Irfs As Competing Pioneers in T-Cell Differentiation

RESEARCH HIGHLIGHT

IRFs as competing pioneers in T-cell differentiation

Andrea Kröger

Cellular & Molecular Immunology (2017) 14, 649–651; doi:10.1038/cmi.2017.37; published online 19 June 2017

CD4-expressing T lymphocytes are combination with IL-6 or IL-21 promote engagement of TCRs on naive CD4+ among of the best-characterized immune TH17 development. These cells produce T cells cultured under Tr1 polarizing system cells.1 They develop in the thy- IL-17, IL-21 and IL-22 and express the conditions. Irf1 and Batf mRNA mus and acquire the potential to differ- lineage-specific transcription factor showed a dual wave expression profile entiate into distinct subpopulations. RORγt. Regulatory T cells (nTreg) can with an early peak between 1 and 6 h Upon leaving the thymus, T helper cells develop directly in the thymus; they after activation. Moreover, stimulation further differentiate in the periphery in express FOXP3 and inhibit T effector of naive CD4+ T cells from knockout response to signals from T-cell receptors, cell functions. Tr1 cells are poorly failed to produce Il10 mRNA or differ- cytokines and other ligands in the micro- defined regulatory T cells;2 they are entiation into Tr1 cells. environment. CD4+ T cells have high FOXP3 negative and express high levels IL-27 receptor signaling is known to plasticity and can differentiate into sev- of anti-inflammatory cytokines like induce Tr1 cell differentiation. Further- eral different subtypes. This subdivision IL-10. more, both STAT1 and STAT3 are is based on the expression of lineage- The diversity of the differentiation required for Tr1 differentiation. Karwacz specific transcription factors, which possibilities of CD4+ T cells raises the and colleagues showed that STAT1 sig- function as ‘mater regulators’ for specific question as to the degree to which a naling was responsible for Irf1 induction, TH subsets. single master regulator contributes to the whereas STAT3 was essential for BATF, TH1 differentiation is driven by IL-12, differentiation, especially because in indicating a distinct regulation of both which promotes the expression of IFNγ some cells similar factors are expressed. transcription factors. The authors also and transcription factor T-BET (encoded Gene expression analysis is typically car- investigated whether both transcription by T-box 21). TH2 cells express the ried out by analyzing induced genes but factors cooperate in Tr1-specificgene master regulator GATA-binding protein does not explain why expression of the expression, whereas IRF1 expression 3 (GATA3) when induced by IL-4 and same transcription factor in the same cell leads to high induction of IL-10. Batf secrete IL-4, IL-5 and IL-13. Transform- types leads to different gene subsets. The overexpression strongly induced Maf and ing growth factor β (TGFβ), in combina- combination of gene expression and Il12,whereasAhr expression was tion with IL-4, induces differentiation to chromatin accessibility analysis allows induced by both. These results suggest TH9 cells, which produce IL-9 and IL-10. analysis of another level of gene regula- that both transcription factors cooperate PU.1 has been suggested as a master tion. Pioneering factors that alter chro- in gene induction and induce a distinct transcription factor. T follicular helper matin also affect the accessibility of set of genes. (TfH) cells are induced by IL-6 and IL-21 transcription factors to specificgenes. To assess the role of IRF1 in auto- and express master regulator BCL6. For the differentiation of TH17 cells, immune disease, Karwacz and coauthors In addition, TGFβ and IL-23 in the cooperative binding of BATF and used an experimental autoimmune ence- interferon regulatory factors (IRF4) phalomyelitis (EAE) model. In previous enables chromatin accessibility and the studies, C57/BL6J Irf1-deficient mice Institute for Medical Microbiology, Molecular subsequent recruitment of RORγtto were found to be resistant to EAE upon Microbiology, Otto-von-Guericke University of regulate selected sets of TH17-relevant immunization with MOG35-55 when Magdeburg, Magdeburg D-39120, Germany genes3–5 (Figure 1). compared with wild-type mice.7,8 This Correspondence: Professor A Kröger, PhD, Group leader, Principle Investigator, Institute for Medical In a recent issue of Nature Immunol- phenotypic characterization was asso- Microbiology, Molecular Microbiology, Otto-von- ogy, Karwacz et al.6 exploited the role ciated with impaired Th1 cell differentia- Guericke University of Magdeburg, Leipziger of IRF1 and BATF as pioneering factors tion and biased development toward Th2 Straße 44, Magdeburg D-39120, Germany. for CD4+ T-cell differentiation to cell phenotype. Thus, Karwacz showed E-mail: [email protected] Received: 21 April 2017; Accepted: 23 April Tr1 cells. The investigators analyzed that loss of IRF1 led to an increased 2017 global gene expression following clinical core upon EAE induction and Research Highlight

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BATF IRF4 IRF1

IL12 TH1 IFNγ T-BET TNFα

IL4 IL4 TH2 GATA3 IL5 IL13

IL4 TH9 IL9 +TGFβ IL10

Naive IL6 T 17 IL17 CD4+ H IL21 +TGFβ RORγt T cell IL22

IL21 Tfh IL21 IL6 BCL6

Tr1 IL10

Treg FOXP3 IL10

+ + Figure 1 IRFs are crucial for the differentiation of CD4 T-cell subsets. CD4 T cells developed in functionally different subsets (TH1, TH2, TH9, TH17, Tfh, Tr1 Treg), some of them are characterized by the expression of lineage-speciﬁc transcription factors (T-BET, GATA3, RORγt or FOXP3). BATF, as a pioneer factor, is expressed in different lineages. IRF1 and IRF4 could cooperate with BATF to landscape the chromatin to promote lineage-speciﬁc gene expression. IRF, interferon regulatory factors.

increased numbers of IL-17- and IFNγ- IRF1 in TH17 cells and vice versa. Over- Karwacz and colleagues used intensive expressing T cells in the central nervous expression of IRF1 in TH17 cells antag- ATAC-seq analyses of Tr1 polarized system of Irf1−/− mice. More impor- onized IRF4-induced IL-14, and the knockout cells to assess the potential tantly, the transfer of Irf1−/− Tcellsinto overexpression of IRF4 in Tr1 cells pioneering roles of BATF and IRF1 Rag2−/− mice and induction of EAE inhibited IRF1-mediated IL-10. Thus, during Tr1 differentiation. They detected resulted in increased disease scores; IRF1 may play the same role as epige- ~ 180 000 accessible regions across the higher numbers of IL-17 producing cells netic pioneer factors in Tr1 cells, such as samples. In contrast to Irf1, c-Maf and −/− were isolated. These data provide evi- IRF4 in TH17 cells. AhR, Batf TH0 and Tr1 cells had dence that IRF1 inhibited Th17 cell To investigate whether BATF or IRF1 distinct chromatin accessibility patterns, differentiation in vivo. Furthermore, could affect epigenetic markers, ChIP- providing high-level support for BATF as Irf1-andBatf-deficient mice were not qPCR assays on the IL-10 locus were a pioneering factor in Tr1 cells. DESeq2 able to generate functional Tr1 cells, performed in Tr1 polarized knockout analysis was used to quantify the number whereas the adaptive transfer of wt cells. Irf1 and Batf deficiency resulted in of transcription-factor-dependent acces- Tr1 cells inhibits disease and the transfer decreased recruitment of activating fac- sible peaks per transcription factor in of Irf1-deficient Tr1 cells exacerbated tors and increased repressive factors. Tr1 conditions. BATF deficiency led to disease. Thus, IRF1 and BATF control Thus, both transcription factors seem altered accessibility at over 20 000 loci, the in vivo generation of Tr1 cells. to induce epigenetic changes during Tr1 IRF1 deficiency of 1200 loci and only Tr1 cells are characterized by high cell differentiation. Reporter assays using minor alterations in Ahr and c-Mafs cells. expression levels of IL-10. To determine promoter elements with high BATF and Although the scale of IRF1- and BATF- whether IRF1 and BATF have to interact IRF1 co-occupancy showed that only dependent changes differs, both tran- on the Il10 promoter, Karwacz et al. IRF1 was able to directly induce the scription factors altered chromatin acces- performed sequential ChIP assays and IL-10 promoter. Moreover, both factors sibility, whereas c-MAF and AhR did showed a strong co-occupancy of IRF-1 provide binding sites for other transcrip- not. Thus, both IRF1 and BATF are and BATF. Because IRF4 and IRF1 share tion factors, suggesting that both factors necessary for additional Tr1 transcription the same DBD, and IRF4 and BATF could induce chromatin changes, which factorstobindchromatinandsupport show a similar dependency in TH17 cells, allow the exclusive or cooperative bind- the role for IRF1 and BATF as pioneer- they also investigated the function of ing of other transcription factors. ing factors.

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Taking the findings together this CONFLICT OF INTEREST 5 Ciofani M, Madar A, Galan C, Sellars M, study uncovered the critical role of Theauthordeclaresnoconflict of interest. Mace K, Pauli F et al. A validated regulatory network for Th17 cell specification. Cell IRF1 and BATF in preparing the chro- 2012; 151:289–303. matin landscape for the induction of 6 Karwacz K, Miraldi ER, Pokrovskii M, the Tr1 gene network in response to 1 Zhu J, Yamane H, Paul WE. Differentiation of Madi A, Yosef N, Wortman I et al. Critical IL-27 signaling. Where BATF acts as a effector CD4 T cell populations. Annu Rev role of IRF1 and BATF in forming chromatin Immunol 2010; 28:445–489. landscape during type 1 regulatory cell dif- pioneer factor and prepares the geno- 2 Zeng H, Zhang R, Jin B, Chen L. Type 1 ferentiation. Nat Immunol 2017; 18: mic landscape for the binding of addi- regulatory T cells: a new mechanism of 412–421. tional transcription factors that define peripheral immune tolerance. Cell Mol 7 Tada Y, Ho A, Matsuyama T, Mak TW. Immunol 2015; 12:566–571. the Tr1 lineage, IRF1 specifically trans- Reduced incidence and severity of antigen- 3 Glasmacher E, Agrawal S, Chang AB, induced autoimmune diseases in mice lack- Murphy TL, Zeng W, Vander Lugt B et al. activates IL-10 gene expression and a ing interferon regulatory factor-1. J Exp Med smaller cluster of genes that character- A genomic regulatory element that directs – assembly and function of immune-specific 1997; 185:231 238. ize the Tr1 lineage while retaining AP-1-IRF complexes. Science 2012; 338: 8 Buch T, Uthoff-Hachenberg C, Waisman A. Protection from autoimmune brain TH17 differentiation. These data indi- 975–980. inflammation in mice lacking IFN- cate that BATF and IRF-1 are drivers 4 Li P, Spolski R, Liao W, Wang L, Murphy TL, Murphy KM et al. BATF-JUN is critical for regulatory factor-1 is associated with of the earliest steps in the induction of IRF4-mediated transcription in T cells. Nat- Th2-type cytokines. Int Immunol 2003; Tr1 lineage (Figure 1). ure 2012; 490:543–546. 15:855–859.

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