control of type 1 regulatory T cell differentiation by AHR and HIF1-α. Nat. Med 21, 638–646 (2015).

    CAS  Article  Google Scholar 

  13. 13.

    Motomura, Y. et al. The transcription factor E4BP4 regulates the production of IL-10 and IL-13 in CD4+ T cells. Nat. Immunol. 12, 450–459 (2011).

    CAS  Article  Google Scholar 

  14. 14.

    Neumann, C. et al. Role of Blimp-1 in programing Th effector cells into IL-10 producers. J. Exp. Med. 211, 1807–1819 (2014).

    CAS  Article  Google Scholar 

  15. 15.

    Rutz, S. et al. Notch regulates IL-10 production by T helper 1 cells. Proc. Natl Acad. Sci. USA 105, 3497–3502 (2008).

    CAS  Article  Google Scholar 

  16. 16.

    Rutz, S. et al. Transcription factor c-Maf mediates the TGF-β-dependent suppression of IL-22 production in TH17 cells. Nat. Immunol.1238–1245 (2011)..

  17. 17.

    Tussiwand, R. et al. Compensatory dendritic cell development mediated by BATF-IRF interactions. Nature 490, 502–507 (2012).

    CAS  Article  Google Scholar 

  18. 18.

    Wan, Y. Y. & Flavell, R. A. Identifying Foxp3-expressing suppressor T cells with a bicistronic reporter. Proc. Natl Acad. Sci. USA 102, 5126–5131 (2005).

    CAS  Article  Google Scholar 

  19. 19.

    Wheaton, J. D., Yeh, C. H. & Ciofani, M. Cutting edge: c-Maf is required for regulatory t cells to adopt RORγt+ and follicular phenotypes. J. Immunol. 199, 3931–3936 (2017).

    CAS  Article  Google Scholar 

  20. 20.

    Xu, M. et al. c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont. Nature 554, 373–377 (2018).

    CAS  Article  Google Scholar 

  21. 21.

    Xu, J. et al. c-Maf regulates IL-10 expression during Th17 polarization. J. Immunol. 182, 6226–6236 (2009).

    CAS  Article  Google Scholar 

  22. 22.

    Eychene, A., Rocques, N. & Pouponnot, C. A new MAFia in cancer. Nat. Rev. Cancer 8, 683–693 (2008).

    CAS  Article  Google Scholar 

  23. 23.

    Yoshida, H. & Hunter, C. A. The immunobiology of interleukin-27. Annu. Rev. Immunol. 33, 417–443 (2015).

    CAS  Article  Google Scholar 

  24. 24.

    Barrat, F. J. et al. In vitro generation of interleukin 10-producing regulatory CD4+ T cells is induced by immunosuppressive drugs and inhibited by T helper type 1 (Th1)- and Th2-inducing cytokines. J. Exp. Med. 195, 603–616 (2002).

    CAS  Article  Google Scholar 

  25. 25.

    Wang, Z. Y. et al. Regulation of IL-10 gene expression in Th2 cells by Jun proteins. J. Immunol. 174, 2098–2105 (2005).

    CAS  Article  Google Scholar 

  26. 26.

    Freitas do Rosario, A. P. et al. IL-27 promotes IL-10 production by effector Th1 CD4+ T cells: a critical mechanism for protection from severe immunopathology during malaria infection. J. Immunol. 188, 1178–1190 (2012).

    CAS  Article  Google Scholar 

  27. 27.

    Wilson, M. S. et al. Suppression of allergic airway inflammation by helminth-induced regulatory T cells. J. Exp. Med. 202, 1199–1212 (2005).

    CAS  Article  Google Scholar 

  28. 28.

    Korn, T. et al. IL-6 controls Th17 immunity in vivo by inhibiting the conversion of conventional T cells into Foxp3+ regulatory T cells. Proc. Natl Acad. Sci. USA 105, 18460–18465 (2008).

    CAS  Article  Google Scholar 

  29. 29.

    Coomes, S.M. et al. CD4 Th2 cells are directly regulated by IL-10 during allergic airway inflammation. Mucosal Immunol. 10, 150–161 (2016).

    Article  Google Scholar 

  30. 30.

    Bettelli, E. et al. IL-10 is critical in the regulation of autoimmune encephalomyelitis as demonstrated by studies of IL-10- and IL-4-deficient and transgenic mice. J. Immunol. 161, 3299–3306 (1998).

    CAS  PubMed  Google Scholar 

  31. 31.

    Honma, S. et al. Dec1 and Dec2 are regulators of the mammalian molecular clock. Nature 419, 841–844 (2002).

    CAS  Article  Google Scholar 

  32. 32.

    Ho, I. C., Hodge, M. R., Rooney, J. W. & Glimcher, L. H. The proto-oncogene c-maf is responsible for tissue-specific expression of interleukin-4. Cell 85, 973–983 (1996).

    CAS  Article  Google Scholar 

  33. 33.

    Ho, I. C., Lo, D. & Glimcher, L. H. c-maf promotes T helper cell type 2 (Th2) and attenuates Th1 differentiation by both interleukin 4-dependent and -independent mechanisms. J. Exp. Med. 188, 1859–1866 (1998).

    CAS  Article  Google Scholar 

  34. 34.

    Andris, F. et al. The transcription factor c-Maf promotes the differentiation of follicular helper T cells. Front. Immunol. 8, 480 (2017).

    Article  Google Scholar 

  35. 35.

    Bauquet, A. T. et al. The costimulatory molecule ICOS regulates the expression of c-Maf and IL-21 in the development of follicular T helper cells and TH-17 cells. Nat. Immunol. 10, 167–175 (2009).

    CAS  Article  Google Scholar 

  36. 36.

    Perez-Mazliah, D. et al. Follicular helper T cells are essential for the elimination of plasmodium infection. EBioMedicine 24, 216–230 (2017).

    Article  Google Scholar 

  37. 37.

    Ma, W., Noble, W. S. & Bailey, T. L. Motif-based analysis of large nucleotide data sets using MEME-ChIP. Nat. Protoc. 9, 1428–1450 (2014).

    CAS  Article  Google Scholar 

  38. 38.

    Chuang, L. S., Ito, K. & Ito, Y. RUNX family: regulation and diversification of roles through interacting proteins. Int. J. Cancer 132, 1260–1271 (2013).

    CAS  Article  Google Scholar 

  39. 39.

    Wang, S. et al. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat. Protoc. 8, 2502–2515 (2013).

    CAS  Article  Google Scholar 

  40. 40.

    BaekS., GoldsteinI. & HagerG. L. Bivariate genomic footprinting detects changes in transcription factor activity. Cell Rep. 19, 1710–1722 (2017).

    CAS  Article  Google Scholar 

  41. 41.

    Djuretic, I. M. et al. Transcription factors T-bet and Runx3 cooperate to activate Ifng and silence Il4 in T helper type 1 cells. Nat. Immunol. 8, 145–153 (2007).

    CAS  Article  Google Scholar 

  42. 42.

    Kataoka, K., Noda, M. & Nishizawa, M. Maf nuclear oncoprotein recognizes sequences related to an AP-1 site and forms heterodimers with both Fos and Jun. Mol. Cell. Biol. 14, 700–712 (1994).

    CAS  Article  Google Scholar 

  43. 43.

    Lin, C. C. et al. Bhlhe40 controls cytokine production by T cells and is essential for pathogenicity in autoimmune neuroinflammation. Nat. Commun. 5, 3551 (2014).

    Article  Google Scholar 

  44. 44.

    Muller, M. R. & Rao, A. NFAT, immunity and cancer: a transcription factor comes of age. Nat. Rev. Immunol. 10, 645–656 (2010).

    Article  Google Scholar 

  45. 45.

    Webster, K. E. et al. In vivo expansion of T reg cells with IL-2-mAb complexes: induction of resistance to EAE and long-term acceptance of islet allografts without immunosuppression. J. Exp. Med. 206, 751–760 (2009).

    CAS  Article  Google Scholar 

  46. 46.

    Laurence, A. et al. Interleukin-2 signaling via STAT5 constrains T helper 17 cell generation. Immunity 26, 371–381 (2007).

    CAS  Article  Google Scholar 

  47. 47.

    Kamanaka, M. et al. Expression of interleukin-10 in intestinal lymphocytes detected by an interleukin-10 reporter knockin tiger mouse. Immunity 25, 941–952 (2006).

    CAS  Article  Google Scholar 

  48. 48.

    Wende, H. et al. The transcription factor c-Maf controls touch receptor development and function. Science 335, 1373–1376 (2012).

    CAS  Article  Google Scholar 

  49. 49.

    Lee, P. P. et al. A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival. Immunity 15, 763–774 (2001).

    CAS  Article  Google Scholar 

  50. 50.

    Kaji, T. et al. Distinct cellular pathways select germline-encoded and somatically mutated antibodies into immunological memory. J. Exp. Med. 209, 2079–2097 (2012).

    CAS  Article  Google Scholar 

  51. 51.

    Freitas do Rosario, A. P. et al. Gradual decline in malaria-specific memory T cell responses leads to failure to maintain long-term protective immunity to Plasmodium chabaudi AS despite persistence of B cell memory and circulating antibody. J. Immunol. 181, 8344–8355 (2008).

    CAS  Article  Google Scholar 

  52. 52.

    Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013).

    CAS  Article  Google Scholar 

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Acknowledgements

We thank R.A. Flavell (Yale University) for Foxp3RFP IL-10GFP mice; M. Sieweke and C. Birchmeier (Max Delbrück Centre for Molecular Medicine) for Maffl/fl mice; G. Trinchieri (Wistar Institute) for anti-IL-12p40 (C17.8.20); The Francis Crick Institute, Biological Services for breeding and maintenance of the mice; the Advanced Sequencing Platform and A. Sesay for help with sequence sample processing; the Flow Cytometry Platform; Bioinformatics Platform and G. Kelly for help with statistics; Photographics and M. Butt for help with figures; V. Stavropoulos for help with in vivo experiments; and A. Singhania and L. Moreira-Teixeira from the AOG laboratory for review and discussion of the manuscript. Supported by the Francis Crick Institute (Crick Core), which since 1 April 2015 has received its core funding from Cancer Research UK (FC001126 and FC010110), the UK Medical Research Council (FC001126 and FC010110) and the Wellcome Trust (FC001126 and FC010110), and before that from the UK Medical Research Council (MRC U117565642) and the European Research Council (294682-TB-PATH (Crick 10127)) (all for A.O.G., L.G., K.P., M.A.-M., L.S.C. and C.W.), the UK Medical Research Council (MRC Centenary Award for L.G.; and MRC eMedLab Medical Bioinformatics Infrastructure Award MR/L016311/1 for N.M.L.), Crick Core projects (10101 for J.L. and FC001051 for J.B. and V.M.), the Wellcome Trust (WT098326MA for J.B. and V.M.; and Joint Investigator Award 103760/Z/14/Z for N.M.L.), Inserm/CNRS and Agence Nationale de la Recherche (ANR-11-BSV3-0026), Fondation pour la Recherche Médicale (DEQ. 20110421320) and the European Research Council (695093 for M.H.S.).

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Contributions

L.G. co-designed the study with A.O.G., executed the experiments, interpreted and analyzed the data, and co-wrote the paper with A.O.G.; M.A.-M. analyzed the ATAC-seq, ChIP-seq and RNA-seq data and contributed to the writing of the paper; R.L. interpreted and analyzed the RNA-seq data and contributed to the writing of the paper; L.S.C. executed and helped design the in vitro experiments with c-Maf-deficient and control CD4+ T cells and analyzed the data; J.S. and C.H. helped execute and interpret malaria experiments; D.P.-M. contributed data for Supplementary Fig. 3; C.W. helped execute EAE experiments; Y.K. and M.W. helped execute and interpret allergy experiments; K.P. performed early RNA-seq analysis; X.W. executed the genetics for obtaining Cd4-cre × Maffl/fl mice and designed and performed all screening and quality control; L.B. performed processing and troubleshooting for RNA-seq analysis; H.W. constructed Maffl/fl mice and provided feedback on the study; M.H.S. provided feedback and suggestions for the study; G.E. supervised analysis of early RNA-seq data; J.B. and V.M. provided advice and input on the ATAC-seq analysis; J.L. provided expertise for the malaria model and feedback on the study; N.M.L. provided advice and input on the RNA-seq analysis and directed the integrated analysis of ATAC-seq, ChIP-seq and RNA-seq; and A.O.G. co-designed the study with L.G., interpreted and analyzed the data, and co-wrote the paper with L.G.

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Correspondence to Anne O’Garra.

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Integrated supplementary information

Supplementary Figure 1 The induction and effect of c-Maf on CD4+ T cell differentiation in vitro

a, Naive CD4+ T cells from Maf fl/fl and Maf fl/flCd4-cre were sorted and stimulated in vitro with anti-CD3 and anti-CD28 in the presence of medium alone, IL-12, IL-27, IL-12 + IL-27, IL-4, TGF-β + IL-6 or TGF-β and assessed for the mRNA expression of Maf, Il10 and master regulator transcription factors Tbx21, Gata3, Rorc and Foxp3 and hallmark cytokines Ifng, Il4 and Il17a as well as Il2ra relative to Hprt as follows. Medium, IL-12, IL-27, IL-12 + IL-27: Maf, Il10, Tbx21, Ifng (day 3); IL-4: Maf (day 5), Il10 (day 5), Gata3 (day 4), Il4 (day 5); TGF-β + IL-6: Maf (day 1), Il10 (day 2), Il17a (day 5); TGF-β: Maf, Il10, Foxp3, Il2ra (day 3) (n = 3 culture wells per condition, mean ± SD; * P< 0.05, ** P< 0.01, *** P< 0.001, **** P< 0.0001, unpaired t-test, two-tailed). Representative data from three biological experiments are shown. b, Naive CD4+ T cells from wild-type mice were sorted, stimulated as in (a) and assessed for intracellular c-Maf on day 3. Depicted are dot plots of c-Maf versus isotype control gated on live CD4+ T cells. Representative data from two independent experiments are shown.

Supplementary Figure 2 Supporting information for differential gene expression analyses

CD4+ T cells from malaria, HDM and EAE challenged Maffl/flCd4-cre vs Maffl/fl mice were profiled by RNA-seq. a, Volcano plots of differentially expressed genes, with previously associated regulators of IL-10 depicted (blue, significantly down-regulated; red, significantly up-regulated; grey, non-differentially expressed) (n = 3 independent animals (malaria) or biologically independent samples (HDM and EAE) per genotype; P< 0.05, absolute FC ≥ 1.5, moderated t-test, two-tailed). b, Manually curated list of top biological pathways as determined by GO enrichment analysis of each differentially up- and down-regulated genes in Maffl/flCd4-cre vs Maffl/fl mice (n = 3 independent animals (malaria) or biologically independent samples (HDM and EAE) per genotype).

Supplementary Figure 3 Effect on pathology and phenotype of TFH cells in acute phase of malaria

a, Schematic of P. chabaudi infection in Bcl6fl/fl and Bcl6fl/flCd4-cre mice, percentage weight loss (n = 5, mean ± SD) and temperature changes (n = 8, mean ± SD) on day 9 post P. chabaudi infection. Representative data from two biological experiments are shown. b, Representative cytokine staining of CD4+ T cells on day 14 post P. chabaudi infection in C57BL/6/J mice, plots are gated on live CD3+CD4+CD44+ T cells. Pooled data from two biological experiments are shown (n = 5, mean ± SD).

Supplementary Figure 4 Changes in chromatin accessibility do not account for transriptional disregulation in the absence of c-Maf

Volcano plots of accessibility changes in ATAC-Seq consensus peak sets in CD4+ T cells from malaria, HDM allergy and EAE challenged Maffl/flCd4-cre vs Maffl/fl mice (n = 3 independent animals (malaria) or biologically independent samples (HDM and EAE) per genotype, statistical significance called using DiffBind 2.02 with FDR < 0.05, absolute fold change ≥ 1.5) assigned to genes (see Supplementary Information for computational methods) and mapped to RNA-seq fold-change values. The top ten peaks ranked by fold-change were labeled with their assigned gene, as well as any remodeled peak assigned to Il10.

Supplementary Figure 5 Framework schematic for the identification of putative direct targets of c-Maf

For each disease model, the c-Maf ChIP-seq (GSE40918) and motif datasets were filtered according to the accessibility as determined by ATAC-seq, allowing the identification of putative c-Maf binding sites and estimation of its relevance in explaining RNA-seq-defined transcriptional changes observed upon c-Maf deletion (see Supplementary Information for computational methods).

Supplementary Figure 6 Genome browser tracks of other key immune genes

Genome browser tracks of read coverage of RNA-seq and ATAC-seq in CD4+ T cells from the malaria, HDM allergy and EAE challenged Maffl/flCd4-cre vs Maffl/fl mice (shown as an overlay of n = 3 independent animals (malaria) or biologically independent samples (HDM and EAE) per genotype), as compared to untreated control and matched to c-Maf ChIP-seq (GSE40918) and motif sites.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1-6

Reporting Summary

Supplementary Table 1

TF correlation lists

Supplementary Table 2

SVD components

Supplementary Table 3

Differentially expressed genes

Supplementary Table 4

Network analysis

Supplementary Table 5

Direct and indirect c-Maf targets

Supplementary Table 6

Combined c-Maf binding evidence for direct effects on differentially expressed genes

Supplementary Table 7

BaGFoot TF statistics

Supplementary Table 8

BaGFoot TFs with altered activity are statistically enriched in differentially expressed genes

Supplementary Data

Supplementary Data for Computational Methods

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Gabryšová, L., Alvarez-Martinez, M., Luisier, R. et al. c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4+ T cells. Nat Immunol 19, 497–507 (2018). https://doi.org/10.1038/s41590-018-0083-5

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