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Caillier A, Oleksyn D, Fowell DJ, Miller J, Oakes PW. T cells use focal adhesions to pull themselves through confined environments. J Cell Biol 2024; 223:e202310067. [PMID: 38889096 PMCID: PMC11187980 DOI: 10.1083/jcb.202310067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 05/16/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
Immune cells are highly dynamic and able to migrate through environments with diverse biochemical and mechanical compositions. Their migration has classically been defined as amoeboid under the assumption that it is integrin independent. Here, we show that activated primary Th1 T cells require both confinement and extracellular matrix proteins to migrate efficiently. This migration is mediated through small and dynamic focal adhesions that are composed of the same proteins associated with canonical mesenchymal cell focal adhesions, such as integrins, talin, and vinculin. These focal adhesions, furthermore, localize to sites of contractile traction stresses, enabling T cells to pull themselves through confined spaces. Finally, we show that Th1 T cells preferentially follow tracks of other T cells, suggesting that these adhesions modify the extracellular matrix to provide additional environmental guidance cues. These results demonstrate not only that the boundaries between amoeboid and mesenchymal migration modes are ambiguous, but that integrin-mediated focal adhesions play a key role in T cell motility.
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Affiliation(s)
- Alexia Caillier
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - David Oleksyn
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, University of Rochester Medical Center, Rochester, NY, USA
| | - Deborah J. Fowell
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Jim Miller
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, University of Rochester Medical Center, Rochester, NY, USA
| | - Patrick W. Oakes
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
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2
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Tsareva A, Shelyakin PV, Shagina IA, Myshkin MY, Merzlyak EM, Kriukova VV, Apt AS, Linge IA, Chudakov DM, Britanova OV. Aberrant adaptive immune response underlies genetic susceptibility to tuberculosis. Front Immunol 2024; 15:1380971. [PMID: 38799462 PMCID: PMC11116662 DOI: 10.3389/fimmu.2024.1380971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/11/2024] [Indexed: 05/29/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb) remains a major threat worldwide, although only a fraction of infected individuals develops tuberculosis (TB). TB susceptibility is shaped by multiple genetic factors, and we performed comparative immunological analysis of two mouse strains to uncover relevant mechanisms underlying susceptibility and resistance. C57BL/6 mice are relatively TB-resistant, whereas I/St mice are prone to develop severe TB, partly due to the MHC-II allelic variant that shapes suboptimal CD4+ T cell receptor repertoire. We investigated the repertoires of lung-infiltrating helper T cells and B cells at the progressed stage in both strains. We found that lung CD4+ T cell repertoires of infected C57BL/6 but not I/St mice contained convergent TCR clusters with functionally confirmed Mtb specificity. Transcriptomic analysis revealed a more prominent Th1 signature in C57BL/6, and expression of pro-inflammatory IL-16 in I/St lung-infiltrating helper T cells. The two strains also showed distinct Th2 signatures. Furthermore, the humoral response of I/St mice was delayed, less focused, and dominated by IgG/IgM isotypes, whereas C57BL/6 mice generated more Mtb antigen-focused IgA response. We conclude that the inability of I/St mice to produce a timely and efficient anti-Mtb adaptive immune responses arises from a suboptimal helper T cell landscape that also impacts the humoral response, leading to diffuse inflammation and severe disease.
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Affiliation(s)
- Anastasiia Tsareva
- Precision Oncology Division, Boston Gene Laboratory, Waltham, MA, United States
| | - Pavel V. Shelyakin
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Abu Dhabi Stem Cells Center, Abu Dhabi, United Arab Emirates
| | - Irina A. Shagina
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Mikhail Yu. Myshkin
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ekaterina M. Merzlyak
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Valeriia V. Kriukova
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Alexander S. Apt
- Laboratory for Immunogenetics, Central Tuberculosis Research Institute, Moscow, Russia
| | - Irina A. Linge
- Laboratory for Immunogenetics, Central Tuberculosis Research Institute, Moscow, Russia
| | - Dmitriy M. Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Abu Dhabi Stem Cells Center, Abu Dhabi, United Arab Emirates
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Olga V. Britanova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
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3
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Brash JT, Diez-Pinel G, Colletto C, Castellan RF, Fantin A, Ruhrberg C. The BulkECexplorer compiles endothelial bulk transcriptomes to predict functional versus leaky transcription. NATURE CARDIOVASCULAR RESEARCH 2024; 3:460-473. [PMID: 38708406 PMCID: PMC7615926 DOI: 10.1038/s44161-024-00436-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/26/2024] [Indexed: 05/07/2024]
Abstract
Transcriptomic data can be mined to understand the molecular activity of cell types. Yet, functional genes may remain undetected in RNA sequencing (RNA-seq) experiments for technical reasons, such as insufficient read depth or gene dropout. Conversely, RNA-seq experiments may detect lowly expressed mRNAs thought to be biologically irrelevant products of leaky transcription. To represent a cell type's functional transcriptome more accurately, we propose compiling many bulk RNA-seq datasets into a compendium and applying established classification models to predict whether detected transcripts are likely products of active or leaky transcription. Here, we present the BulkECexplorer (bulk RNA-seq endothelial cell explorer) compendium of 240 bulk RNA-seq datasets from five vascular endothelial cell subtypes. This resource reports transcript counts for genes of interest and predicts whether detected transcripts are likely the products of active or leaky gene expression. Beyond its usefulness for vascular biology research, this resource provides a blueprint for developing analogous tools for other cell types.
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Affiliation(s)
- James T. Brash
- UCL Institute of Ophthalmology, University College London, London, UK
| | | | - Chiara Colletto
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Alessandro Fantin
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Biosciences, University of Milan, Milan, Italy
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Hughes K, Conaway E, Blackwell E, Rout E, Yoshimoto J, Burnett R, Avery A. Canine T zone lymphoma is a tumor of mature, previously activated αβ T cells. Vet Immunol Immunopathol 2024; 269:110725. [PMID: 38359755 DOI: 10.1016/j.vetimm.2024.110725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 02/17/2024]
Abstract
T cell lymphomas are a diverse group of tumors found in both dogs and humans, originating from various normal T cell types. Identifying the origin of neoplastic lymphocytes can offer valuable insights into the pathogenesis and clinical behavior of these tumors. T zone lymphoma (TZL) in dogs is characterized by the absence of CD45 expression, a strong breed predilection, and its association with adult-onset demodicosis-a condition believed to be linked to immunosuppression. In this study, our aim was to employ transcriptomic and functional data to determine the normal counterpart of TZL. Identifying the normal counterpart may help us understand both how these tumors arise and explain their clinical behavior. Gene expression profiling using NanoString and RNA seq was used to compare the transcriptome between neoplastic T zone cells, normal canine T cells and publicly available gene sets using Gene Set Enrichment Analysis. Mitogen, anti-CD3 stimulation and PMA/ionomycin stimulation were used to assess T cell proliferation in vitro, and intracellular cytokine production was measured by flow cytometry. Gene expression profiling revealed that TZL is most likely derived from an activated or memory alpha-beta T cell but the cells do not fall cleanly into an effector subtype. TZL cells express CD4-specific transcription factors GATA3 and THPOK, even though TZL cells more commonly express CD8, or neither CD4 nor CD8. TZL cells produce high levels of interferon gamma and tumor necrosis factor alpha when stimulated, further supporting the hypothesis that they are derived from an antigen experienced T cell. TZL cells do not proliferate when stimulated through the T cell receptor but will divide when the T cell receptor is bypassed with PMA and ionomycin. The observation that these cells are derived from a mature, previously activated T cell is the first step in understanding the genesis of this unique T cell tumor.
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Affiliation(s)
- Kelly Hughes
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States
| | - Evan Conaway
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States
| | - Emily Blackwell
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States
| | - Emily Rout
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States
| | - Janna Yoshimoto
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States
| | - Robert Burnett
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States
| | - Anne Avery
- Clinical Hematopathology Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Science, Colorado State University, Fort Collins, CO 80523, United States.
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5
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Yang F, Zhou L, Shen Y, Wang X, Fan X, Yang L. Multi-omics approaches for drug-response characterization in primary biliary cholangitis and autoimmune hepatitis variant syndrome. J Transl Med 2024; 22:214. [PMID: 38424613 PMCID: PMC10902991 DOI: 10.1186/s12967-024-05029-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/24/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Primary biliary cholangitis (PBC) and autoimmune hepatitis (AIH) variant syndrome (VS) exhibit a complex overlap of AIH features with PBC, leading to poorer prognoses than those with PBC or AIH alone. The biomarkers associated with drug response and potential molecular mechanisms in this syndrome have not been fully elucidated. METHODS Whole-transcriptome sequencing was employed to discern differentially expressed (DE) RNAs within good responders (GR) and poor responders (PR) among patients with PBC/AIH VS. Subsequent gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted for the identified DE RNAs. Plasma metabolomics was employed to delineate the metabolic profiles distinguishing PR and GR groups. The quantification of immune cell profiles and associated cytokines was achieved through flow cytometry and immunoassay technology. Uni- and multivariable logistic regression analyses were conducted to construct a predictive model for insufficient biochemical response. The performance of the model was assessed by computing the area under the receiver operating characteristic (AUC) curve, sensitivity, and specificity. FINDINGS The analysis identified 224 differentially expressed (DE) mRNAs, 189 DE long non-coding RNAs, 39 DE circular RNAs, and 63 DE microRNAs. Functional pathway analysis revealed enrichment in lipid metabolic pathways and immune response. Metabolomics disclosed dysregulated lipid metabolism and identified PC (18:2/18:2) and PC (16:0/20:3) as predictors. CD4+ T helper (Th) cells, including Th2 cells and regulatory T cells (Tregs), were upregulated in the GR group. Pro-inflammatory cytokines (IFN-γ, TNF-α, IL-9, and IL-17) were downregulated in the GR group, while anti-inflammatory cytokines (IL-10, IL-4, IL-5, and IL-22) were elevated. Regulatory networks were constructed, identifying CACNA1H and ACAA1 as target genes. A predictive model based on these indicators demonstrated an AUC of 0.986 in the primary cohort and an AUC of 0.940 in the validation cohort for predicting complete biochemical response. CONCLUSION A combined model integrating genomic, metabolic, and cytokinomic features demonstrated high accuracy in predicting insufficient biochemical response in patients with PBC/AIH VS. Early recognition of individuals at elevated risk for insufficient response allows for the prompt initiation of additional treatments.
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Affiliation(s)
- Fan Yang
- Department of Gastroenterology and Hepatology and Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, West China Hospital, Sichuan University, #37 Guoxue Road, Chengdu, 610041, Sichuan, China
| | - Leyu Zhou
- Department of Gastroenterology and Hepatology and Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, West China Hospital, Sichuan University, #37 Guoxue Road, Chengdu, 610041, Sichuan, China
| | - Yi Shen
- Department of Gastroenterology and Hepatology and Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, West China Hospital, Sichuan University, #37 Guoxue Road, Chengdu, 610041, Sichuan, China
| | - Xianglin Wang
- Department of Gastroenterology and Hepatology and Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, West China Hospital, Sichuan University, #37 Guoxue Road, Chengdu, 610041, Sichuan, China
| | - Xiaoli Fan
- Department of Gastroenterology and Hepatology and Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, West China Hospital, Sichuan University, #37 Guoxue Road, Chengdu, 610041, Sichuan, China.
| | - Li Yang
- Department of Gastroenterology and Hepatology and Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, West China Hospital, Sichuan University, #37 Guoxue Road, Chengdu, 610041, Sichuan, China.
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Cox LS, Alvarez-Martinez M, Wu X, Gabryšová L, Luisier R, Briscoe J, Luscombe NM, O'Garra A. Blimp-1 and c-Maf regulate Il10 and negatively regulate common and unique proinflammatory gene networks in IL-12 plus IL-27-driven T helper-1 cells. Wellcome Open Res 2023; 8:403. [PMID: 38074197 PMCID: PMC10709690 DOI: 10.12688/wellcomeopenres.19680.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2023] [Indexed: 02/12/2024] Open
Abstract
Background CD4 + Th1 cells producing IFN-γ are required to eradicate intracellular pathogens, however if uncontrolled these cells can cause immunopathology. The cytokine IL-10 is produced by multiple immune cells including Th1 cells during infection and regulates the immune response to minimise collateral host damage. In this study we aimed to elucidate the transcriptional network of genes controlling the expression of Il10 and proinflammatory cytokines, including Ifng in Th1 cells differentiated from mouse naive CD4 + T cells. Methods We applied computational analysis of gene regulation derived from temporal profiling of gene expression clusters obtained from bulk RNA sequencing (RNA-seq) of flow cytometry sorted naïve CD4 + T cells from mouse spleens differentiated in vitro into Th1 effector cells with IL-12 and IL-27 to produce Ifng and Il10, compared to IL-27 alone which express Il10 only , or IL-12 alone which express Ifng and no Il10, or medium control driven-CD4 + T cells which do not express effector cytokines . Data were integrated with analysis of active genomic regions from these T cells using an assay for transposase-accessible chromatin with sequencing (ATAC)-seq, integrated with literature derived-Chromatin-immunoprecipitation (ChIP)-seq data and the RNA-seq data, to elucidate the transcriptional network of genes controlling expression of Il10 and pro-inflammatory effector genes in Th1 cells. The co-dominant role for the transcription factors, Prdm1 (encoding Blimp-1) and Maf (encoding c-Maf) , in cytokine gene regulation in Th1 cells, was confirmed using T cells obtained from mice with T-cell specific deletion of these transcription factors. Results We show that the transcription factors Blimp-1 and c-Maf each have unique and common effects on cytokine gene regulation and not only co-operate to induce Il10 gene expression in IL-12 plus IL-27 differentiated mouse Th1 cells, but additionally directly negatively regulate key proinflammatory cytokines including Ifng, thus providing mechanisms for reinforcement of regulated Th1 cell responses. Conclusions These data show that Blimp-1 and c-Maf positively and negatively regulate a network of both unique and common anti-inflammatory and pro-inflammatory genes to reinforce a Th1 response in mice that will eradicate pathogens with minimum immunopathology.
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Affiliation(s)
- Luke S. Cox
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
| | - Marisol Alvarez-Martinez
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
| | - Xuemei Wu
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
| | - Leona Gabryšová
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
| | - Raphaëlle Luisier
- Computational Biology Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
| | - James Briscoe
- Developmental Dynamics Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
| | - Nicholas M. Luscombe
- Computational Biology Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, England, UK
| | - Anne O'Garra
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
- National Heart and Lung Institute, Imperial College London, London, England, UK
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7
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Fassett MS, Braz JM, Castellanos CA, Salvatierra JJ, Sadeghi M, Yu X, Schroeder AW, Caston J, Munoz-Sandoval P, Roy S, Lazarevsky S, Mar DJ, Zhou CJ, Shin JS, Basbaum AI, Ansel KM. IL-31-dependent neurogenic inflammation restrains cutaneous type 2 immune response in allergic dermatitis. Sci Immunol 2023; 8:eabi6887. [PMID: 37831760 PMCID: PMC10890830 DOI: 10.1126/sciimmunol.abi6887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/18/2023] [Indexed: 10/15/2023]
Abstract
Despite robust literature associating IL-31 with pruritic inflammatory skin diseases, its influence on cutaneous inflammation and the interplay between inflammatory and neurosensory pathways remain unmapped. Here, we examined the consequences of disrupting Il31 and its receptor Il31ra in a mouse model of house dust mite (HDM)-induced allergic dermatitis. Il31-deficient mice displayed a deficit in HDM dermatitis-associated scratching, consistent with its well-established role as a pruritogen. In contrast, Il31 deficiency increased the number and proportion of cutaneous type 2 cytokine-producing CD4+ T cells and serum IgE in response to HDM. Furthermore, Il4ra+ monocytes and macrophages capable of fueling a feedforward type 2 inflammatory loop were selectively enriched in Il31ra-deficient HDM dermatitis skin. Thus, IL-31 is not strictly a proinflammatory cytokine but rather an immunoregulatory factor that limits the magnitude of type 2 inflammatory responses in skin. Our data support a model wherein IL-31 activation of IL31RA+ pruritoceptors triggers release of calcitonin gene-related protein (CGRP), which can mediate neurogenic inflammation, inhibit CD4+ T cell proliferation, and reduce T cell production of the type 2 cytokine IL-13. Together, these results illustrate a previously unrecognized neuroimmune pathway that constrains type 2 tissue inflammation in the setting of chronic cutaneous allergen exposure and may explain paradoxical dermatitis flares in atopic patients treated with anti-IL31RA therapy.
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Affiliation(s)
- Marlys S Fassett
- Department of Dermatology, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center (SABRe), San Francisco, CA, USA
| | - Joao M Braz
- Department of Anatomy, University of California, San Francisco, CA, USA
| | - Carlos A Castellanos
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center (SABRe), San Francisco, CA, USA
| | | | - Mahsa Sadeghi
- Department of Anatomy, University of California, San Francisco, CA, USA
| | - Xiaobing Yu
- Department of Anatomy, University of California, San Francisco, CA, USA
- Department of Anesthesiology, University of California, San Francisco, CA, USA
| | | | - Jaela Caston
- Department of Dermatology, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Priscila Munoz-Sandoval
- Department of Dermatology, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center (SABRe), San Francisco, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA 94143, USA
| | - Suparna Roy
- Department of Dermatology, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center (SABRe), San Francisco, CA, USA
| | - Steven Lazarevsky
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Darryl J Mar
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Connie J Zhou
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Jeoung-Sook Shin
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center (SABRe), San Francisco, CA, USA
| | - Allan I Basbaum
- Department of Anatomy, University of California, San Francisco, CA, USA
| | - K Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center (SABRe), San Francisco, CA, USA
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8
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Caillier A, Oleksyn D, Fowell DJ, Miller J, Oakes PW. T cells Use Focal Adhesions to Pull Themselves Through Confined Environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562587. [PMID: 37904911 PMCID: PMC10614902 DOI: 10.1101/2023.10.16.562587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Immune cells are highly dynamic and able to migrate through environments with diverse biochemical and mechanical composition. Their migration has classically been defined as amoeboid under the assumption that it is integrin-independent. Here we show that activated primary Th1 T cells require both confinement and extracellular matrix protein to migrate efficiently. This migration is mediated through small and dynamic focal adhesions that are composed of the same proteins associated with canonical mesenchymal focal adhesions, such as integrins, talin, and vinculin. These focal adhesions, furthermore, localize to sites of contractile traction stresses, enabling T cells to pull themselves through confined spaces. Finally, we show that Th1 T cell preferentially follows tracks of other T cells, suggesting that these adhesions are modifying the extracellular matrix to provide additional environmental guidance cues. These results demonstrate not only that the boundaries between amoeboid and mesenchymal migration modes are ambiguous, but that integrin-mediated adhesions play a key role in T cell motility.
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Affiliation(s)
- Alexia Caillier
- Department of Cell & Molecular Physiology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL 60153, USA
| | - David Oleksyn
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Deborah J Fowell
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jim Miller
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Patrick W Oakes
- Department of Cell & Molecular Physiology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL 60153, USA
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9
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Braband KL, Nedwed AS, Helbich SS, Simon M, Beumer N, Brors B, Marini F, Delacher M. Using single-cell chromatin accessibility sequencing to characterize CD4+ T cells from murine tissues. Front Immunol 2023; 14:1232511. [PMID: 37908367 PMCID: PMC10613658 DOI: 10.3389/fimmu.2023.1232511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/29/2023] [Indexed: 11/02/2023] Open
Abstract
The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a cutting-edge technology that enables researchers to assess genome-wide chromatin accessibility and to characterize cell type specific gene-regulatory programs. Recent technological progress allows for using this technology also on the single-cell level. In this article, we describe the whole value chain from the isolation of T cells from murine tissues to a complete bioinformatic analysis workflow. We start with methods for isolating scATAC-seq-ready CD4+ T cells from murine tissues such as visceral adipose tissue, skin, colon, and secondary lymphoid tissues such as the spleen. We describe the preparation of nuclei and quality control parameters during library preparation. Based on publicly available sequencing data that was generated using these protocols, we describe a step-by-step bioinformatic analysis pipeline for data pre-processing and downstream analysis. Our analysis workflow will follow the R-based bioinformatics framework ArchR, which is currently well established for scATAC-seq datasets. All in all, this work serves as a one-stop shop for generating and analyzing chromatin accessibility landscapes in T cells.
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Affiliation(s)
- Kathrin Luise Braband
- Institute of Immunology, University Medical Center Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center Mainz, Mainz, Germany
| | - Annekathrin Silvia Nedwed
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Mainz, Germany
| | - Sara Salome Helbich
- Institute of Immunology, University Medical Center Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center Mainz, Mainz, Germany
| | - Malte Simon
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Niklas Beumer
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKFZ-Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany
- Division of Personalized Medical Oncology (A420), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Personalized Oncology, University Hospital Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Federico Marini
- Research Center for Immunotherapy (FZI), University Medical Center Mainz, Mainz, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, Mainz, Germany
| | - Michael Delacher
- Institute of Immunology, University Medical Center Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center Mainz, Mainz, Germany
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10
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Burt P, Thurley K. Distribution modeling quantifies collective T H cell decision circuits in chronic inflammation. SCIENCE ADVANCES 2023; 9:eadg7668. [PMID: 37703364 PMCID: PMC10881075 DOI: 10.1126/sciadv.adg7668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/11/2023] [Indexed: 09/15/2023]
Abstract
Immune responses are tightly regulated by a diverse set of interacting immune cell populations. Alongside decision-making processes such as differentiation into specific effector cell types, immune cells initiate proliferation at the beginning of an inflammation, forming two layers of complexity. Here, we developed a general mathematical framework for the data-driven analysis of collective immune cell dynamics. We identified qualitative and quantitative properties of generic network motifs, and we specified differentiation dynamics by analysis of kinetic transcriptome data. Furthermore, we derived a specific, data-driven mathematical model for T helper 1 versus T follicular helper cell-fate decision dynamics in acute and chronic lymphocytic choriomeningitis virus infections in mice. The model recapitulates important dynamical properties without model fitting and solely by using measured response-time distributions. Model simulations predict different windows of opportunity for perturbation in acute and chronic infection scenarios, with potential implications for optimization of targeted immunotherapy.
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Affiliation(s)
- Philipp Burt
- Systems Biology of Inflammation, German Rheumatism Research Center (DRFZ), a Leibniz Institute, Berlin, Germany
- Institute for Theoretical Biophysics, Humboldt University, Berlin, Germany
| | - Kevin Thurley
- Systems Biology of Inflammation, German Rheumatism Research Center (DRFZ), a Leibniz Institute, Berlin, Germany
- Biomathematics Division, Institute of Experimental Oncology, University Hospital Bonn, Bonn, Germany
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11
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Clement M, Ladell K, Miners KL, Marsden M, Chapman L, Cardus Figueras A, Scott J, Andrews R, Clare S, Kriukova VV, Lupyr KR, Britanova OV, Withers DR, Jones SA, Chudakov DM, Price DA, Humphreys IR. Inhibitory IL-10-producing CD4 + T cells are T-bet-dependent and facilitate cytomegalovirus persistence via coexpression of arginase-1. eLife 2023; 12:e79165. [PMID: 37440306 PMCID: PMC10344424 DOI: 10.7554/elife.79165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/11/2023] [Indexed: 07/14/2023] Open
Abstract
Inhibitory CD4+ T cells have been linked with suboptimal immune responses against cancer and pathogen chronicity. However, the mechanisms that underpin the development of these regulatory cells, especially in the context of ongoing antigen exposure, have remained obscure. To address this knowledge gap, we undertook a comprehensive functional, phenotypic, and transcriptomic analysis of interleukin (IL)-10-producing CD4+ T cells induced by chronic infection with murine cytomegalovirus (MCMV). We identified these cells as clonally expanded and highly differentiated TH1-like cells that developed in a T-bet-dependent manner and coexpressed arginase-1 (Arg1), which promotes the catalytic breakdown of L-arginine. Mice lacking Arg1-expressing CD4+ T cells exhibited more robust antiviral immunity and were better able to control MCMV. Conditional deletion of T-bet in the CD4+ lineage suppressed the development of these inhibitory cells and also enhanced immune control of MCMV. Collectively, these data elucidated the ontogeny of IL-10-producing CD4+ T cells and revealed a previously unappreciated mechanism of immune regulation, whereby viral persistence was facilitated by the site-specific delivery of Arg1.
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Affiliation(s)
- Mathew Clement
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
- Systems Immunity Research Institute, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Kristin Ladell
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Kelly L Miners
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Morgan Marsden
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Lucy Chapman
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Anna Cardus Figueras
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Jake Scott
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Robert Andrews
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
- Systems Immunity Research Institute, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Simon Clare
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Valeriia V Kriukova
- Center of Life Sciences, Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussian Federation
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of KielKielGermany
| | - Ksenia R Lupyr
- Center of Life Sciences, Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussian Federation
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Olga V Britanova
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussian Federation
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of KielKielGermany
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - David R Withers
- Institute of Immunology and Immunotherapy, University of BirminghamBirminghamUnited Kingdom
| | - Simon A Jones
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
- Systems Immunity Research Institute, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussian Federation
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Abu Dhabi Stem Cell CenterAl MuntazahUnited Arab Emirates
| | - David A Price
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
- Systems Immunity Research Institute, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Ian R Humphreys
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
- Systems Immunity Research Institute, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
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12
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Cordner R, Jhun M, Panwar A, Wang H, Gull N, Murali R, McAbee JH, Mardiros A, Sanchez-Takei A, Mazer MW, Fan X, Jouanneau E, Yu JS, Black KL, Wheeler CJ. Glioma immunotherapy enhancement and CD8-specific sialic acid cleavage by isocitrate dehydrogenase (IDH)-1. Oncogene 2023:10.1038/s41388-023-02713-7. [PMID: 37161052 DOI: 10.1038/s41388-023-02713-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/11/2023]
Abstract
The promise of adaptive cancer immunotherapy in treating highly malignant tumors such as glioblastoma multiforme (GBM) can only be realized through expanding its benefits to more patients. Alleviating various modes of immune suppression has so far failed to achieve such expansion, but exploiting endogenous immune enhancers among mutated cancer genes could represent a more direct approach to immunotherapy improvement. We found that Isocitrate Dehydrogenase-1 (IDH1), which is commonly mutated in gliomas, enhances glioma vaccine efficacy in mice and discerns long from short survivors after vaccine therapy in GBM patients. Extracellular IDH1 directly enhanced T cell responses to multiple tumor antigens, and prolonged experimental glioma cell lysis. Moreover, IDH1 specifically bound to and exhibited sialidase activity against CD8. By contrast, mutant IDH1R132H lacked sialidase activity, delayed killing in glioma cells, and decreased host survival after immunotherapy. Overall, our findings identify IDH1 as an immunotherapeutic enhancer that mediates the known T cell-enhancing reaction of CD8 desialylation. This uncovers a new axis for immunotherapeutic improvement in GBM and other cancers, reveals novel physiological and molecular functions of IDH1, and hints at an unexpectedly direct link between lytic T cell function and metabolic activity in target cells.
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Affiliation(s)
- Ryan Cordner
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Microbiology and Molecular Biology, Brigham Young University, UT, Provo, USA
| | - Michelle Jhun
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Akanksha Panwar
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - HongQiang Wang
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Nicole Gull
- Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joseph H McAbee
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Armen Mardiros
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- A2 Biotherapeutics, Agoura Hills, CA, USA
| | - Akane Sanchez-Takei
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mia W Mazer
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xuemo Fan
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, 8700 Beverly Blvd., Los Angeles, CA, USA
| | - Emmanuel Jouanneau
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Neurosurgery, Neurological Hospital and INSERM 842 Research Unit, Claude Bernard University, Lyon, France
| | - John S Yu
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Keith L Black
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Christopher J Wheeler
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- International Brain Mapping Foundation, Society for Brain Mapping & Therapeutics, 860 Via De La Paz, Suite E-1, Pacific Palisades, CA, USA.
- StemVax Therapeutics (subsidiary of NovAccess Global), 8584 E. Washington St. #127, Chagrin Falls, OH, USA.
- T-Neuro Pharma, PO Box 781, Aptos, CA, USA.
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13
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Gocher-Demske AM, Cui J, Szymczak-Workman AL, Vignali KM, Latini JN, Pieklo GP, Kimball JC, Avery L, Cipolla EM, Huckestein BR, Hedden L, Meisel M, Alcorn JF, Kane LP, Workman CJ, Vignali DAA. IFNγ-induction of T H1-like regulatory T cells controls antiviral responses. Nat Immunol 2023; 24:841-854. [PMID: 36928412 PMCID: PMC10224582 DOI: 10.1038/s41590-023-01453-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/06/2023] [Indexed: 03/18/2023]
Abstract
Regulatory T (Treg) cells are an immunosuppressive population that are required to maintain peripheral tolerance and prevent tissue damage from immunopathology, via anti-inflammatory cytokines, inhibitor receptors and metabolic disruption. Here we show that Treg cells acquire an effector-like state, yet remain stable and functional, when exposed to interferon gamma (IFNγ) during infection with lymphocytic choriomeningitis and influenza A virus. Treg cell-restricted deletion of the IFNγ receptor (encoded by Ifngr1), but not the interleukin 12 (IL12) receptor (encoded by Il12rb2), prevented TH1-like polarization (decreased expression of T-bet, CXC motif chemokine receptor 3 and IFNγ) and promoted TH2-like polarization (increased expression of GATA-3, CCR4 and IL4). TH1-like Treg cells limited CD8+ T cell effector function, proliferation and memory formation during acute and chronic infection. These findings provide fundamental insights into how Treg cells sense inflammatory cues from the environment (such as IFNγ) during viral infection to provide guidance to the effector immune response. This regulatory circuit prevents prolonged immunoinflammatory responses and shapes the quality and quantity of the memory T cell response.
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Affiliation(s)
- Angela M Gocher-Demske
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Jian Cui
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | | | - Kate M Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Julianna N Latini
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Gwen P Pieklo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Jesse C Kimball
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Lyndsay Avery
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Program in Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Ellyse M Cipolla
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
- Program in Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Brydie R Huckestein
- Program in Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
- Program in Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lee Hedden
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marlies Meisel
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - John F Alcorn
- Program in Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Lawrence P Kane
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Creg J Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Tumor Microenvironment Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA.
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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14
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Delgobo M, Weiß E, Ashour D, Richter L, Popiolkowski L, Arampatzi P, Stangl V, Arias-Loza P, Mariotti-Ferrandiz E, Rainer PP, Saliba AE, Ludewig B, Hofmann U, Frantz S, Campos Ramos G. Myocardial Milieu Favors Local Differentiation of Regulatory T Cells. Circ Res 2023; 132:565-582. [PMID: 36744467 DOI: 10.1161/circresaha.122.322183] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND In the past years, several studies investigated how distinct immune cell subsets affects post-myocardial infarction repair. However, whether and how the tissue environment controls these local immune responses has remained poorly understood. We sought to investigate how antigen-specific T-helper cells differentiate under myocardial milieu's influence. METHODS We used a transgenic T cell receptor (TCR-M) model and major histocompatibility complex-II tetramers, both myosin-specific, combined with single-cell transcriptomics (single-cell RNA sequencing [scRNA-seq]) and functional phenotyping to elucidate how the antigen-specific CD4+ T cells differentiate in the murine infarcted myocardium and influence tissue repair. Additionally, we transferred proinflammatory versus regulatory predifferentiated TCR-M-cells to dissect how they specially contribute to post-myocardial infarction inflammation. RESULTS Flow cytometry and scRNA-/TCR-seq analyses revealed that transferred TCR-M cells acquired an induced regulatory phenotype (induced regulatory T cell) in the infarcted myocardium and blunted local inflammation. Myocardial TCR-M cells differentiated into 2 main lineages enriched with either cell activation and profibrotic transcripts (eg, Tgfb1) or suppressor immune checkpoints (eg, Pdcd1), which we also found in human myocardial tissue. These cells produced high levels of LAP (latency-associated peptide) and inhibited IL-17 (interleukin-17) responses. Endogenous myosin-specific T-helper cells, identified using genetically barcoded tetramers, also accumulated in infarcted hearts and exhibited a regulatory phenotype. Notably, TCR-M cells that were predifferentiated toward a regulatory phenotype in vitro maintained stable in vivo FOXP3 (Forkhead box P3) expression and anti-inflammatory activity whereas TH17 partially converted toward a regulatory phenotype in the injured myocardium. Overall, the myosin-specific Tregs dampened post-myocardial infarction inflammation, suppressed neighboring T cells, and were associated with improved cardiac function. CONCLUSIONS These findings provide novel evidence that the heart and its draining lymph nodes actively shape local immune responses by promoting the differentiation of antigen-specific Tregs poised with suppressive function.
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Affiliation(s)
- Murilo Delgobo
- Department of Internal Medicine I (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany.,Comprehensive Heart Failure Center (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany
| | - Emil Weiß
- Department of Internal Medicine I (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany.,Comprehensive Heart Failure Center (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany
| | - DiyaaElDin Ashour
- Department of Internal Medicine I (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany.,Comprehensive Heart Failure Center (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany
| | - Leon Richter
- Department of Internal Medicine I (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany.,Comprehensive Heart Failure Center (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany
| | - Lisa Popiolkowski
- Department of Internal Medicine I (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany.,Comprehensive Heart Failure Center (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany
| | | | - Verena Stangl
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Austria (V.S.)
| | - Paula Arias-Loza
- Department of Nuclear Medicine (P.A.-L.), University Hospital Würzburg, Germany
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Université, INSERM, UMRS959, Immunology-Immunopathology-Immunotherapy (i3) lab, Paris France (E.M.-F.).,Institut Universitaire de France (IUF) (E.M.-F.)
| | - Peter P Rainer
- Division of Cardiology at the Medical University of Graz, Austria (P.P.R.).,BioTechMed Graz, Austria (P.P.R.)
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany (A.-E.S.)
| | - Burkhard Ludewig
- Institute of Immunobiology, Kantonsspital St. Gallen, Switzerland (B.L.)
| | - Ulrich Hofmann
- Department of Internal Medicine I (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany.,Comprehensive Heart Failure Center (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany
| | - Stefan Frantz
- Department of Internal Medicine I (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany.,Comprehensive Heart Failure Center (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany
| | - Gustavo Campos Ramos
- Department of Internal Medicine I (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany.,Comprehensive Heart Failure Center (M.D., E.W., D.E.A., L.R., L.P., U.H., S.F., G.C.R.), University Hospital Würzburg, Germany
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15
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Thelen B, Schipperges V, Knörlein P, Hummel JF, Arnold F, Kupferschmid L, Klose CSN, Arnold SJ, Boerries M, Tanriver Y. Eomes is sufficient to regulate IL-10 expression and cytotoxic effector molecules in murine CD4 + T cells. Front Immunol 2023; 14:1058267. [PMID: 36756120 PMCID: PMC9901365 DOI: 10.3389/fimmu.2023.1058267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/02/2023] [Indexed: 01/20/2023] Open
Abstract
The T-box transcription factors T-bet and Eomesodermin regulate type 1 immune responses in innate and adaptive lymphocytes. T-bet is widely expressed in the immune system but was initially identified as the lineage-specifying transcription factor of Th1 CD4+ T cells, where it governs expression of the signature cytokine IFN- γ and represses alternative cell fates like Th2 and Th17. T-bet's paralog Eomes is less abundantly expressed and Eomes+ CD4+ T cells are mostly found in the context of persistent antigen exposure, like bone marrow transplantation, chronic infection or inflammation as well as malignant disorders. However, it has remained unresolved whether Eomes executes similar transcriptional activities as T-bet in CD4+ T cells. Here we use a novel genetic approach to show that Eomes expression in CD4+ T cells drives a distinct transcriptional program that shows only partial overlap with T-bet. We found that Eomes is sufficient to induce the expression of the immunoregulatory cytokine IL-10 and, together with T-bet, promotes a cytotoxic effector profile, including Prf1, Gzmb, Gzmk, Nkg7 and Ccl5, while repressing alternative cell fates. Our results demonstrate that Eomes+ CD4+ T cells, which are often found in the context of chronic antigen stimulation, are likely to be a unique CD4+ T cell subset that limits inflammation and immunopathology as well as eliminates antigen-presenting and malignant cells.
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Affiliation(s)
- Benedikt Thelen
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Vincent Schipperges
- Institute of Medical Bioinformatics and Systems Medicine, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Paulina Knörlein
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jonas F. Hummel
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Frederic Arnold
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany,Department of Internal Medicine IV, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany,Berta-Ottenstein-Programme, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Laurence Kupferschmid
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph S. N. Klose
- Department of Microbiology, Infectious Diseases and Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sebastian J. Arnold
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany,CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany,German Cancer Consortium (Deutsches Konsortium für Translationale Krebsforschung, DKTK), Partner Site Freiburg, and German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany
| | - Yakup Tanriver
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany,Department of Internal Medicine IV, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany,*Correspondence: Yakup Tanriver,
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16
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Burt P, Peine M, Peine C, Borek Z, Serve S, Floßdorf M, Hegazy AN, Höfer T, Löhning M, Thurley K. Dissecting the dynamic transcriptional landscape of early T helper cell differentiation into Th1, Th2, and Th1/2 hybrid cells. Front Immunol 2022; 13:928018. [PMID: 36052070 PMCID: PMC9424495 DOI: 10.3389/fimmu.2022.928018] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Selective differentiation of CD4+ T helper (Th) cells into specialized subsets such as Th1 and Th2 cells is a key element of the adaptive immune system driving appropriate immune responses. Besides those canonical Th-cell lineages, hybrid phenotypes such as Th1/2 cells arise in vivo, and their generation could be reproduced in vitro. While master-regulator transcription factors like T-bet for Th1 and GATA-3 for Th2 cells drive and maintain differentiation into the canonical lineages, the transcriptional architecture of hybrid phenotypes is less well understood. In particular, it has remained unclear whether a hybrid phenotype implies a mixture of the effects of several canonical lineages for each gene, or rather a bimodal behavior across genes. Th-cell differentiation is a dynamic process in which the regulatory factors are modulated over time, but longitudinal studies of Th-cell differentiation are sparse. Here, we present a dynamic transcriptome analysis following Th-cell differentiation into Th1, Th2, and Th1/2 hybrid cells at 3-h time intervals in the first hours after stimulation. We identified an early bifurcation point in gene expression programs, and we found that only a minority of ~20% of Th cell-specific genes showed mixed effects from both Th1 and Th2 cells on Th1/2 hybrid cells. While most genes followed either Th1- or Th2-cell gene expression, another fraction of ~20% of genes followed a Th1 and Th2 cell-independent transcriptional program associated with the transcription factors STAT1 and STAT4. Overall, our results emphasize the key role of high-resolution longitudinal data for the characterization of cellular phenotypes.
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Affiliation(s)
- Philipp Burt
- Systems Biology of Inflammation, German Rheumatism Research Center (DRFZ), a Leibniz Institute, Berlin, Germany
- Institute for Theoretical Biology, Humboldt University, Berlin, Germany
| | - Michael Peine
- Pitzer Laboratory of Osteoarthritis Research, German Rheumatism Research Center (DRFZ), a Leibniz Institute, Berlin, Germany
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin, Berlin, Germany
| | - Caroline Peine
- Pitzer Laboratory of Osteoarthritis Research, German Rheumatism Research Center (DRFZ), a Leibniz Institute, Berlin, Germany
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin, Berlin, Germany
| | - Zuzanna Borek
- Systems Biology of Inflammation, German Rheumatism Research Center (DRFZ), a Leibniz Institute, Berlin, Germany
- Department of Gastroenterology, Infectious Diseases and Rheumatology, Charité-Universitätsmedizin, Berlin, Germany
- Inflammatory Mechanisms, German Rheumatism Research Center (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Sebastian Serve
- Systems Biology of Inflammation, German Rheumatism Research Center (DRFZ), a Leibniz Institute, Berlin, Germany
- Pitzer Laboratory of Osteoarthritis Research, German Rheumatism Research Center (DRFZ), a Leibniz Institute, Berlin, Germany
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin, Berlin, Germany
| | - Michael Floßdorf
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ahmed N. Hegazy
- Department of Gastroenterology, Infectious Diseases and Rheumatology, Charité-Universitätsmedizin, Berlin, Germany
- Inflammatory Mechanisms, German Rheumatism Research Center (DRFZ), a Leibniz Institute, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Max Löhning
- Pitzer Laboratory of Osteoarthritis Research, German Rheumatism Research Center (DRFZ), a Leibniz Institute, Berlin, Germany
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin, Berlin, Germany
- *Correspondence: Max Löhning, ; Kevin Thurley,
| | - Kevin Thurley
- Systems Biology of Inflammation, German Rheumatism Research Center (DRFZ), a Leibniz Institute, Berlin, Germany
- Institute for Theoretical Biology, Humboldt University, Berlin, Germany
- Institute for Experimental Oncology, Biomathematics Division, University Hospital Bonn, Bonn, Germany
- *Correspondence: Max Löhning, ; Kevin Thurley,
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17
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Soichot J, Guttmann N, Rehrauer H, Joller N, Tritten L. Nematode microRNAs can Individually Regulate Interferon Regulatory Factor 4 and mTOR in Differentiating T Helper 2 Lymphocytes and Modulate Cytokine Production in Macrophages. Front Mol Biosci 2022; 9:909312. [PMID: 35836928 PMCID: PMC9274173 DOI: 10.3389/fmolb.2022.909312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022] Open
Abstract
Parasitic nematodes are masterful immunomodulators. This class of pathogens has evolved a spectrum of sophisticated strategies to regulate and evade host immune responses, mediated through the release of various molecules. In this context, the release of microRNAs (miRNAs), short post-transcriptional regulators of gene expression, has been of particular interest in the host-parasite interplay. Evidence that parasite-derived miRNAs modulate host innate and adaptive immune responses has become increasingly compelling. However, since miRNAs are usually contained in extracellular vesicles containing other mediators, it is difficult to assign an observed effect on host cells to miRNAs specifically. Here, the effects of some abundantly secreted miRNAs by nematodes used as models of gastrointestinal infections (Heligmosomoides polygyrus bakeri, Trichuris muris and Ascaris suum) were evaluated, addressing the potential of parasite miRNAs to impair in vitro differentiation of two important types of immune cells in the context of helminth infections, Th2 lymphocytes and macrophages. Mimicking a continuous exposure to low concentrations of nematode miRNAs, the interferon gamma signaling, the IL-2/STAT5 signaling, and the mTOR signaling pathways were identified as downregulated by Hpo-miR-71-5p. Interferon regulatory factor 4 (Irf4) was validated as a target of Hpo-miR-71-5p, while Mtor is targeted by Asu-miR-791-3p, abundant in the T. muris secretions. By trend, Hpo-miR-71-5p impacts mildly but consistently on the amounts of inflammatory cytokines in unpolarized macrophages but leads to slightly increased IL-10 level in alternatively activated cells. In addition, our data suggests that transfected miRNAs remain for days in recipient cells, and that Hpo-miR-71-5p can incorporate into mouse Argonaute protein complexes. Nematode miRNAs can impair both innate and adaptive arms of host immunity. Hpo-miR-71-5p in particular, absent in mammals, interacts with host genes and pathways with crucial involvement in anthelmintic immune responses. This report brings new insights into the dynamics of miRNA-driven immunomodulation and highlights putative targeted pathways. Although the absolute repression is subtle, it is expected that the dozens of different miRNAs released by nematodes may have a synergistic effect on surrounding host cells.
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Affiliation(s)
- Julien Soichot
- Institute of Parasitology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Nathalie Guttmann
- Institute of Parasitology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Nicole Joller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Lucienne Tritten
- Institute of Parasitology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- *Correspondence: Lucienne Tritten,
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18
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Trabanelli S, Ercolano G, Wyss T, Gomez-Cadena A, Falquet M, Cropp D, Imbratta C, Leblond MM, Salvestrini V, Curti A, Adotevi O, Jandus C, Verdeil G. c-Maf enforces cytokine production and promotes memory-like responses in mouse and human type 2 innate lymphoid cells. EMBO J 2022; 41:e109300. [PMID: 35467036 PMCID: PMC9194744 DOI: 10.15252/embj.2021109300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/13/2022] Open
Abstract
Group‐2 innate lymphoid cells (ILC2s), which are involved in type 2 inflammatory diseases such as allergy, can exhibit immunological memory, but the basis of this ILC2 "trained immunity" has remained unclear. Here, we found that stimulation with IL‐33/IL‐25 or exposure to the allergen papain induces the expression of the transcription factor c‐Maf in mouse ILC2s. Chronic papain exposure results in high production of IL‐5 and IL‐13 cytokines and lung eosinophil recruitment, effects that are blocked by c‐Maf deletion in ILCs. Transcriptomic analysis revealed that knockdown of c‐Maf in ILC2s suppresses expression of type 2 cytokine genes, as well as of genes linked to a memory‐like phenotype. Consistently, c‐Maf was found highly expressed in human adult ILC2s but absent in cord blood and required for cytokine production in isolated human ILC2s. Furthermore, c‐Maf‐deficient mouse or human ILC2s failed to exhibit strengthened (“trained”) responses upon repeated challenge. Thus, the expression of c‐Maf is indispensable for optimal type 2 cytokine production and proper memory‐like responses in group‐2 innate lymphoid cells.
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Affiliation(s)
- Sara Trabanelli
- Departement of Oncology, UNIL-CHUV, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Giuseppe Ercolano
- Departement of Oncology, UNIL-CHUV, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Tania Wyss
- Departement of Oncology, UNIL-CHUV, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Alejandra Gomez-Cadena
- Departement of Oncology, UNIL-CHUV, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Maryline Falquet
- Departement of Oncology, UNIL-CHUV, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Daniela Cropp
- Departement of Oncology, UNIL-CHUV, University of Lausanne, Lausanne, Switzerland
| | - Claire Imbratta
- Departement of Oncology, UNIL-CHUV, University of Lausanne, Lausanne, Switzerland
| | - Marine M Leblond
- Departement of Oncology, UNIL-CHUV, University of Lausanne, Lausanne, Switzerland
| | - Valentina Salvestrini
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Antonio Curti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Olivier Adotevi
- INSERM, UMR1098 RIGHT, EFS-BFC, University of Bourgogne Franche-Comté, Besançon, France
| | - Camilla Jandus
- Departement of Oncology, UNIL-CHUV, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Grégory Verdeil
- Departement of Oncology, UNIL-CHUV, University of Lausanne, Lausanne, Switzerland
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19
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Smita S, Chikina M, Shlomchik MJ, Tilstra JS. Heterogeneity and clonality of kidney-infiltrating T cells in murine lupus nephritis. JCI Insight 2022; 7:e156048. [PMID: 35271505 PMCID: PMC9089785 DOI: 10.1172/jci.insight.156048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/04/2022] [Indexed: 11/17/2022] Open
Abstract
We previously found that kidney-infiltrating T cells (KITs) in murine lupus nephritis (LN) resembled dysfunctional T cells that infiltrate tumors. This unexpected finding raised the question of how to reconcile the "exhausted" phenotype of KITs with ongoing tissue destruction in LN. To address this, we performed single-cell RNA-Seq and TCR-Seq of KITs in murine lupus models. We found that CD8+ KITs existed first in a transitional state, before clonally expanding and evolving toward exhaustion. On the other hand, CD4+ KITs did not fit into current differentiation paradigms but included both hypoxic and cytotoxic subsets with a pervasive exhaustion signature. Thus, autoimmune nephritis is unlike acute pathogen immunity; rather, the kidney microenvironment suppresses T cells by progressively inducing exhausted states. Our findings suggest that LN, a chronic condition, results from slow evolution of damage caused by dysfunctional T cells and their precursors on the way to exhaustion. These findings have implications for both autoimmunity and tumor immunology.
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Affiliation(s)
- Shuchi Smita
- Department of Immunology
- Department of Computational and Systems Biology
| | | | | | - Jeremy S. Tilstra
- Department of Medicine, and
- Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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20
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Erdogmus S, Concepcion AR, Yamashita M, Sidhu I, Tao AY, Li W, Rocha PP, Huang B, Garippa R, Lee B, Lee A, Hell JW, Lewis RS, Prakriya M, Feske S. Cavβ1 regulates T cell expansion and apoptosis independently of voltage-gated Ca 2+ channel function. Nat Commun 2022; 13:2033. [PMID: 35440113 PMCID: PMC9018955 DOI: 10.1038/s41467-022-29725-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 03/22/2022] [Indexed: 12/11/2022] Open
Abstract
TCR stimulation triggers Ca2+ signals that are critical for T cell function and immunity. Several pore-forming α and auxiliary β subunits of voltage-gated Ca2+ channels (VGCC) were reported in T cells, but their mechanism of activation remains elusive and their contribution to Ca2+ signaling in T cells is controversial. We here identify CaVβ1, encoded by Cacnb1, as a regulator of T cell function. Cacnb1 deletion enhances apoptosis and impairs the clonal expansion of T cells after lymphocytic choriomeningitis virus (LCMV) infection. By contrast, Cacnb1 is dispensable for T cell proliferation, cytokine production and Ca2+ signaling. Using patch clamp electrophysiology and Ca2+ recordings, we are unable to detect voltage-gated Ca2+ currents or Ca2+ influx in human and mouse T cells upon depolarization with or without prior TCR stimulation. mRNAs of several VGCC α1 subunits are detectable in human (CaV3.3, CaV3.2) and mouse (CaV2.1) T cells, but they lack transcription of many 5' exons, likely resulting in N-terminally truncated and non-functional proteins. Our findings demonstrate that although CaVβ1 regulates T cell function, these effects are independent of VGCC channel activity.
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Affiliation(s)
- Serap Erdogmus
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Axel R Concepcion
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Megumi Yamashita
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Ikjot Sidhu
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Anthony Y Tao
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Wenyi Li
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
- National Cancer Institute, NIH, Bethesda, MD, USA
| | - Bonnie Huang
- National Institute of Allergy and Infectious Disease, Bethesda, MD, USA
- National Human Genome Research Institute, Bethesda, MD, USA
| | - Ralph Garippa
- Department of Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Boram Lee
- Department of Pharmacology, University of California, Davis, CA, USA
| | - Amy Lee
- Department of Neuroscience, University of Texas-Austin, Austin, TX, USA
| | - Johannes W Hell
- Department of Pharmacology, University of California, Davis, CA, USA
| | - Richard S Lewis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Murali Prakriya
- Department of Pharmacology, Northwestern University, Chicago, IL, USA.
| | - Stefan Feske
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.
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21
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Sariol A, Zhao J, Abrahante JE, Perlman S. Virus-Specific Regulatory T Cells Persist as Memory in a Neurotropic Coronavirus Infection. THE JOURNAL OF IMMUNOLOGY 2022; 208:1989-1997. [PMID: 35365567 PMCID: PMC9012697 DOI: 10.4049/jimmunol.2100794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/04/2022] [Indexed: 11/19/2022]
Abstract
Regulatory T cells (Tregs) are critical for regulating immunopathogenic responses in a variety of infections, including infection of mice with JHM strain of mouse hepatitis virus (JHMV), a neurotropic coronavirus that causes immune-mediated demyelinating disease. Although virus-specific Tregs are known to mitigate disease in this infection by suppressing pathogenic effector T cell responses of the same specificity, it is unclear whether these virus-specific Tregs form memory populations and persist similar to their conventional T cell counterparts of the same epitope specificity. Using congenically labeled JHMV-specific Tregs, we found that virus-specific Tregs persist long-term after murine infection, through at least 180 d postinfection and stably maintain Foxp3 expression. We additionally demonstrate that these cells are better able to proliferate and inhibit virus-specific T cell responses postinfection than naive Tregs of the same specificity, further suggesting that these cells differentiate into memory Tregs upon encountering cognate Ag. Taken together, these data suggest that virus-specific Tregs are able to persist long-term in the absence of viral Ag as memory Tregs.
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Affiliation(s)
- Alan Sariol
- Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; and
| | | | - Stanley Perlman
- Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA;
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA
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22
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Chauss D, Freiwald T, McGregor R, Yan B, Wang L, Nova-Lamperti E, Kumar D, Zhang Z, Teague H, West EE, Vannella KM, Ramos-Benitez MJ, Bibby J, Kelly A, Malik A, Freeman AF, Schwartz DM, Portilla D, Chertow DS, John S, Lavender P, Kemper C, Lombardi G, Mehta NN, Cooper N, Lionakis MS, Laurence A, Kazemian M, Afzali B. Autocrine vitamin D signaling switches off pro-inflammatory programs of T H1 cells. Nat Immunol 2022; 23:62-74. [PMID: 34764490 PMCID: PMC7612139 DOI: 10.1038/s41590-021-01080-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/26/2021] [Indexed: 12/15/2022]
Abstract
The molecular mechanisms governing orderly shutdown and retraction of CD4+ type 1 helper T (TH1) cell responses remain poorly understood. Here we show that complement triggers contraction of TH1 responses by inducing intrinsic expression of the vitamin D (VitD) receptor and the VitD-activating enzyme CYP27B1, permitting T cells to both activate and respond to VitD. VitD then initiated the transition from pro-inflammatory interferon-γ+ TH1 cells to suppressive interleukin-10+ cells. This process was primed by dynamic changes in the epigenetic landscape of CD4+ T cells, generating super-enhancers and recruiting several transcription factors, notably c-JUN, STAT3 and BACH2, which together with VitD receptor shaped the transcriptional response to VitD. Accordingly, VitD did not induce interleukin-10 expression in cells with dysfunctional BACH2 or STAT3. Bronchoalveolar lavage fluid CD4+ T cells of patients with COVID-19 were TH1-skewed and showed de-repression of genes downregulated by VitD, from either lack of substrate (VitD deficiency) and/or abnormal regulation of this system.
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Affiliation(s)
- Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, USA
| | - Tilo Freiwald
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, USA
- Medic Clinic III, Department of Nephrology, University Hospital Frankfurt, Goethe-University, Frankfurt, Germany
| | - Reuben McGregor
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, USA
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Bingyu Yan
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Luopin Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Estefania Nova-Lamperti
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepcion, Concepcion, Chile
| | - Dhaneshwar Kumar
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Zonghao Zhang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, USA
| | - Heather Teague
- Laboratory of Inflammation & Cardiometabolic Diseases, Cardiovascular Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, USA
| | - Erin E West
- Complement and Inflammation Research Section, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, USA
| | - Kevin M Vannella
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD, USA
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Marcos J Ramos-Benitez
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD, USA
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Jack Bibby
- Complement and Inflammation Research Section, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, USA
| | - Audrey Kelly
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Amna Malik
- Department of Medicine, Imperial College London, London, UK
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD, USA
| | - Daniella M Schwartz
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD, USA
| | - Didier Portilla
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, USA
- Division of Nephrology and the Center for Immunity, Inflammation and Regenerative Medicine, University of Virginia, Charlottesville, VA, USA
| | - Daniel S Chertow
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD, USA
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Susan John
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Paul Lavender
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Claudia Kemper
- Complement and Inflammation Research Section, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, USA
- Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany
| | - Giovanna Lombardi
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Nehal N Mehta
- Laboratory of Inflammation & Cardiometabolic Diseases, Cardiovascular Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, USA
| | - Nichola Cooper
- Department of Medicine, Imperial College London, London, UK
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD, USA
| | - Arian Laurence
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA.
- Department of Computer Science, Purdue University, West Lafayette, IN, USA.
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, USA.
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23
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Vecchio E, Caiazza C, Mimmi S, Avagliano A, Iaccino E, Brusco T, Nisticò N, Maisano D, Aloisio A, Quinto I, Renna M, Divisato G, Romano S, Tufano M, D’Agostino M, Vigliar E, Iaccarino A, Mignogna C, Andreozzi F, Mannino GC, Spiga R, Stornaiuolo M, Arcucci A, Mallardo M, Fiume G. Metabolites Profiling of Melanoma Interstitial Fluids Reveals Uridine Diphosphate as Potent Immune Modulator Capable of Limiting Tumor Growth. Front Cell Dev Biol 2021; 9:730726. [PMID: 34604232 PMCID: PMC8486041 DOI: 10.3389/fcell.2021.730726] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022] Open
Abstract
Tumor interstitial fluid (TIF) surrounds and perfuses tumors and collects ions, metabolites, proteins, and extracellular vesicles secreted by tumor and stromal cells. Specific metabolites, accumulated within the TIF, could induce metabolic alterations of immune cells and shape the tumor microenvironment. We deployed a metabolomic approach to analyze the composition of melanoma TIF and compared it to the plasma of C57BL6 mice, engrafted or not with B16-melanoma cells. Among the classes of metabolites analyzed, monophosphate and diphosphate nucleotides resulted enriched in TIF compared to plasma samples. The analysis of the effects exerted by guanosine diphosphate (GDP) and uridine diphosphate (UDP) on immune response revealed that GDP and UDP increased the percentage of CD4+CD25+FoxP3- and, on isolated CD4+ T-cells, induced the phosphorylation of ERK, STAT1, and STAT3; increased the activity of NF-κB subunits p65, p50, RelB, and p52; increased the expression of Th1/Th17 markers including IFNγ, IL17, T-bet, and RORγt; and reduced the expression of IL13, a Th2 marker. Finally, we observed that local administrations of UDP in B16-engrafted C57BL6 mice reduced tumor growth and necrotic areas. In addition, UDP-treated tumors showed a higher presence of MHCIIhi tumor-associated macrophage (TAM) and of CD3+CD8+ and CD3+CD4+ tumor-infiltrating T-lymphocytes (TILs), both markers of anti-tumor immune response. Consistent with this, intra-tumoral gene expression analysis revealed in UDP-treated tumors an increase in the expression of genes functionally linked to anti-tumor immune response. Our analysis revealed an important metabolite acting as mediator of immune response, which could potentially represent an additional tool to be used as an adjuvant in cancer immunotherapy.
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Affiliation(s)
- Eleonora Vecchio
- Department of Experimental and Clinical Medicine, University of Catanzaro “Magna Graecia”, Catanzaro, Italy
| | - Carmen Caiazza
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Selena Mimmi
- Department of Experimental and Clinical Medicine, University of Catanzaro “Magna Graecia”, Catanzaro, Italy
| | - Angelica Avagliano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Enrico Iaccino
- Department of Experimental and Clinical Medicine, University of Catanzaro “Magna Graecia”, Catanzaro, Italy
| | - Teresa Brusco
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Nancy Nisticò
- Department of Experimental and Clinical Medicine, University of Catanzaro “Magna Graecia”, Catanzaro, Italy
| | - Domenico Maisano
- Department of Experimental and Clinical Medicine, University of Catanzaro “Magna Graecia”, Catanzaro, Italy
| | - Annamaria Aloisio
- Department of Experimental and Clinical Medicine, University of Catanzaro “Magna Graecia”, Catanzaro, Italy
| | - Ileana Quinto
- Department of Experimental and Clinical Medicine, University of Catanzaro “Magna Graecia”, Catanzaro, Italy
| | - Maurizio Renna
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Giuseppina Divisato
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Simona Romano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Martina Tufano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Massimo D’Agostino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Chiara Mignogna
- Department of Health Sciences, Magna Graecia University, Catanzaro, Italy
| | - Francesco Andreozzi
- Department of Medical and Surgical Sciences, University “Magna Graecia” of Catanzaro, Catanzaro, Italy
| | - Gaia Chiara Mannino
- Department of Medical and Surgical Sciences, University “Magna Graecia” of Catanzaro, Catanzaro, Italy
| | - Rosangela Spiga
- Department of Medical and Surgical Sciences, University “Magna Graecia” of Catanzaro, Catanzaro, Italy
| | | | - Alessandro Arcucci
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Massimo Mallardo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Giuseppe Fiume
- Department of Experimental and Clinical Medicine, University of Catanzaro “Magna Graecia”, Catanzaro, Italy
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24
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Qian Y, Arellano G, Ifergan I, Lin J, Snowden C, Kim T, Thomas JJ, Law C, Guan T, Balabanov RD, Kaech SM, Miller SD, Choi J. ZEB1 promotes pathogenic Th1 and Th17 cell differentiation in multiple sclerosis. Cell Rep 2021; 36:109602. [PMID: 34433042 PMCID: PMC8431781 DOI: 10.1016/j.celrep.2021.109602] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 05/18/2021] [Accepted: 08/04/2021] [Indexed: 12/28/2022] Open
Abstract
Inappropriate CD4+ T helper (Th) differentiation can compromise host immunity or promote autoimmune disease. To identify disease-relevant regulators of T cell fate, we examined mutations that modify risk for multiple sclerosis (MS), a canonical organ-specific autoimmune disease. This analysis identified a role for Zinc finger E-box-binding homeobox (ZEB1). Deletion of ZEB1 protects against experimental autoimmune encephalitis (EAE), a mouse model of multiple sclerosis (MS). Mechanistically, ZEB1 in CD4+ T cells is required for pathogenic Th1 and Th17 differentiation. Genomic analyses of paired human and mouse expression data elucidated an unexpected role for ZEB1 in JAK-STAT signaling. ZEB1 inhibits miR-101-3p that represses JAK2 expression, STAT3/STAT4 phosphorylation, and subsequent expression of interleukin-17 (IL-17) and interferon gamma (IFN-γ). Underscoring its clinical relevance, ZEB1 and JAK2 downregulation decreases pathogenic cytokines expression in T cells from MS patients. Moreover, a Food and Drug Administration (FDA)-approved JAK2 inhibitor is effective in EAE. Collectively, these findings identify a conserved, potentially targetable mechanism regulating disease-relevant inflammation. Qian et al. show that ZEB1 is required for the development of the autoimmune disease multiple sclerosis (MS). ZEB1, a transcription factor, promotes JAK-STAT signaling during Th1/Th17 differentiation by repressing expression of a JAK2-targeting miRNA. ZEB1 and JAK2 are potentially clinically relevant therapeutic targets for MS.
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Affiliation(s)
- Yuan Qian
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Gabriel Arellano
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Igal Ifergan
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jean Lin
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA; Department of Medicine, Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Caroline Snowden
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Taehyeung Kim
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Jane Joy Thomas
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Calvin Law
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Tianxia Guan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Roumen D Balabanov
- Department of Neurology, Northwestern University, Chicago, IL 60611, USA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Stephen D Miller
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Jaehyuk Choi
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA; Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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25
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Canaria DA, Yan B, Clare MG, Zhang Z, Taylor GA, Boone DL, Kazemian M, Olson MR. STAT5 Represses a STAT3-Independent Th17-like Program during Th9 Cell Differentiation. THE JOURNAL OF IMMUNOLOGY 2021; 207:1265-1274. [PMID: 34348976 DOI: 10.4049/jimmunol.2100165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/30/2021] [Indexed: 12/13/2022]
Abstract
IL-9-producing Th cells, termed Th9 cells, contribute to immunity against parasites and cancers but have detrimental roles in allergic disease and colitis. Th9 cells differentiate in response to IL-4 and TGF-β, but these signals are insufficient to drive Th9 differentiation in the absence of IL-2. IL-2-induced STAT5 activation is required for chromatin accessibility within Il9 enhancer and promoter regions and directly transactivates the Il9 locus. STAT5 also suppresses gene expression during Th9 cell development, but these roles are less well defined. In this study, we demonstrate that human allergy-associated Th9 cells exhibited a signature of STAT5-mediated gene repression that is associated with the silencing of a Th17-like transcriptional signature. In murine Th9 cell differentiation, blockade of IL-2/STAT5 signaling induced the expression of IL-17 and the Th17-associated transcription factor Rorγt. However, IL-2-deprived Th9 cells did not exhibit a significant Th17- or STAT3-associated transcriptional signature. Consistent with these observations, differentiation of IL-17-producing cells under these conditions was STAT3-independent but did require Rorγt and BATF. Furthermore, ectopic expression of Rorγt and BATF partially rescued IL-17 production in STAT3-deficient Th17 cells, highlighting the importance of these factors in this process. Although STAT3 was not required for the differentiation of IL-17-producing cells under IL-2-deprived Th9 conditions, their prolonged survival was STAT3-dependent, potentially explaining why STAT3-independent IL-17 production is not commonly observed in vivo. Together, our data suggest that IL-2/STAT5 signaling plays an important role in controlling the balance of a Th9 versus a Th17-like differentiation program in vitro and in allergic disease.
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Affiliation(s)
| | - Bingyu Yan
- Department of Biochemistry, Purdue University, West Lafayette, IN
| | - Maia G Clare
- Department of Biological Sciences, Purdue University, West Lafayette, IN
| | - Zonghao Zhang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN
| | - Grace A Taylor
- Department of Biological Sciences, Purdue University, West Lafayette, IN
| | - David L Boone
- Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN; and
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, IN.,Department of Computer Science, Purdue University, West Lafayette, IN
| | - Matthew R Olson
- Department of Biological Sciences, Purdue University, West Lafayette, IN;
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26
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Haim-Vilmovsky L, Henriksson J, Walker JA, Miao Z, Natan E, Kar G, Clare S, Barlow JL, Charidemou E, Mamanova L, Chen X, Proserpio V, Pramanik J, Woodhouse S, Protasio AV, Efremova M, Griffin JL, Berriman M, Dougan G, Fisher J, Marioni JC, McKenzie ANJ, Teichmann SA. Mapping Rora expression in resting and activated CD4+ T cells. PLoS One 2021; 16:e0251233. [PMID: 34003838 PMCID: PMC8130942 DOI: 10.1371/journal.pone.0251233] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/22/2021] [Indexed: 11/19/2022] Open
Abstract
The transcription factor Rora has been shown to be important for the development of ILC2 and the regulation of ILC3, macrophages and Treg cells. Here we investigate the role of Rora across CD4+ T cells in general, but with an emphasis on Th2 cells, both in vitro as well as in the context of several in vivo type 2 infection models. We dissect the function of Rora using overexpression and a CD4-conditional Rora-knockout mouse, as well as a RORA-reporter mouse. We establish the importance of Rora in CD4+ T cells for controlling lung inflammation induced by Nippostrongylus brasiliensis infection, and have measured the effect on downstream genes using RNA-seq. Using a systematic stimulation screen of CD4+ T cells, coupled with RNA-seq, we identify upstream regulators of Rora, most importantly IL-33 and CCL7. Our data suggest that Rora is a negative regulator of the immune system, possibly through several downstream pathways, and is under control of the local microenvironment.
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MESH Headings
- Animals
- Antigens, Helminth/immunology
- Antigens, Helminth/metabolism
- CD4-Positive T-Lymphocytes/immunology
- Cells, Cultured
- Cytokines/metabolism
- Disease Models, Animal
- Female
- Gene Expression Regulation/immunology
- Lymphocyte Activation
- Macrophages/immunology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Nippostrongylus/immunology
- Nuclear Receptor Subfamily 1, Group F, Member 1/immunology
- Nuclear Receptor Subfamily 1, Group F, Member 1/metabolism
- Pneumonia/immunology
- Pneumonia/parasitology
- Pneumonia/pathology
- Strongylida Infections/immunology
- Strongylida Infections/parasitology
- Th2 Cells/immunology
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Affiliation(s)
- Liora Haim-Vilmovsky
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Johan Henriksson
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jennifer A. Walker
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Zhichao Miao
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Eviatar Natan
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gozde Kar
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Simon Clare
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jillian L. Barlow
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Evelina Charidemou
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Xi Chen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Valentina Proserpio
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jhuma Pramanik
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Steven Woodhouse
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust—Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Anna V. Protasio
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mirjana Efremova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Julian L. Griffin
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Metabolism, Digestion and Reproduction, Biomolecular Medicine, Imperial College London, London, United Kingdom
| | - Matt Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gordon Dougan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | | | - John C. Marioni
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Andrew N. J. McKenzie
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sarah A. Teichmann
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Theory of Condensed Matter, Cavendish Laboratory, Cambridge, United Kingdom
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27
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Durante M, Squillace S, Lauro F, Giancotti LA, Coppi E, Cherchi F, Di Cesare Mannelli L, Ghelardini C, Kolar G, Wahlman C, Opejin A, Xiao C, Reitman ML, Tosh DK, Hawiger D, Jacobson KA, Salvemini D. Adenosine A3 agonists reverse neuropathic pain via T cell-mediated production of IL-10. J Clin Invest 2021; 131:139299. [PMID: 33621215 DOI: 10.1172/jci139299] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 02/19/2021] [Indexed: 12/16/2022] Open
Abstract
The A3 adenosine receptor (A3AR) has emerged as a therapeutic target with A3AR agonists to tackle the global challenge of neuropathic pain, and investigation into its mode of action is essential for ongoing clinical development. Immune cell A3ARs, and their activation during pathology, modulate cytokine release. Thus, the use of immune cells as a cellular substrate for the pharmacological action of A3AR agonists is enticing, but unknown. The present study discovered that Rag-KO mice lacking T and B cells, as compared with WT mice, are insensitive to the anti-allodynic effects of A3AR agonists. Similar findings were observed in interleukin-10 and interleukin-10 receptor knockout mice. Adoptive transfer of CD4+ T cells from WT mice infiltrated the dorsal root ganglion (DRG) and restored A3AR agonist-mediated anti-allodynia in Rag-KO mice. CD4+ T cells from Adora3-KO or Il10-KO mice did not. Transfer of CD4+ T cells from WT mice, but not Il10-KO mice, into Il10-KO mice or Adora3-KO mice fully reinstated the anti-allodynic effects of A3AR activation. Notably, A3AR agonism reduced DRG neuron excitability when cocultured with CD4+ T cells in an IL-10-dependent manner. A3AR action on CD4+ T cells infiltrated in the DRG decreased phosphorylation of GluN2B-containing N-methyl-D-aspartate receptors at Tyr1472, a modification associated with regulating neuronal hypersensitivity. Our findings establish that activation of A3AR on CD4+ T cells to release IL-10 is required and sufficient evidence for the use of A3AR agonists as therapeutics.
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Affiliation(s)
- Mariaconcetta Durante
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.,Department of Neuroscience, Psychology, Drug Research and Child Health, Section of Pharmacology, University of Florence, Florence, Italy
| | - Silvia Squillace
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.,Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, St. Louis, Missouri, USA.,Department of Physiology and Pharmacology "V. Erspamer," Sapienza University of Rome, Rome, Italy
| | - Filomena Lauro
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.,Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, St. Louis, Missouri, USA.,Institute of Research for Food Safety & Health, Department of Health Sciences, University "Magna Graecia" of Catanzaro, Catanzaro, Italy
| | - Luigino Antonio Giancotti
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.,Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Elisabetta Coppi
- Department of Neuroscience, Psychology, Drug Research and Child Health, Section of Pharmacology, University of Florence, Florence, Italy
| | - Federica Cherchi
- Department of Neuroscience, Psychology, Drug Research and Child Health, Section of Pharmacology, University of Florence, Florence, Italy
| | - Lorenzo Di Cesare Mannelli
- Department of Neuroscience, Psychology, Drug Research and Child Health, Section of Pharmacology, University of Florence, Florence, Italy
| | - Carla Ghelardini
- Department of Neuroscience, Psychology, Drug Research and Child Health, Section of Pharmacology, University of Florence, Florence, Italy
| | - Grant Kolar
- Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, St. Louis, Missouri, USA.,Department of Pathology, and
| | - Carrie Wahlman
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Adeleye Opejin
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Cuiying Xiao
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - Marc L Reitman
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - Dilip K Tosh
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - Daniel Hawiger
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Kenneth A Jacobson
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - Daniela Salvemini
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.,Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, St. Louis, Missouri, USA
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28
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Luff DH, Wojdyla K, Oxley D, Chessa T, Hudson K, Hawkins PT, Stephens LR, Barry ST, Okkenhaug K. PI3Kδ Forms Distinct Multiprotein Complexes at the TCR Signalosome in Naïve and Differentiated CD4 + T Cells. Front Immunol 2021; 12:631271. [PMID: 33763075 PMCID: PMC7982423 DOI: 10.3389/fimmu.2021.631271] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/02/2021] [Indexed: 11/14/2022] Open
Abstract
Phosphoinositide 3-kinases (PI3Ks) play a central role in adaptive immunity by transducing signals from the T cell antigen receptor (TCR) via production of PIP3. PI3Kδ is a heterodimer composed of a p110δ catalytic subunit associated with a p85α or p85β regulatory subunit and is preferentially engaged by the TCR upon T cell activation. The molecular mechanisms leading to PI3Kδ recruitment and activation at the TCR signalosome remain unclear. In this study, we have used quantitative mass spectrometry, biochemical approaches and CRISPR-Cas9 gene editing to uncover the p110δ interactome in primary CD4+ T cells. Moreover, we have determined how the PI3Kδ interactome changes upon the differentiation of small naïve T cells into T cell blasts expanded in the presence of IL-2. Our interactomic analyses identified multiple constitutive and inducible PI3Kδ-interacting proteins, some of which were common to naïve and previously-activated T cells. Our data reveals that PI3Kδ rapidly interacts with as many as seven adaptor proteins upon TCR engagement, including the Gab-family proteins, GAB2 and GAB3, a CD5-CBL signalosome and the transmembrane proteins ICOS and TRIM. Our results also suggest that PI3Kδ pre-forms complexes with the adaptors SH3KBP1 and CRKL in resting cells that could facilitate the localization and activation of p110δ at the plasma membrane by forming ternary complexes during early TCR signalling. Furthermore, we identify interactions that were not previously known to occur in CD4+ T cells, involving BCAP, GAB3, IQGAP3 and JAML. We used CRISPR-Cas9-mediated gene knockout in primary T cells to confirm that BCAP is a positive regulator of PI3K-AKT signalling in CD4+ T cell blasts. Overall, our results provide evidence for a large protein network that regulates the recruitment and activation of PI3Kδ in T cells. Finally, this work shows how the PI3Kδ interactome is remodeled as CD4+ T cells differentiate from naïve T cells to activated T cell blasts. These activated T cells upregulate additional PI3Kδ adaptor proteins, including BCAP, GAB2, IQGAP3 and ICOS. This rewiring of TCR-PI3K signalling that occurs upon T cell differentiation may serve to reduce the threshold of activation and diversify the inputs for the PI3K pathway in effector T cells.
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Affiliation(s)
- Daisy H Luff
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
| | - Katarzyna Wojdyla
- Mass Spectrometry Facility, The Babraham Institute, Cambridge, United Kingdom.,Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - David Oxley
- Mass Spectrometry Facility, The Babraham Institute, Cambridge, United Kingdom
| | - Tamara Chessa
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Kevin Hudson
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Phillip T Hawkins
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Len R Stephens
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Simon T Barry
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Klaus Okkenhaug
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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29
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Scheer S, Runting J, Bramhall M, Russ B, Zaini A, Ellemor J, Rodrigues G, Ng J, Zaph C. The Methyltransferase DOT1L Controls Activation and Lineage Integrity in CD4 + T Cells during Infection and Inflammation. Cell Rep 2020; 33:108505. [PMID: 33326781 DOI: 10.1016/j.celrep.2020.108505] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/05/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022] Open
Abstract
CD4+ T helper (Th) cell differentiation is controlled by lineage-specific expression of transcription factors and effector proteins, as well as silencing of lineage-promiscuous genes. Lysine methyltransferases (KMTs) comprise a major class of epigenetic enzymes that are emerging as important regulators of Th cell biology. Here, we show that the KMT DOT1L regulates Th cell function and lineage integrity. DOT1L-dependent dimethylation of lysine 79 of histone H3 (H3K79me2) is associated with lineage-specific gene expression. However, DOT1L-deficient Th cells overproduce IFN-γ under lineage-specific and lineage-promiscuous conditions. Consistent with the increased IFN-γ response, mice with a T-cell-specific deletion of DOT1L are susceptible to infection with the helminth parasite Trichuris muris and are resistant to the development of allergic lung inflammation. These results identify a central role for DOT1L in Th2 cell lineage commitment and stability and suggest that inhibition of DOT1L may provide a therapeutic strategy to limit type 2 immune responses.
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Affiliation(s)
- Sebastian Scheer
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton VIC 3800, Australia.
| | - Jessica Runting
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton VIC 3800, Australia
| | - Michael Bramhall
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton VIC 3800, Australia
| | - Brendan Russ
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Department of Microbiology, Monash University, Clayton VIC 3800, Australia
| | - Aidil Zaini
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton VIC 3800, Australia
| | - Jessie Ellemor
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton VIC 3800, Australia
| | - Grace Rodrigues
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton VIC 3800, Australia
| | - Judy Ng
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton VIC 3800, Australia
| | - Colby Zaph
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton VIC 3800, Australia.
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30
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Radens CM, Blake D, Jewell P, Barash Y, Lynch KW. Meta-analysis of transcriptomic variation in T-cell populations reveals both variable and consistent signatures of gene expression and splicing. RNA (NEW YORK, N.Y.) 2020; 26:1320-1333. [PMID: 32554554 PMCID: PMC7491319 DOI: 10.1261/rna.075929.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Human CD4+ T cells are often subdivided into distinct subtypes, including Th1, Th2, Th17, and Treg cells, that are thought to carry out distinct functions in the body. Typically, these T-cell subpopulations are defined by the expression of distinct gene repertoires; however, there is variability between studies regarding the methods used for isolation and the markers used to define each T-cell subtype. Therefore, how reliably studies can be compared to one another remains an open question. Moreover, previous analysis of gene expression in CD4+ T-cell subsets has largely focused on gene expression rather than alternative splicing. Here we take a meta-analysis approach, comparing eleven independent RNA-seq studies of human Th1, Th2, Th17, and/or Treg cells to determine the consistency in gene expression and splicing within each subtype across studies. We find that known master-regulators are consistently enriched in the appropriate subtype; however, cytokines and other genes often used as markers are more variable. Importantly, we also identify previously unknown transcriptomic markers that appear to consistently differentiate between subsets, including a few Treg-specific splicing patterns. Together this work highlights the heterogeneity in gene expression between samples designated as the same subtype, but also suggests additional markers that can be used to define functional groupings.
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Affiliation(s)
- Caleb M Radens
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Davia Blake
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Paul Jewell
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Computer Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yoseph Barash
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Computer Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kristen W Lynch
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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31
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Ren HM, Kolawole EM, Ren M, Jin G, Netherby-Winslow CS, Wade Q, Shwetank, Rahman ZSM, Evavold BD, Lukacher AE. IL-21 from high-affinity CD4 T cells drives differentiation of brain-resident CD8 T cells during persistent viral infection. Sci Immunol 2020; 5:5/51/eabb5590. [PMID: 32948671 DOI: 10.1126/sciimmunol.abb5590] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/25/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022]
Abstract
Development of tissue-resident memory (TRM) CD8 T cells depends on CD4 T cells. In polyomavirus central nervous system infection, brain CXCR5hi PD-1hi CD4 T cells produce interleukin-21 (IL-21), and CD8 T cells lacking IL-21 receptors (IL21R-/-) fail to become bTRM IL-21+ CD4 T cells exhibit elevated T cell receptor (TCR) affinity and higher TCR density. IL21R-/- brain CD8 T cells do not express CD103, depend on vascular CD8 T cells for maintenance, are antigen recall defective, and lack TRM core signature genes. CD4 T cell-deficient and IL21R-/- brain CD8 T cells show similar deficiencies in expression of genes for oxidative metabolism, and intrathecal delivery of IL-21 to CD4 T cell-depleted mice restores expression of electron transport genes in CD8 T cells to wild-type levels. Thus, high-affinity CXCR5hi PD-1hi CD4 T cells in the brain produce IL-21, which drives CD8 bTRM differentiation in response to a persistent viral infection.
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Affiliation(s)
- Heather M Ren
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Elizabeth M Kolawole
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Mingqiang Ren
- Consortium for Health and Military Performance, Department of Military & Emergency Medicine, Uniformed Services University, Bethesda, MD 20814, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Ge Jin
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | | | - Quinn Wade
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Shwetank
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Ziaur S M Rahman
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Brian D Evavold
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Aron E Lukacher
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA.
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32
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Lee M, Lee E, Han SK, Choi YH, Kwon DI, Choi H, Lee K, Park ES, Rha MS, Joo DJ, Shin EC, Kim S, Kim JK, Lee YJ. Single-cell RNA sequencing identifies shared differentiation paths of mouse thymic innate T cells. Nat Commun 2020; 11:4367. [PMID: 32868763 PMCID: PMC7459300 DOI: 10.1038/s41467-020-18155-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 08/09/2020] [Indexed: 12/19/2022] Open
Abstract
Invariant natural killer T (iNKT), mucosal-associated invariant T (MAIT), and γδ T cells are innate T cells that acquire memory phenotype in the thymus and share similar biological characteristics. However, how their effector differentiation is developmentally regulated is still unclear. Here, we identify analogous effector subsets of these three innate T cell types in the thymus that share transcriptional profiles. Using single-cell RNA sequencing, we show that iNKT, MAIT and γδ T cells mature via shared, branched differentiation rather than linear maturation or TCR-mediated instruction. Simultaneous TCR clonotyping analysis reveals that thymic maturation of all three types is accompanied by clonal selection and expansion. Analyses of mice deficient of TBET, GATA3 or RORγt and additional in vivo experiments corroborate the predicted differentiation paths, while human innate T cells from liver samples display similar features. Collectively, our data indicate that innate T cells share effector differentiation processes in the thymus. Innate T cells such as iNKT, MAIT and γδ T cells all develop in the thymus, but their differentiation paths are still unclear. Here, the authors show, using single-cell RNA sequencing, that all three cell types develop via shared and branched differentiation paths that are corroborated by additional results from gene-deficient mice and human liver T cells.
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Affiliation(s)
- Minji Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Eunmin Lee
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Seong Kyu Han
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Yoon Ha Choi
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Dong-Il Kwon
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Hyobeen Choi
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Kwanghwan Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Eun Seo Park
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Min-Seok Rha
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea
| | - Dong Jin Joo
- Department of Surgery, Yonsei University, College of Medicine, Seoul, Republic of Korea.,The Research Institute for Transplantation, Yonsei University, College of Medicine, Seoul, Republic of Korea
| | - Eui-Cheol Shin
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
| | - You Jeong Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
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33
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Li J, Comeau HY, Zhang Z, Ren X. Landscape of transcript isoforms in single T cells infiltrating in non-small-cell lung cancer. J Genet Genomics 2020; 47:373-388. [PMID: 32998846 DOI: 10.1016/j.jgg.2020.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/08/2020] [Accepted: 06/21/2020] [Indexed: 01/14/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) has enabled high-resolution characterization of molecular signatures of tumor-infiltrating lymphocytes. However, analyses at the transcript isoform level are rarely reported. As alternative splicing is critical to T-cell differentiation and activation, here, we proposed a computational method named IDEA (Isoform Detection, Enrichment, and functional Annotation) to comprehensively detect and annotate differentially used isoforms across cell subtypes. We applied IDEA on a scRNA-seq data set of 12,346 T cells from non-small-cell lung cancer (NSCLC). We found that most genes tend to dominantly express one isoform in single T cells, enabling typing T cells based on the isotypes, given a gene. Isotype analysis suggested that tumor-infiltrating T cells significantly preferred specific isotypes for 245 genes in CD8+ T cells and 456 genes in CD4+ T cells. Functional annotation suggests that the preferred isoforms involved in coding/noncoding switches, transcription start site changes, gains/losses of domains, and subcellular translocation. Clonal analysis revealed that isoform switching occurred during T-cell activation/differentiation. Our analysis provides precise characterization of the molecular events in tumor-infiltrating T cells and sheds new light on the regulatory mechanisms of tumor-infiltrating T cells.
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Affiliation(s)
- Jiesheng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Hannah Y Comeau
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zemin Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China; BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Xianwen Ren
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, 100871, China.
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34
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Wolf D, Gerhardt T, Winkels H, Michel NA, Pramod AB, Ghosheh Y, Brunel S, Buscher K, Miller J, McArdle S, Baas L, Kobiyama K, Vassallo M, Ehinger E, Dileepan T, Ali A, Schell M, Mikulski Z, Sidler D, Kimura T, Sheng X, Horstmann H, Hansen S, Mitre LS, Stachon P, Hilgendorf I, Gaddis DE, Hedrick C, Benedict CA, Peters B, Zirlik A, Sette A, Ley K. Pathogenic Autoimmunity in Atherosclerosis Evolves From Initially Protective Apolipoprotein B 100-Reactive CD4 + T-Regulatory Cells. Circulation 2020; 142:1279-1293. [PMID: 32703007 PMCID: PMC7515473 DOI: 10.1161/circulationaha.119.042863] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Throughout the inflammatory response that accompanies atherosclerosis, autoreactive CD4+ T-helper cells accumulate in the atherosclerotic plaque. Apolipoprotein B100 (apoB), the core protein of low-density lipoprotein, is an autoantigen that drives the generation of pathogenic T-helper type 1 (TH1) cells with proinflammatory cytokine secretion. Clinical data suggest the existence of apoB-specific CD4+ T cells with an atheroprotective, regulatory T cell (Treg) phenotype in healthy individuals. Yet, the function of apoB-reactive Tregs and their relationship with pathogenic TH1 cells remain unknown. METHODS To interrogate the function of autoreactive CD4+ T cells in atherosclerosis, we used a novel tetramer of major histocompatibility complex II to track T cells reactive to the mouse self-peptide apo B978-993 (apoB+) at the single-cell level. RESULTS We found that apoB+ T cells build an oligoclonal population in lymph nodes of healthy mice that exhibit a Treg-like transcriptome, although only 21% of all apoB+ T cells expressed the Treg transcription factor FoxP3 (Forkhead Box P3) protein as detected by flow cytometry. In single-cell RNA sequencing, apoB+ T cells formed several clusters with mixed TH signatures that suggested overlapping multilineage phenotypes with pro- and anti-inflammatory transcripts of TH1, T helper cell type 2 (TH2), and T helper cell type 17 (TH17), and of follicular-helper T cells. ApoB+ T cells were increased in mice and humans with atherosclerosis and progressively converted into pathogenic TH1/TH17-like cells with proinflammatory properties and only a residual Treg transcriptome. Plaque T cells that expanded during progression of atherosclerosis consistently showed a mixed TH1/TH17 phenotype in single-cell RNA sequencing. In addition, we observed a loss of FoxP3 in a fraction of apoB+ Tregs in lineage tracing of hyperlipidemic Apoe-/- mice. In adoptive transfer experiments, converting apoB+ Tregs failed to protect from atherosclerosis. CONCLUSIONS Our results demonstrate an unexpected mixed phenotype of apoB-reactive autoimmune T cells in atherosclerosis and suggest an initially protective autoimmune response against apoB with a progressive derangement in clinical disease. These findings identify apoB autoreactive Tregs as a novel cellular target in atherosclerosis.
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Affiliation(s)
- Dennis Wolf
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA.,Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Teresa Gerhardt
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA.,Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Department of Cardiology, Charité - University Medicine Berlin (Campus Benjamin Franklin), Germany (T.G.)
| | - Holger Winkels
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Nathaly Anto Michel
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Department of Cardiology, Medical University Graz, Austria (N.A.M., A.Z.)
| | - Akula Bala Pramod
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA.,Department of Psychiatry, University of California San Diego, La Jolla (A.B.P.)
| | - Yanal Ghosheh
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Simon Brunel
- Division of Immune Regulation (S.B., D.S., C.A.B.), La Jolla Institute for Immunology, CA
| | - Konrad Buscher
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Jacqueline Miller
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Sara McArdle
- Microscopy Core Facility (S.M.), La Jolla Institute for Immunology, CA
| | - Livia Baas
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Kouji Kobiyama
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Melanie Vassallo
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Erik Ehinger
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | | | - Amal Ali
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Maximilian Schell
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Zbigniew Mikulski
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Daniel Sidler
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Takayuki Kimura
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA
| | - Xia Sheng
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Hauke Horstmann
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Sophie Hansen
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Lucia Sol Mitre
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Peter Stachon
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Ingo Hilgendorf
- Department of Cardiology/Angiology I, University Heart Center Freiburg-Bad Krozingen, Germany (D.W., T.G., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.).,Medical Faculty, University of Freiburg, Germany (D.W., N.A.M., X.S., H.H., S.H., L.S.M., P.S., I.H.)
| | - Dalia E Gaddis
- Center for Autoimmunity and Inflammation (D.E.G., C.H., K.L.), La Jolla Institute for Immunology, CA
| | - Catherine Hedrick
- Center for Autoimmunity and Inflammation (D.E.G., C.H., K.L.), La Jolla Institute for Immunology, CA
| | - Chris A Benedict
- Division of Immune Regulation (S.B., D.S., C.A.B.), La Jolla Institute for Immunology, CA
| | - Bjoern Peters
- Division of Vaccine Discovery (B.P., A.S.), La Jolla Institute for Immunology, CA
| | - Andreas Zirlik
- Department of Cardiology, Medical University Graz, Austria (N.A.M., A.Z.)
| | - Alessandro Sette
- Division of Vaccine Discovery (B.P., A.S.), La Jolla Institute for Immunology, CA
| | - Klaus Ley
- Laboratory of Inflammation Biology(D.W., T.G., H.W., A.B.P., Y.G., K.B., J.M., L.B., K.K., M.V., E.E., A.A., M.S., T.K., K.L.), La Jolla Institute for Immunology, CA.,Center for Autoimmunity and Inflammation (D.E.G., C.H., K.L.), La Jolla Institute for Immunology, CA
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McGregor R, Chauss D, Freiwald T, Yan B, Wang L, Nova-Lamperti E, Zhang Z, Teague H, West EE, Bibby J, Kelly A, Malik A, Freeman AF, Schwartz D, Portilla D, John S, Lavender P, Lionakis MS, Mehta NN, Kemper C, Cooper N, Lombardi G, Laurence A, Kazemian M, Afzali B. An autocrine Vitamin D-driven Th1 shutdown program can be exploited for COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32743590 DOI: 10.1101/2020.07.18.210161] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pro-inflammatory immune responses are necessary for effective pathogen clearance, but cause severe tissue damage if not shut down in a timely manner 1,2 . Excessive complement and IFN-γ-associated responses are known drivers of immunopathogenesis 3 and are among the most highly induced immune programs in hyper-inflammatory SARS-CoV2 lung infection 4 . The molecular mechanisms that govern orderly shutdown and retraction of these responses remain poorly understood. Here, we show that complement triggers contraction of IFN-γ producing CD4 + T helper (Th) 1 cell responses by inducing expression of the vitamin D (VitD) receptor (VDR) and CYP27B1, the enzyme that activates VitD, permitting T cells to both activate and respond to VitD. VitD then initiates the transition from pro-inflammatory IFN-γ + Th1 cells to suppressive IL-10 + Th1 cells. This process is primed by dynamic changes in the epigenetic landscape of CD4 + T cells, generating superenhancers and recruiting c-JUN and BACH2, a key immunoregulatory transcription factor 5-7 . Accordingly, cells in psoriatic skin treated with VitD increased BACH2 expression, and BACH2 haplo-insufficient CD4 + T cells were defective in IL-10 production. As proof-of-concept, we show that CD4 + T cells in the bronchoalveolar lavage fluid (BALF) of patients with COVID-19 are Th1-skewed and that VDR is among the top regulators of genes induced by SARS-CoV2. Importantly, genes normally down-regulated by VitD were de-repressed in CD4 + BALF T cells of COVID-19, indicating that the VitD-driven shutdown program is impaired in this setting. The active metabolite of VitD, alfacalcidol, and cortico-steroids were among the top predicted pharmaceuticals that could normalize SARS-CoV2 induced genes. These data indicate that adjunct therapy with VitD in the context of other immunomodulatory drugs may be a beneficial strategy to dampen hyperinflammation in severe COVID-19.
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36
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ADAM12 is a costimulatory molecule that determines Th1 cell fate and mediates tissue inflammation. Cell Mol Immunol 2020; 18:1904-1919. [PMID: 32572163 PMCID: PMC8322154 DOI: 10.1038/s41423-020-0486-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/31/2020] [Indexed: 12/18/2022] Open
Abstract
A disintegrin and metalloproteinase (ADAM)12 was previously found to be expressed in T cells in the inflamed brain. However, the function of ADAM12 in T-cell responses in general and in tissue inflammation has not been examined. Here, we studied the role of ADAM12 in T-cell responses, fate determination on activation, and its functions in T cells to mediate tissue inflammation. We identified ADAM12 as a costimulatory molecule that is expressed on naive T cells and downregulated on stimulation. ADAM12 mimics CD28 costimulatory signaling to activate and induce the proliferation of T-helper 1 (Th1) cells. Monoclonal ADAM12 Fab antibodies trigger T-cell activation by amplifying TCR signaling to stimulate T-bet-mediated IFNγ production. Lack of genomic ADAM12 and its knockdown in T cells diminished T-bet and IFNγ production in Th1 cells, whereas other T cells, including Th17 cells, were unaffected. ADAM12 had similar functions in vivo on myelin antigen (MOG35–55)-induced T-cell activation. We found that genetic loss of ADAM12 profoundly alleviated Th1-mediated neuroinflammation and thus disease severity in experimental autoimmune encephalomyelitis, a model of multiple sclerosis. Transcriptomic profiling of MOG35–55-specific ADAM12−/− T cells revealed differentially expressed genes that are important for T-cell activation, proliferation, and costimulatory signaling and Th1 pathogenicity, consistent with their inability to cause T-cell-mediated skin inflammation in a model of adoptive delayed-type hypersensitivity. We conclude that ADAM12 is a T-cell costimulatory molecule that contributes to the pathogenesis of tissue inflammation and a potential target for the treatment of Th1-mediated diseases.
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37
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Palmer LD, Maloney KN, Boyd KL, Goleniewska AK, Toki S, Maxwell CN, Chazin WJ, Peebles RS, Newcomb DC, Skaar EP. The Innate Immune Protein S100A9 Protects from T-Helper Cell Type 2-mediated Allergic Airway Inflammation. Am J Respir Cell Mol Biol 2020; 61:459-468. [PMID: 30943376 DOI: 10.1165/rcmb.2018-0217oc] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Calprotectin is a heterodimer of the proteins S100A8 and S100A9, and it is an abundant innate immune protein associated with inflammation. In humans, calprotectin transcription and protein abundance are associated with asthma and disease severity. However, mechanistic studies in experimental asthma models have been inconclusive, identifying both protective and pathogenic effects of calprotectin. To clarify the role of calprotectin in asthma, calprotectin-deficient S100A9-/- and wild-type (WT) C57BL/6 mice were compared in a murine model of allergic airway inflammation. Mice were intranasally challenged with extracts of the clinically relevant allergen, Alternaria alternata (Alt Ext), or PBS every third day over 9 days. On Day 10, BAL fluid and lung tissue homogenates were harvested and allergic airway inflammation was assessed. Alt Ext challenge induced release of S100A8/S100A9 to the alveolar space and increased protein expression in the alveolar epithelium of WT mice. Compared with WT mice, S100A9-/- mice displayed significantly enhanced allergic airway inflammation, including production of IL-13, CCL11, CCL24, serum IgE, eosinophil recruitment, and airway resistance and elastance. In response to Alt Ext, S100A9-/- mice accumulated significantly more IL-13+IL-5+CD4+ T-helper type 2 cells. S100A9-/- mice also accumulated a significantly lower proportion of CD4+ T regulatory (Treg) cells in the lung that had significantly lower expression of CD25. Calprotectin enhanced WT Treg cell suppressive activity in vitro. Therefore, this study identifies a role for the innate immune protein, S100A9, in protection from CD4+ T-helper type 2 cell hyperinflammation in response to Alt Ext. This protection is mediated, at least in part, by CD4+ Treg cell function.
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Affiliation(s)
- Lauren D Palmer
- Department of Pathology, Microbiology, and Immunology.,Vanderbilt Institute for Infection, Immunology and Inflammation, and
| | - K Nichole Maloney
- Department of Pathology, Microbiology, and Immunology.,Vanderbilt Institute for Infection, Immunology and Inflammation, and
| | - Kelli L Boyd
- Department of Pathology, Microbiology, and Immunology.,Vanderbilt Institute for Infection, Immunology and Inflammation, and
| | - A Kasia Goleniewska
- Vanderbilt Institute for Infection, Immunology and Inflammation, and.,Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; and
| | - Shinji Toki
- Vanderbilt Institute for Infection, Immunology and Inflammation, and.,Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; and
| | - C Noel Maxwell
- Department of Biochemistry and.,Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee
| | - Walter J Chazin
- Vanderbilt Institute for Infection, Immunology and Inflammation, and.,Department of Biochemistry and.,Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee
| | - R Stokes Peebles
- Department of Pathology, Microbiology, and Immunology.,Vanderbilt Institute for Infection, Immunology and Inflammation, and.,Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; and
| | - Dawn C Newcomb
- Department of Pathology, Microbiology, and Immunology.,Vanderbilt Institute for Infection, Immunology and Inflammation, and.,Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; and
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology.,Vanderbilt Institute for Infection, Immunology and Inflammation, and
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38
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CRISPR screen in regulatory T cells reveals modulators of Foxp3. Nature 2020; 582:416-420. [PMID: 32499641 PMCID: PMC7305989 DOI: 10.1038/s41586-020-2246-4] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 02/26/2020] [Indexed: 12/26/2022]
Abstract
Regulatory T cells (Tregs) are required to control immune responses and maintain homeostasis, but are a significant barrier to anti-tumor immunity1. Conversely, Treg instability, characterized by loss of the master transcription factor Foxp3 and acquisition of pro-inflammatory properties2, can promote autoimmunity and/or facilitate more effective tumor immunity3,4. A comprehensive understanding of the pathways that regulate Foxp3 could lead to more effective Treg therapies for autoimmune disease and cancer. Despite improved functional genetic tools that now allow for systematic interrogation, dissection of the gene regulatory programs that modulate Foxp3 expression has not yet been reported. In this study, we developed a CRISPR-based pooled screening platform for phenotypes in primary mouse Tregs and applied this technology to perform a targeted loss-of-function screen of ~490 nuclear factors to identify gene regulatory programs that promote or disrupt Foxp3 expression. We discovered several novel modulators including ubiquitin-specific peptidase 22 (Usp22) and ring finger protein 20 (Rnf20). Usp22, a member of the deubiquitination module of the SAGA chromatin modifying complex, was discovered to be a positive regulator that stabilized Foxp3 expression; whereas the screen suggested Rnf20, an E3 ubiquitin ligase, can serve as a negative regulator of Foxp3. Treg-specific ablation of Usp22 in mice reduced Foxp3 protein and created defects in their suppressive function that led to spontaneous autoimmunity but protected against tumor growth in multiple cancer models. Foxp3 destabilization in Usp22-deficient Tregs could be rescued by ablation of Rnf20, revealing a reciprocal ubiquitin switch in Tregs. These results reveal novel modulators of Foxp3 and demonstrate a screening method that can be broadly applied to discover new targets for Treg immunotherapies for cancer and autoimmune disease.
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39
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Stampouloglou E, Cheng N, Federico A, Slaby E, Monti S, Szeto GL, Varelas X. Yap suppresses T-cell function and infiltration in the tumor microenvironment. PLoS Biol 2020; 18:e3000591. [PMID: 31929526 PMCID: PMC6980695 DOI: 10.1371/journal.pbio.3000591] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 01/24/2020] [Accepted: 12/18/2019] [Indexed: 12/11/2022] Open
Abstract
A major challenge for cancer immunotherapy is sustaining T-cell activation and recruitment in immunosuppressive solid tumors. Here, we report that the levels of the Hippo pathway effector Yes-associated protein (Yap) are sharply induced upon the activation of cluster of differentiation 4 (CD4)-positive and cluster of differentiation 8 (CD8)-positive T cells and that Yap functions as an immunosuppressive factor and inhibitor of effector differentiation. Loss of Yap in T cells results in enhanced T-cell activation, differentiation, and function, which translates in vivo to an improved ability for T cells to infiltrate and repress tumors. Gene expression analyses of tumor-infiltrating T cells following Yap deletion implicates Yap as a mediator of global T-cell responses in the tumor microenvironment and as a negative regulator of T-cell tumor infiltration and patient survival in diverse human cancers. Collectively, our results indicate that Yap plays critical roles in T-cell biology and suggest that Yap inhibition improves T-cell responses in cancer.
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MESH Headings
- Adaptor Proteins, Signal Transducing/antagonists & inhibitors
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/physiology
- Animals
- Cell Cycle Proteins/antagonists & inhibitors
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/physiology
- Cell Proliferation/genetics
- Cells, Cultured
- Chemotaxis, Leukocyte/genetics
- Down-Regulation/genetics
- Down-Regulation/immunology
- Immunotherapy, Adoptive
- Melanoma, Experimental/immunology
- Melanoma, Experimental/pathology
- Melanoma, Experimental/therapy
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Skin Neoplasms/immunology
- Skin Neoplasms/pathology
- Skin Neoplasms/therapy
- T-Lymphocytes/physiology
- Tumor Microenvironment/genetics
- Tumor Microenvironment/immunology
- YAP-Signaling Proteins
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Affiliation(s)
- Eleni Stampouloglou
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Nan Cheng
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Anthony Federico
- Division of Computational Biology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Emily Slaby
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
| | - Stefano Monti
- Division of Computational Biology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Gregory L. Szeto
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland, United States of America
- Translational Center for Age-Related Disease and Disparities, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, United States of America
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40
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Ranu N, Villani AC, Hacohen N, Blainey PC. Targeting individual cells by barcode in pooled sequence libraries. Nucleic Acids Res 2019; 47:e4. [PMID: 30256981 PMCID: PMC6326790 DOI: 10.1093/nar/gky856] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/12/2018] [Indexed: 01/02/2023] Open
Abstract
Transcriptional profiling of thousands of single cells in parallel by RNA-seq is now routine. However, due to reliance on pooled library preparation, targeting analysis to particular cells of interest is difficult. Here, we present a multiplexed PCR method for targeted sequencing of select cells from pooled single-cell sequence libraries. We demonstrated this molecular enrichment method on multiple cell types within pooled single-cell RNA-seq libraries produced from primary human blood cells. We show how molecular enrichment can be combined with FACS to efficiently target ultra-rare cell types, such as the recently identified AXL+SIGLEC6+ dendritic cell (AS DC) subset, in order to reduce the required sequencing effort to profile single cells by 100-fold. Our results demonstrate that DNA barcodes identifying cells within pooled sequencing libraries can be used as targets to enrich for specific molecules of interest, for example reads from a set of target cells.
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Affiliation(s)
- Navpreet Ranu
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
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41
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Gaylo-Moynihan A, Prizant H, Popović M, Fernandes NRJ, Anderson CS, Chiou KK, Bell H, Schrock DC, Schumacher J, Capece T, Walling BL, Topham DJ, Miller J, Smrcka AV, Kim M, Hughson A, Fowell DJ. Programming of Distinct Chemokine-Dependent and -Independent Search Strategies for Th1 and Th2 Cells Optimizes Function at Inflamed Sites. Immunity 2019; 51:298-309.e6. [PMID: 31399281 PMCID: PMC6904228 DOI: 10.1016/j.immuni.2019.06.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/18/2019] [Accepted: 06/26/2019] [Indexed: 02/08/2023]
Abstract
T-helper (Th) cell differentiation drives specialized gene programs that dictate effector T cell function at sites of infection. Here, we have shown Th cell differentiation also imposes discrete motility gene programs that shape Th1 and Th2 cell navigation of the inflamed dermis. Th1 cells scanned a smaller tissue area in a G protein-coupled receptor (GPCR) and chemokine-dependent fashion, while Th2 cells scanned a larger tissue area independent of GPCR signals. Differential chemokine reliance for interstitial migration was linked to STAT6 transcription-factor-dependent programming of integrin αVβ3 expression: Th2 cell differentiation led to high αVβ3 expression relative to Th1 cells. Th1 and Th2 cell modes of motility could be switched simply by manipulating the amount of αVβ3 on the cell surface. Deviating motility modes from those established during differentiation impaired effector function. Thus, programmed expression of αVβ3 tunes effector T cell reliance on environmental cues for optimal exploration of inflamed tissues.
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Affiliation(s)
- Alison Gaylo-Moynihan
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Hen Prizant
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Milan Popović
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ninoshka R J Fernandes
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; Department of Biomedical Engineering, University of Rochester, Rochester, NY 14642, USA
| | - Christopher S Anderson
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Kevin K Chiou
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hannah Bell
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Dillon C Schrock
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Justin Schumacher
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14642, USA
| | - Tara Capece
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Brandon L Walling
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - David J Topham
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jim Miller
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Alan V Smrcka
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Minsoo Kim
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Angela Hughson
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Deborah J Fowell
- David H. Smith Center for Vaccine Biology and Immunology, Aab Institute of Biomedical Sciences, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA.
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42
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Tibbitt CA, Stark JM, Martens L, Ma J, Mold JE, Deswarte K, Oliynyk G, Feng X, Lambrecht BN, De Bleser P, Nylén S, Hammad H, Arsenian Henriksson M, Saeys Y, Coquet JM. Single-Cell RNA Sequencing of the T Helper Cell Response to House Dust Mites Defines a Distinct Gene Expression Signature in Airway Th2 Cells. Immunity 2019; 51:169-184.e5. [PMID: 31231035 DOI: 10.1016/j.immuni.2019.05.014] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 02/28/2019] [Accepted: 05/23/2019] [Indexed: 12/24/2022]
Abstract
Naive CD4+ T cells differentiate into functionally diverse T helper (Th) cell subsets. Th2 cells play a pathogenic role in asthma, yet a clear picture of their transcriptional profile is lacking. We performed single-cell RNA sequencing (scRNA-seq) of T helper cells from lymph node, lung, and airways in the house dust mite (HDM) model of allergic airway disease. scRNA-seq resolved transcriptional profiles of naive CD4+ T, Th1, Th2, regulatory T (Treg) cells, and a CD4+ T cell population responsive to type I interferons. Th2 cells in the airways were enriched for transcription of many genes, including Cd200r1, Il6, Plac8, and Igfbp7, and their mRNA profile was supported by analysis of chromatin accessibility and flow cytometry. Pathways associated with lipid metabolism were enriched in Th2 cells, and experiments with inhibitors of key metabolic pathways supported roles for glucose and lipid metabolism. These findings provide insight into the differentiation of pathogenic Th2 cells in the context of allergy.
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Affiliation(s)
| | - Julian Mario Stark
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Liesbet Martens
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Junjie Ma
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Jeff Eron Mold
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Kim Deswarte
- VIB Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Ganna Oliynyk
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Xiaogang Feng
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Bart Norbert Lambrecht
- VIB Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Pieter De Bleser
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Susanne Nylén
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Hamida Hammad
- VIB Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | | | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Jonathan Marie Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden.
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43
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Effector and Regulatory T Cells Roll at High Shear Stress by Inducible Tether and Sling Formation. Cell Rep 2019; 21:3885-3899. [PMID: 29281835 DOI: 10.1016/j.celrep.2017.11.099] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/04/2017] [Accepted: 11/28/2017] [Indexed: 01/07/2023] Open
Abstract
The adaptive immune response involves T cell differentiation and migration to sites of inflammation. T cell trafficking is initiated by rolling on inflamed endothelium. Tethers and slings, discovered in neutrophils, facilitate cell rolling at high shear stress. Here, we demonstrate that the ability to form tethers and slings during rolling is highly inducible in T helper 1 (Th1), Th17, and regulatory T (Treg) cells but less in Th2 cells. In vivo, endogenous Treg cells rolled stably in cremaster venules at physiological shear stress. Quantitative dynamic footprinting nanoscopy of Th1, Th17, and Treg cells uncovered the formation of multiple tethers per cell. Human Th1 cells also showed tethers and slings. RNA sequencing (RNA-seq) revealed the induction of cell migration and cytoskeletal genes in sling-forming cells. We conclude that differentiated CD4 T cells stabilize rolling by inducible tether and sling formation. These phenotypic changes approximate the adhesion phenotype of neutrophils and support CD4 T cell access to sites of inflammation.
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44
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Hewitson JP, Shah KM, Brown N, Grevitt P, Hain S, Newling K, Sharp TV, Kaye PM, Lagos D. miR-132 suppresses transcription of ribosomal proteins to promote protective Th1 immunity. EMBO Rep 2019; 20:embr.201846620. [PMID: 30833344 DOI: 10.15252/embr.201846620] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 02/01/2019] [Accepted: 02/06/2019] [Indexed: 01/01/2023] Open
Abstract
Determining the mechanisms that distinguish protective immunity from pathological chronic inflammation remains a fundamental challenge. miR-132 has been shown to play largely immunoregulatory roles in immunity; however, its role in CD4+ T cell function is poorly understood. Here, we show that CD4+ T cells express high levels of miR-132 and that T cell activation leads to miR-132 up-regulation. The transcriptomic hallmark of splenic CD4+ T cells lacking the miR-132/212 cluster during chronic infection is an increase in mRNA levels of ribosomal protein (RP) genes. BTAF1, a co-factor of B-TFIID and novel miR-132/212-3p target, and p300 contribute towards miR-132/212-mediated regulation of RP transcription. Following infection with Leishmania donovani, miR-132 -/- CD4+ T cells display enhanced expression of IL-10 and decreased IFNγ. This is associated with reduced hepatosplenomegaly and enhanced pathogen load. The enhanced IL-10 expression in miR-132 -/- Th1 cells is recapitulated in vitro following treatment with phenylephrine, a drug reported to promote ribosome synthesis. Our results uncover that miR-132/212-mediated regulation of RP expression is critical for optimal CD4+ T cell activation and protective immunity against pathogens.
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Affiliation(s)
- James P Hewitson
- Centre for Immunology and Infection and York Biomedical Research Institute, Hull York Medical School and Department of Biology, University of York, York, UK
| | - Kunal M Shah
- Centre of Molecular Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University London, London, UK
| | - Najmeeyah Brown
- Centre for Immunology and Infection and York Biomedical Research Institute, Hull York Medical School and Department of Biology, University of York, York, UK
| | - Paul Grevitt
- Centre of Molecular Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University London, London, UK
| | - Sofia Hain
- Centre for Immunology and Infection and York Biomedical Research Institute, Hull York Medical School and Department of Biology, University of York, York, UK
| | - Katherine Newling
- Genomics and Bioinformatics Laboratory, Bioscience Technology Facility, Department of Biology, University of York, York, UK
| | - Tyson V Sharp
- Centre of Molecular Oncology, Barts Cancer Institute, John Vane Science Centre, Charterhouse Square, Queen Mary University London, London, UK
| | - Paul M Kaye
- Centre for Immunology and Infection and York Biomedical Research Institute, Hull York Medical School and Department of Biology, University of York, York, UK
| | - Dimitris Lagos
- Centre for Immunology and Infection and York Biomedical Research Institute, Hull York Medical School and Department of Biology, University of York, York, UK
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45
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Henriksson J, Chen X, Gomes T, Ullah U, Meyer KB, Miragaia R, Duddy G, Pramanik J, Yusa K, Lahesmaa R, Teichmann SA. Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation. Cell 2019; 176:882-896.e18. [PMID: 30639098 PMCID: PMC6370901 DOI: 10.1016/j.cell.2018.11.044] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 09/19/2018] [Accepted: 11/28/2018] [Indexed: 12/24/2022]
Abstract
T helper type 2 (Th2) cells are important regulators of mammalian adaptive immunity and have relevance for infection, autoimmunity, and tumor immunology. Using a newly developed, genome-wide retroviral CRISPR knockout (KO) library, combined with RNA-seq, ATAC-seq, and ChIP-seq, we have dissected the regulatory circuitry governing activation and differentiation of these cells. Our experiments distinguish cell activation versus differentiation in a quantitative framework. We demonstrate that these two processes are tightly coupled and are jointly controlled by many transcription factors, metabolic genes, and cytokine/receptor pairs. There are only a small number of genes regulating differentiation without any role in activation. By combining biochemical and genetic data, we provide an atlas for Th2 differentiation, validating known regulators and identifying factors, such as Pparg and Bhlhe40, as part of the core regulatory network governing Th2 helper cell fates.
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Affiliation(s)
- Johan Henriksson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
| | - Xi Chen
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ubaid Ullah
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6 FI-20520, Turku, Finland
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ricardo Miragaia
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Graham Duddy
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jhuma Pramanik
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kosuke Yusa
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6 FI-20520, Turku, Finland
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, UK.
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46
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Tripathi SK, Välikangas T, Shetty A, Khan MM, Moulder R, Bhosale SD, Komsi E, Salo V, De Albuquerque RS, Rasool O, Galande S, Elo LL, Lahesmaa R. Quantitative Proteomics Reveals the Dynamic Protein Landscape during Initiation of Human Th17 Cell Polarization. iScience 2018; 11:334-355. [PMID: 30641411 PMCID: PMC6330361 DOI: 10.1016/j.isci.2018.12.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 08/08/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022] Open
Abstract
Th17 cells contribute to the pathogenesis of inflammatory and autoimmune diseases and cancer. To reveal the Th17 cell-specific proteomic signature regulating Th17 cell differentiation and function in humans, we used a label-free mass spectrometry-based approach. Furthermore, a comprehensive analysis of the proteome and transcriptome of cells during human Th17 differentiation revealed a high degree of overlap between the datasets. However, when compared with corresponding published mouse data, we found very limited overlap between the proteins differentially regulated in response to Th17 differentiation. Validations were made for a panel of selected proteins with known and unknown functions. Finally, using RNA interference, we showed that SATB1 negatively regulates human Th17 cell differentiation. Overall, the current study illustrates a comprehensive picture of the global protein landscape during early human Th17 cell differentiation. Poor overlap with mouse data underlines the importance of human studies for translational research. Quantitative proteomics analysis of early human Th17 cell polarization The proteome and transcriptome highly correlate during early Th17 polarization Poor overlap of proteome profiles of human and mouse during early Th17 polarization The results underline the importance of human studies for translational research
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Affiliation(s)
- Subhash K Tripathi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland
| | - Tommi Välikangas
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland; Doctoral Programme in Mathematics and Computer Sciences (MATTI), University of Turku, University Hill, FI-20014 Turku, Finland
| | - Ankitha Shetty
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland; Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Mohd Moin Khan
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland; Turku Doctoral Programme of Molecular Medicine (TuDMM), University of Turku, Tykistökatu 6, FI-20520 Turku, Finland
| | - Robert Moulder
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland
| | - Santosh D Bhosale
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland; Turku Doctoral Programme of Molecular Medicine (TuDMM), University of Turku, Tykistökatu 6, FI-20520 Turku, Finland
| | - Elina Komsi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland
| | - Verna Salo
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland; Turku Doctoral Programme of Molecular Medicine (TuDMM), University of Turku, Tykistökatu 6, FI-20520 Turku, Finland
| | - Rafael Sales De Albuquerque
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland
| | - Omid Rasool
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland
| | - Sanjeev Galande
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Laura L Elo
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland.
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland.
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Brajic A, Franckaert D, Burton O, Bornschein S, Calvanese AL, Demeyer S, Cools J, Dooley J, Schlenner S, Liston A. The Long Non-coding RNA Flatr Anticipates Foxp3 Expression in Regulatory T Cells. Front Immunol 2018; 9:1989. [PMID: 30319599 PMCID: PMC6167443 DOI: 10.3389/fimmu.2018.01989] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/13/2018] [Indexed: 12/30/2022] Open
Abstract
Mammalian genomes encode a plethora of long non-coding RNA (lncRNA). These transcripts are thought to regulate gene expression, influencing biological processes from development to pathology. Results from the few lncRNA that have been studied in the context of the immune system have highlighted potentially critical functions as network regulators. Here we explored the nature of the lncRNA transcriptome in regulatory T cells (Tregs), a subset of CD4+ T cells required to establish and maintain immunological self-tolerance. The identified Treg lncRNA transcriptome showed distinct differences from that of non-regulatory CD4+ T cells, with evidence of direct shaping of the lncRNA transcriptome by Foxp3, the master transcription factor driving the distinct mRNA profile of Tregs. Treg lncRNA changes were disproportionally reversed in the absence of Foxp3, with an enrichment for colocalisation with Foxp3 DNA binding sites, indicating a direct coordination of transcription by Foxp3 independent of the mRNA coordination function. We further identified a novel lncRNA Flatr, as a member of the core Treg lncRNA transcriptome. Flatr expression anticipates Foxp3 expression during in vitro Treg conversion, and Flatr-deficient mice show a mild delay in in vitro and peripheral Treg induction. These results implicate Flatr as part of the upstream cascade leading to Treg conversion, and may provide clues as to the nature of this process.
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Affiliation(s)
- Aleksandra Brajic
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Dean Franckaert
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Oliver Burton
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Simon Bornschein
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium.,VIB Cancer Research Center, VIB, Leuven, Belgium
| | - Anna L Calvanese
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | | | - Jan Cools
- VIB Cancer Research Center, VIB, Leuven, Belgium
| | - James Dooley
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Susan Schlenner
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Adrian Liston
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
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48
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Matthews AL, Koo CZ, Szyroka J, Harrison N, Kanhere A, Tomlinson MG. Regulation of Leukocytes by TspanC8 Tetraspanins and the "Molecular Scissor" ADAM10. Front Immunol 2018; 9:1451. [PMID: 30013551 PMCID: PMC6036176 DOI: 10.3389/fimmu.2018.01451] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/12/2018] [Indexed: 01/16/2023] Open
Abstract
A disintegrin and metalloproteinase 10 (ADAM10) is a ubiquitous transmembrane protein that functions as a "molecular scissor" to cleave the extracellular regions from its transmembrane target proteins. ADAM10 is well characterized as the ligand-dependent activator of Notch proteins, which control cell fate decisions. Indeed, conditional knockouts of ADAM10 in mice reveal impaired B-, T-, and myeloid cell development and/or function. ADAM10 cleaves many other leukocyte-expressed substrates. On B-cells, ADAM10 cleavage of the low-affinity IgE receptor CD23 promotes allergy and asthma, cleavage of ICOS ligand impairs antibody responses, and cleavage of the BAFF-APRIL receptor transmembrane activator and CAML interactor, and BAFF receptor, reduce B-cell survival. On microglia, increased ADAM10 cleavage of a rare variant of the scavenger receptor triggering receptor expressed on myeloid cells 2 may increase susceptibility to Alzheimer's disease. We and others recently showed that ADAM10 interacts with one of six different regulatory tetraspanin membrane proteins, which we termed the TspanC8 subgroup, comprising Tspan5, Tspan10, Tspan14, Tspan15, Tspan17, and Tspan33. The TspanC8s are required for ADAM10 exit from the endoplasmic reticulum, and emerging evidence suggests that they dictate ADAM10 subcellular localization and substrate specificity. Therefore, we propose that ADAM10 should not be regarded as a single scissor, but as six different scissors with distinct substrate specificities, depending on the associated TspanC8. In this review, we collate recent transcriptomic data to present the TspanC8 repertoires of leukocytes, and we discuss the potential role of the six TspanC8/ADAM10 scissors in leukocyte development and function.
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Affiliation(s)
- Alexandra L Matthews
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Chek Ziu Koo
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, United Kingdom
| | - Justyna Szyroka
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Neale Harrison
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Aditi Kanhere
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Michael G Tomlinson
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom.,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, United Kingdom
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49
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Mohammad I, Nousiainen K, Bhosale SD, Starskaia I, Moulder R, Rokka A, Cheng F, Mohanasundaram P, Eriksson JE, Goodlett DR, Lähdesmäki H, Chen Z. Quantitative proteomic characterization and comparison of T helper 17 and induced regulatory T cells. PLoS Biol 2018; 16:e2004194. [PMID: 29851958 PMCID: PMC5979006 DOI: 10.1371/journal.pbio.2004194] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 04/25/2018] [Indexed: 12/14/2022] Open
Abstract
The transcriptional network and protein regulators that govern T helper 17 (Th17) cell differentiation have been studied extensively using advanced genomic approaches. For a better understanding of these biological processes, we have moved a step forward, from gene- to protein-level characterization of Th17 cells. Mass spectrometry–based label-free quantitative (LFQ) proteomics analysis were made of in vitro differentiated murine Th17 and induced regulatory T (iTreg) cells. More than 4,000 proteins, covering almost all subcellular compartments, were detected. Quantitative comparison of the protein expression profiles resulted in the identification of proteins specifically expressed in the Th17 and iTreg cells. Importantly, our combined analysis of proteome and gene expression data revealed protein expression changes that were not associated with changes at the transcriptional level. Our dataset provides a valuable resource, with new insights into the proteomic characteristics of Th17 and iTreg cells, which may prove useful in developing treatment of autoimmune diseases and developing tumor immunotherapy. T helper 17 (Th17) cells and induced regulatory T (iTreg) cells are two subsets of T helper cells differentiated from naïve cells that play important roles in autoimmune diseases, immune homeostasis, and tumor immunity. The differentiation process is achieved by changes in numerous proteins, including transcription regulators, enzymes, membrane receptors, and cytokines, which are critical in lineage commitment. To profile protein expression changes in Th17 and iTreg cells, we polarized murine naïve CD4+ T (Thp) cells in vitro to Th17 and iTreg cells and performed quantitative proteomic analysis of these cells. More than 4,000 proteins, covering almost all subcellular compartments, were detected. Quantitative comparison of the protein expression profiles resulted in the identification of proteins specifically expressed in the Th17 and iTreg cells. Importantly, our combined analysis of proteome and gene expression data revealed protein expression changes that were not associated with changes at the transcriptional level. The present study serves as a valuable resource that may prove useful in developing treatment of autoimmune diseases and cancer.
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Affiliation(s)
- Imran Mohammad
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Kari Nousiainen
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Santosh D. Bhosale
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Inna Starskaia
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Robert Moulder
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Anne Rokka
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Fang Cheng
- Cell Biology, Biosciences, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Ponnuswamy Mohanasundaram
- Cell Biology, Biosciences, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - John E. Eriksson
- Cell Biology, Biosciences, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - David R. Goodlett
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, United States of America
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Zhi Chen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
- * E-mail:
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50
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Kwon DI, Lee YJ. Lineage Differentiation Program of Invariant Natural Killer T Cells. Immune Netw 2017; 17:365-377. [PMID: 29302250 PMCID: PMC5746607 DOI: 10.4110/in.2017.17.6.365] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 10/27/2017] [Accepted: 11/02/2017] [Indexed: 02/07/2023] Open
Abstract
Invariant natural killer T (iNKT) cells are innate T cells restricted by CD1d molecules. They are positively selected in the thymic cortex and migrate to the medullary area, in which they differentiate into 3 different lineages. Promyelocytic leukemia zinc finger (PLZF) modulates this process, and PLZFhigh, PLZFintermediate, and PLZFlow iNKT cells are designated as NKT2, NKT17, and NKT1 cells, respectively. Analogous to conventional helper CD4 T cells, each subset expresses distinct combinations of transcription factors and produces different cytokines. In lymphoid organs, iNKT subsets have unique localizations, which determine their cytokine responses upon antigenic challenge. The lineage differentiation programs of iNKT cells are differentially regulated in various mice strains in a cell-intrinsic manner, and BALB/c mice contain a high frequency of NKT2 cells. In the thymic medulla, steady state IL-4 from NKT2 cells directly conditions CD8 T cells to become memory-like cells expressing Eomesodermin, which function as premade memory effectors. The genetic signature of iNKT cells is more similar to that of γδ T cells and innate lymphoid cells (ILCs) than of conventional helper T cells, suggesting that ILCs and innate T cells share common developmental programs.
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Affiliation(s)
- Dong-Il Kwon
- Academy of Immunology and Microbiology, Institute for Basic Science, Pohang 37673, Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 37673, Korea
| | - You Jeong Lee
- Academy of Immunology and Microbiology, Institute for Basic Science, Pohang 37673, Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 37673, Korea
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