ABSTRACT
Tissue adaptation is required for regulatory T (Treg) cell function within organs. Whether this program shares aspects with other tissue-localized immune populations is unclear. Here, we analyzed single-cell chromatin accessibility data, including the transposable element (TE) landscape of CD45+ immune cells from colon, skin, adipose tissue, and spleen. We identified features of organ-specific tissue adaptation across different immune cells. Focusing on tissue Treg cells, we found conservation of the Treg tissue adaptation program in other tissue-localized immune cells, such as amphiregulin-producing T helper (Th)17 cells. Accessible TEs can act as regulatory elements, but their contribution to tissue adaptation is not understood. TE landscape analysis revealed an enrichment of specific transcription factor binding motifs in TE regions within accessible chromatin peaks. TEs, specifically from the LTR family, were located in enhancer regions and associated with tissue adaptation. These findings broaden our understanding of immune tissue residency and provide an important step toward organ-specific immune interventions.
Subject(s)
Chromatin , DNA Transposable Elements , Single-Cell Analysis , T-Lymphocytes, Regulatory , Animals , Chromatin/metabolism , Chromatin/genetics , T-Lymphocytes, Regulatory/immunology , DNA Transposable Elements/genetics , Mice , Organ Specificity/genetics , Transcription Factors/metabolism , Transcription Factors/genetics , Mice, Inbred C57BL , HumansABSTRACT
FOXP3 hijacks DNA-binding proteins to regulate gene expression. In this issue of JEM, He et al. (https://doi.org/10.1084/jem.20232068) propose a dynamic model in which FOXP3 associates with DNA-binding proteins to regulate Treg cell function in response to environmental cues.
Subject(s)
Forkhead Transcription Factors , T-Lymphocytes, Regulatory , Forkhead Transcription Factors/metabolism , Forkhead Transcription Factors/genetics , Humans , T-Lymphocytes, Regulatory/immunology , T-Lymphocytes, Regulatory/metabolism , Animals , Gene Expression Regulation , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Transcription Factors/metabolism , Transcription Factors/geneticsABSTRACT
CD8 T lymphocytes are classically viewed as cytotoxic T cells. Whether human CD8 T cells can, in parallel, induce a tissue regeneration program is poorly understood. Here, antigen-specific assay systems revealed that human CD8 T cells not only mediated cytotoxicity but also promoted tissue remodeling. Activated CD8 T cells could produce the epidermal growth factor receptor (EGFR)-ligand amphiregulin (AREG) and sensitize epithelial cells for enhanced regeneration potential. Blocking the EGFR or the effector cytokines IFN-γ and TNF could inhibit tissue remodeling. This regenerative program enhanced tumor spheroid and stem cell-mediated organoid growth. Using single-cell gene expression analysis, we identified an AREG+, tissue-resident CD8 T cell population in skin and adipose tissue from patients undergoing abdominal wall or abdominoplasty surgery. These tissue-resident CD8 T cells showed a strong TCR clonal relation to blood PD1+TIGIT+ CD8 T cells with tissue remodeling abilities. These findings may help to understand the complex CD8 biology in tumors and could become relevant for the design of therapeutic T cell products.
Subject(s)
CD8-Positive T-Lymphocytes , T-Lymphocytes, Cytotoxic , Humans , ErbB Receptors , Adipose Tissue , Cell CycleABSTRACT
Regulatory T (Treg) cells ensure tolerance against self-antigens, limit excessive inflammation, and support tissue repair processes. Therefore, Treg cells are currently attractive candidates for the treatment of certain inflammatory diseases, autoimmune disorders, or transplant rejection. Early clinical trials have proved the safety and efficacy of certain Treg cell therapies in inflammatory diseases. We summarize recent advances in engineering Treg cells, including the concept of biosensors for inflammation. We assess Treg cell engineering possibilities for novel functional units, including Treg cell modifications influencing stability, migration, and tissue adaptation. Finally, we outline perspectives of engineered Treg cells going beyond inflammatory diseases by using custom-designed receptors and read-out systems, aiming to use Treg cells as in vivo diagnostic tools and drug delivery vehicles.
Subject(s)
Autoimmune Diseases , T-Lymphocytes, Regulatory , Humans , Autoimmune Diseases/therapy , Immune Tolerance , Immunotherapy, Adoptive , Inflammation/therapyABSTRACT
Engineered regulatory T cell (Treg cell) therapy is a promising strategy to treat patients suffering from inflammatory diseases, autoimmunity, and transplant rejection. However, in many cases, disease-related antigens that can be targeted by Treg cells are not available. In this study, we introduce a class of synthetic biosensors, named artificial immune receptors (AIRs), for murine and human Treg cells. AIRs consist of three domains: (a) extracellular binding domain of a tumor necrosis factor (TNF)-receptor superfamily member, (b) intracellular costimulatory signaling domain of CD28, and (c) T cell receptor signaling domain of CD3-ζ chain. These AIR receptors equip Treg cells with an inflammation-sensing machinery and translate this environmental information into a CD3-ζ chain-dependent TCR-activation program. Different AIRs were generated, recognizing the inflammatory ligands of the TNF-receptor superfamily, including LIGHT, TNFα, and TNF-like ligand 1A (TL1A), leading to activation, differentiation, and proliferation of AIR-Treg cells. In a graft-versus-host disease model, Treg cells expressing lymphotoxin ß receptor-AIR, which can be activated by the ligand LIGHT, protect significantly better than control Treg cells. Expression and signaling of the corresponding human AIR in human Treg cells prove that this concept can be translated. Engineering Treg cells that target inflammatory ligands leading to TCR signaling and activation might be used as a Treg cell-based therapy approach for a broad range of inflammation-driven diseases.
Subject(s)
Biosensing Techniques , Cell Engineering , Cell- and Tissue-Based Therapy , Inflammation , T-Lymphocytes, Regulatory , Animals , CD28 Antigens/metabolism , Humans , Inflammation/therapy , Ligands , Lymphotoxin beta Receptor/metabolism , Mice , Receptors, Antigen, T-Cell/metabolism , Receptors, Tumor Necrosis Factor/metabolism , T-Lymphocytes, Regulatory/transplantation , Tumor Necrosis Factor-alphaABSTRACT
Accelerated glycolysis leads to secretion and accumulation of lactate and protons in the tumor environment and determines the efficacy of adoptive T cell and checkpoint inhibition therapy. Here, we analyzed effects of lactic acid on different human CD4 T cell subsets and aimed to increase CD4 T cell resistance towards lactic acid. In all CD4 T cell subsets analyzed, lactic acid inhibited metabolic activity (glycolysis and respiration), cytokine secretion, and cell proliferation. Overexpression of the lactate-metabolizing isoenzyme LDHB increased cell respiration and mitigated lactic acid effects on intracellular cytokine production. Strikingly, LDHB-overexpressing cells preferentially migrated into HCT116 tumor spheroids and displayed higher expression of cytotoxic effector molecules. We conclude, that LDHB overexpression might be a promising strategy to increase the efficacy of adoptive T cell transfer therapy.
Subject(s)
Lactate Dehydrogenases/metabolism , Lactic Acid , Neoplasms , Cell Line, Tumor , Cytokines/metabolism , Glycolysis , Humans , L-Lactate Dehydrogenase/genetics , L-Lactate Dehydrogenase/metabolism , Lactic Acid/metabolism , Neoplasms/metabolism , T-Lymphocytes/metabolismABSTRACT
Tertiary lymphoid structures (TLS) are highly organized ectopic structures found in nonlymphoid organs under chronic inflammatory conditions, including cancer. A recent study by Chaurio et al. reports that repression of Satb1 in CD4+ T cells can lead to increased Tfh cell differentiation, driving intratumoral TLS formation, resulting in reduced tumor growth in mice.
Subject(s)
Matrix Attachment Region Binding Proteins , Neoplasms , Tertiary Lymphoid Structures , Animals , Cell Differentiation , Humans , Mice , T Follicular Helper Cells , Tertiary Lymphoid Structures/pathologyABSTRACT
T cell exhaustion limits anti-tumor immunity and responses to immunotherapy. Here, we explored the microenvironmental signals regulating T cell exhaustion using a model of chronic lymphocytic leukemia (CLL). Single-cell analyses identified a subset of PD-1hi, functionally impaired CD8+ T cells that accumulated in secondary lymphoid organs during disease progression and a functionally competent PD-1int subset. Frequencies of PD-1int TCF-1+ CD8+ T cells decreased upon Il10rb or Stat3 deletion, leading to accumulation of PD-1hi cells and accelerated tumor progression. Mechanistically, inhibition of IL-10R signaling altered chromatin accessibility and disrupted cooperativity between the transcription factors NFAT and AP-1, promoting a distinct NFAT-associated program. Low IL10 expression or loss of IL-10R-STAT3 signaling correlated with increased frequencies of exhausted CD8+ T cells and poor survival in CLL and in breast cancer patients. Thus, balance between PD-1hi, exhausted CD8+ T cells and functional PD-1int TCF-1+ CD8+ T cells is regulated by cell-intrinsic IL-10R signaling, with implications for immunotherapy.
Subject(s)
CD8-Positive T-Lymphocytes/immunology , Immunotherapy/methods , Leukemia, Lymphocytic, Chronic, B-Cell/immunology , Receptors, Interleukin-10/metabolism , T-Lymphocyte Subsets/immunology , Animals , Cell Line, Tumor , Cells, Cultured , Cellular Microenvironment , Hepatocyte Nuclear Factor 1-alpha/metabolism , Humans , Immunity , Mice , Mice, Inbred C57BL , NFATC Transcription Factors/metabolism , Programmed Cell Death 1 Receptor/metabolism , Receptors, Interleukin-10/genetics , STAT3 Transcription Factor/genetics , STAT3 Transcription Factor/metabolism , Signal Transduction , Transcription Factor AP-1/metabolismABSTRACT
Murine regulatory T (Treg) cells in tissues promote tissue homeostasis and regeneration. We sought to identify features that characterize human Treg cells with these functions in healthy tissues. Single-cell chromatin accessibility profiles of murine and human tissue Treg cells defined a conserved, microbiota-independent tissue-repair Treg signature with a prevailing footprint of the transcription factor BATF. This signature, combined with gene expression profiling and TCR fate mapping, identified a population of tissue-like Treg cells in human peripheral blood that expressed BATF, chemokine receptor CCR8 and HLA-DR. Human BATF+CCR8+ Treg cells from normal skin and adipose tissue shared features with nonlymphoid T follicular helper-like (Tfh-like) cells, and induction of a Tfh-like differentiation program in naive human Treg cells partially recapitulated tissue Treg regenerative characteristics, including wound healing potential. Human BATF+CCR8+ Treg cells from healthy tissue share features with tumor-resident Treg cells, highlighting the importance of understanding the context-specific functions of these cells.
Subject(s)
Chromatin/immunology , T-Lymphocytes, Regulatory/immunology , Wound Healing/immunology , Adult , Animals , Basic-Leucine Zipper Transcription Factors/immunology , Cell Differentiation/immunology , Cell Line , Female , Gene Expression Profiling/methods , Gene Expression Regulation/immunology , HaCaT Cells , Humans , Male , Mice , Mice, Inbred C57BL , Middle Aged , Receptors, CCR8/immunology , T Follicular Helper Cells/immunologyABSTRACT
The macroscopic and microscopic anatomy of the oral cavity is complex and unique in the human body. Soft-tissue structures are in close interaction with mineralized bone, but also dentine, cementum and enamel of our teeth. These are exposed to intense mechanical and chemical stress as well as to dense microbiologic colonization. Teeth are susceptible to damage, most commonly to caries, where microorganisms from the oral cavity degrade the mineralized tissues of enamel and dentine and invade the soft connective tissue at the core, the dental pulp. However, the pulp is well-equipped to sense and fend off bacteria and their products and mounts various and intricate defense mechanisms. The front rank is formed by a layer of odontoblasts, which line the pulp chamber towards the dentine. These highly specialized cells not only form mineralized tissue but exert important functions as barrier cells. They recognize pathogens early in the process, secrete antibacterial compounds and neutralize bacterial toxins, initiate the immune response and alert other key players of the host defense. As bacteria get closer to the pulp, additional cell types of the pulp, including fibroblasts, stem and immune cells, but also vascular and neuronal networks, contribute with a variety of distinct defense mechanisms, and inflammatory response mechanisms are critical for tissue homeostasis. Still, without therapeutic intervention, a deep carious lesion may lead to tissue necrosis, which allows bacteria to populate the root canal system and invade the periradicular bone via the apical foramen at the root tip. The periodontal tissues and alveolar bone react to the insult with an inflammatory response, most commonly by the formation of an apical granuloma. Healing can occur after pathogen removal, which is achieved by disinfection and obturation of the pulp space by root canal treatment. This review highlights the various mechanisms of pathogen recognition and defense of dental pulp cells and periradicular tissues, explains the different cell types involved in the immune response and discusses the mechanisms of healing and repair, pointing out the close links between inflammation and regeneration as well as between inflammation and potential malignant transformation.
Subject(s)
Dental Pulp/pathology , Periapical Periodontitis/pathology , Periapical Tissue/pathology , Pulpitis/pathology , Animals , Antigens, Neoplasm/immunology , Carcinogenesis/immunology , Carcinoma, Squamous Cell/etiology , Carcinoma, Squamous Cell/immunology , Carcinoma, Squamous Cell/physiopathology , Chemokines/metabolism , Complement System Proteins/metabolism , Dental Caries/physiopathology , Dental Pulp/microbiology , Dentin/blood supply , Dentin/innervation , Dentin/metabolism , Fibroblasts/immunology , Fibroblasts/metabolism , Humans , Intracellular Signaling Peptides and Proteins/physiology , Mesenchymal Stem Cells/physiology , Mouth Neoplasms/etiology , Mouth Neoplasms/immunology , Mouth Neoplasms/physiopathology , Nerve Net/physiology , Neuropeptides/metabolism , Nitric Oxide/physiology , Odontoblasts/physiology , Periapical Granuloma/etiology , Periapical Granuloma/pathology , Periapical Tissue/microbiology , Radicular Cyst/etiology , Radicular Cyst/physiopathologyABSTRACT
The vast majority of Foxp3+ regulatory T cells (Tregs) are generated in the thymus, and several factors, such as cytokines and unique thymic antigen-presenting cells, are known to contribute to the development of these thymus-derived Tregs (tTregs). Here, we report the existence of a specific subset of Foxp3+ Tregs within the thymus that is characterized by the expression of IL-1R2, which is a decoy receptor for the inflammatory cytokine IL-1. Detailed flow cytometric analysis of the thymocytes from Foxp3hCD2xRAG1GFP reporter mice revealed that the IL-1R2+ Tregs are mainly RAG1GFP- and CCR6+CCR7-, demonstrating that these Tregs are recirculating cells entering the thymus from the periphery and that they have an activated phenotype. In the spleen, the majority of IL-1R2+ Tregs express neuropilin-1 (Nrp-1) and Helios, suggesting a thymic origin for these Tregs. Interestingly, among all tissues studied, the highest frequency of IL-1R2+ Tregs was observed in the thymus, indicating preferential recruitment of this Treg subset by the thymus. Using fetal thymic organ cultures (FTOCs), we demonstrated that increased concentrations of exogenous IL-1ß blocked intrathymic Treg development, resulting in a decreased frequency of CD25+Foxp3+ tTregs and an accumulation of CD25+Foxp3- Treg precursors. Interestingly, the addition of IL-1R2+ Tregs, but not IL-1R2- Tregs, to reaggregated thymic organ cultures (RTOCs) abrogated the IL-1ß-mediated blockade, demonstrating that these recirculating IL-1R2+ Tregs can quench IL-1 signaling in the thymus and thereby maintain thymic Treg development even under inflammatory conditions.
Subject(s)
Cell Differentiation , Forkhead Transcription Factors/physiology , Inflammation/immunology , Receptors, Interleukin-1 Type II/metabolism , T-Lymphocytes, Regulatory/cytology , Thymocytes/cytology , Animals , Cytokines/metabolism , Homeodomain Proteins/physiology , Inflammation/metabolism , Inflammation/pathology , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Spleen/cytology , Spleen/immunology , Spleen/metabolism , T-Lymphocytes, Regulatory/immunology , T-Lymphocytes, Regulatory/metabolism , Thymocytes/immunology , Thymocytes/metabolismABSTRACT
Regulatory T cells are important regulators of the immune system and have versatile functions for the homeostasis and repair of tissues. They express the forkhead box transcription factor Foxp3 as a lineage-defining protein. Negative regulators of Foxp3 expression are not well understood. Here, we generated double-stranded DNA probes complementary to the Foxp3 promoter sequence and performed a pull-down with nuclear protein in vitro, followed by elution of bound proteins and quantitative mass spectrometry. Of the Foxp3-promoter-binding transcription factors identified with this approach, one was T cell factor 1 (TCF1). Using viral over-expression, we identified TCF1 as a repressor of Foxp3 expression. In TCF1-deficient animals, increased levels of Foxp3intermediateCD25negative T cells were identified. CRISPR-Cas9 knockout studies in primary human and mouse conventional CD4 T (Tconv) cells revealed that TCF1 protects Tconv cells from inadvertent Foxp3 expression. Our data implicate a role of TCF1 in suppressing Foxp3 expression in activated T cells.
ABSTRACT
Specialized regulatory T (Treg) cells accumulate and perform homeostatic and regenerative functions in nonlymphoid tissues. Whether common precursors for nonlymphoid-tissue Treg cells exist and how they differentiate remain elusive. Using transcription factor nuclear factor, interleukin 3 regulated (Nfil3) reporter mice and single-cell RNA-sequencing (scRNA-seq), we identified two precursor stages of interleukin 33 (IL-33) receptor ST2-expressing nonlymphoid tissue Treg cells, which resided in the spleen and lymph nodes. Global chromatin profiling of nonlymphoid tissue Treg cells and the two precursor stages revealed a stepwise acquisition of chromatin accessibility and reprogramming toward the nonlymphoid-tissue Treg cell phenotype. Mechanistically, we identified and validated the transcription factor Batf as the driver of the molecular tissue program in the precursors. Understanding this tissue development program will help to harness regenerative properties of tissue Treg cells for therapy.
Subject(s)
Basic-Leucine Zipper Transcription Factors/metabolism , Lymph Nodes/immunology , Spleen/immunology , T-Lymphocytes, Regulatory/cytology , Adoptive Transfer , Animals , Basic-Leucine Zipper Transcription Factors/deficiency , Basic-Leucine Zipper Transcription Factors/genetics , Cell Differentiation/genetics , Chromatin/metabolism , GATA3 Transcription Factor/genetics , GATA3 Transcription Factor/metabolism , Gene Expression Profiling , Gene Expression Regulation/immunology , Interleukin-1 Receptor-Like 1 Protein/metabolism , Lectins, C-Type/genetics , Lectins, C-Type/metabolism , Mice , Organ Specificity/immunology , Receptors, Immunologic/genetics , Receptors, Immunologic/metabolism , T-Lymphocytes, Regulatory/metabolismABSTRACT
BACKGROUND: NY-BR-1 has been described as a breast cancer associated differentiation antigen with intrinsic immunogenicity giving rise to endogenous T and B cell responses. The current study presents the first murine tumor model allowing functional investigation of NY-BR-1-specific immune responses in vivo. METHODS: A NY-BR-1 expressing tumor model was established in DR4tg mice based on heterotopic transplantation of stable transfectant clones derived from the murine H2 compatible breast cancer cell line EO771. Composition and phenotype of tumor infiltrating immune cells were analyzed by qPCR and FACS. MHC I binding affinity of candidate CTL epitopes predicted in silico was determined by FACS using the mutant cell line RMA-S. Frequencies of NY-BR-1 specific CTLs among splenocytes of immunized mice were quantified by FACS with an epitope loaded Db-dextramer. Functional CTL activity was determined by IFNγ catch or IFNγ ELISpot assays and statistical analysis was done applying the Mann Whitney test. Tumor protection experiments were performed by immunization of DR4tg mice with replication deficient recombinant adenovirus followed by s.c. challenge with NY-BR-1 expressing breast cancer cells. RESULTS: Our results show spontaneous accumulation of CD8+ T cells and F4/80+ myeloid cells preferentially in NY-BR-1 expressing tumors. Upon NY-BR-1-specific immunization experiments combined with in silico prediction and in vitro binding assays, the first NY-BR-1-specific H2-Db-restricted T cell epitope could be identified. Consequently, flow cytometric analysis with fluorochrome conjugated multimers showed enhanced frequencies of CD8+ T cells specific for the newly identified epitope in spleens of immunized mice. Moreover, immunization with Ad.NY-BR-1 resulted in partial protection against outgrowth of NY-BR-1 expressing tumors and promoted intratumoral accumulation of macrophages. CONCLUSION: This study introduces the first H2-Db-resctricted CD8+ T cell epitope-specific for the human breast cancer associated tumor antigen NY-BR-1. Our novel, partially humanized tumor model enables investigation of the interplay between HLA-DR4-restricted T cell responses and CTLs within their joint attack of NY-BR-1 expressing tumors.
Subject(s)
Antigens, Neoplasm/immunology , Epitopes, T-Lymphocyte/immunology , HLA-DRB1 Chains/genetics , Neoplasms/etiology , Neoplasms/pathology , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , Animals , Antigens, Neoplasm/genetics , Biomarkers , Cell Line, Tumor , Disease Models, Animal , HLA-DRB1 Chains/immunology , Heterografts , Humans , Immunization , Immunophenotyping , Leukocytes/immunology , Leukocytes/metabolism , Mice , Mice, Transgenic , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolismABSTRACT
The transcriptional regulator Rbpj is involved in T-helper (TH) subset polarization, but its function in Treg cells remains unclear. Here we show that Treg-specific Rbpj deletion leads to splenomegaly and lymphadenopathy despite increased numbers of Treg cells with a polyclonal TCR repertoire. A specific defect of Rbpj-deficient Treg cells in controlling TH2 polarization and B cell responses is observed, leading to the spontaneous formation of germinal centers and a TH2-associated immunoglobulin class switch. The observed phenotype is environment-dependent and can be induced by infection with parasitic nematodes. Rbpj-deficient Treg cells adopt open chromatin landscapes and gene expression profiles reminiscent of tissue-derived TH2-polarized Treg cells, with a prevailing signature of the transcription factor Gata-3. Taken together, our study suggests that Treg cells require Rbpj to specifically restrain TH2 responses, including their own excessive TH2-like differentiation potential.
Subject(s)
Immunity, Cellular , Immunoglobulin J Recombination Signal Sequence-Binding Protein/metabolism , Strongyloidiasis/immunology , T-Lymphocytes, Regulatory/immunology , Th2 Cells/immunology , Animals , Cell Differentiation/immunology , Disease Models, Animal , Female , GATA3 Transcription Factor/metabolism , Gene Expression Profiling , Gene Expression Regulation/immunology , Germinal Center/immunology , Humans , Immunoglobulin J Recombination Signal Sequence-Binding Protein/genetics , Immunoglobulin J Recombination Signal Sequence-Binding Protein/immunology , Lymphocyte Activation , Male , Mice , Mice, Inbred C57BL , Mice, Transgenic , Strongyloides ratti/immunology , Strongyloides ratti/pathogenicity , Strongyloidiasis/parasitology , T-Lymphocytes, Regulatory/metabolism , Transcriptome/immunologyABSTRACT
During the last decade, advances in sequencing technologies allowed production of a wealth of information on epigenetic modifications in T cells. Epigenome maps, in combination with mechanistic studies, have demonstrated that T cells undergo extensive epigenome remodeling in response to signals, which has a strong effect on phenotypic stability and function of lymphocytes. In this review we focus on DNA methylation, histone modifications, and chromatin structure as important epigenetic mechanisms involved in controlling T-cell responses. In particular, we discuss epigenetic processes in light of the development, activation, and differentiation of CD4+ T helper (TH), regulatory T, and CD8+ T cells. As central aspects of the adaptive immune system, we review mechanisms that ensure molecular memory, stability, plasticity, and exhaustion of T cells. We further discuss the effect of the tissue environment on imprinting T-cell epigenomes with potential implications for immunotherapy.
Subject(s)
Epigenesis, Genetic , T-Lymphocytes/cytology , Animals , Cell Differentiation , Humans , Thymus Gland/cytologyABSTRACT
This corrects the article DOI: 10.1038/ni.3799.