Author Correction: Circadian circuits control plasticity of group 3 innate lymphoid cells by sustaining epigenetic configuration of RORγt

Nature Immunology · 2026-03-27

Cell type-specific enhancers regulate IL-22 expression in innate and adaptive type 3 lymphoid cells

Nature Communications · 2026-03-14

IL-22, a signature cytokine for type 3 lymphoid cells, including T helper 17/22 (Th17/22) and type 3 innate lymphoid cells (ILC3), mediates epithelial homeostasis and protective pathogen responses in barrier tissues. Upon dysregulation, IL-22 can drive chronic inflammatory diseases, yet little is known about transcriptional elements modulating its expression. Here, we identify two enhancers, E22-1 and E22-2, with distinct capacities for regulating Il22 expression in type 3 lymphoid cells. Both enhancers are necessary for protection from Citrobacter rodentium infection and for the onset of IL-22-mediated psoriasis. E22-2 is specifically required for IL-22 expression in ILC3s, while E22-1 functions in both Th17/22 and ILC3. The ILC3 specificity of E22-2 is attributed to the presence of multiple Runx3 sites and the lack of a functional RORγt motif. We conclude that Th17/22 and ILC3 cells use distinct cis-elements to differentially regulate IL-22 expression, while orchestrating homeostatic protection and pathogen defense in barrier tissues. In healthy barrier tissues, type 3 lymphoid cells express IL-22 to maintain a protective immune balance, while IL-22 dysregulation contributes to disease. Here, the authors identify E22-1 and E22-2 as enhancers regulating IL-22 expression in health and disease; with E22-2 being restricted to IL-22 regulation in ILC3s.

Histone demethylases KDM5A/B regulate epigenetic programming of exhausted T cells and restrain immunotherapy responses 4207

The Journal of Immunology · 2025-11-01

Abstract Description Epigenetic silencing of effector and stemness genes in exhausted CD8 T cells (TEX) poses a considerable hurdle to effective T cell immunotherapies. While de novo DNA methylation is known to enforce T cell exhaustion, the role of histone modifications in shaping these methylation patterns remains unclear. Notably, H3K4me3 marks, which hinder Dnmt3a-mediated de novo DNA methylation, are enriched at effector/memory-associated genes in the cytolytic subset of TEX cells but are lost in terminally exhausted cells. Through integrated epigenetic profiling in both our in vitro model of human T cell dysfunction and a preclinical model of exhaustion, we observed characteristic patterns of H3K4me1/3 modifications and DNA methylation that distinctly map to different TEX subsets. Importantly, our findings demonstrate that therapeutic inhibition or genetic targeting of the H3K4 demethylases KDM5A/KDM5B enhanced effector function and cytotoxicity in dysfunctional human CD8 T cells. Furthermore, combined KDM5A/B blockade with anti-PD-L1 therapy expanded both progenitor and cytolytic TEX populations during chronic LCMV infection or cancer. These findings reveal a novel epigenetic histone-DNA methylation axis underlying terminal exhaustion and identify H3K4 demethylases as potential therapeutic targets for enhancing immunotherapy efficacy. Funding Sources Supported by NIH R01AI170926; NIH T32AI165391; Ohio State College of Medicine/Comprehensive Cancer Center funding Topic Categories Tumor Immunology: Checkpoints, Prevention, and Treatment (TIPT)

Transcriptional regulation of Ligase IV by an intronic regulatory element directs thymocyte development

Genes and Immunity · 2025-09-05

Double-strand breaks represent the most dangerous form of DNA damage, and in resting cells, these breaks are sealed via the non-homologous end joining (NHEJ) factor Ligase IV (LIG4). Excessive NHEJ may be genotoxic, necessitating multiple mechanisms to control NHEJ activity. However, a clear mechanism of transcriptional control for them has not yet been identified. Here, we examine mechanisms governing Lig4 transcription in mammals, finding that most tissues maintain very low levels of LIG4 production. Select tissues upregulate LIG4, employing different strategies for genomic regulation. In developing lymphocytes, the Lig4 locus is devoid of long-range chromatin contacts; instead, its expression and role in immune development depend upon a promoter-proximal intronic regulatory element. Deletion of the Lig4 intronic regulatory element results in thymocyte-specific loss of Lig4 upregulation, defects in lymphocyte development, and altered antigen receptor rearrangement. Our findings show the NHEJ gene, Lig4, is transcriptionally controlled to support stage-specific function concurrent with programmed DSBs. Moreover, we provide an example of how DNA cis-regulatory elements very close to a promoter can have substantial transcriptional effects.

Caspase11 modulates the adaptive immune response in SARS-CoV-2 infection through innate immune regulation 4503

The Journal of Immunology · 2025-11-01

Abstract Description Caspase 11 is a critical component of the noncanonical inflammasome with multifaceted roles in the innate immune response, contributing to host defense against pathogens. We demonstrated that Casp11 deletion improved disease outcomes in SARS-CoV-2 infection by modulating the innate inflammatory response. However, its role in shaping adaptive immune responses after SARS-CoV-2 infection remains unclear. We found that Casp11-/- MA10 infected mice exhibited higher numbers of activated lung resident memory T cells at Day 7 post-infection compared to wild-type (WT) controls, independent of lung viral load. Ex vivo stimulation of lung-resident T cells with SARS-CoV-2 peptides and tetramer staining revealed that T cells from Casp11-/- mice retained their activation status, antigen specificity, and phenotype. This suggests that Casp11 deletion promotes the expansion and activation of lung resident T cells without impairing their functionality. Using Casp11-/- bone marrow chimera and Casp11-/- Cre-flox mouse models, we identified that the enhanced adaptive immune response was mediated by Casp11 in peripheral immune cells, particularly myeloid cells. These findings indicate that Casp11 deletion leads to a more robust lung-resident adaptive immune response by modulating the early innate immune response. This enhanced adaptive immunity contributed to more effective viral clearance, improved infection control, and reduced progression to severe disease in a P30 severe infection model. Funding Sources NIH 1P01AI175399-01A1 NIH 5R01HL168501-02 Topic Categories Viral Immunology (VIR)

Locus folding mechanisms determine modes of antigen receptor gene assembly

immuneACCESS · 2025-05-09

The dynamic folding of genomes regulates numerous biological processes, including antigen receptor (AgR) gene assembly. We show that, unlike other AgR loci, homotypic chromatin interactions and bidirectional chromosome looping both contribute to structuring Tcrb for efficient long-range V(D)J recombination. Inactivation of the CTCF binding element (CBE) or promoter at the most 5'Vβ segment (Trbv1) impaired loop extrusion originating locally and extending to DβJβ CBEs at the opposite end of Tcrb. Promoter or CBE mutation nearly eliminated Trbv1 contacts and decreased RAG endonuclease-mediated Trbv1 recombination. Importantly, Trbv1 rearrangement can proceed independent of substrate orientation, ruling out scanning by DβJβ-bound RAG as the sole mechanism of Vβ recombination, distinguishing it from Igh. Our data indicate that CBE-dependent generation of loops cooperates with promoter-mediated activation of chromatin to juxtapose Vβ and DβJβ segments for recombination through diffusion-based synapsis. Thus, the mechanisms that fold a genomic region can influence molecular processes occurring in that space, which may include recombination, repair, and transcriptional programming.

Faithful Modeling of Terminal CD8 T Cell Dysfunction and Epigenetic Stabilization <i>In Vitro</i>

bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-27 · 1 citations

Abstract Epigenetic scarring of terminally dysfunctional CD8 T cells hinders long-term protection and response to immune checkpoint blockade during chronic infections and cancer. We developed a faithful in vitro model for CD8 T cell terminal dysfunction as a platform to advance T cell immunotherapy. Using TCR-transgenic CD8 T cells, we found that 1-week peptide stimulation, mimicking conditions in previous models, failed to induce a stable exhaustion program in CD8 T cells. In contrast, prolonged stimulation for 2-3 weeks induced T cell dysfunction but triggered activation-induced cell death, precluding long-term investigation of exhaustion programs. To better mimic in vivo exhaustion, we provided post-effector, chronic TGFβ1 signals, enabling survival of chronically stimulated CD8 T cells for over 3 weeks. These conditions induced a stable state of terminal dysfunction (T Dysf ), marked by a stable loss of effector, cytotoxicity, and memory programs, along with mitochondrial stress and impaired protein translation. Importantly, transcriptomic and epigenetic analyses confirmed the development of terminal exhaustion-specific signatures in T Dysf cells. Adoptive transfer of T Dysf cells revealed their inability to recall effector functions or proliferate after acute LCMV rechallenge. This novel tractable model system enables investigation of molecular pathways driving T cell terminal dysfunction and discovery of new therapeutic targets for cancer or chronic infections.

Circadian circuits control plasticity of group 3 innate lymphoid cells by sustaining epigenetic configuration of RORγt

Nature Immunology · 2025-08-13 · 11 citations

Phosphorylation of GSK3β at Ser389 prevents thymocyte necroptosis and influences the diversity of the Tcr repertoire 4584

The Journal of Immunology · 2025-11-01

Abstract Description The recombination of Tcrb and Tcra genes requires several cycles of programmed DNA double-strand breaks (DSBs) in double-negative (DN) thymocytes, along with effective repair mechanisms. However, the regulatory processes governing cell cycle checkpoints and survival pathways during this repair process are still elusive. Here, we report high-resolution single-cell RNA sequencing (scRNA-seq) analyses of individually sorted DN3 and DN4 thymocytes. We show the presence of a G2/M cell cycle checkpoint as well as the known G1 checkpoint during Tcrb and Tcra recombination. We demonstrate that the inactivation of GSK3β through phosphorylation at Ser389 is crucial for the survival of DN3 and DN4 thymocytes while they are stalled at the G1 and G2/M checkpoints. GSK3β promotes cell death by necroptosis, rather than by apoptosis, during V(D)J recombination of DN3 and DN4 thymocytes. If GSK3β is not inactivated in DN3 thymocytes, it can alter the Tcrb gene repertoire primarily through changes in Trbv segment utilization. GSK3b alters the nucleotide composition of the N2 region of Tcrb by suppressing the expression of the Apobec3 deaminase during Tcrb V(D)J recombination. Additionally, the preferential recombination of proximal V segments in Tcra relies on the inactivation of GSK3β, and this change is induced by necroptosis. Our study identifies a unique survival pathway in thymocytes that helps them navigate cell cycle checkpoints for DNA repair during Tcr gene V(D)J recombination. Funding Sources NIH R01 AI051454 Topic Categories Hematopoiesis and Immune System Development (HEM)

Inactivation of GSK3β by Ser389 phosphorylation prevents thymocyte necroptosis and impacts Tcr repertoire diversity

Cell Death and Differentiation · 2025-01-08