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Roux H, Lantz O. [Role of CD4 T cells in the immune response]. Med Sci (Paris) 2025; 41:336-345. [PMID: 40293150 DOI: 10.1051/medsci/2025048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2025] Open
Abstract
CD4 T cells orchestrate the immune response, facilitating cytotoxic and humoral responses while preventing the destruction of one's own tissues by more autoreactive T cells. However, unlike complete CD4 T cell deficiency, the apparent deficiency caused by mutations in the CD4 gene that prevent its expression does not result in severe combined immunodeficiency in humans. The absence of the CD4 molecule limits the number of clones selected in the thymus on the basis of major histocompatibility complex type II, but does not prevent the acquisition of the T helper lymphocyte program, allowing them to retain most of their effector capacity. This observation raises new questions about the function of CD4 T cells and, in particular, the intrinsic role of the CD4 molecule.
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Affiliation(s)
- Hugo Roux
- Institut Curie, Université Paris Sciences et Lettres, Inserm U932, Immunité et cancer, Paris, France
| | - Olivier Lantz
- Institut Curie, Université Paris Sciences et Lettres, Inserm U932, Immunité et cancer, Paris, France - Laboratoire d'immunologie clinique, Institut Curie, Paris, France - Centre d'investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428) Institut Curie, Paris, France
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2
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Zhang JB, Chaurasia P, Nguyen A, Huang Z, Nguyen TT, Xu H, Tran MT, Reid HH, Jones CM, Schattgen SA, Thiele D, Thomas PG, Rientjes J, Good-Jacobson KL, Ruscher R, Littler DR, Rossjohn J, Zareie P, La Gruta NL. LCK-co-receptor association ensures T cell lineage fidelity and maximizes epitope-specific TCR diversity. Sci Immunol 2025; 10:eadp5016. [PMID: 39982976 DOI: 10.1126/sciimmunol.adp5016] [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: 03/27/2024] [Accepted: 01/30/2025] [Indexed: 02/23/2025]
Abstract
The interaction between the CD4/CD8 co-receptors and LCK (an Src family tyrosine kinase) is thought to augment T cell activation upon recognition of peptide-loaded major histocompatibility complexes (pMHCs). How this interaction influences antigen-specific T cell development is unclear however, as is its impact on naïve and immune antigen-specific T cell repertoires. In mice expressing mutated endogenous LCK unable to bind co-receptors (LCKFREE mice), we show that influenza A virus (IAV)-derived pMHC-specific CD8 and CD4 T cell responses had a significantly narrowed T cell receptor (TCR) repertoire, favoring high-affinity TCRs. This narrowing was established during T cell development and was exacerbated after viral infection. The dissociation of LCK from co-receptors also resulted in the redirection of CD4-fated T cells to the CD8 lineage, with expanded pMHCII-specific cytotoxic CD8 T cells observed after IAV infection. Thus, LCK-co-receptor association is critical for ensuring T cell lineage fidelity and maximizing antigen-specific T cell repertoire diversity.
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Affiliation(s)
- Justin B Zhang
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Priyanka Chaurasia
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Angela Nguyen
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Zijian Huang
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Trang T Nguyen
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Hui Xu
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Mai T Tran
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Hugh H Reid
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Claerwen M Jones
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Stefan A Schattgen
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel Thiele
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Paul G Thomas
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeanette Rientjes
- Genome Modification Platform, Monash University, Clayton, VIC, Australia
| | - Kim L Good-Jacobson
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Roland Ruscher
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Dene R Littler
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jamie Rossjohn
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Pirooz Zareie
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Nicole L La Gruta
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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Swan GA, Fujii C, Guzynski ME, Page SM, Meyers IV, Penev YP, Littleton S, Azzahra A, Richardson C, Sarafova SD. A conserved element in the first intron of Cd4 has a lineage specific, TCR signal-responsive, canonical enhancer function that matches the timing of cell surface CD4 upregulation required to prevent lineage choice error. Front Immunol 2025; 15:1469402. [PMID: 39882239 PMCID: PMC11774700 DOI: 10.3389/fimmu.2024.1469402] [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: 07/23/2024] [Accepted: 12/19/2024] [Indexed: 01/31/2025] Open
Abstract
Introduction The regulation of Cd4 expression during T-cell development and immune responses is essential for proper lineage commitment and function in the periphery. However, the mechanisms of genetic and epigenetic regulation are complex, and their interplay not entirely understood. Previously, we demonstrated the need for CD4 upregulation during positive selection to ensure faithful commitment of MHC-II-restricted T cells to the CD4 lineage. In this study, we investigate whether a conserved region, here called NCE, that is proximal to the Cd4 silencer and contains E4m has the required developmental-stage-specific canonical enhancer function and TCR responsiveness to mediate the CD4 upregulation required to prevent lineage errors. Methods To investigate the role of NCE, transient transfection of reporter plasmids was performed in thymoma cell lines arrested at the double-positive (DP, CD4+CD8+) and intermediate (INT, CD4+CD8lo) stages of development. CRISPR/Cas9-mediated deletion of the coreNCE/E4m region was carried out in these cell lines to assess its impact on CD4 surface expression, re-expression rates, and TCR signaling responsiveness. To avoid developmental alterations from direct manipulation of the endogenous Cd4 locus in vivo, BAC-transgenic reporter mice were generated with the locus modified to express EGFP in the presence or absence of NCE. EGFP mRNA levels were measured via RT-qPCR, and EGFP fluorescence was analyzed in post-selection thymocytes. Results Our in vitro experiments demonstrate that NCE by itself can function as an enhancer at the INT, but not the DP stage of development. Furthermore, CRISPR/Cas9-mediated deletion of coreNCE/E4m resulted in reduced CD4 surface levels, slower re-expression rates, and reduced TCR signaling responsiveness in INT cells, but not in DP cells. In vivo, NCE-sufficient transgenic mice exhibited upregulation of Cd4 reporter EGFP mRNA levels at the INT stage and a corresponding upregulation of EGFP fluorescence, whereas NCE-deficient mice showed a significant loss of Cd4 reporter EGFP mRNA and no detectable EGFP production in any post-selection thymocytes. Discussion This study demonstrates that the canonical enhancer function of coreNCE/E4m is essential for CD4 upregulation following positive selection. The NCE region, with its developmental-stage-specific activity and its known epigenetic regulatory capabilities, ensures faithful lineage commitment to the CD4 lineage.
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Affiliation(s)
- Gregory A. Swan
- Integrative Immunobiology Department, Duke University, Durham, NC, United States
- Biology Department, Davidson College, Davidson, NC, United States
| | - Chika Fujii
- Biology Department, Davidson College, Davidson, NC, United States
| | - Mia E. Guzynski
- Biology Department, Davidson College, Davidson, NC, United States
| | - Sheridan M. Page
- Biology Department, Davidson College, Davidson, NC, United States
| | | | - Yordan P. Penev
- Biology Department, Davidson College, Davidson, NC, United States
| | - Sejiro Littleton
- Integrative Immunobiology Department, Duke University, Durham, NC, United States
- Biology Department, Davidson College, Davidson, NC, United States
| | - Adinda Azzahra
- Biology Department, Davidson College, Davidson, NC, United States
| | - Christine Richardson
- Department of Biological Sciences, University of North Carolina-Charlotte, Charlotte, NC, United States
| | - Sophia D. Sarafova
- Integrative Immunobiology Department, Duke University, Durham, NC, United States
- Biology Department, Davidson College, Davidson, NC, United States
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Golzari-Sorkheh M, Yoganathan K, Chen ELY, Singh J, Zúñiga-Pflücker JC. T Cell Development: From T-Lineage Specification to Intrathymic Maturation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2025; 1471:81-137. [PMID: 40067585 DOI: 10.1007/978-3-031-77921-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2025]
Abstract
T cell development occurs in the thymus in both mice and humans. Upon entry into the thymus, bone marrow-derived blood-borne progenitors receive instructive signals, including Notch signaling, to eliminate their potential to develop into alternative immune lineages while committing to the T cell fate. Upon T-lineage commitment, developing T cells receive further instructional cues to generate different T cell sublineages, which together possess diverse immunological functions to provide host immunity. Over the years, numerous studies have contributed to a greater understanding of key thymic signals that govern T cell differentiation and subset generation. Here, we review these critical signaling factors that govern the different stages of both mouse and human T cell development, while also focusing on the transcriptional changes that mediate T cell identity and diversity.
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Affiliation(s)
- Mahdieh Golzari-Sorkheh
- Department of Immunology, University of Toronto & Sunnybrook Research Institute, Toronto, ON, Canada
| | - Kogulan Yoganathan
- Department of Immunology, University of Toronto & Sunnybrook Research Institute, Toronto, ON, Canada
| | - Edward L Y Chen
- Department of Immunology, University of Toronto & Sunnybrook Research Institute, Toronto, ON, Canada
| | - Jastaranpreet Singh
- Department of Immunology, University of Toronto & Sunnybrook Research Institute, Toronto, ON, Canada
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Baldwin I, Robey EA. Adjusting to self in the thymus: CD4 versus CD8 lineage commitment and regulatory T cell development. J Exp Med 2024; 221:e20230896. [PMID: 38980291 PMCID: PMC11232887 DOI: 10.1084/jem.20230896] [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: 03/22/2024] [Revised: 05/22/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024] Open
Abstract
During thymic development, thymocytes adjust their TCR response based on the strength of their reactivity to self-peptide MHC complexes. This tuning process allows thymocytes with a range of self-reactivities to survive positive selection and contribute to a diverse T cell pool. In this review, we will discuss recent advances in our understanding of how thymocytes tune their responsiveness during positive selection, and we present a "sequential selection" model to explain how MHC specificity influences lineage choice. We also discuss recent evidence for cell type diversity in the medulla and discuss how this heterogeneity may contribute to medullary niches for negative selection and regulatory T cell development.
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Affiliation(s)
- Isabel Baldwin
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ellen A. Robey
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
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6
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Lo WL, Huseby ES. The partitioning of TCR repertoires by thymic selection. J Exp Med 2024; 221:e20230897. [PMID: 39167074 PMCID: PMC11338286 DOI: 10.1084/jem.20230897] [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: 03/04/2024] [Revised: 05/22/2024] [Accepted: 07/09/2024] [Indexed: 08/23/2024] Open
Abstract
αβ T cells are critical components of the adaptive immune system; they maintain tissue and immune homeostasis during health, provide sterilizing immunity after pathogen infection, and are capable of eliminating transformed tumor cells. Fundamental to these distinct functions is the ligand specificity of the unique antigen receptor expressed on each mature T cell (TCR), which endows lymphocytes with the ability to behave in a cell-autonomous, disease context-specific manner. Clone-specific behavioral properties are initially established during T cell development when thymocytes use TCR recognition of major histocompatibility complex (MHC) and MHC-like ligands to instruct survival versus death and to differentiate into a plethora of inflammatory and regulatory T cell lineages. Here, we review the ligand specificity of the preselection thymocyte repertoire and argue that developmental stage-specific alterations in TCR signaling control cross-reactivity and foreign versus self-specificity of T cell sublineages.
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Affiliation(s)
- Wan-Lin Lo
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Eric S Huseby
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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Engesser J, Wang H, Kapffer S, Kaffke A, Peters A, Paust HJ, Geissen M, Krebs CF, Panzer U, Asada N. S1PR1 mediates Th17 cell migration from the thymus to the skin in health and disease. Front Immunol 2024; 15:1473130. [PMID: 39380990 PMCID: PMC11459589 DOI: 10.3389/fimmu.2024.1473130] [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: 07/30/2024] [Accepted: 08/23/2024] [Indexed: 10/10/2024] Open
Abstract
Th17 cells play crucial roles in host defense and the pathogenesis of autoimmune diseases in the skin. While their differentiation mechanisms have been extensively studied, the origin of skin Th17 cells remains unclear. In this study, we analyzed single-cell RNA-sequencing data and identify the presence of Th17 cells in the human thymus. Thymic Th17 cells were characterized by high expression levels of Sphingosine-1-Phosphate Receptor 1 (S1PR1), a receptor crucial for T cell egress from lymphoid tissues. In mice, Th17 cell-specific knockout of S1pr1 resulted in the accumulation of Th17 cells in the thymus and a corresponding decrease in their numbers in the skin. Th17 cells that accumulated in the thymus exhibited a lower IL-17A production capacity compared to those in the skin, indicating that the local environment in the skin is important for maintaining the Th17 cell phenotype. Additionally, using a murine psoriasis model, we demonstrated that Th17 cell-specific knockout of S1pr1 reduced their migration to the inflamed skin, thereby ameliorating disease progression. Collectively, our data suggest that S1PR1 mediates Th17 cell migration from the thymus to the skin, thereby modulating their functional engagement in both homeostatic and inflammatory conditions.
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Affiliation(s)
- Jonas Engesser
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Huiying Wang
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Sonja Kapffer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Kaffke
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Anett Peters
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Hans-Joachim Paust
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Markus Geissen
- Clinic and Polyclinic for Vascular Medicine, University Heart and Vascular Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian F. Krebs
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Ulf Panzer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Nariaki Asada
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg Eppendorf, Hamburg, Germany
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Miao C, Chen Y, Zhang H, Zhao W, Wang C, Ma Z, Zhu S, Hu X. Heterogeneity of lymphocyte subsets in predicting immune checkpoint inhibitor treatment response in advanced lung cancer: an analysis across different pathological types, therapeutic drugs, and age groups. Transl Lung Cancer Res 2024; 13:1264-1276. [PMID: 38973958 PMCID: PMC11225043 DOI: 10.21037/tlcr-24-109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/19/2024] [Indexed: 07/09/2024]
Abstract
Background Immune checkpoint inhibitor (ICI) has become pivotal in the treatment of advanced lung cancer, yet the absence of reliable biomarkers for assessing treatment response poses a significant challenge. This study aims to explore the predictive value of various lymphocyte subsets in different lung cancer subtypes, thus potentially identifying novel biomarkers to improve ICI treatment stratification and outcomes. Methods We conducted a retrospective analysis of 146 stage III or IV lung cancer patients undergoing ICI treatment. The study focused on exploring the relationship between various lymphocyte subsets and the efficacy of ICIs, aiming to determine their predictive value for post-treatment outcomes. Results Subgroup analysis revealed a positive correlation (P=0.01) between lower CD3+CD8+ T lymphocyte levels and treatment response in squamous cell carcinoma patients. However, no significance was observed in lung adenocarcinoma patients. Additionally, the predictive ability of lymphocyte subsets for different immunotherapy drugs varies. In individuals receiving anti-programmed cell death ligand 1 (PD-L1) treatment, a lower CD3+CD8+ T lymphocyte levels is significantly associated with a positive treatment outcome (P=0.002), while there is no difference for programmed death 1 (PD-1) drugs. Among patients under 60, higher expression of CD3+CD4+ T lymphocytes (P=0.03) combined with lower CD3+CD8+ T lymphocyte levels (P=0.006) showed a statistically significant association with improved treatment response. However, in patients aged over 60, no discernible correlation was ascertained between lymphocyte subsets and therapeutic response. Through prognostic analysis, two distinct lymphocyte subsets were identified, both exerting considerable impact on progression-free survival subsequent to ICIs treatment: CD3+CD4+ T lymphocytes [hazard ratio (HR) =0.50, P=0.006] and CD3+CD8+ T lymphocytes (HR =1.78, P=0.02). Conclusions Our findings underscore the significant heterogeneity in the predictive value of distinct lymphocyte subsets for lung cancer patients undergoing ICI treatment. These findings are particularly salient when considering various pathological types, immunotherapeutic agents, and patient age groups.
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Affiliation(s)
- Chuanwang Miao
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Yuanji Chen
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Hao Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Wei Zhao
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Cunliang Wang
- Department of Radiotherapy, Linyi Cancer Hospital, Linyi, China
| | - Zeliang Ma
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Shan Zhu
- Department of Radiation Oncology, Shandong Provincial ENT Hospital, Shandong University, Jinan, China
| | - Xudong Hu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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Steier Z, Kim EJY, Aylard DA, Robey EA. The CD4 Versus CD8 T Cell Fate Decision: A Multiomics-Informed Perspective. Annu Rev Immunol 2024; 42:235-258. [PMID: 38271641 DOI: 10.1146/annurev-immunol-083122-040929] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
The choice of developing thymocytes to become CD8+ cytotoxic or CD4+ helper T cells has been intensely studied, but many of the underlying mechanisms remain to be elucidated. Recent multiomics approaches have provided much higher resolution analysis of gene expression in developing thymocytes than was previously achievable, thereby offering a fresh perspective on this question. Focusing on our recent studies using CITE-seq (cellular indexing of transcriptomes and epitopes) analyses of mouse thymocytes, we present a detailed timeline of RNA and protein expression changes during CD8 versus CD4 T cell differentiation. We also revisit our current understanding of the links between T cell receptor signaling and expression of the lineage-defining transcription factors ThPOK and RUNX3. Finally, we propose a sequential selection model to explain the tight linkage between MHC-I versus MHC-II recognition and T cell lineage choice. This model incorporates key aspects of previously proposed kinetic signaling, instructive, and stochastic/selection models.
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Affiliation(s)
- Zoë Steier
- Department of Bioengineering and Center for Computational Biology, University of California, Berkeley, California, USA
- Graduate Program in Bioengineering, University of California, Berkeley, and University of California, San Francisco, Berkeley and San Francisco, California, USA
- Current affiliation: Institute for Medical Engineering and Science, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard; and Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Esther Jeong Yoon Kim
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Dominik A Aylard
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Ellen A Robey
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
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Liu Z, Li X, Muhammad A, Sun Q, Zhang Q, Wang Y, Wang Y, Ren J, Wang D. PACSIN1 promotes immunosuppression in gastric cancer by degrading MHC-I. Acta Biochim Biophys Sin (Shanghai) 2024; 56:1473-1482. [PMID: 38826133 PMCID: PMC11532212 DOI: 10.3724/abbs.2024059] [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: 01/19/2024] [Accepted: 03/07/2024] [Indexed: 06/04/2024] Open
Abstract
Gastric cancer (GC) is a common gastrointestinal system malignancy. PACSIN1 functions as an oncogene in various cancers. This study aims to investigate the potential of PACSIN1 as a target in GC treatment. Gene expression is determined by RT-qPCR, immunofluorescence staining, and immunohistochemistry assay. FISH is performed to determine the colocalization of PACSIN1 and the major histocompatibility complex (MHC-I). Cytokine release and cell functions are analyzed by flow cytometry. In vivo assays are also conducted. Histological analysis is performed using H&E staining. The results show that PACSIN1 is overexpressed in GC patients, especially in those with immunologically-cold tumors. A high level of PACSIN1 is associated with poor prognosis. PACSIN1 deficiency inhibits autophagy but increases antigen presentation in GC cells. Moreover, PACSIN1 deficiency inhibits the lysosomal fusion and selective autophagy of MHC-I, increases CD8 + T-cell infiltration, and suppresses tumor growth and liver metastasis in vivo. Additionally, PACSIN1 knockout enhances the chemosensitivity of cells to immune checkpoint blockade. In summary, PACSIN1 mediates lysosomal fusion and selective autophagy of MHC-I and suppresses antigen presentation and CD8 + T-cell infiltration, thus inhibiting antitumor immunity in GC.
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Affiliation(s)
- Zhu Liu
- The Yangzhou School of Clinical Medicine of Nanjing Medical UniversityYangzhou225001China
- Northern Jiangsu People’s HospitalYangzhou225001China
- General Surgery Institute of YangzhouYangzhou UniversityYangzhou225001China
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic DiseasesYangzhou225001China
| | - Xin Li
- Northern Jiangsu People’s HospitalYangzhou225001China
- Department of PharmacyClinical Medical CollegeYangzhou UniversityNorthern Jiangsu People’s HospitalYangzhou225001China
| | - Ali Muhammad
- Clinical Medical CollegeYangzhou UniversityYangzhou225001China
- General Surgery Institute of YangzhouYangzhou UniversityYangzhou225001China
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic DiseasesYangzhou225001China
| | - Qiannan Sun
- Northern Jiangsu People’s HospitalYangzhou225001China
- General Surgery Institute of YangzhouYangzhou UniversityYangzhou225001China
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic DiseasesYangzhou225001China
| | - Qi Zhang
- Northern Jiangsu People’s HospitalYangzhou225001China
- General Surgery Institute of YangzhouYangzhou UniversityYangzhou225001China
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic DiseasesYangzhou225001China
| | - Yang Wang
- Clinical Medical CollegeYangzhou UniversityYangzhou225001China
- General Surgery Institute of YangzhouYangzhou UniversityYangzhou225001China
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic DiseasesYangzhou225001China
| | - Yong Wang
- Northern Jiangsu People’s HospitalYangzhou225001China
- General Surgery Institute of YangzhouYangzhou UniversityYangzhou225001China
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic DiseasesYangzhou225001China
| | - Jun Ren
- Clinical Medical CollegeYangzhou UniversityYangzhou225001China
- Northern Jiangsu People’s HospitalYangzhou225001China
- General Surgery Institute of YangzhouYangzhou UniversityYangzhou225001China
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic DiseasesYangzhou225001China
| | - Daorong Wang
- The Yangzhou School of Clinical Medicine of Nanjing Medical UniversityYangzhou225001China
- Clinical Medical CollegeYangzhou UniversityYangzhou225001China
- Northern Jiangsu People’s HospitalYangzhou225001China
- General Surgery Institute of YangzhouYangzhou UniversityYangzhou225001China
- Yangzhou Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic DiseasesYangzhou225001China
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Guérin A, Moncada-Vélez M, Jackson K, Ogishi M, Rosain J, Mancini M, Langlais D, Nunez A, Webster S, Goyette J, Khan T, Marr N, Avery DT, Rao G, Waterboer T, Michels B, Neves E, Iracema Morais C, London J, Mestrallet S, Quartier dit Maire P, Neven B, Rapaport F, Seeleuthner Y, Lev A, Simon AJ, Montoya J, Barel O, Gómez-Rodríguez J, Orrego JC, L’Honneur AS, Soudée C, Rojas J, Velez AC, Sereti I, Terrier B, Marin N, García LF, Abel L, Boisson-Dupuis S, Reis J, Marinho A, Lisco A, Faria E, Goodnow CC, Vasconcelos J, Béziat V, Ma CS, Somech R, Casanova JL, Bustamante J, Franco JL, Tangye SG. Helper T cell immunity in humans with inherited CD4 deficiency. J Exp Med 2024; 221:e20231044. [PMID: 38557723 PMCID: PMC10983808 DOI: 10.1084/jem.20231044] [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: 06/19/2023] [Revised: 01/04/2024] [Accepted: 01/31/2024] [Indexed: 04/04/2024] Open
Abstract
CD4+ T cells are vital for host defense and immune regulation. However, the fundamental role of CD4 itself remains enigmatic. We report seven patients aged 5-61 years from five families of four ancestries with autosomal recessive CD4 deficiency and a range of infections, including recalcitrant warts and Whipple's disease. All patients are homozygous for rare deleterious CD4 variants impacting expression of the canonical CD4 isoform. A shorter expressed isoform that interacts with LCK, but not HLA class II, is affected by only one variant. All patients lack CD4+ T cells and have increased numbers of TCRαβ+CD4-CD8- T cells, which phenotypically and transcriptionally resemble conventional Th cells. Finally, patient CD4-CD8- αβ T cells exhibit intact responses to HLA class II-restricted antigens and promote B cell differentiation in vitro. Thus, compensatory development of Th cells enables patients with inherited CD4 deficiency to acquire effective cellular and humoral immunity against an unexpectedly large range of pathogens. Nevertheless, CD4 is indispensable for protective immunity against at least human papillomaviruses and Trophyrema whipplei.
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Affiliation(s)
- Antoine Guérin
- Garvan Institute of Medical Research, Darlinghurst, Australia
- Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, Australia
| | - Marcela Moncada-Vélez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia UdeA, Medellin, Colombia
| | | | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jérémie Rosain
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Mathieu Mancini
- Department of Human Genetics, McGill University, Montreal, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
- Dahdaleh Institute of Genomic Medicine, McGill Research Centre on Complex Traits, McGill University, Montreal, Canada
| | - David Langlais
- Department of Human Genetics, McGill University, Montreal, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
- Dahdaleh Institute of Genomic Medicine, McGill Research Centre on Complex Traits, McGill University, Montreal, Canada
| | - Andrea Nunez
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Samantha Webster
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Jesse Goyette
- Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Taushif Khan
- Department of Human Immunology, Sidra Medicine, Doha, Qatar
- The Jackson Laboratory, Farmington, CT, USA
| | - Nico Marr
- Department of Human Immunology, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Danielle T. Avery
- Garvan Institute of Medical Research, Darlinghurst, Australia
- Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, Australia
| | - Geetha Rao
- Garvan Institute of Medical Research, Darlinghurst, Australia
- Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, Australia
| | - Tim Waterboer
- Division of Infections and Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Birgitta Michels
- Division of Infections and Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Esmeralda Neves
- Immunology Department—Pathology, University Hospital Center of Porto, Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Cátia Iracema Morais
- Immunology Department—Pathology, University Hospital Center of Porto, Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Jonathan London
- Service of Internal Medicine, Diaconesse-Croix Saint Simon Hospital, Paris, France
| | - Stéphanie Mestrallet
- Department of Internal Medicine and Infectious Diseases, Manchester Hospital, Charleville-Mézières, France
| | - Pierre Quartier dit Maire
- Pediatric Immunology-Hematology and Rheumatology Unit, Necker Hospital for Sick Children, Paris, France
| | - Bénédicte Neven
- Pediatric Immunology-Hematology and Rheumatology Unit, Necker Hospital for Sick Children, Paris, France
| | - Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Atar Lev
- Department of Pediatrics and Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Aviv School of Medicine, Tel Aviv, Israel
| | - Amos J. Simon
- Department of Pediatrics and Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Aviv School of Medicine, Tel Aviv, Israel
| | - Jorge Montoya
- San Vicente de Paul University Hospital, Medellin, Colombia
| | - Ortal Barel
- The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
| | - Julio Gómez-Rodríguez
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Julio C. Orrego
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia UdeA, Medellin, Colombia
| | - Anne-Sophie L’Honneur
- Department of Virology, Paris Cité University and Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Camille Soudée
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Jessica Rojas
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia UdeA, Medellin, Colombia
| | - Alejandra C. Velez
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia UdeA, Medellin, Colombia
| | - Irini Sereti
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin Terrier
- Department of Internal Medicine, Cochin Hospital, Assistance Publique–Hôpitaux de Paris, Paris Cité University, Paris, France
| | - Nancy Marin
- Cellular Immunology and Immunogenetics Group, University of Antioquia UdeA, Medellin, Colombia
| | - Luis F. García
- Cellular Immunology and Immunogenetics Group, University of Antioquia UdeA, Medellin, Colombia
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Joel Reis
- Dermatology Service, University Hospital Center of Porto, Porto, Portugal
| | - Antonio Marinho
- School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- Department of Clinical Immunology, University Hospital Center of Porto, Porto, Portugal
| | - Andrea Lisco
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emilia Faria
- Allergy and Clinical Immunology Department, University Hospital Center of Coimbra, Coimbra, Portugal
| | - Christopher C. Goodnow
- Garvan Institute of Medical Research, Darlinghurst, Australia
- Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, Australia
| | - Julia Vasconcelos
- Immunology Department—Pathology, University Hospital Center of Porto, Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Vivien Béziat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Cindy S. Ma
- Garvan Institute of Medical Research, Darlinghurst, Australia
- Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, Australia
| | - Raz Somech
- Department of Pediatrics and Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Aviv School of Medicine, Tel Aviv, Israel
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Jose Luis Franco
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia UdeA, Medellin, Colombia
| | - Stuart G. Tangye
- Garvan Institute of Medical Research, Darlinghurst, Australia
- Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, Australia
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12
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Hagen RR, Xu C, Koay HF, Konstantinov IE, Berzins SP, Kedzierska K, van de Sandt CE. Methodological optimisation of thymocyte isolation and cryopreservation of human thymus samples. J Immunol Methods 2024; 528:113651. [PMID: 38417671 DOI: 10.1016/j.jim.2024.113651] [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: 01/28/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Premature lymphocytes develop into non-autoreactive, mature naïve CD4+ or CD8+ T cells in the thymus before entering the circulation. However, in-depth characterization of human thymocyte development remains challenging due to limited availability of human thymus samples and the fragile nature of thymocyte populations. Thymocytes often do not survive cryopreservation and thawing procedures, especially the fragile CD4+CD8+ double positive population. It is generally recommended to use fresh human thymus tissue on the day of excision to avoid any biases in thymocyte composition. This hampers the possibility to perform multiple experiments on the same thymus sample. To establish how the thymocyte viability and composition can be maintained, we compared two thymocyte isolation methods used for human and/or mice thymi, three cryopreservation methods in combination with our most gentle thawing technique. Based on our findings we established that fresh human thymi remain viable in cold storage for up to two days post-surgery without compromising thymocyte composition. Thymocytes can be cryopreserved if required, although the CD4+CD8+ double positive populations may be reduced. Our study provides thoroughly optimized methods to study human thymocyte development over a considerable time-frame post-surgery.
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Affiliation(s)
- Ruth R Hagen
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, the University of Melbourne, Parkville, Australia
| | - Calvin Xu
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, the University of Melbourne, Parkville, Australia
| | - Hui-Fern Koay
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, the University of Melbourne, Parkville, Australia
| | - Igor E Konstantinov
- Murdoch Children's Research Institute, Melbourne, Australia; Deparment of Paediatrics, the University of Melbourne, Parkville, Australia; Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, Melbourne, Australia; Cardiothoracic Surgery, Royal Children's Hospital, Melbourne, Australia
| | - Stuart P Berzins
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, the University of Melbourne, Parkville, Australia; Federation University Australia, Ballarat, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, the University of Melbourne, Parkville, Australia
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, the University of Melbourne, Parkville, Australia.
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13
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Li C, Lanasa D, Park JH. Pathways and mechanisms of CD4 +CD8αα + intraepithelial T cell development. Trends Immunol 2024; 45:288-302. [PMID: 38514370 PMCID: PMC11015970 DOI: 10.1016/j.it.2024.02.006] [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: 02/02/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
The mammalian small intestine epithelium harbors a peculiar population of CD4+CD8αα+ T cells that are derived from mature CD4+ T cells through reprogramming of lineage-specific transcription factors. CD4+CD8αα+ T cells occupy a unique niche in T cell biology because they exhibit mixed phenotypes and functional characteristics of both CD4+ helper and CD8+ cytotoxic T cells. The molecular pathways driving their generation are not fully mapped. However, recent studies demonstrate the unique role of the commensal gut microbiota as well as distinct cytokine and chemokine requirements in the differentiation and survival of these cells. We review the established and newly identified factors involved in the generation of CD4+CD8αα+ intraepithelial lymphocytes (IELs) and place them in the context of the molecular machinery that drives their phenotypic and functional differentiation.
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Affiliation(s)
- Can Li
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dominic Lanasa
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jung-Hyun Park
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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14
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Weerakoon H, Mohamed A, Wong Y, Chen J, Senadheera B, Haigh O, Watkins TS, Kazakoff S, Mukhopadhyay P, Mulvenna J, Miles JJ, Hill MM, Lepletier A. Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation. NPJ Syst Biol Appl 2024; 10:21. [PMID: 38418561 PMCID: PMC10901835 DOI: 10.1038/s41540-024-00346-4] [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: 08/03/2023] [Accepted: 01/25/2024] [Indexed: 03/01/2024] Open
Abstract
Engagement of the T cell receptor (TCR) triggers molecular reprogramming leading to the acquisition of specialized effector functions by CD4 helper and CD8 cytotoxic T cells. While transcription factors, chemokines, and cytokines are known drivers in this process, the temporal proteomic and transcriptomic changes that regulate different stages of human primary T cell activation remain to be elucidated. Here, we report an integrative temporal proteomic and transcriptomic analysis of primary human CD4 and CD8 T cells following ex vivo stimulation with anti-CD3/CD28 beads, which revealed major transcriptome-proteome uncoupling. The early activation phase in both CD4 and CD8 T cells was associated with transient downregulation of the mRNA transcripts and protein of the central glucose transport GLUT1. In the proliferation phase, CD4 and CD8 T cells became transcriptionally more divergent while their proteome became more similar. In addition to the kinetics of proteome-transcriptome correlation, this study unveils selective transcriptional and translational metabolic reprogramming governing CD4 and CD8 T cell responses to TCR stimulation. This temporal transcriptome/proteome map of human T cell activation provides a reference map exploitable for future discovery of biomarkers and candidates targeting T cell responses.
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Affiliation(s)
- Harshi Weerakoon
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
- Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Ahmed Mohamed
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Yide Wong
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Jinjin Chen
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | | | - Oscar Haigh
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Thomas S Watkins
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Stephen Kazakoff
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | - Jason Mulvenna
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - John J Miles
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Ailin Lepletier
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.
- Institute for Glycomics, Griffith Univeristy, Gold Coast, QLD, Australia.
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15
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Tai X, Singer A. New insights into developmental fate decisions by autoreactive CD4 thymocytes. Clin Transl Med 2024; 14:e1590. [PMID: 38362613 PMCID: PMC10870014 DOI: 10.1002/ctm2.1590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/17/2024] Open
Affiliation(s)
- Xuguang Tai
- Experimental Immunology Branch, National Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Alfred Singer
- Experimental Immunology Branch, National Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
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16
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Abstract
The thymus is an evolutionarily conserved organ that supports the development of T cells. Not only does the thymic environment support the rearrangement and expression of diverse T cell receptors but also provides a unique niche for the selection of appropriate T cell clones. Thymic selection ensures that the repertoire of available T cells is both useful (being MHC-restricted) and safe (being self-tolerant). The unique antigen-presentation features of the thymus ensure that the display of self-antigens is optimal to induce tolerance to all types of self-tissue. MHC class-specific functions of CD4+ T helper cells, CD8+ killer T cells and CD4+ regulatory T cells are also established in the thymus. Finally, the thymus provides signals for the development of several minor T cell subsets that promote immune and tissue homeostasis. This Review provides an introductory-level overview of our current understanding of the sophisticated thymic selection mechanisms that ensure T cells are useful and safe.
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Affiliation(s)
- K Maude Ashby
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
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17
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Amable L, Ferreira Martins LA, Pierre R, Do Cruseiro M, Chabab G, Sergé A, Kergaravat C, Delord M, Viret C, Jaubert J, Liu C, Karray S, Marie JC, Irla M, Georgiev H, Clave E, Toubert A, Lucas B, Klibi J, Benlagha K. Intrinsic factors and CD1d1 but not CD1d2 expression levels control invariant natural killer T cell subset differentiation. Nat Commun 2023; 14:7922. [PMID: 38040679 PMCID: PMC10692182 DOI: 10.1038/s41467-023-43424-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 11/08/2023] [Indexed: 12/03/2023] Open
Abstract
Invariant natural killer T (NKT) cell subsets are defined based on their cytokine-production profiles and transcription factors. Their distribution is different in C57BL/6 (B6) and BALB/c mice, with a bias for NKT1 and NKT2/NKT17 subsets, respectively. Here, we show that the non-classical class I-like major histocompatibility complex CD1 molecules CD1d2, expressed in BALB/c and not in B6 mice, could not account for this difference. We find however that NKT cell subset distribution is intrinsic to bone marrow derived NKT cells, regardless of syngeneic CD1d-ligand recognition, and that multiple intrinsic factors are likely involved. Finally, we find that CD1d expression levels in combination with T cell antigen receptor signal strength could also influence NKT cell distribution and function. Overall, this study indicates that CD1d-mediated TCR signals and other intrinsic signals integrate to influence strain-specific NKT cell differentiation programs and subset distributions.
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Affiliation(s)
- Ludivine Amable
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), EMiLy, Paris, France
| | | | - Remi Pierre
- Plateforme de recombinaison homologue et de cryoconservation (PRHTEC), Institut Cochin, Université Paris Descartes, Paris, France
| | - Marcio Do Cruseiro
- Plateforme de recombinaison homologue et de cryoconservation (PRHTEC), Institut Cochin, Université Paris Descartes, Paris, France
| | - Ghita Chabab
- Tumor Escape Resistance and Immunity department, Cancer Research Center of Lyon INSERM U1052, CNRS UMR 5286, Centre Léon Bérard, Lyon, France
| | - Arnauld Sergé
- Laboratoire Adhésion Inflammation (LAI), CNRS, INSERM, Aix-Marseille Université, Marseille, France
| | - Camille Kergaravat
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), EMiLy, Paris, France
| | | | - Christophe Viret
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Jean Jaubert
- Mouse Genetics Unit, Institut Pasteur, Paris, France
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, China
| | - Saoussen Karray
- Université Paris Cité, INSERM U976, Institut de Recherche Saint-Louis (IRSL), Hôpital Saint-Louis, Paris, France
| | - Julien C Marie
- Tumor Escape Resistance and Immunity department, Cancer Research Center of Lyon INSERM U1052, CNRS UMR 5286, Centre Léon Bérard, Lyon, France
| | - Magali Irla
- Centre d'Immunologie de Marseille-Luminy (CIML), CNRS, INSERM, Aix-Marseille Université, Marseille, France
| | - Hristo Georgiev
- Institute of immunology, Hannover Medical School, Hannover, Germany
| | - Emmanuel Clave
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), EMiLy, Paris, France
| | - Antoine Toubert
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), EMiLy, Paris, France
| | - Bruno Lucas
- Institut Cochin, Centre National de la Recherche Scientifique UMR8104, INSERM U1016, Université Paris Descartes, Paris, France
| | - Jihene Klibi
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), EMiLy, Paris, France
| | - Kamel Benlagha
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), EMiLy, Paris, France.
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18
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Badr ME, Zhang Z, Tai X, Singer A. CD8 T cell tolerance results from eviction of immature autoreactive cells from the thymus. Science 2023; 382:534-541. [PMID: 37917689 PMCID: PMC11302524 DOI: 10.1126/science.adh4124] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/22/2023] [Indexed: 11/04/2023]
Abstract
CD8 T cell tolerance is thought to result from clonal deletion of autoreactive thymocytes before they differentiate into mature CD8 T cells in the thymus. However, we report that, in mice, CD8 T cell tolerance instead results from premature thymic eviction of immature autoreactive CD8 thymocytes into the periphery, where they differentiate into self-tolerant mature CD8 T cells. Premature thymic eviction is triggered by T cell receptor (TCR)-driven down-regulation of the transcriptional repressor Gfi1, which induces expression of sphingosine-1-phosphate receptor-1 (S1P1) on negatively selected immature CD8 thymocytes. Thus, premature thymic eviction is the basis for CD8 T cell tolerance and is the mechanism responsible for the appearance in the periphery of mature CD8 T cells bearing autoreactive TCRs that are absent from the thymus.
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Affiliation(s)
- Mohamed Elsherif Badr
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhongmei Zhang
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuguang Tai
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alfred Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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19
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Wang S, Liu Y, Sun Q, Zeng B, Liu C, Gong L, Wu H, Chen L, Jin M, Guo J, Gao Z, Huang W. Triple Cross-linked Dynamic Responsive Hydrogel Loaded with Selenium Nanoparticles for Modulating the Inflammatory Microenvironment via PI3K/Akt/NF-κB and MAPK Signaling Pathways. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303167. [PMID: 37740428 PMCID: PMC10625091 DOI: 10.1002/advs.202303167] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/27/2023] [Indexed: 09/24/2023]
Abstract
Modulating the inflammatory microenvironment can inhibit the process of inflammatory diseases (IDs). A tri-cross-linked inflammatory microenvironment-responsive hydrogel with ideal mechanical properties achieves triggerable and sustained drug delivery and regulates the inflammatory microenvironment. Here, this study develops an inflammatory microenvironment-responsive hydrogel (OD-PP@SeNPs) composed of phenylboronic acid grafted polylysine (PP), oxidized dextran (OD), and selenium nanoparticles (SeNPs). The introduction of SeNPs as initiators and nano-fillers into the hydrogel results in extra cross-linking of the polymer network through hydrogen bonding. Based on Schiff base bonds, Phenylboronate ester bonds, and hydrogen bonds, a reactive oxygen species (ROS)/pH dual responsive hydrogel with a triple-network is achieved. The hydrogel has injectable, self-healing, adhesion, outstanding flexibility, suitable swelling capacity, optimal biodegradability, excellent stimuli-responsive active substance release performance, and prominent biocompatibility. Most importantly, the hydrogel with ROS scavenging and pH-regulating ability protects cells from oxidative stress and induces macrophages into M2 polarization to reduce inflammatory cytokines through PI3K/AKT/NF-κB and MAPK pathways, exerting anti-inflammatory effects and reshaping the inflammatory microenvironment, thereby effectively treating typical IDs, including S. aureus infected wound and rheumatoid arthritis in rats. In conclusion, this dynamically responsive injectable hydrogel with a triple-network structure provides an effective strategy to treat IDs, holding great promise in clinical application.
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Affiliation(s)
- Shuangqing Wang
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Beijing Key Laboratory of Drug Delivery Technology and Novel FormulationsDepartment of PharmaceuticsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Key Laboratory of Natural Medicines of the Changbai MountainMinistry of EducationCollege of PharmacyYanbian UniversityYanjiJilin Province133002China
| | - Yanhong Liu
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Beijing Key Laboratory of Drug Delivery Technology and Novel FormulationsDepartment of PharmaceuticsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
| | - Qianwen Sun
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Beijing Key Laboratory of Drug Delivery Technology and Novel FormulationsDepartment of PharmaceuticsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
| | - Bowen Zeng
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Beijing Key Laboratory of Drug Delivery Technology and Novel FormulationsDepartment of PharmaceuticsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
| | - Chao Liu
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Beijing Key Laboratory of Drug Delivery Technology and Novel FormulationsDepartment of PharmaceuticsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
| | - Liming Gong
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Beijing Key Laboratory of Drug Delivery Technology and Novel FormulationsDepartment of PharmaceuticsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
| | - Hao Wu
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Beijing Key Laboratory of Drug Delivery Technology and Novel FormulationsDepartment of PharmaceuticsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Key Laboratory of Natural Medicines of the Changbai MountainMinistry of EducationCollege of PharmacyYanbian UniversityYanjiJilin Province133002China
| | - Liqing Chen
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Beijing Key Laboratory of Drug Delivery Technology and Novel FormulationsDepartment of PharmaceuticsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
| | - Mingji Jin
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Beijing Key Laboratory of Drug Delivery Technology and Novel FormulationsDepartment of PharmaceuticsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
| | - Jianpeng Guo
- Key Laboratory of Natural Medicines of the Changbai MountainMinistry of EducationCollege of PharmacyYanbian UniversityYanjiJilin Province133002China
| | - Zhonggao Gao
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Beijing Key Laboratory of Drug Delivery Technology and Novel FormulationsDepartment of PharmaceuticsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Key Laboratory of Natural Medicines of the Changbai MountainMinistry of EducationCollege of PharmacyYanbian UniversityYanjiJilin Province133002China
| | - Wei Huang
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
- Beijing Key Laboratory of Drug Delivery Technology and Novel FormulationsDepartment of PharmaceuticsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100050China
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20
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Steier Z, Aylard DA, McIntyre LL, Baldwin I, Kim EJY, Lutes LK, Ergen C, Huang TS, Robey EA, Yosef N, Streets A. Single-cell multiomic analysis of thymocyte development reveals drivers of CD4 + T cell and CD8 + T cell lineage commitment. Nat Immunol 2023; 24:1579-1590. [PMID: 37580604 PMCID: PMC10457207 DOI: 10.1038/s41590-023-01584-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 07/12/2023] [Indexed: 08/16/2023]
Abstract
The development of CD4+ T cells and CD8+ T cells in the thymus is critical to adaptive immunity and is widely studied as a model of lineage commitment. Recognition of self-peptide major histocompatibility complex (MHC) class I or II by the T cell antigen receptor (TCR) determines the CD8+ or CD4+ T cell lineage choice, respectively, but how distinct TCR signals drive transcriptional programs of lineage commitment remains largely unknown. Here we applied CITE-seq to measure RNA and surface proteins in thymocytes from wild-type and T cell lineage-restricted mice to generate a comprehensive timeline of cell states for each T cell lineage. These analyses identified a sequential process whereby all thymocytes initiate CD4+ T cell lineage differentiation during a first wave of TCR signaling, followed by a second TCR signaling wave that coincides with CD8+ T cell lineage specification. CITE-seq and pharmaceutical inhibition experiments implicated a TCR-calcineurin-NFAT-GATA3 axis in driving the CD4+ T cell fate. Our data provide a resource for understanding cell fate decisions and implicate a sequential selection process in guiding lineage choice.
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Affiliation(s)
- Zoë Steier
- University of California, Berkeley, Department of Bioengineering, Berkeley, CA, USA
- UC Berkeley - UCSF Graduate Program in Bioengineering, Berkeley and San Francisco, CA, USA
- University of California, Berkeley, Center for Computational Biology, Berkeley, CA, USA
- Massachusetts Institute of Technology, Institute for Medical Engineering and Science, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Dominik A Aylard
- University of California, Berkeley, Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, Berkeley, CA, USA
| | - Laura L McIntyre
- University of California, Berkeley, Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, Berkeley, CA, USA
| | - Isabel Baldwin
- University of California, Berkeley, Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, Berkeley, CA, USA
| | - Esther Jeong Yoon Kim
- University of California, Berkeley, Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, Berkeley, CA, USA
| | - Lydia K Lutes
- University of California, Berkeley, Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, Berkeley, CA, USA
| | - Can Ergen
- University of California, Berkeley, Center for Computational Biology, Berkeley, CA, USA
- University of California, Berkeley, Department of Electrical Engineering and Computer Sciences, Berkeley, CA, USA
| | | | - Ellen A Robey
- University of California, Berkeley, Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, Berkeley, CA, USA.
| | - Nir Yosef
- University of California, Berkeley, Center for Computational Biology, Berkeley, CA, USA.
- University of California, Berkeley, Department of Electrical Engineering and Computer Sciences, Berkeley, CA, USA.
- Weizmann Institute of Science, Department of Systems Immunology, Rehovot, Israel.
| | - Aaron Streets
- University of California, Berkeley, Department of Bioengineering, Berkeley, CA, USA.
- UC Berkeley - UCSF Graduate Program in Bioengineering, Berkeley and San Francisco, CA, USA.
- University of California, Berkeley, Center for Computational Biology, Berkeley, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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21
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Tai X, Indart A, Rojano M, Guo J, Apenes N, Kadakia T, Craveiro M, Alag A, Etzensperger R, Badr ME, Zhang F, Zhang Z, Mu J, Guinter T, Crossman A, Granger L, Sharrow S, Zhou X, Singer A. How autoreactive thymocytes differentiate into regulatory versus effector CD4 + T cells after avoiding clonal deletion. Nat Immunol 2023; 24:637-651. [PMID: 36959291 PMCID: PMC10063450 DOI: 10.1038/s41590-023-01469-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/14/2023] [Indexed: 03/25/2023]
Abstract
Thymocytes bearing autoreactive T cell receptors (TCRs) are agonist-signaled by TCR/co-stimulatory molecules to either undergo clonal deletion or to differentiate into specialized regulatory T (Treg) or effector T (Teff) CD4+ cells. How these different fates are achieved during development remains poorly understood. We now document that deletion and differentiation are agonist-signaled at different times during thymic selection and that Treg and Teff cells both arise after clonal deletion as alternative lineage fates of agonist-signaled CD4+CD25+ precursors. Disruption of agonist signaling induces CD4+CD25+ precursors to initiate Foxp3 expression and become Treg cells, whereas persistent agonist signaling induces CD4+CD25+ precursors to become IL-2+ Teff cells. Notably, we discovered that transforming growth factor-β induces Foxp3 expression and promotes Treg cell development by disrupting weaker agonist signals and that Foxp3 expression is not induced by IL-2 except under non-physiological in vivo conditions. Thus, TCR signaling disruption versus persistence is a general mechanism of lineage fate determination in the thymus that directs development of agonist-signaled autoreactive thymocytes.
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Affiliation(s)
- Xuguang Tai
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alyssa Indart
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mirelle Rojano
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jie Guo
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Nicolai Apenes
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tejas Kadakia
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marco Craveiro
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amala Alag
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ruth Etzensperger
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mohamed Elsherif Badr
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Flora Zhang
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhongmei Zhang
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jie Mu
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Terry Guinter
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Assiatu Crossman
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Larry Granger
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Susan Sharrow
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xuyu Zhou
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Alfred Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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22
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Michaels YS, Durland LJ, Zandstra PW. Engineering T Cell Development for the Next Generation of Stem Cell-Derived Immunotherapies. GEN BIOTECHNOLOGY 2023; 2:106-119. [PMID: 37928777 PMCID: PMC10624212 DOI: 10.1089/genbio.2023.0008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/31/2023] [Indexed: 11/07/2023]
Abstract
Engineered T cells are at the leading edge of clinical cell therapy. T cell therapies have had a remarkable impact on patient care for a subset of hematological malignancies. This foundation has motivated the development of off-the-shelf engineered cell therapies for a broad range of devastating indications. Achieving this vision will require cost-effective manufacturing of precision cell products capable of addressing multiple process and clinical-design challenges. Pluripotent stem cell (PSC)-derived engineered T cells are emerging as a solution of choice. To unleash the full potential of PSC-derived T cell therapies, the field will require technologies capable of robustly orchestrating the complex series of time- and dose-dependent signaling events needed to recreate functional T cell development in the laboratory. In this article, we review the current state of allogenic T cell therapies, focusing on strategies to generate engineered lymphoid cells from PSCs. We highlight exciting recent progress in this field and outline timely opportunities for advancement with an emphasis on niche engineering and synthetic biology.
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Affiliation(s)
- Yale S. Michaels
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; University of British Columbia, Vancouver, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada; University of British Columbia, Vancouver, Canada
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, Canada; and University of British Columbia, Vancouver, Canada
| | - Lauren J. Durland
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; University of British Columbia, Vancouver, Canada
| | - Peter W. Zandstra
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
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23
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Mørch AM, Schneider F, Jenkins E, Santos AM, Fraser SE, Davis SJ, Dustin ML. The kinase occupancy of T cell coreceptors reconsidered. Proc Natl Acad Sci U S A 2022; 119:e2213538119. [PMID: 36454761 PMCID: PMC9894195 DOI: 10.1073/pnas.2213538119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/01/2022] [Indexed: 12/05/2022] Open
Abstract
The sensitivity of the αβ T cell receptor (TCR) is enhanced by the coreceptors CD4 and CD8αβ, which are expressed primarily by cells of the helper and cytotoxic T cell lineages, respectively. The coreceptors bind to major histocompatibility complex (MHC) molecules and associate intracellularly with the Src-family kinase Lck, which catalyzes TCR phosphorylation during receptor triggering. Although coreceptor/kinase occupancy was initially believed to be high, a recent study suggested that most coreceptors exist in an Lck-free state, and that this low occupancy helps to effect TCR antigen discrimination. Here, using the same method, we found instead that the CD4/Lck interaction was stoichiometric (~100%) and that the CD8αβ/Lck interaction was substantial (~60%). We confirmed our findings in live cells using fluorescence cross-correlation spectroscopy (FCCS) to measure coreceptor/Lck codiffusion in situ. After introducing structurally guided mutations into the intracellular domain of CD4, we used FCCS to also show that stoichiometric coupling to Lck required an amphipathic α-helix present in CD4 but not CD8α. In double-positive cells expressing equal numbers of both coreceptors, but limiting amounts of kinase, CD4 outcompeted CD8αβ for Lck. In T cells, TCR signaling induced CD4/Lck oligomerization but did not affect the high levels of CD4/Lck occupancy. These findings help settle the question of kinase occupancy and suggest that the binding advantages that CD4 has over CD8 could be important when Lck levels are limiting.
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Affiliation(s)
- Alexander M. Mørch
- Kennedy Institute of Rheumatology, University of Oxford, OxfordOX3 7FY, United Kingdom
- Medical Research Council Human Immunology Unit, and Medical Research Council Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, OxfordOX3 9DS, United Kingdom
| | - Falk Schneider
- Translational Imaging Center, University of Southern California, Los Angeles, CA90089
| | - Edward Jenkins
- Medical Research Council Human Immunology Unit, and Medical Research Council Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, OxfordOX3 9DS, United Kingdom
| | - Ana Mafalda Santos
- Medical Research Council Human Immunology Unit, and Medical Research Council Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, OxfordOX3 9DS, United Kingdom
| | - Scott E. Fraser
- Translational Imaging Center, University of Southern California, Los Angeles, CA90089
| | - Simon J. Davis
- Medical Research Council Human Immunology Unit, and Medical Research Council Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, OxfordOX3 9DS, United Kingdom
| | - Michael L. Dustin
- Kennedy Institute of Rheumatology, University of Oxford, OxfordOX3 7FY, United Kingdom
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24
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MacDonald KN, Salim K, Levings MK. Manufacturing next-generation regulatory T-cell therapies. Curr Opin Biotechnol 2022; 78:102822. [PMID: 36332342 DOI: 10.1016/j.copbio.2022.102822] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/11/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022]
Abstract
Regulatory T-cell (Treg) therapy has shown promise in treating autoimmune diseases, transplant rejection, or graft-versus-host disease in early clinical trials. These trials have demonstrated that cell therapy using polyclonal Tregs is feasible and safe, however, the field has been limited by the lack of polyclonal cell specificity and consequent large cell numbers required, and the difficulty in generating autologous products for some patients. Thus, the field is moving toward 'next generation' Treg cell therapies that include genetic modification strategies to engineer specificity and/or modify function, as well as methods to generate Tregs in vitro. In this review, we describe how genetic modification of Tregs using viral transduction or gene editing may be incorporated into Treg manufacturing protocols. We also describe how Tregs may be generated via FOXP3 gene editing or overexpression, or by differentiation from pluripotent stem cells. The application of these various types of engineered Tregs is discussed.
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Affiliation(s)
- Katherine N MacDonald
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Kevin Salim
- BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Megan K Levings
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Surgery, University of British Columbia, Vancouver, BC, Canada.
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25
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Clonal dynamics underlying the skewed CD4/CD8 ratio of mouse thymocytes revealed by TCR-independent barcoding. Commun Biol 2022; 5:911. [PMID: 36064961 PMCID: PMC9445074 DOI: 10.1038/s42003-022-03870-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
T cell differentiation in the thymus generates CD4+ helper and cytotoxic CD8+ cells as the two principal T cell lineages. Curiously, at the end of this complex selection process, CD4+ cells invariably outnumber CD8+ cells. Here, we examine the dynamics of repertoire formation and the emergence of the skewed CD4/CD8 ratio using high-resolution endogenous CRISPR/Cas9 barcoding that indelibly marks immature T cells at the DN2/DN3 pre-TCR stage. In wild-type mice, greater clone size of CD4+ cells and an intrinsically greater probability of Tcr β clonotypes for pMHCII interactions are major contributors to the skewed CD4/CD8 ratio. Clonal perturbations of thymocyte differentiation following the precocious expression of a rearranged iNKT invariant TCR α chain are due to loss of Tcr β clonotypes from the CD4 lineage-committed pre-selection repertoire. The present barcoding scheme offers a novel means to examine the clonal dynamics of lymphocyte differentiation orthogonal to that using TCR clonotypes. CRSIPR-mediated barcoding of pre-TCR-expressing T cells is used to investigate the clonal dynamics of thymic T cells and reveals new fundamental understanding of how the skewed CD4/CD8 ratio arises during thymic selection.
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26
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Damen H, Tebid C, Viens M, Roy DC, Dave VP. Negative Regulation of Zap70 by Lck Forms the Mechanistic Basis of Differential Expression in CD4 and CD8 T Cells. Front Immunol 2022; 13:935367. [PMID: 35860252 PMCID: PMC9289233 DOI: 10.3389/fimmu.2022.935367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/07/2022] [Indexed: 11/24/2022] Open
Abstract
Lck and Zap70, two non-receptor tyrosine kinases, play a crucial role in the regulation of membrane proximal TCR signaling critical for thymic selection, CD4/CD8 lineage choice and mature T cell function. Signal initiation upon TCR/CD3 and peptide/MHC interaction induces Lck-mediated phosphorylation of CD3 ITAMs. This is necessary for Zap70 recruitment and its phosphorylation by Lck leading to full Zap70 activation. In its native state Zap70 maintains a closed conformation creating an auto-inhibitory loop, which is relieved by Lck-mediated phosphorylation of Y315/Y319. Zap70 is differentially expressed in thymic subsets and mature T cells with CD8 T cells expressing the highest amount compared to CD4 T cells. However, the mechanistic basis of differential Zap70 expression in thymic subsets and mature T cells is not well understood. Here, we show that Zap70 is degraded relatively faster in DP and mature CD4 T cells compared to CD8 T cells, and inversely correlated with relative level of activated Zap70. Importantly, we found that Zap70 expression is negatively regulated by Lck activity: augmented Lck activity resulting in severe diminution in total Zap70. Moreover, Lck-mediated phosphorylation of Y315/Y319 was essential for Zap70 degradation. Together, these data shed light on the underlying mechanism of Lck-mediated differential modulation of Zap70 expression in thymic subsets and mature T cells.
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Affiliation(s)
- Hassan Damen
- Institute for Hematology-Oncology, Cell and Gene Therapy, Hopital Maisonneuve-Rosemont Research Center, Montreal, QC, Canada
| | - Christian Tebid
- Institute for Hematology-Oncology, Cell and Gene Therapy, Hopital Maisonneuve-Rosemont Research Center, Montreal, QC, Canada
| | - Melissa Viens
- Institute for Hematology-Oncology, Cell and Gene Therapy, Hopital Maisonneuve-Rosemont Research Center, Montreal, QC, Canada
| | - Denis-Claude Roy
- Institute for Hematology-Oncology, Cell and Gene Therapy, Hopital Maisonneuve-Rosemont Research Center, Montreal, QC, Canada
- Department of Medicine, University of Montreal, Montreal, QC, Canada
- *Correspondence: Denis-Claude Roy, ; Vibhuti P. Dave,
| | - Vibhuti P. Dave
- Institute for Hematology-Oncology, Cell and Gene Therapy, Hopital Maisonneuve-Rosemont Research Center, Montreal, QC, Canada
- *Correspondence: Denis-Claude Roy, ; Vibhuti P. Dave,
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27
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Vogt N. FlipFlop of the T cell immune system. Nat Methods 2022; 19:781. [PMID: 35804242 DOI: 10.1038/s41592-022-01555-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Signal length not strength guides T cell fate. Nat Rev Immunol 2022; 22:407. [DOI: 10.1038/s41577-022-00736-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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