TIF1γ regulates stability of regulatory T cells during inflammation

H3.3 chaperone Hira primes the effector program and function of regulatory T cells

It is shown that the histone variant H3.3 is enriched in tissue Tregs compared to splenic Tregs and its chaperone Hira is a critical regulator of Treg effector program, revealing a previously unreported epigenetic mechanism critical for Treg effector differentiation and function.

Deletion of a distal IRF4 element prevents inflammation-induced reprogramming of human regulatory T cell fate.

Regulatory T (Treg) cells in mice can lose lineage identity and acquire proinflammatory functions, but whether human Treg cells are similarly susceptible to cytokine-driven destabilization remains unclear. Here we established an in vitro model of human Treg cell destabilization defined by silencing of the lineage-specifying transcription factor FOXP3, loss of suppressive function and acquisition of proinflammatory activity. Single-cell chromatin accessibility and transcriptomic profiling revealed a genome-wide increase in accessibility at AP-1-binding sites, including a putative regulatory element distal to IRF4. Increased accessibility at this element correlated with increased IRF4 expression during Treg cell destabilization, and its excision conferred resistance to inflammatory cytokine-induced reprogramming. Conversely, forced expression of IRF4 together with BATF promoted Treg cell destabilization. These data identify a distal IRF4 regulatory element as a critical node enabling heightened AP-1-IRF4 cooperative activity to drive Treg cell destabilization, with implications for the design of more stable and effective Treg cell-based therapies.

KLF2 regulates CD8 T cell differentiation and migration in infection and cancer 2254075

Besides acute infection, CX3CR1+ effector-like CD8 T cells also appear in chronic infection and cancer. Whether there is a central transcriptional regulator of the effector fate is unclear. Here, using joint single-cell profiling of the transcriptome and epigenome of chimeric antigen receptor (CAR) T cells, we identified KLF2 as a hub transcription factor in the gene regulatory network of effector-like CAR T cells. KLF2 deficiency abolished effector-like differentiation in both CAR T cells and antiviral CD8 T cells. KLF2 deficiency also impaired the differentiation of the stem-like subset. In both chronic viral infection and cancer, KLF2 deficiency impaired CD8 T cell infiltration to non-lymphoid tissues. However, unlike CAR T cells, KLF2-deficient antiviral CD8 T cells showed a greater expansion in the lymphoid tissue. Single-cell transcriptomics analysis revealed that KLF2-deficient CD8 T cells upregulated the transcriptional signature of terminally exhausted T cells and downregulated the signature of effector-like T cells, suggesting a central role of KLF2 in regulating the bifurcation of effector versus terminal exhaustion cell fates. In addition, the TOX-controlled transcriptional program was upregulated in KLF2-deficient CD8 T cells. KLF2 deficiency downregulated multiple genes associated with T cell migration including S1pr1. S1PR1 deficiency impaired the effector-like subset, whereas deficiency of CD69, a negative regulator of S1PR1, increased the effector-like subset. Notably, aging downregulated KLF2 in antigen-specific CD8 T cells, impaired the differentiation of the CX3CR1+ subset, and upregulated the TOX-mediated transcriptional program. Thus, our study demonstrates KLF2 as a central regulator of the effector fate and migration of CD8 T cells. NIH, CRI, AFAR, V Foundation Immune Response Regulation: Molecular Mechanisms (IRM)

Atherosclerosis destabilizes regulatory T cells (Tregs) resulting in multiple families of exTregs

MAP4K2 promotes regulatory T cell differentiation and attenuates T cell immunity 2256886

MAP4K family kinases are key kinases for T-cell-mediated immune responses; however, in vivo roles of MAP4K2 in immune regulation remain unclear. We used T-cell-specific MAP4K2 conditional knockout (T-MAP4K2 cKO) mice, single-cell RNA sequencing (scRNA-seq), and mass spectrometry analysis to study the role of MAP4K2 in T cell function and regulation. We found that MAP4K2 protein levels were increased in Treg cells compared to other T helper cells. We found that MAP4K2 interacted with DDX39, induced Foxp3 gene expression, and promoted Treg differentiation. Mechanistically, MAP4K2 directly phosphorylated the DEAD box protein DDX39, leading to DDX39 nuclear translocation and subsequent Foxp3 RNA splicing. MAP4K2-induced Foxp3 mRNA levels were abolished in DDX39 knockout Jurkat T cells. Furthermore, T-MAP4K2 cKO mice displayed the reduction of Treg population and sustained inflammation during remission phase of EAE autoimmune disease model. Remarkably, the anti-PD-1 immunotherapeutic effect on pancreatic cancer was drastically improved in T-MAP4K2 cKO mice, Treg-specific MAP4K2-deficient mice, or MAP4K2-inhibitor-treated mice. Consistently, scRNA-seq analysis of human pancreatic or lung cancer patients showed an increase of MAP4K2 levels in the tumor-infiltrating Treg cells; MAP4K2 mRNA levels were correlated with Foxp3 mRNA levels in the tumor-infiltrating T cells. Collectively, MAP4K2 promotes Treg differentiation by inducing DDX39 nuclear translocation, leading to the attenuation of tumor immunity. n/a Immune Response Regulation: Molecular Mechanisms (IRM)

The transcription factor NF-Y promotes myeloid cell survival and protects from inflammatory vascular disease.

Myeloid cells orchestrate vascular inflammation through transcriptional programs that control their maturation, effector function, and survival. While lineage-determining transcription factors establish myeloid identity, our understanding of the transcriptional regulation of myeloid cell behavior in chronic inflammatory contexts remains limited. Nuclear factor-Y (NF-Y) is a trimeric CCAAT-binding transcription factor that regulates cell proliferation and differentiation and is essential for maintaining stem and progenitor cell fitness. Here, we investigate NF-Y activity in myeloid cell function and survival using integrated single-cell transcriptomics and myeloid-specific deletion of the NF-YA subunit. At RNA level, NF-Y subunit transcripts were detected across myeloid compartments, with NF-YA enriched in proliferative macrophages and immature neutrophils. In mouse atherosclerotic lesions, low NF-YA levels were associated with macrophages exhibiting lipid-handling and phagocytic signatures and with neutrophils displaying a proinflammatory phenotype. NF-Y deficiency impaired neutrophil adhesion and rolling, increased their susceptibility to apoptosis, and promoted activation and lipid accumulation in macrophages. In vivo, myeloid NF-YA deficiency reduced circulating neutrophil counts, increased macrophage and neutrophil apoptosis during acute inflammation, expanded necrotic cores, leading to larger and more unstable atherosclerotic lesions, and aggravated both atherosclerosis and injury-induced neointimal thickening. These findings identify NF-Y as a transcriptional safeguard of myeloid cell survival during inflammatory stress, thereby shaping disease progression and outcomes in vascular disease.