Research ArticleIMMUNE REGULATION

Conversion of antigen-specific effector/memory T cells into Foxp3-expressing Treg cells by inhibition of CDK8/19

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Science Immunology  25 Oct 2019:
Vol. 4, Issue 40, eaaw2707
DOI: 10.1126/sciimmunol.aaw2707

Pharmacological retraining for T cells

Regulatory T (Treg) cells expressing the Foxp3 transcription factor play a critical role in dampening overactive immune responses including autoimmune diseases. Akamatsu et al. screened a library of small molecules and identified a compound that promotes Treg differentiation on the basis of its ability to inhibit the cyclin-dependent kinases CDK8 and CDK19. The Treg-promoting activity of the CDK8/19 inhibitor did not require transforming growth factor–β (TGF-β) and reduced disease activity in mouse models of autoimmune diabetes and encephalomyelitis. These findings indicate that CDK8/19 inhibitors are a new class of immunomodulatory drugs capable of generating Treg cells with potential clinical applications in promoting tolerance and squelching autoimmunity.

Abstract

A promising way to restrain hazardous immune responses, such as autoimmune disease and allergy, is to convert disease-mediating T cells into immunosuppressive regulatory T (Treg) cells. Here, we show that chemical inhibition of the cyclin-dependent kinase 8 (CDK8) and CDK19, or knockdown/knockout of the CDK8 or CDK19 gene, is able to induce Foxp3, a key transcription factor controlling Treg cell function, in antigen-stimulated effector/memory as well as naïve CD4+ and CD8+ T cells. The induction was associated with STAT5 activation, independent of TGF-β action, and not affected by inflammatory cytokines. Furthermore, in vivo administration of a newly developed CDK8/19 inhibitor along with antigen immunization generated functionally stable antigen-specific Foxp3+ Treg cells, which effectively suppressed skin contact hypersensitivity and autoimmune disease in animal models. The results indicate that CDK8/19 is physiologically repressing Foxp3 expression in activated conventional T cells and that its pharmacological inhibition enables conversion of antigen-specific effector/memory T cells into Foxp3+ Treg cells for the treatment of various immunological diseases.

INTRODUCTION

Naturally occurring CD4+ regulatory T (Treg) cells expressing the transcription factor forkhead box protein 3 (Foxp3) are essential for the maintenance of immunological self-tolerance and homeostasis (1). Anomalies of Foxp3+ natural Treg (nTreg) cells in number or function, such as those associated with loss-of-function mutations of the Foxp3 gene, cause various immunological diseases including autoimmune disease, allergy, and inflammatory bowel disease (1, 2). Moreover, increasing the number of Foxp3+ nTreg cells or augmenting their suppressive function is able to treat immunological diseases and control graft rejection in organ transplantation (1). Although the majority of nTreg cells are produced by the thymus as a functionally distinct and mature T cell population (tTreg cells), conventional T (Tconv) cells in the periphery can acquire similar Treg phenotype and function [peripherally induced Treg (pTreg) cells], for example, in response to a particular species of commensal bacteria in the intestine (3). On the basis of these findings on physiological generation of Foxp3+ Treg cells in the thymus and the periphery, a promising approach for promoting antigen-specific immune suppression is the development of methods for converting antigen-specific Tconv cells, especially effector or memory T cells mediating harmful immune responses, into functionally stable Foxp3-expressing Treg cells in vivo and in vitro.

It has been well established that in vitro antigenic stimulation in the presence of transforming growth factor–β (TGF-β) is able to elicit Foxp3 expression in Tconv cells (4, 5). This in vitro TGF-β–dependent generation of induced Treg (iTreg) cells is, however, only attainable from naïve Tconv cells, not from effector or memory T cells, and hindered by the presence of proinflammatory cytokines (4, 5). In addition, TGF-β–induced iTreg cells are unstable in sustaining in vivo suppressive function mainly because of their failure to acquire stable Treg-specific epigenomic changes in Foxp3 and other Treg signature genes, which limits their therapeutic application (57). These findings prompted us to search for chemical compounds that can convert not only naïve but also effector or memory Tconv cells into functionally stable, antigen-specific Foxp3+ Treg cells in a TGF-β–independent manner even in the presence of proinflammatory cytokines.

We conducted a screen of chemical compounds for the in vitro capacity to generate Foxp3+ T cells from Tconv cells. We found that pharmacological inhibition of cyclin-dependent kinase 8 (CDK8) and its paralog CDK19, which are reversibly associated with the Mediator complex and mainly control the function of transcription factors positively and negatively (8), is able to induce Foxp3 not only in naïve T cells but also in effector/memory-type T cells. The converted Treg cells are capable of suppressing autoimmune and allergic immune responses in animal models. Our results indicate that the CDK8/19 signaling physiologically represses Foxp3 expression in activated Tconv cells and that the inhibition of the signaling is sufficient to induce Foxp3 in activated and differentiated Tconv cells, converting them into antigen-specific Treg-like suppressive T cells with potential clinical applications. These findings would enhance our understanding of physiological mechanisms of pTreg cell generation and peripheral immune tolerance.

RESULTS

Induction of Foxp3 expression in effector/memory T cells and naïve T cells by a chemical compound

We first screened our chemical library composed of ~5000 structurally different small molecules for the compounds capable of generating Foxp3+ Treg cells from Tconv cells upon in vitro polyclonal T cell receptor (TCR) stimulation. When mouse Tconv cells were stimulated in vitro with anti-CD3 and anti-CD28 monoclonal antibody (mAb)–coated beads in the presence of interleukin-2 (IL-2), the compound AS2863619 (4-[1-(2-methyl-1H-benzimidazol-5-yl)-1H-imidazo[4,5-c]pyridin-2-yl]-1,2,5-oxadiazol-3-amine dihydrochloride) (AS) (Fig. 1A) was found to generate Foxp3+ T cells from naïve Foxp3CD4+ Tconv cells in a dose-dependent fashion (fig. S1A). It did not exhibit cellular toxicity or hinder proliferative activity of Tconv cells in the concentration range having Foxp3-inducing activity (fig. S1A). Similar AS treatment induced Foxp3 in CD8+ Tconv cells as well (Fig. 1B). It also substantially enhanced FOXP3 expression in human CD4+ and CD8+ Tconv cells in the peripheral blood, although TCR stimulation per se elicited the expression at a low level (fig. S2) (9, 10).

Fig. 1 AS2863619 is a potent Foxp3 inducer in Tconv cells.

(A) Chemical structure of AS2863619, hereafter designated AS. (B) In vitro induction of Foxp3 expression in AS-treated mouse effector/memory and naïve CD4+ T cells as CD44highCD62Llow and CD44lowCD62Lhigh cells, respectively, and also in CD8+ T cells. Cells were stimulated with anti-CD3/CD28 mAb-coated beads and IL-2 in the presence or absence of AS (1.0 μM) or TGF-β (2.5 ng/ml) for 72 hours. Representative Foxp3 staining and percentages of Foxp3+ cells among CD4+ or CD8+ T cells after respective stimulation are shown (n = 3). (C and D) Foxp3+ cells generation by AS under TH1-, TH2-, TH17-, or TH9-inducing conditions. Naïve CD4+ T cells were anti-CD3/CD28–stimulated in the presence of IL-12 (10 ng/ml; TH1 condition, n = 5), IL-4 (10 ng/ml; TH2 condition, n = 4), IL-6 (20 ng/ml) + TGF-β (2.5 ng/ml; TH17 condition, n = 4), or IL-4 (10 ng/ml) + TGF-β (2.5 ng/ml; TH9 condition, n = 3). (E and F) Foxp3+ T cell generation from antigen-stimulated T cells. DO11.10 naïve CD4+ T cells were cocultured with APCs, 5 μM OVA peptide, and 1.0 μM AS and assessed for Foxp3 and DO11.10 TCR expression by flow cytometry (n = 3). (G) Expression of Treg signature molecules in AS- or TGF-β–treated anti-CD3/CD28–stimulated T cells assessed by flow cytometry. Data are representative of three independent experiments. (H) In vitro suppression assay using in vitro activated nTreg cells and TGF-β– or AS-induced iTreg cells (n = 3). Treg versus responder T cell ratio was 1:10. Vertical bars indicate means ± SD. **P < 0.01 by SNK method. ns, not significant.

AS induced Foxp3 in phenotypically effector/memory (CD44highCD62Llow) CD4+ Tconv cells as well as naïve (CD44lowCD62Lhigh) Foxp3CD4+ Tconv cells (Fig. 1B). A combination of AS and TGF-β synergistically induced Foxp3 in both naïve and effector/memory populations, whereas TGF-β alone generated Foxp3+ cells only from naïve Tconv cells.

Unlike other reported Foxp3-inducing substances, such as retinoic acid (fig. S1B), which requires exogenous TGF-β for iTreg cell induction (1113), TGF-β neutralization (Fig. 1B) or serum-free conditions (fig. S1C) did not affect the AS-dependent in vitro Foxp3 induction. IL-2 neutralization or IL-2 addition dampened or enhanced, respectively, the induction, indicating a requirement for IL-2 for the AS-induced generation of Foxp3+ T cells (fig. S1D). Furthermore, use of T helper 1 (TH1)–, TH2-, TH17-, or TH9-inducing culture conditions containing inflammatory cytokines such as IL-12, IL-4, and IL-6 that inhibited TGF-β–dependent Foxp3 induction (14, 15) did not hamper the AS-dependent Foxp3 induction in CD4+ Tconv cells (Fig. 1, C and D).

With CD4+ Tconv cells from DO11.10 transgenic mice expressing an ovalbumin (OVA) peptide-specific transgenic TCR, which can be detected by the clonotype-specific KJ1-26 mAb (16), the AS compound induced Foxp3 expression in OVA-stimulated KJ1-26+ T cells but not in nonstimulated KJ1-26 T cells (Fig. 1, E and F), indicating a requirement for antigenic stimulation for the AS-dependent Foxp3+ cell generation.

Although TGF-β was not required for Treg induction, AS-induced iTreg cells were similar to TGF-β–induced ones in expression of Treg function–associated cell surface molecules, such as CD25, CTLA-4 (cytotoxic T lymphocyte antigen–4), and GITR (glucocorticoid-induced tumor necrosis factor receptor family-related protein) (Fig. 1G); in in vitro suppressive activity (Fig. 1H); and in the absence of Treg-specific DNA hypomethylation (fig. S3) (17). AS scarcely affected nTreg function and proliferation in vitro (fig. S4).

RNA sequencing (RNA-seq) analysis of AS-treated or untreated CD4+ Tconv cells, B cells, or dendritic cells (DCs) revealed differentially expressed genes (DEGs) in each population. The compound up-regulated the transcription of a limited number (~20) of genes, including Foxp3, in CD4+ Tconv cells, without up-regulation of these genes in B cells or DCs (fig. S5).

These results together indicate that AS is able to directly, without antigen-presenting cells (APCs), induce Foxp3 in vitro not only in naïve Tconv cells but also in antigen-activated or effector/memory Tconv cells even in the presence of various inflammatory cytokines. The induction is TGF-β independent and IL-2 dependent and requires TCR stimulation, thus enabling conversion of antigen-specific Tconv cells into Foxp3+-suppressive T cells without TGF-β.

CDK8/19 as a target of Foxp3-inducing AS

To determine the target molecule(s) of AS in its Foxp3 induction, we conducted affinity purification (18) of AS-bound proteins by conjugating AS3309191, an active AS analog, to a photoreactive affinity capture linker and mixing the conjugate with the lysates of mouse EL4 T cell lymphoma cells in the presence or absence of an excess amount of AS analogs (fig. S6, A and B). This affinity purification followed by mass spectrometry analysis identified CDK8, CDK19, GSK3α, and GSK3β as candidate AS-binding proteins (Fig. 2A). We therefore assessed several compounds, including AS, two AS analogs (AS3334366 and AS3196162; fig. S6C), a CDK8/19 inhibitor [senexin A; (19)], and a GSK3α/β inhibitor [CHIR99021; (20)], for their activity to inhibit these kinases and thereby induce Foxp3 in CD4+ Tconv cells (Fig. 2B). The Foxp3-inducing potency of these compounds correlated well with their inhibitory activities on CDK8 and CDK19 but not on the GSK3 isoforms. In addition, in a kinase selectivity profiling assay for evaluating 189 other kinases, AS inhibited glycogen synthase kinases (GSKs) by ~50% and ribosomal protein S6 kinases (RSKs) by 60 to 80%, whereas AS3334366, a more CDK8/19-specific inhibitor and more potent Foxp3 inducer (Fig. 2B), scarcely inhibited these kinases (table S1). Thus, CDK8 and CDK19 are most likely the target molecules of AS in its Foxp3 induction.

Fig. 2 CDK8/19 as a key target of AS.

(A) Candidate target molecules of AS revealed by tandem mass spectrometry (also see fig. S6 for chemical proteomics workflow). m/z, mass/charge ratio. (B) Correlation of Treg induction with the degree of CDK8/19 kinase inhibition. Five different kinase inhibitors including AS were examined for their Treg-inducing potency and their inhibitory activity of various kinases. Kinase inhibition was assessed in vitro using recombinant CDK8/cyclin C complex, CDK19/cyclin C complex, GSK3α, or GSK3β. IC50 was defined as the concentration of an inhibitor that reduced phosphorylation by half compared with DMSO control. EC150 for Treg induction was defined as the concentration of the compound that induced Foxp3+ Treg cells to 150% of DMSO control when mouse naїve CD4+ T cells were treated with anti-CD3/CD28 for 44 hours in the presence of the compound. Values are geometric mean of three (Treg induction, CDK19, GSK3α, and GSK3β) or four (CDK8) independent experiments. Pearson r, Pearson’s correlation coefficient (versus Treg induction). (C) Expression of CDK8, CDK19, and cyclin C after stimulation. Mouse CD4+ T cells stimulated with anti-CD3/CD28 were lysed for immunoblotting of these molecules at various time points. Data are representative of three independent experiments. (D) Effects of CDK8 or CDK19 knockdown on Foxp3 mRNA expression. Mouse CD4+ T cells were transfected with siRNA for CDK8 or CDK19; stimulated with anti-CD3/CD28, TGF-β, and IL-2; and examined for CDK8 and CDK19 expression by immunoblotting (left) or Foxp3 mRNA expression by quantitative RT-PCR (n = 3) (right). (E) Effects of retroviral expression of WT or KD CDK8 or CDK19 on Foxp3+ cell generation. Mouse CD4+ T cells infected with retroviruses harboring GFP (mock control), WT or KD CDK8, and WT or KD CDK19 were stimulated with anti-CD3/CD28 and IL-2 and examined for CDK8 and CDK19 expression by immunoblotting (left) and for the percentages of Foxp3+ cells among CD4+ T cells by flow cytometry (n = 5) (right). (F) Luciferase assay using CDK8 and/or CDK19 KO EL4 cell lines and a Foxp3 promoter plasmid (triplicate). Data are representative of two independent experiments. RLU, relative light unit. (G and H) Foxp3 induction in CDK8-KD–transfected CD4+ T cells by antigenic stimulation. Naїve CD4+ T cells isolated from DO11.10Rag2−/−Foxp3-eGFP reporter mice were stimulated with anti-CD3/CD28 for 22 hours, infected with mock or CDK8-KD or CDK8-WT–carrying retroviruses, incubated for another 22 hours in the absence of IL-2, and rested for 10 days in the presence of IL-2 (100 U/ml). LNGFR was used as a marker of infection. BALB/c-nu/nu mice were transferred with infected T cells on day 0 and treated with IL-2/anti–IL-2 Ab complexes on day 7 and then immunized with OVA/CFA on day 14. Draining lymph nodes were collected and examined for expression of Foxp3 by flow cytometry on day 20. Representative staining (G) and percentages of Foxp3+ cells among live LNGFR+ or LNGFRCD4+ cells in lymph nodes are shown (n = 6) (H). Vertical bars indicate means ± SD. ***P < 0.001, **P < 0.01, and *P < 0.05 (Dunnett’s test).

The expression of CDK8 was low in naïve CD4+ Tconv cells and increased within 24 hours after in vitro TCR stimulation, whereas CDK19 and cyclin C, another component of the CDK8 kinase module, were constitutively expressed before and after stimulation (Fig. 2C), suggesting that CDK8, either alone or together with CDK19, might be repressing Foxp3 expression in activated Tconv cells. To assess this possibility, we depleted CDK8 and CDK19 in CD4+ Tconv cells by RNA interference (RNAi) and found a significant increase of Foxp3 transcription not only in CDK8-depleted cells but also in CDK19-depleted cells upon TCR stimulation (Fig. 2D). In addition, retroviral overexpression of the kinase-dead (KD) mutants, D173A CDK8 and D173A CDK19, which had dominant-negative effects on wild-type (WT) CDK8/19 (fig. S7A), generated Foxp3+ cells from CD4+ Tconv cells even in the absence of TGF-β or in the presence of IL-6, whereas overexpression of WT CDK8 or CDK19 did not (Fig. 2E and fig. S7B). Luciferase reporter assays harboring the Foxp3 promoter sequence also showed that AS enhanced Foxp3 transcriptional activity in WT and CDK8- or CDK19-deficient EL4 cells but not in CDK8/19 double-deficient EL4 cells (Fig. 2F and fig. S8). The latter were still responsive to TGF-β–dependent Foxp3 induction in luciferase assay with a SMAD3-responsive Foxp3 CNS1-containing construct (fig. S8).

Next, to examine whether CDK8 dysfunction in primary Tconv cells could induce Foxp3 expression upon in vivo antigenic stimulation, we retrovirally overexpressed the KD mutant of CDK8, together with the low-affinity nerve growth factor receptor (LNGFR) reporter, in DO11.10 TCR+CD4+ T cells and transferred them into T cell–deficient BALB/c nude (nu/nu) mice, expanded the transferred T cells in an antigen-nonspecific manner by administration of one dose of the IL-2/anti–IL-2 complex, and then immunized the mice with OVA (Fig. 2, G and H, and fig. S9). The transferred CD4+ T cells expressing the KD mutant CDK8 gave rise to Foxp3+ T cells after OVA immunization, whereas those overexpressing WT CDK8 did not.

These in vitro and in vivo results collectively indicate that AS is able to elicit transcription of the Foxp3 gene in activated Tconv cells by inhibiting the kinase activity of CDK8/19, which appears to physiologically repress Foxp3 expression in activated Tconv cells.

Interaction of CDK8/19 with STAT5 in Foxp3 induction

The following findings suggested the possible involvement of signal transducer and activator of transcription 5 (STAT5) in the CDK8/19 inhibition-dependent Foxp3 induction: CDK8 phosphorylates the serine residue in the PSP (Pro-Ser-Pro) motif of the STAT proteins including STAT5 (21); AS and IL-2, whose signaling requires STAT5, synergistically enhanced Foxp3+ T cell generation (fig. S1D); and constitutive activation of STAT5 is able to induce Foxp3 expression in Tconv cells (22, 23). We therefore examined the possible effects of AS on the phosphorylation of STAT5 in inducing Foxp3 in Tconv cells. Immunoprecipitation with anti-CDK8 coprecipitated STAT5b, together with MED12, a component of the CDK8 kinase module of the Mediator complex, from activated CD4+ Tconv cells and more strongly from those retrovirally overexpressing both CDK8 and STAT5b (Fig. 3A). Incubation of recombinant WT CDK8 with recombinant STAT5b resulted in phosphorylation of the serine residue of the latter, whereas incubation of KD CDK8 with STAT5b did not; furthermore, AS inhibited the STAT5b serine phosphorylation by WT CDK8 (Fig. 3B). In addition, anti-CD3/anti-CD28 mAb stimulation induced phosphorylation of both serine and tyrosine residues of STAT5 in CD4+ T cells, and AS suppressed serine phosphorylation of the PSP motif of STAT5b to ~40% while enhancing tyrosine phosphorylation in the C-terminal domain to ~160% of control-treated samples (Fig. 3C). The AS inhibition of STAT5b-serine phosphorylation was correlated with Foxp3 induction in a dose-dependent manner (fig. S10). In addition, CDK8 and STAT5 formed endogenous complexes in activated CD4+ Tconv cells as indicated by their colocalization shown by proximity ligation assay (PLA) (Fig. 3, D and E) and by costaining by anti-CDK8 and anti-STAT5 antibodies (Fig. 3F). Furthermore, overexpression in CD4+ T cells of S730A-STAT5b, a serine phosphorylation–resistant STAT5b mutant shown to exhibit increased tyrosine phosphorylation (24, 25), generated Foxp3+ T cells more efficiently than WT-STAT5 overexpression. AS augmented the WT-STAT5–induced generation to an equivalent level as attained by the mutant (Fig. 3G). It was also noted in these experiments that AS treatment of S730A-STAT5b–overexpressing cells significantly increased Foxp3+ T cells, suggesting a possible involvement of a signaling pathway other than the STAT5-mediated one in the Foxp3 induction by CDK8/19 inhibition. Thus, a potential contributing mechanism is AS inhibiting the ability of activated CDK8/19 to phosphorylate the serine residue in the PSP motif of STAT5; the diminished serine phosphorylation augments the retention of the tyrosine-phosphorylated STAT5 in the nucleus, leading to enhanced activation of STAT5, which consequently activates the Foxp3 gene.

Fig. 3 Interaction of CDK8/19 and STAT5 in inducing Foxp3 expression.

(A) Mouse CD4+ T cells were mock-infected or infected with retrovirus harboring the WT CDK8 and STAT5b genes, stimulated with anti-CD3/CD28 and IL-2, and subjected to immunoprecipitation and immunoblotting for CDK8, STAT5b, and MED12. Data are representative of two independent experiments. (B) STAT5 serine phosphorylation by CDK8. Recombinant GST-STAT5b incubated with recombinant WT or KD CDK8 in the presence or absence of 1.0 μM AS with 100 μM ATP and 10 mM MgCl2 was subjected to immunoblotting for phosphoserine (pS) of STAT5b. Data are representative of two independent experiments. (C) Control of serine and tyrosine phosphorylation by AS in activated T cells. Mouse CD4+ T cells were stimulated with anti-CD3/CD28 in the presence or absence of TGF-β for 22 hours and in the absence (DMSO) or presence of 100 nM AS, lysed, and subjected to immunoblot analysis for STAT5b, pS-STAT5b, or pY-STAT5. Signal intensity was quantified and normalized by GAPDH (n = 3 or 4). **P < 0.01 (Student’s t test). AU, arbitrary units. (D and E) Mouse naїve CD4+ T cells were incubated in the presence or absence of anti-CD3/28 for 22 hours, and PLA was performed to assess interaction between CDK8 and STAT5. Images were obtained using an LSM710 confocal microscope. Data were presented as maximum intensity projection (n = 3). Each red spot represents a single interaction, and DNA was stained with DAPI. (F) Mouse naїve CD4+ T cells were incubated in the presence or absence of anti-CD3/CD28 for 22 hours and examined for expression of CDK8 and STAT5. DNA was stained with Hoechst33342. Images were obtained using an LSM710 confocal microscope. Data are representative of two independent experiments. (G) Mouse CD4+ T cells infected with retrovirus encoding WT or S730A mutant STAT5b were stimulated with anti-CD3/CD28 and IL-2, without TGF-β, and subjected to immunoblotting for STAT5b (left), or assessed for the percentage of Foxp3+ cells among live virus–infected (i.e., GFP+) CD4+ T cells by flow cytometry (n = 7) (right). ***P < 0.001 (Student’s t test).

Genome-wide enhancement of STAT5 binding by AS

To determine then whether AS augmented STAT5 binding in the genome, we conducted whole-genome chromatin immunoprecipitation (IP) sequencing (ChIP-seq) of AS-treated activated Tconv cells. At the Foxp3 gene locus, AS enhanced STAT5 binding to the Foxp3 CNS0 region, which is the enhancer region first activated in thymic Treg cell development (26), and, to a lesser extent, to the Foxp3 promoter and the CNS2 region, a critical enhancer site for Foxp3 transcription (Fig. 4A) (27). ChIP–quantitative polymerase chain reaction (qPCR) with anti-STAT5 or anti-pSTAT5 confirmed STAT5 and pSTAT5 binding to these regions, especially to the CNS0 region (Fig. 4B). CDK8 also bound to the CNS0 and the promoter regions in AS-treated activated Tconv cells (fig. S11). The CNS0 enhancer region in AS-treated or nontreated Tconv cell equally had activated H3K27ac as assessed by H3K27ac-ChIP-seq and was in an open chromatin state by assay for transposase-accessible chromatin sequencing (ATAC-seq) (Fig. 4A). The STAT5 ChIP-seq also revealed globally increased STAT5 binding at activated enhancer regions, marked by H3K4me1 or H3K27ac modifications (Fig. 4C). When STAT5-binding peaks were separated into two groups consisting of those unchanged (5353 peaks) or augmented (876 peaks) by AS treatment, the AS-increased peaks were mainly in introns and intergenic regions, whereas the unchanged peaks were mainly in promoter regions (Fig. 4D). Expression of STAT5-associated genes with STAT5 binding in enhancers was highly up-regulated by AS treatment, whereas expression of those with STAT5 binding in promoters was not (Fig. 4E). The former genes up-regulated by AS in Tconv cells included various Treg function–associated genes (e.g., Foxp3, Il2ra, Tnfrsf18, Foxo1, Ccr4, and Icos). STAT5 ChIP-seq analyses also revealed little direct histone modification by AS itself (fig. S11). Together, STAT5 activation enhanced by AS inhibition of CDK8/19 and consequent transcription of STAT5-bound genes including Foxp3 is a key mechanism of AS-induced Foxp3 expression in activated Tconv cells.

Fig. 4 Genome-wide enhancement of STAT5-dependent gene expression by AS.

(A) Mouse CD4+ T cells stimulated with anti-CD3/CD28 with or without 1.0 μM AS were analyzed at the Foxp3 gene locus for STAT5 binding, H3K27ac, and chromatin status by ChIP-seq and ATAC-seq. (B) Mouse CD4+ T cells stimulated with anti-CD3/CD28 and TGF-β with or without 1.0 μM AS were subjected to ChIP-qPCR assay for pY-STAT5 binding at Foxp3 CNS0, CNS2, and core promoter regions (n = 3). *P < 0.05. (C) Density of STAT5 binding and indicated histone modifications in AS-treated or untreated T cells. Normalized ChIP-seq signal density is plotted for AS–up-regulated STAT5-binding sites ±2 kb. (D) STAT5-binding peaks were separated into two groups, i.e., unchanged or up-regulated peaks after AS treatment, and the frequency of the peaks located in promoter, intron, exon, intergenic, 3′ untranslated region (3′UTR) or 5′UTR of mRNAs, noncoding RNAs (ncRNA), and others was calculated in each group by using annotatePeaks.pl. of homer v4.8 in default settings. (E) Cumulative histogram of fold change on average (AS–up-regulated versus AS unchanged STAT5 peak sites) of three independent RNA-seq results. STAT5-binding peaks were classified into proximal promoter or enhancer regions (within 1000 bases in the H3K4me1 or H3K27ac-positive region). Statistical significance was determined by the Kolmogorov-Smirnov test.

AS-induced in vivo Foxp3 induction in antigen-activated T cells

To determine then whether AS was able to induce Foxp3 in vivo in Tconv cells in an antigen-specific manner, we orally administered AS to DO11.10 TCR transgenic mice on the RAG2-deficient background, which harbored no thymus-derived Treg cells (1), and immunized the mice with OVA during AS treatment (Fig. 5A). Treatment with the 30 mg/kg dose, which attained a serum concentration equivalent to an in vitro Foxp3-inducing dose without discernible in vivo toxicity (fig. S12) (28), induced Foxp3 in KJ1-26+ T cells, whereas AS administration alone did not. Similarly in RAG2-sufficient DO11.10 mice, OVA immunization followed by AS treatment specifically generated KJ1.26+Foxp3+ T cells, with concurrent antigen-specific suppression of the activation of KJ1.26+ but not KJ1.26Foxp3 Tconv cells (fig. S13).

Fig. 5 In vivo induction of antigen-specific pTreg cells by AS.

(A) Flow cytometry of Foxp3+ cells in DO11.10RAG2−/−Foxp3-eGFP reporter mice with or without subcutaneous OVA immunization. CD4+ T cells in the draining lymph nodes of mice treated orally with AS (30 mg/kg) every day for 7 days were stained for Foxp3 on day 8. Representative staining (left) and percentages of Foxp3+ cells among CD4+ T cells (n = 6) (right). (B) Gene expression pattern of Foxp3+ T cells from OVA- and AS-treated DO11.10RAG2−/−Foxp3-eGFP reporter mice (designated as DO/Rag AS-pTreg), as shown in (A), compared with Foxp3+ T cells (DO nTreg) and Tconv cells (DO effector T cells) in OVA-immunized DO11.10 mice or Tconv cells (DO naїve T cells) in OVA-nonimmunized mice. Heat map shows the expression of Treg signature genes analyzed by RNA-seq. Hierarchical cluster analysis was conducted on all expressed genes. (C) Flow cytometry of Treg signature molecules expressed by AS-iTreg cells (AS-pTreg) in (A) or nTreg cells from OVA-immunized DO.11.10 mice. Itgb8 expression was assessed by mRNA staining. Data are representative of at least three experiments. (D) Bisulfite sequencing showing Treg-specific demethylated regions at Foxp3 CNS2, Eos int1b, and Helios int3a. Data are representative of two to four experiments. (E) Suppression assay performed by coculturing of VPD-labeled responder CD4+ T cells, APCs, and nTreg or pTreg cells, shown in (A), in the presence of soluble anti-CD3 mAb. Representative result (left) and total results (n = 3) (right). Vertical bars indicate means ± SD. Statistical significance was assessed by the SNK method, Student’s t test, or Kaplan-Meier method. **P < 0.01 and *P < 0.05.

RNA-seq analysis of the AS-induced pTreg cells in RAG2-deficient DO11.10 TCR transgenic mice revealed their gene expression pattern to be more similar to nTreg cells, especially activated nTreg cells, compared with AS-treated or nontreated Foxp3 Tconv cells (Fig. 5B and fig. S14). The analysis also depicted Klrg1 as being highly expressed in AS-induced pTreg cells but not in nTreg cells or Tconv cells after antigen immunization (fig. S14). Flow cytometric analysis of AS-induced pTreg cells showed an expression pattern of Treg signature molecules with a slightly less activated profile (i.e., slightly lower expression of CD25, GITR, and CTLA-4) and lower neuropilin-1 (NRP1) and negative expression of integrin β8, both profiles being indicative of pTreg cells (Fig. 5C) (7, 2931). Consistent with the gene expression profile, a population of AS-induced pTreg cells showed high expression of the KLRG1 protein, a possible marker for terminally differentiated Treg cells (32). Moreover, Treg-specific DNA demethylation status, assessed by bisulfite sequencing (17, 33), revealed that, unlike in vitro AS-induced Foxp3+ cells, the in vivo AS-induced pTreg cells had stable Treg-specific demethylation at the Foxp3 and Helios gene loci (Fig. 5D). These pTreg cells also exhibited suppressive activity as potently as nTreg cells (Fig. 5E). In addition, injection of IL-2/anti–IL-2 mAb complexes augmented in vivo AS-dependent KLRG1+ pTreg cell induction after OVA immunization in RAG-deficient DO11.10 mice (fig. S15).

Thus, the combination of AS treatment with antigenic stimulation enables in vivo generation of antigen-specific, functionally stable, and highly differentiated Foxp3+ pTreg cells from Tconv cells.

Therapeutic effects of AS on allergy and autoimmunity in animal models

The above results prompted us to assess in vivo therapeutic effects of AS in several disease models. In a skin contact hypersensitivity model, AS treatment after sensitization with 2,4-dinitrofluorobenzene (DNFB) dampened the degree of the secondary response, with milder infiltration of inflammatory cells into the skin and decreased ratios of interferon-γ+ (IFN-γ+) cells in the regional lymph nodes when compared with vehicle-treated control mice (Fig. 6, A to D). Treg depletion before the elicitation of the secondary response abolished AS-induced suppression. KLRG1+Foxp3+ T cells were specifically increased in DNFB-sensitized AS-treated mice (Fig. 6E). An increase of total Foxp3+ cells, mainly KLRG1Foxp3+ cells, was also noticed in nonimmunized AS-treated mice, suggesting that AS might have converted some self-reactive Tconv cells into Foxp3+ cells or transiently expanded self-reactive nTreg cells via activating DCs presenting self-antigens (fig. S16). AS treatment also suppressed delayed-type hypersensitivity (DTH) against OVA in normal mice, with an increase of KLRG1+ Foxp3+ T cells in draining lymph nodes, contrasting with dexamethasone as a control, which exhibited nonspecific suppression of effector T cells without increasing Treg cells (fig. S17). In addition, in nonobese diabetic (NOD) mice, which spontaneously developed histologically evident insulitis by 8 weeks of age in our mouse facility, AS treatment from 8 weeks of age significantly reduced the incidence of clinically evident diabetes (Fig. 6F), with much milder insulitis development (Fig. 6G), significantly higher ratios of KLRG1+Foxp3+ T cells (Fig. 6H), and smaller ratios of TH1 cells in the regional lymph nodes (Fig. 6H). Similar AS treatment also suppressed mouse experimental allergic encephalomyelitis with a significant increase of KLRG1+Foxp3+ T cells and a decrease of TH17 cells in the regional lymph nodes (Fig. 6, I and J). These results collectively indicate that AS is able to control acute and chronic immune responses whether physiological or pathological, such as allergy and autoimmunity, by generating antigen-specific pTreg cells.

Fig. 6 Therapeutic effects of AS on autoimmunity and allergy.

(A to E) AS treatment of DNFB-induced contact skin hypersensitivity. Mice expressing diphtheria toxin receptor under the Foxp3 promoter were sensitized epicutaneously with DNFB on the abdominal skin on days 0 and 7 and challenged on day 14 by applying DNFB on the ear, whereas some of them were orally administered with AS (30 mg/kg) daily for 2 weeks (n = 4). A group of mice (n = 6) were also treated with diphtheria toxin daily from days 0 to 14 to deplete Foxp3+ cells. Ear swelling was measured 24 hours after challenge (A), with preparation of histology (hematoxylin and eosin staining) (B). Percentages of Foxp3+ cells (C) and IFN-γ+ cells (D) among CD4+ T cells and KLRG1+ cells among Foxp3+CD4+ T cells (E) in the regional lymph nodes on day 14 (n = 3 or 4). (F) AS treatment of NOD mice. NOD mice (n = 10) were treated daily with AS (30 mg/kg, p.o.) from 8 to 10 weeks of age and assessed for urinary glucose once a week (left). Histological severity of insulitis was scored from 0 to 2 at 10 weeks of age (n = 9 to 11) (middle and right). (G) Percentages of Foxp3+ T cells among CD4+ T cells and KLRG1+Foxp3+CD4+ T cells among Foxp3+CD4+ T cells in the regional lymph nodes of NOD mice (n = 4) were assessed by flow cytometry. (H) Percentages of IFN-γ+ T cells in the regional lymph nodes of 10-week-old NOD mice (n = 4) were assessed by flow cytometry. (I and J) EAE was induced by MOG immunization, and AS (30 mg/kg) was administered daily from day 0 to day 14 (n = 7 or 8 per group). (I) EAE clinical scores and histology of spinal cords were assessed from day 8 to 28 after immunization. Spinal cords from EAE-induced mice were stained with Luxol fast blue. Percentages of Foxp3+, KLRG1+, and IL-17+ cells (J) among CD4+ T cells in the regional lymph nodes were analyzed by flow cytometry on day 14 (n = 3 or 4). Vertical bars indicate means ± SD. Statistical significance was assessed by the SNK method, Student’s t test, or Kaplan-Meier method. **P < 0.01 and *P < 0.05. AUC, area under the curve.

DISCUSSION

A key feature of Foxp3 induction in Tconv cells by pharmacological inhibition of CDK8/19 [or knockdown/knockout (KO) of the CDK8 or CDK19 gene] is that it does not require exogenous TGF-β. This was demonstrated by AS induction of Foxp3 in vitro under conditions of TGF-β neutralization and in the absence of APCs and serum. The CDK8/19 inhibitor AS is therefore distinct from other Foxp3-inducing substances such as rapamycin, retinoic acid, and butyrate (1113), which all require TGF-β for initial Foxp3 induction. In addition, unlike TGF-β–induced iTreg cells, AS-induced iTreg cells can be induced in the presence of inflammatory cytokines such as IL-4, IL-6, and IFN-γ, which appear to hamper Foxp3 gene activation via activation of STATs (34). Unlike TGF-β, AS is able to generate iTreg cells not only from naïve Tconv cells but also from effector/memory Tconv cells. Furthermore, AS cannot induce Foxp3 in CDK8 and CDK19 double-deficient T cells, whereas TGF-β can. Yet, there are also common properties between the TGF-β– and AS-induced iTreg cells; for example, both require TCR and IL-2 stimulation for their generation, and both are devoid of Treg-type DNA hypomethylation, which is present in nTreg cells and required for stable Treg function (17). This combination of distinct and shared immunological properties, together with a synergism of AS and TGF-β in Foxp3 induction, suggests that the CDK8/19- and TGF-β–dependent signaling pathways are distinct but converge on the activation of Foxp3 gene, as discussed below.

CDK8 and its paralog CDK19, which assemble with cyclin C, Med12, and Med13 to form the Mediator kinase module, are reversibly associated with the Mediator complex, controlling gene transcription positively and negatively (35). Although CDK8 and CDK19 are reported to be mutually exclusive in the association with the kinase module, knockdown/KO of either CDK8 or CDK19 or the expression of a KD form of either one was sufficient to induce Foxp3 expression in primary Tconv cells. This finding suggests that CDK8 and CDK19 are not mutually compensatory or redundant in Foxp3 induction in Tconv cells. CDK8 has been implicated in the regulation of cytokine signaling, for example, via controlling STATs (21, 36). Although CDK8 has been shown to be involved in oncogenic pathways such as the Wnt–β-catenin, p53, nuclear factor κB (NF-κB), microRNA, or TGF-β pathways (3739), inhibitors of NF-κB, GSK3, or other pathways failed to hamper in vitro AS-mediated Foxp3 induction (fig. S18). It is required to determine how each CDK8 inhibitor affects the structure and function of CDK8 and consequently modulates distinct signaling pathways to further understand the role of CDK8/19 in Foxp3 induction.

AS-inhibited CDK8/19 suppresses the serine phosphorylation in the PSP motif of STAT5 and somehow augments phosphorylation of the tyrosine residue in the C-terminal domain, leading to enhanced activation of STAT5 and consequently the activation of various STAT5-bound genes including Treg signature genes such as Foxp3 and Cd25. At the Foxp3 gene locus, pSTAT5 strongly binds to the CNS0 region and, to a lesser extent, to the promoter and the CNS2 region. We have previously shown that CNS0 is an enhancer region first and profoundly activated in the differentiation of tTreg cells in the thymus and also slightly activated (e.g., H3K27ac modified) in Tconv cells from their thymic CD4+CD8+ stage on but not in other immune cell lineages such as B cells and DCs (24). This T cell–specific role of the CNS0 enhancer region and STAT5 binding to the region might contribute to T cell–specific expression of Foxp3 by AS. Together, these findings suggest that, in TCR-stimulated Tconv cells expressing the IL-2 receptor, CDK8/19 activated by TCR signals physiologically suppresses IL-2–dependent STAT5 activation, thus attenuating STAT5-dependent gene activation to a certain extent and thereby suppressing Foxp3 expression (fig. S19). The balance between the TCR-CDK8/19-STAT5 signaling pathway inhibiting Foxp3 expression and the IL-2R/STAT5 pathway inducing Foxp3 expression might be altered transiently in Tconv cells upon TCR stimulation, resulting in transient and low-level Foxp3 expression in activated human Tconv cells without exhibiting suppressive activity or acquiring Treg-specific epigenetic changes (10, 40).

In contrast with in vitro AS or TGF-β–induced iTreg cells, which were devoid of Treg-specific hypomethylation in Treg signature genes, in vivo AS-induced pTreg cells had stable Treg-specific demethylation at the Foxp3, Helios, and other gene loci and robust suppressive activity similar to activated nTreg cells. Their low expression of NRP1 and integrin β8 indicates that they are similar to pTreg cells naturally induced from Tconv cells, for example, by homeostatic Tconv activation and differentiation in a T-lymphopenic environment (17). In addition, they characteristically express KLRG1, suggesting that they are in a highly activated or differentiated state with strong suppressive activity (32). These results collectively indicate that in vivo AS-induced Foxp3+ T cells are able to gradually acquire Treg-specific epigenetic alterations, differentiating into functionally stable Foxp3+ pTreg cells having a more nTreg-like gene expression profile. AS treatment for a limited period may thus enable establishing long-term immunosuppression by generating functionally stable pTreg cells. It remains to be determined what in vivo host-derived factors, which appear to be missing in vitro, are responsible for the epigenetic conversion of Tconv into Treg cells by in vivo AS treatment.

We have thus shown that pharmacological inhibition of CDK8/19 or knockdown/KO of the CDK8 or CDK19 gene is sufficient to induce Foxp3 in activated Tconv cells by mainly, if not solely, modulating STAT5. A key therapeutic advantage of this AS-dependent generation of Foxp3+ T cells is that effector/memory or antigen-primed T cells mediating a particular pathological (e.g., autoimmunity and allergy) or a physiological immune response (e.g., rejection of an organ transplant) can be converted into antigen-specific Treg cells even in a cytokine-abundant inflammatory environment. Further elucidation of the molecular basis of CDK8/19-STAT5 signal-dependent Foxp3 induction, particularly in effector/memory Tconv cells, will facilitate our understanding of peripheral immune tolerance contributed by pTreg cells and enable design of innovative therapies for immunological diseases relying on de novo pharmacologically induced Foxp3+ Treg cells generated in vivo and/or in vitro.

MATERIALS AND METHODS

Study design

The goal of this study was to determine the mechanism of action of AS2863619, a small-molecule CDK8/19 inhibitor identified through a screen for compounds capable of converting Tconv cells into Foxp3-expressing Treg cells. Cellular proteins binding to AS and its active analogs were identified using a photoreactive affinity probe and mass spectrometry. Immunoprecipitation experiments were used to identify other proteins contributing to AS induction of Foxp3. RNA-seq analysis was performed to investigate the effects of AS on gene expression by activated mouse T cells. Gene expression profiles assessed by RNA-seq analysis were obtained from biological replicates. Mouse models of contact hypersensitivity and autoimmunity were used to examine the in vivo therapeutic potential of AS. Sufficient numbers (more than three) of adult mice with matched age (6 to 12 weeks) and both sexes were used for each in vitro or in vivo experiment. In vitro Treg inductions, in vivo therapeutic effect, CDK8/19 knockdown experiments, and STAT5-binding assay were reproduced in two independent laboratories.

Mice

C57BL/6, BALB/c, NOD, and BALB/c-nu/nu mice were purchased from SLC or CLEA. DO.10.11 TCR transgenic mice, RAG2-deficient mice, Foxp3-DTR–green fluorescent protein (GFP) (FDG), and Foxp3–enhanced green fluorescent protein (eGFP) (eFox) reporter mice have already been described (4143). All procedures were in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals and approved by the Committee on Animal Research of Kyoto University Faculty of Medicine or Osaka University.

Antibodies and reagents

Antibodies are listed in table S2. AS2863619, AS3334366, AS3196162, AS3293990, and AS3309191 were synthesized by Astellas Pharma Inc. (chemical structures of these compounds are shown in Fig. 1A and fig. S6). CHIR99021 and CP690550 were purchased from Selleckchem; senexin A, nuclear factor of activated T cell inhibitor (CAS:249537-73-3), and SP 100030 (AP-1/NF-κB dual inhibitor) were acquired from Tocris Bioscience; rapamycin was obtained from Cell Signaling Technology; STAT5 inhibitor (CAS:285986-31-4), GSK-3β inhibitor (CAS:99-73-0), Foxo1 inhibitor (CAS:836620-48-5), and BAY-11-7082 were purchased from Cayman Chemical Company; all trans-retinoic acid and dexamethasone were obtained from Sigma-Aldrich; OVA (323-339) and MOG (35-55) peptides were purchased from Medical & Biological Laboratories (MBL). For the enrichment of CD4+ cells, CD4+ T cell isolation kit, human (Miltenyi Biotec), and Mouse CD4 T Lymphocyte Enrichment Set (BD) were used. For intracellular cytokine staining, Cell Stimulation Cocktail (plus protein transport inhibitors) (eBioscience) was used. StemXVivo Serum-Free Human T Cell Base Media (R&D Systems) was used for serum-free culture.

Cell sorting and in vitro cell culture

T cell sorting and culture were performed as previously described (44). Briefly, lymph node cells derived from eFox mice were stained with antibodies. Then, CD4+GFP+ cells were sorted as nTreg cells, and CD4+GFPCD44lowCD62Lhigh cells were sorted as naïve T cells by FACSAria II (BD). In some experiments, CD4+GFPCD44highCD62Llow cells were prepared as effector/memory T cells.

For cell culture, we used RPMI 1640 supplemented with 10% fetal calf serum (FCS) (v/v), penicillin G (60 μg/ml), streptomycin (100 μg/ml), and 0.1 mM 2-mercaptoethanol. Sorted T cells were stimulated by using Dynabeads Mouse T-Activator CD3/CD28 in the presence of IL-2 (50 U/ml).

In coculture assay, 2 × 105 CD4+ DO11.10 T cells were plated with 4 × 104 T cell–depleted splenocytes in the presence of 5 μM OVA peptide. AS was used at 1.0 μM, except where noted.

Carboxyfluorescein diacetate succinimidyl ester or violet proliferation dye (VPD) labeling was performed by incubating with 5 μM reagents at room temperature for 5 min. Labeling reaction was quenched by adding five volumes of cold medium and incubated for 20 min on ice. After washing, cells were stimulated, and proliferation was determined by fluorescence-activated cell sorting (FACS).

Human CD4+ T cells were purified from peripheral blood mononuclear cells (PBMCs) of healthy donors. Pre-enriched PBMCs were stained with anti-CD4, anti-CD25, and anti-CD45RA mAb for 30 min on ice. After washing, CD4+CD25CD45RA+ cells were sorted by FACSAria II. Cells were cultured with IL-2 (50 U/ml) and Dynabeads Human T-Activator CD3/CD28 in the presence or absence of AS. All donors provided written informed consent before sampling according to the Declaration of Helsinki. The present study was approved by the institutional ethics committees of Osaka University.

Flow cytometry analysis

Flow cytometry analysis was performed as previously described (44). Cytokine staining was carried out after incubation of cells with Cell Stimulation Cocktail (eBioscience) for 4 hours at 37°C. Cells were fixed by eBioscence Foxp3/Transcription Factor Staining Buffer Set or BD Pharmingen Transcription Factor Buffer Set according to the manufacturer’s instructions. Flow cytometric in situ hybridization of Itgb8 mRNA was carried out by PrimeFlow RNA Assay (eBioscience) according to the manufacturer’s instructions.

CpG methylation analysis by bisulfite sequencing

Bisulfite sequencing analysis was performed as previously described (14). Cells were collected by FACSAria II, and DNA was extracted by phenol extraction and ethanol precipitation. Bisulfite reaction was carried out using the MethylEasy Xceed Rapid DNA Bisulphite Modification Kit (Human Genetic Signatures).

Affinity purification using chemical probes and protein identification

EL4 cells were purchased from DS Pharma Biomedical and maintained in Dulbecco’s modified Eagle’s medium (Thermo Fisher Scientific) supplemented with 10% FCS (Sigma-Aldrich). Pull-down experiments and mass spectrometry analyses were performed as previously described (18). Cell lysate was made from EL4 lysed in 0.2% CHAPS lysis buffer (0.2% CHAPS, EDTA-free Protease Inhibitor in HBS-N). AS3309191 was coupled to the photoreactive affinity capture linker (18) by amine coupling using O-(1H-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium tetrafluoroborate and 1-hydroxybenztriazole.

Treg cell induction EC150

Mouse naїve CD4+ T cells were purified with mouse naїve CD4+ T Cell Isolation Kit (Miltenyi Biotec) from spleens of C57BL6 mice. T cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% FCS (Sigma-Aldrich), 2-mercapthoethanol (Sigma-Aldrich), and streptomycin (50 μg/ml) and penicillin (50 U/ml; Thermo Fisher Scientific). To induce mouse iTreg cells, we cultured mouse naїve CD4+ T cells with Dynabeads Mouse T-Activator CD3/CD28 (Thermo Fisher Scientific) at a bead-to-cell ratio of 1:1 for 44 hours. The cells were then stained with anti-mouse CD4 and anti-mouse Foxp3 mAbs and were analyzed by flow cytometry. EC150 was defined as the concentration of compounds that induced 150% of Foxp3+ CD4+ cells compared with dimethyl sulfoxide (DMSO) control. When EC150 could not be calculated, the maximum concentration of compounds evaluated in this assay (10 μM) was used for the calculation of the geometric mean.

RNAi in mouse CD4+ T cells

RNAi in mouse CD4+ T cells was achieved by transfection with GenomONE-Si (Ishihara Sangyo) and predesigned small interfering RNAs (siRNAs) purchased from Thermo Fisher Scientific (negative control siRNA, CDK8 siRNA, ID no. s113914; CDK19 siRNA, ID no. s95476) according to the manufacturer’s instructions. Mouse CD4+ T cells were purified with CD4 (L3T4) MicroBeads (Miltenyi Biotec) from spleens of C57BL/6 mice. The cells were transfected with 250 nM siRNA and stimulated by plate-bound anti-CD3/CD28. After 24 hours, the cells were transfected again with siRNAs and incubated for another 24 hours. After samples were collected for immunoblotting, the cells were stimulated with TGF-β (5 ng/ml) and IL-2 (250 U/ml; R&D Systems) and Dynabeads Mouse T-Activator CD3/CD28 for 22 hours. RNA was isolated from T cells by using the RNeasy Plus Micro Kit (Qiagen), and complementary DNA (cDNA) was prepared with the SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific). Reverse transcription polymerase chain reaction (RT-PCR) was performed by using TaqMan Fast Advanced Master Mix (Thermo Fisher Scientific), and predesigned TaqMan probe sets were purchased from Thermo Fisher Scientific (18S, Mm03928990_g1; Foxp3, Mm00475162_m1). Foxp3 expression level was normalized to 18S ribosomal RNA.

Retroviral transduction

A fragment encoding mouse CDK8, CDK19, or STAT5b cDNA was obtained from pCMV6-CDK8 (OriGene, MR218219), pCMV6-CDK19 (OriGene, MR215712), or pCMV6-STAT5b (OriGene, MR210649) and subcloned into a retroviral plasmid pMCs-IRES-GFP (Cell Biolabs). D173A mutation of CDK8 or CDK19 (45, 46) was induced with primers as follows: CDK8 D173A forward: GAGTAAAAATTGCTGCCATGGGCTTTGCCCG; CDK8 D173A reverse: CGGGCAAAGCCCATGGCAGCAATTTTTACTC; CDK19 D173A forward: GAGTCAAAATAGCTGCCATGGGTTTTGCCAG; CDK19 D173A reverse: CTGGCAAAACCCATGGCAGCTATTTTGACTC. S730A mutation of STAT5b was induced with primers as follows: STAT5b S730A forward: ATGGATCAGGCTCCTGCCCCAGTCGTGTGCC; STAT5b S730A reverse: GGCACACGACTGGGGCAGGAGCCTGATCCAT. Gene transduction of retroviral constructs into mouse CD4+ T cells was performed by stimulating cells by plate-bound anti-CD3/CD28. After 24 hours of culture, activated T cells were infected with viral supernatants supplemented with Polybrene (5 μg/ml), followed by centrifugation for 1 hour at 3200 rpm. Infected cells were then stimulated with Dynabeads Mouse T-Activator CD3/CD28 and IL-2 (250 U/ml) for 44 hours. The cells were stained with phycoerythrin (PE)–Cy7–labeled anti-mouse CD4, allophycocyanin-Cy7–labeled anti mouse-CD25, and allophycocyanin-labeled anti-mouse Foxp3 and were analyzed by flow cytometry. The rest of the cells were lysed for immunoblotting for CDK8 and CDK19. For the assessment of interaction between CDK8 and STAT5b, cell lysates were subjected to immunoprecipitation with anti-CDK8 or rabbit isotype control antibody (Ab) with Dynabeads Protein A (Thermo Fisher Scientific).

Luciferase reporter assay

Luciferase reporter assay was carried out by using the PicaGene Dual Seapangy Luminescence kit (Promega). Briefly, 1.6 μg of PGL4.10-luciferase vectors was transfected into 1 × 106 EL4 cells by using Nucleofector Amaxa Cell Line Nucleofector Kit L (Lonza) according to the manufacturer’s instructions. After 24 hours, cells were stimulated with Dynabeads Mouse T-Activator CD3/CD28 and AS (1 μM) for another 24 hours. Luciferase activity was recorded using the GloMax Luminometer (Promega).

Establishment of CDK8/19 KO EL4 cells

Designed guide RNAs were ligated into pSpCas9-T2A-GFP/single-guide RNA (sgRNA) {original vector was supplied by F. Zhang [pSpCas9n(BB)-2A-GFP (PX461)]; Addgene plasmid no. 48140} (47) after Bbs I digestion. Guide RNA sequences are described as follows: sgCDK8: AAGTTGGTCGAGGCACTTAC; sgCDK19: GAGGATCTGTTTGAGTACGA.

Cas9 and sgRNA expression vectors were transfected into EL4 cells using the Nucleofector L system (Lonza). After sorting of GFP+ cells by FACSAria II, cells were diluted into single-cell suspension and clonally expanded by maintenance in culture medium with penicillin/streptomycin for 1 to 2 weeks. Target deletion was confirmed by Western blot and DNA sequencing.

Immunoblotting

Antibody binding on polyvinylidene difluoride membrane (Immobilon P, Merck Millipore) was detected by using the ECL Prime Western Blotting Detection Reagent (GE Healthcare) and ImageQuant LAS4000 system (Fujifilm). Signal intensity was quantified and normalized with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) by using MultiGauge 3.2 (Fiji Image Analyzing).

RNA-seq analysis

For in vitro Foxp3 induction, 1 × 106 naïve T cells were cultured in 1 ml of 10% FCS-supplemented RPMI 1640, with the stimulation of 25 μl of Dynabeads Mouse T-Activator CD3/CD28 and IL-2 (50 U/ml, final concentration) for 18 hours followed by AS treatment for 6 hours. CD19+ B cells and bone marrow–derived DCs (BMDCs) were cultured under the same condition for 18 hours followed by AS treatment for 6 hours. For in vivo pTreg collection, DO11.10/RAG2 KO/eFox mice were immunized with OVA (200 μg subcutaneously) and treated with AS [30 mg/kg, orally (p.o.)]. One week after treatment, Foxp3+ cells in draining lymph nodes were sorted using FACSAria II. Cells were lysed in RLT buffer (Qiagen) containing 1% 2-mercaptoethanol, followed by RNA reverse transcription by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). Before preparation of the cDNA library using KAPA Library preparation kit (Kapa Biosystems), cDNA samples were fragmented by Covaris S220 Focused-ultrasonicator.

Sequence of the cDNA libraries was analyzed by Ion Proton (Thermo Fisher Scientific). Sequencing results were mapped to the reference genome information [mm9, provided by the University of California, Santa Cruz (UCSC)] using Tophat2, and unmapped sequences were analyzed again by Bowtie2. Normalized FPKM (fragments per kilobase of transcript per million mapped reads) values were provided by Cuffnorm of Cufflinks package (version 2.2.1, Trapnell Lab). To analyze DEGs in each comparison, raw tag count data were generated from mapped reads by using featureCounts in Subread packages [version 1.5.0-p3, Walter and Eliza Hall Institute; (48)]. Normalized tag count value and false discovery rate were calculated using DESeq2 package in R (version 3.2.2). Genes of false discovery rate > 0.25 in each comparison were assigned to the group of DEG.

In situ PLA

In situ PLA was performed with Duolink PLA probes and reagents (Sigma-Aldrich). Cultured cells were fixed for 10 min with 4% paraformaldehyde in phosphate-buffered saline (PBS), permeabilized for 15 min with 0.3% Triton X-100 in PBS, and incubated with 1% bovine serum albumin (BSA) in PBS for 45 min and then with primary antibodies (rabbit polyclonal anti-CDK8 Ab and mouse monoclonal anti-STAT5 Ab) overnight at 4°C. After incubation with the primary antibodies, the cells were incubated with the PLA probes (secondary antibodies against two different species bound to two oligonucleotides: anti-mouse MINUS and anti-rabbit PLUS). Annealing of the PLUS and MINUS PLA probes occurs when CDK8 and STAT5 are in close proximity, and repeat sequences in the annealed oligonucleotide complexes are amplified and then recognized by a fluorescently labeled oligonucleotide probe. After the amplifying reaction, the cells were mounted with Duolink in situ mounting medium containing 4′,6-diamidino-2-phenylindole (DAPI). PLA signals were obtained using an LSM710 confocal microscope. Z stacks were captured with sections spanning entire cells, and images were presented as maximum intensity projection.

Immunofluorescence test

Cultured cells were fixed for 10 min with 4% paraformaldehyde in PBS and permeabilized for 15 min with 0.3% Triton X-100 in PBS. The cells were incubated with 1% BSA in PBS for 45 min and then incubated with the primary antibodies [rabbit polyclonal anti-CDK8 Ab (Thermo Fisher Scientific) and mouse monoclonal anti-STAT5 Ab (BioLegend)] overnight at 4°C. After incubation with the primary antibodies, the cells were incubated with the secondary antibodies [Alexa Fluor 488–conjugated anti-rabbit immunoglobulin G (IgG) (Thermo Fisher Scientific) and Alexa Fluor 594–conjugated anti-mouse IgG (Thermo Fisher Scientific)] for 1 hour at room temperature. After incubation with Hoechst33342 in PBS, the cells were mounted with ProLong Diamond (Thermo Fischer Scientific). Confocal images were obtained using an LSM710 confocal microscope.

Assay for transposase-accessible chromatin sequencing

ATAC-seq was performed as previously described (24). Naïve T cells (1 × 106) were cultured in 1 ml of 10% FCS-supplemented RPMI 1640, with the stimulation of 25 μl of Dynabeads Mouse T-Activator CD3/CD28, IL-2 (50 U/ml, final concentration), and AS for 24 hours. ATAC peaks were visualized with the Integrative Genomics Viewer genome browser.

Chromatin immunoprecipitation sequencing

ChIP-seq analysis was performed as previously described (23), with 1 × 106 naïve T cells cultured as described in the method for RNA-seq analysis. ChIP experiments used 5 × 105 cells for each histone modification (H3K27ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3), 1 × 107 cells for Stat5, and 5 × 106 cells for CDK8. Chromatin protein–DNA interaction was fixed by 1% formaldehyde for 5 min (histone modification: H3K27ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3) or 30 min (DNA binding proteins: STAT5 and CDK8). The sonication-fragmented lysate was incubated with Dynabeads IgG magnetic beads (Thermo Fisher Scientific) precoated with 2.5 to 5 μg of antibody at 4°C for at least 6 hours. For reverse cross-linking of precipitated DNA–protein complex, DNA-protein solution was incubated with gently shaking at 65°C for precisely 24 hours. If needed, further fragmentation was performed using Covaris S220 Focused-ultrasonicator. Genomic DNA libraries were prepared using KAPA Library Preparation Kit Ion Torrent (Kapa Biosystems), with the same protocol for cDNA library preparation in RNA-seq analysis, except the number of PCR cycles (histone modification: 11 cycles, DNA binding proteins: 10 cycles) followed by DNA sequencing by IonS5 sequencing system (Thermo Fisher Scientific). Raw sequence fastq files were mapped to the reference mouse genome (mm9 provided by UCSC, 2007) by using Bowtie2.2.6 followed by calling ChIP peak region and defined differential/undifferential peak region using MACS2.

As for AS-enhanced STAT5-binding regions, annotating peak regions for the nearest transcription start site (TSS), tag coverage of given region, and motif enrichment analysis were performed using Homer2. In each defined peak region, the peak whose center was within ±1000 bases from the TSS was classified as “promoter-related modification” and the gene under that promoter was defined as “promoter peak-related gene.” For the definition of “enhancer-related genes,” TSSs within ±10,000 bases from the H3K4me1 or H3K27ac peak regions were regarded as the genes under regulation of these histone modifications (H3K4me1 or H3K27ac peak areas within 3000 bases were treated as one broad peak region). After classifying peak regions and defining related genes, expression fold changes in AS-treated/nontreated cells were calculated from RNA-seq data (normalized tag counts) and shown as a cumulative histogram. Statistical significance was determined by the Kolmogorov-Smirnov test.

ChIP assay

Mouse CD4+ T cells were stimulated by plate-bound anti-CD3/CD28 and TGF-β (5 ng/ml), and cultured with DMSO or 1000 nM AS for 22 hours. The cells were subjected to ChIP assay with the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s instructions with the use of phospho-STAT5 (Tyr694) antibody and rabbit isotype control antibody. The ChIP primer sequences used were as follows: core promoter forward: CTCACTCAGAGACTCGCAGCA; core promoter reverse: GCAAGCATGCATATGATCACC; CNS2 forward: TACAGGATAGACTAGCCACTT; CNS2 reverse: AATATGTTTTCCTATCGGGGT. Relative enrichment was calculated as a ratio to input chromatin.

Kinase assay

To evaluate compounds and calculate their IC50 (median inhibitory concentration), we performed CDK8 and CDK19 kinase assays with QSS Assist CDK8/CycC_ELISA Kit and QSS Assist CDK19/CycC_ELISA Kit (Carna Biosciences) according to the manufacturer’s instructions. GSK3α and GSK3β kinase assays were performed with GSK3α, GSK3β (Carna Biosciences), and Z-Lyte Kinase assay kit-Ser/Thr9 peptide (Thermo Fisher Scientific) according to the manufacturer’s instructions. Kinase inhibition IC50 is defined as the concentration of inhibitor that reduces phosphorylation by half compared with DMSO control.

For the evaluation of STAT5b phosphorylation by CDK8, GST-STAT5b was purified with Glutathione Sepharose 4B (GE Healthcare) from BL21 lysates transfected with pGEX 6P-1 (GE Healthcare) harboring STAT5b (709 to 786 amino acids) subcloned from pCMV6-STAT5b. 293T cells were transfected with pCMV6-CDK8 (WT or KD), pCMV–cyclin C (OriGene, RC220544), pCMV6-MED13 (OriGene, MR224038), and pF4K-CMV harboring MED12 subcloned from pF1K-MED12 (Promega, FXC12080). CDK8 submodules were pulled down with Anti-FLAG(R) M2 Magnetic Beads (Sigma-Aldrich) from the 293T lysates. The purified kinases were incubated with 10 ng of GST-STAT5b in kinase assay buffer [5 mM tris-HCl (pH 7.5), 10 mM MgCl2, 2 mM dithiothreitol, 100 mM KCl, 0.01% Brij35, and 100 μM adenosine triphosphate (ATP)]. The reaction products were subjected to immunoblotting with anti–phospho-Stat5b (S731).

Kinase selectivity profiles of compounds were evaluated by biochemical assays with a panel of recombinant kinases at Carna Biosciences. Compounds were assayed at 100 nM (duplicate). Assay formats included IMAP assays and off-chip mobility shift assays. ATP concentrations were set near kilometer values. Data are expressed as percent inhibition of the kinase activity compared with DMSO control.

Determination of drug concentration in the peripheral blood

BALB/c mice were orally administered with AS (3, 10, or 30 mg/kg). Plasma samples were collected from mice at 1, 2, 4, 8, and 24 hours after administration to measure drug levels using high-performance liquid chromatography–tandem mass spectrometry.

OVA immunization

DO11.10 mice were immunized subcutaneously with 100 μl of an emulsion containing 200 μg of OVA (323-339) in 50 μl of PBS and 50 μl of complete Freund’s adjuvant (CFA). AS was administrated (30 mg/kg, p.o.) for 7 days, and draining lymph nodes were collected for flow cytometry analysis, bisulfite sequencing analysis, and RNA-seq analysis.

Adoptive transfer of retrovirus-infected CD4+ T cells

Naїve CD4+ T cells were isolated from DO11.10Rag2−/−Foxp3-eGFP reporter mice. The cells were stimulated with anti-CD3/CD28 mAbs for 22 hours and infected with retroviruses and incubated for 22 hours in the absence of IL-2. For this experiment, truncated LNGFR, instead of eGFP, was inserted into a retroviral plasmid as a marker of infection. Then, cells were rested for 10 days in the presence of IL-2 (100 U/ml) until cell transfer into mice. BALB/c-nu/nu mice were transferred with the retrovirus-infected cells on day 0, treated with IL-2/anti–IL-2 Ab complexes on day 7, and then immunized with 100 μg of OVA emulsified with CFA at the base of the tail on day 14. Inguinal lymph node cells were collected from the mice and examined by flow cytometry on day 20.

DNFB-induced contact hypersensitivity

Mice were sensitized epicutaneously at days 0 and 7 by applying 100 μl of 0.5% DNFB diluted in acetone on the abdominal skin and challenged at day 14 by applying 20 μl of 0.5% DNFB on the ear. To deplete Treg, we treated FDG mice with 1000 ng of diphtheria toxin (daily intraperitoneally) from days 0 to 14.

Experimental autoimmune encephalomyelitis

Mice were immunized subcutaneously with 100 μl of an emulsion containing 100 μg of MOG peptide in 50 μl of PBS and 50 μl of CFA on day 0. CFA was prepared by mixing incomplete Freund’s adjuvant (Difco) with Mycobacterium tuberculosis H37RA (20 mg/ml; Difco). Pertussis toxin (List Biological Laboratories Inc., Campbell, CA) was injected on days 0 and 2 (100 ng per mouse, intraperitoneally). Clinical scoring was performed according to the following scale: 0, no clinical signs of experimental autoimmune encephalomyelitis (EAE); 1, tail weakness or tail paralysis; 2, hind leg paraparesis or hemiparesis; 3, hind leg paralysis or hemiparalysis; 4, tetraplegia or moribund; 5, death. Statistical analysis was performed according to a previous discussion (49). Histological analysis was carried out by using the Luxol Fast Blue Stain Kit (ScyTek Laboratories Inc.).

NOD mice

In this study, 8-week-old female NOD mice were prepared and maintained with tap water. The incidence of diabetes was determined by monitoring blood glucose levels. Histological analysis was performed by using pancreas tissue from 10-week-old mice. Insulitis scoring was performed according to the following scale: 0, no insulitis; 1, peri-insulitis and insulitis involving less than 25% islet infiltration; 2, more than 25% islet infiltration; 3, more than 75% islet infiltration.

DTH induction and assessment

Eight-week-old female BALB/c mice were immunized subcutaneously with 50 μg of OVA (Sigma-Aldrich) emulsified with CFA (Difco) in both hind footpads. Seven days after immunization, the mice were challenged with the intradermal injection of 20 μl of OVA (1 mg/ml in PBS) in the left ear. AS and dexamethasone were orally administered once a day during the whole experimental period. The vehicle for both compounds was 0.5% methylcellulose solution. DTH was assessed by measuring the thickness of the ear before and 24 hours after the challenge by a micrometer (TECLOCK). Mice were euthanized, and single-cell suspensions of auricular lymph nodes were prepared. The cells were then stained with PE-Cy7–labeled anti-mouse CD4, fluorescein isothiocyanate–labeled anti-mouse CD25, PerCP-Cy5.5–labeled anti-mouse KLRG1, and allophycocyanin-labeled anti-mouse Foxp3 and were assessed by flow cytometry.

BMDC culture

BMDCs were generated in vitro as previously described (50). Briefly, the bone marrow cells were cultured in culture medium containing mouse granulocyte-macrophage colony-stimulating factor (20 ng/ml) for 8 to 10 days. These DCs were stimulated with lipopolysaccharide (0.1 μg/ml) or AS (1 μM) for 24 hours.

Statistics

Values were expressed as means ± SD. Statistical significance was assessed by Student’s t test (two groups), Kaplan-Meier log-rank test (disease incidence), or non–repeated-measures analysis of variance (ANOVA) followed by the Bonferroni test (versus control), Dunnett’s test, or Student-Newman-Keuls (SNK) test (multiple comparisons). A P value <0.05 was considered statistically significant.

SUPPLEMENTARY MATERIALS

immunology.sciencemag.org/cgi/content/full/4/40/eaaw2707/DC1

Fig. S1. AS dose, TGF-β, and IL-2 in AS-dependent in vitro induction of Foxp3+ T cells.

Fig. S2. In vitro induction of FOXP3 in human Tconv cells by AS.

Fig. S3. Inability of AS to induce Treg-specific DNA hypomethylation in vitro in Tconv cells.

Fig. S4. In vitro effects of AS on the proliferative activity and the phenotype of nTreg cells.

Fig. S5. Effects of AS on gene expression by T cells, B cells, and DCs.

Fig. S6. Identification of AS targets by chemical proteomics.

Fig. S7. Dominant–negative type impaired kinase activity of KD CDK8 or CDK19 and Foxp3 induction in CD4+ T cells by their retroviral expression.

Fig. S8. Generation of CDK8/19 KO EL4 cell lines.

Fig. S9. Retroviral expression of KD or WT CDK8 in CD4+ T cells.

Fig. S10. Effects of AS on serine phosphorylation of STAT5.

Fig. S11. Effects of AS on genome-wide STAT5 binding.

Fig. S12. Plasma concentration and body weight of mice treated with various doses of AS.

Fig. S13. Induction of pTreg cells by AS treatment and antigen immunization.

Fig. S14. RNA-seq analysis of AS-induced pTreg cells.

Fig. S15. IL-2 augments in vivo AS-mediated pTreg induction.

Fig. S16. Activation of DCs by AS.

Fig. S17. Suppression of OVA-induced DTH by AS.

Fig. S18. In vitro Foxp3-inducing effects of AS in the presence of various inhibitors.

Fig. S19. Inhibition of STAT5 by CDK8/19 in activated Tconv cells and their Foxp3 expression induced by CDK8/19 inhibition via activating STAT5.

Table S1. Kinase selectivity profiles of AS2863619 and AS3334366.

Table S2. List of antibodies.

Table S3. Raw data.

REFERENCES AND NOTES

Acknowledgments: We thank M. Hattori (Kyoto University Graduate School of Medicine), K. Tamura, N. Morikawa, R. Murakami, and A. Katoh (Astellas Pharma Inc.) for constructive discussion; E. Moriyoshi, T. Ushitani, and S. Chuganji for technical assistance; and A. Tanaka (Hyogo University of Health Science) for providing the photoreactive linker compound. Funding: This work was supported by the Special Coordination Funds by the Ministry of Education, Culture, Sports, Science, and Technology of Japan and Astellas Pharma Inc. Author contributions: M.A., N.M., N.O., Y.M., I.A., S.N. and S.S. designed the study. N.N. and S.U. performed the chemical biology experiments. M.A., N.M., N.O., R.K., Y.K., A.S., K.H., and G.X. performed the cell biology experiments. T.K., H. Hamaguchi, and H. Harada performed the medicinal chemistry experiments. M.A., N.M., R.K., N.N., S.U., G.X., T.K., H. Hamaguchi, and H. Harada planned the experiments and analyzed the data. All the authors discussed the results and edited the manuscript written by M.A., N.M., S.N., and S.S. Competing interests: M.A., N.N., S.U., T.K., H. Hamaguchi, H. Harada, Y.M., and I.A. are employees of Astellas Pharma Inc. S.N. is a scientific adviser to Astellas Pharma Inc. S.S., N.O., N.M., S.N., M.A., G.X., H. Hamaguchi, N.N., S.U., and H. Harada are the authors on a patent application related to this work placed by Kyoto University and Astellas Pharma Inc. (PCT/JP2018/2826; Novel Compound, and Method for Producing Regulatory T Cells). The other authors declare that they have no competing interests. Data and materials availability: The raw data (fastq files) from the RNA-seq, ATAC-seq, and ChIP-seq experiments have been deposited at the DDBJ Sequence Read Archive under accession no. DRA006379. All data needed to evaluate the conclusions in the paper are present in the paper or the Supplementary Materials.

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