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Le HN, de Freitas MV, Antunes DA. Strengths and limitations of web servers for the modeling of TCRpMHC complexes. Comput Struct Biotechnol J 2024; 23:2938-2948. [PMID: 39104710 PMCID: PMC11298609 DOI: 10.1016/j.csbj.2024.06.028] [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: 03/31/2024] [Revised: 06/22/2024] [Accepted: 06/23/2024] [Indexed: 08/07/2024] Open
Abstract
Cellular immunity relies on the ability of a T-cell receptor (TCR) to recognize a peptide (p) presented by a class I major histocompatibility complex (MHC) receptor on the surface of a cell. The TCR-peptide-MHC (TCRpMHC) interaction is a crucial step in activating T-cells, and the structural characteristics of these molecules play a significant role in determining the specificity and affinity of this interaction. Hence, obtaining 3D structures of TCRpMHC complexes offers valuable insights into various aspects of cellular immunity and can facilitate the development of T-cell-based immunotherapies. Here, we aimed to compare three popular web servers for modeling the structures of TCRpMHC complexes, namely ImmuneScape (IS), TCRpMHCmodels, and TCRmodel2, to examine their strengths and limitations. Each method employs a different modeling strategy, including docking, homology modeling, and deep learning. The accuracy of each method was evaluated by reproducing the 3D structures of a dataset of 87 TCRpMHC complexes with experimentally determined crystal structures available on the Protein Data Bank (PDB). All selected structures were limited to human MHC alleles, presenting a diverse set of peptide ligands. A detailed analysis of produced models was conducted using multiple metrics, including Root Mean Square Deviation (RMSD) and standardized assessments from CAPRI and DockQ. Special attention was given to the complementarity-determining region (CDR) loops of the TCRs and to the peptide ligands, which define most of the unique features and specificity of a given TCRpMHC interaction. Our study provides an optimistic view of the current state-of-the-art for TCRpMHC modeling but highlights some remaining challenges that must be addressed in order to support the future application of these tools for TCR engineering and computer-aided design of TCR-based immunotherapies.
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Affiliation(s)
- Hoa Nhu Le
- University of Houston, Departments of Biology and Biochemistry, Houston, 77204, TX, USA
| | | | - Dinler Amaral Antunes
- University of Houston, Departments of Biology and Biochemistry, Houston, 77204, TX, USA
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2
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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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3
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T. RR, Demerdash ONA, Smith JC. TCR-H: explainable machine learning prediction of T-cell receptor epitope binding on unseen datasets. Front Immunol 2024; 15:1426173. [PMID: 39221256 PMCID: PMC11361934 DOI: 10.3389/fimmu.2024.1426173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
Artificial-intelligence and machine-learning (AI/ML) approaches to predicting T-cell receptor (TCR)-epitope specificity achieve high performance metrics on test datasets which include sequences that are also part of the training set but fail to generalize to test sets consisting of epitopes and TCRs that are absent from the training set, i.e., are 'unseen' during training of the ML model. We present TCR-H, a supervised classification Support Vector Machines model using physicochemical features trained on the largest dataset available to date using only experimentally validated non-binders as negative datapoints. TCR-H exhibits an area under the curve of the receiver-operator characteristic (AUC of ROC) of 0.87 for epitope 'hard splitting' (i.e., on test sets with all epitopes unseen during ML training), 0.92 for TCR hard splitting and 0.89 for 'strict splitting' in which neither the epitopes nor the TCRs in the test set are seen in the training data. Furthermore, we employ the SHAP (Shapley additive explanations) eXplainable AI (XAI) method for post hoc interrogation to interpret the models trained with different hard splits, shedding light on the key physiochemical features driving model predictions. TCR-H thus represents a significant step towards general applicability and explainability of epitope:TCR specificity prediction.
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Affiliation(s)
- Rajitha Rajeshwar T.
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Omar N. A. Demerdash
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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4
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Gu R, Pan J, Awan MUN, Sun X, Yan F, Bai L, Bai J. The major histocompatibility complex participates in Parkinson's disease. Pharmacol Res 2024; 203:107168. [PMID: 38583689 DOI: 10.1016/j.phrs.2024.107168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 03/23/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease characterized by progressive loss of dopaminergic neurons in the substantia nigra and the aggregation of alpha-synuclein (α-syn). The central nervous system (CNS) has previously been considered as an immune-privileged area. However, studies have shown that the immune responses are involved in PD. The major histocompatibility complex (MHC) presents antigens from antigen-presenting cells (APCs) to T lymphocytes, immune responses will be induced. MHCs are expressed in microglia, astrocytes, and dopaminergic neurons. Single nucleotide polymorphisms in MHC are related to the risk of PD. The aggregated α-syn triggers the expression of MHCs by activating glia cells. CD4+ and CD8+ T lymphocytes responses and microglia activation are detected in brains of PD patients. In addiction immune responses further increase blood-brain barrier (BBB) permeability and T cell infiltration in PD. Thus, MHCs are involved in PD through participating in immune and inflammatory responses.
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Affiliation(s)
- Rou Gu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Jianyu Pan
- Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Maher Un Nisa Awan
- Medical School, Kunming University of Science and Technology, Kunming 650500, China; Department of Neurology, The Affiliated Hospital of Yunnan University, Kunming 650500, China
| | - Xiaowei Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Fang Yan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Liping Bai
- Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Jie Bai
- Medical School, Kunming University of Science and Technology, Kunming 650500, China.
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5
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Yin R, Melton S, Huseby ES, Kardar M, Chakraborty AK. How persistent infection overcomes peripheral tolerance mechanisms to cause T cell-mediated autoimmune disease. Proc Natl Acad Sci U S A 2024; 121:e2318599121. [PMID: 38446856 PMCID: PMC10945823 DOI: 10.1073/pnas.2318599121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
T cells help orchestrate immune responses to pathogens, and their aberrant regulation can trigger autoimmunity. Recent studies highlight that a threshold number of T cells (a quorum) must be activated in a tissue to mount a functional immune response. These collective effects allow the T cell repertoire to respond to pathogens while suppressing autoimmunity due to circulating autoreactive T cells. Our computational studies show that increasing numbers of pathogenic peptides targeted by T cells during persistent or severe viral infections increase the probability of activating T cells that are weakly reactive to self-antigens (molecular mimicry). These T cells are easily re-activated by the self-antigens and contribute to exceeding the quorum threshold required to mount autoimmune responses. Rare peptides that activate many T cells are sampled more readily during severe/persistent infections than in acute infections, which amplifies these effects. Experiments in mice to test predictions from these mechanistic insights are suggested.
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Affiliation(s)
- Rose Yin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Samuel Melton
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Eric S. Huseby
- Basic Pathology, Department of Pathology, University of Massachusetts Medical School, Worcester, MA01655
| | - Mehran Kardar
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Arup K. Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
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Zhou Y, Jadlowsky J, Baiduc C, Klattenhoff AW, Chen Z, Bennett AD, Pumphrey NJ, Jakobsen BK, Riley JL. Chimeric antigen receptors enable superior control of HIV replication by rapidly killing infected cells. PLoS Pathog 2023; 19:e1011853. [PMID: 38100526 PMCID: PMC10773964 DOI: 10.1371/journal.ppat.1011853] [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: 08/26/2023] [Revised: 01/08/2024] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Engineered T cells hold great promise to become part of an effective HIV cure strategy, but it is currently unclear how best to redirect T cells to target HIV. To gain insight, we generated engineered T cells using lentiviral vectors encoding one of three distinct HIV-specific T cell receptors (TCRs) or a previously optimized HIV-targeting chimeric antigen receptor (CAR) and compared their functional capabilities. All engineered T cells had robust, antigen-specific polyfunctional cytokine profiles when mixed with artificial antigen-presenting cells. However, only the CAR T cells could potently control HIV replication. TCR affinity enhancement did not augment HIV control but did allow TCR T cells to recognize common HIV escape variants. Interestingly, either altering Nef activity or adding additional target epitopes into the HIV genome bolstered TCR T cell anti-HIV activity, but CAR T cells remained superior in their ability to control HIV replication. To better understand why CAR T cells control HIV replication better than TCR T cells, we performed a time course to determine when HIV-specific T cells were first able to activate Caspase 3 in HIV-infected targets. We demonstrated that CAR T cells recognized and killed HIV-infected targets more rapidly than TCR T cells, which correlates with their ability to control HIV replication. These studies suggest that the speed of target recognition and killing is a key determinant of whether engineered T cell therapies will be effective against infectious diseases.
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Affiliation(s)
- Yuqi Zhou
- Department of Microbiology and Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Julie Jadlowsky
- Department of Microbiology and Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Caitlin Baiduc
- Department of Microbiology and Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alex W. Klattenhoff
- Department of Microbiology and Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhilin Chen
- Department of Microbiology and Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | | | - Bent K. Jakobsen
- Adaptimmune Ltd, Abingdon, United Kingdom
- Immunocore Ltd., Abingdon, United Kingdom
| | - James L. Riley
- Department of Microbiology and Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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7
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He M, Borlak J. A genomic perspective of the aging human and mouse lung with a focus on immune response and cellular senescence. Immun Ageing 2023; 20:58. [PMID: 37932771 PMCID: PMC10626779 DOI: 10.1186/s12979-023-00373-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/12/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND The aging lung is a complex process and influenced by various stressors, especially airborne pathogens and xenobiotics. Additionally, a lifetime exposure to antigens results in structural and functional changes of the lung; yet an understanding of the cell type specific responses remains elusive. To gain insight into age-related changes in lung function and inflammaging, we evaluated 89 mouse and 414 individual human lung genomic data sets with a focus on genes mechanistically linked to extracellular matrix (ECM), cellular senescence, immune response and pulmonary surfactant, and we interrogated single cell RNAseq data to fingerprint cell type specific changes. RESULTS We identified 117 and 68 mouse and human genes linked to ECM remodeling which accounted for 46% and 27%, respectively of all ECM coding genes. Furthermore, we identified 73 and 31 mouse and human genes linked to cellular senescence, and the majority code for the senescence associated secretory phenotype. These cytokines, chemokines and growth factors are primarily secreted by macrophages and fibroblasts. Single-cell RNAseq data confirmed age-related induced expression of marker genes of macrophages, neutrophil, eosinophil, dendritic, NK-, CD4+, CD8+-T and B cells in the lung of aged mice. This included the highly significant regulation of 20 genes coding for the CD3-T-cell receptor complex. Conversely, for the human lung we primarily observed macrophage and CD4+ and CD8+ marker genes as changed with age. Additionally, we noted an age-related induced expression of marker genes for mouse basal, ciliated, club and goblet cells, while for the human lung, fibroblasts and myofibroblasts marker genes increased with age. Therefore, we infer a change in cellular activity of these cell types with age. Furthermore, we identified predominantly repressed expression of surfactant coding genes, especially the surfactant transporter Abca3, thus highlighting remodeling of surfactant lipids with implications for the production of inflammatory lipids and immune response. CONCLUSION We report the genomic landscape of the aging lung and provide a rationale for its growing stiffness and age-related inflammation. By comparing the mouse and human pulmonary genome, we identified important differences between the two species and highlight the complex interplay of inflammaging, senescence and the link to ECM remodeling in healthy but aged individuals.
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Affiliation(s)
- Meng He
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Jürgen Borlak
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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Pospiech M, Tamizharasan M, Wei YC, Kumar AMS, Lou M, Milstein J, Alachkar H. Features of the TCR repertoire associate with patients' clinical and molecular characteristics in acute myeloid leukemia. Front Immunol 2023; 14:1236514. [PMID: 37928542 PMCID: PMC10620936 DOI: 10.3389/fimmu.2023.1236514] [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: 06/07/2023] [Accepted: 09/07/2023] [Indexed: 11/07/2023] Open
Abstract
Background Allogeneic hematopoietic stem cell transplant remains the most effective strategy for patients with high-risk acute myeloid leukemia (AML). Leukemia-specific neoantigens presented by the major histocompatibility complexes (MHCs) are recognized by the T cell receptors (TCR) triggering the graft-versus-leukemia effect. A unique TCR signature is generated by a complex V(D)J rearrangement process to form TCR capable of binding to the peptide-MHC. The generated TCR repertoire undergoes dynamic changes with disease progression and treatment. Method Here we applied two different computational tools (TRUST4 and MIXCR) to extract the TCR sequences from RNA-seq data from The Cancer Genome Atlas (TCGA) and examine the association between features of the TCR repertoire in adult patients with AML and their clinical and molecular characteristics. Results We found that only ~30% of identified TCR CDR3s were shared by the two computational tools. Yet, patterns of TCR associations with patients' clinical and molecular characteristics based on data obtained from either tool were similar. The numbers of unique TCR clones were highly correlated with patients' white blood cell counts, bone marrow blast percentage, and peripheral blood blast percentage. Multivariable regressions of TCRA and TCRB median normalized number of unique clones with mutational status of AML patients using TRUST4 showed significant association of TCRA or TCRB with WT1 mutations, WBC count, %BM blast, and sex (adjusted in TCRB model). We observed a correlation between TCRA/B number of unique clones and the expression of T cells inhibitory signal genes (TIGIT, LAG3, CTLA-4) and foxp3, but not IL2RA, CD69 and TNFRSF9 suggestive of exhausted T cell phenotypes in AML. Conclusion Benchmarking of computational tools is needed to increase the accuracy of the identified clones. The utilization of RNA-seq data enables identification of highly abundant TCRs and correlating these clones with patients' clinical and molecular characteristics. This study further supports the value of high-resolution TCR-Seq analyses to characterize the TCR repertoire in patients.
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Affiliation(s)
- Mateusz Pospiech
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Mukund Tamizharasan
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Department of Computer Science, University of Southern California, Los Angeles, CA, United States
| | - Yu-Chun Wei
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Advaith Maya Sanjeev Kumar
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Department of Computer Science, University of Southern California, Los Angeles, CA, United States
| | - Mimi Lou
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Joshua Milstein
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Houda Alachkar
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States
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Lee DY, Song WH, Lim YS, Lee C, Rajbongshi L, Hwang SY, Kim BS, Lee D, Song YJ, Kim HG, Yoon S. Fish Collagen Peptides Enhance Thymopoietic Gene Expression, Cell Proliferation, Thymocyte Adherence, and Cytoprotection in Thymic Epithelial Cells via Activation of the Nuclear Factor-κB Pathway, Leading to Thymus Regeneration after Cyclophosphamide-Induced Injury. Mar Drugs 2023; 21:531. [PMID: 37888466 PMCID: PMC10608061 DOI: 10.3390/md21100531] [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: 09/19/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023] Open
Abstract
Prolonged thymic involution results in decreased thymopoiesis and thymic output, leading to peripheral T-cell deficiency. Since the thymic-dependent pathway is the only means of generating fully mature T cells, the identification of strategies to enhance thymic regeneration is crucial in developing therapeutic interventions to revert immune suppression in immunocompromised patients. The present study clearly shows that fish collagen peptides (FCPs) stimulate activities of thymic epithelial cells (TECs), including cell proliferation, thymocyte adhesion, and the gene expression of thymopoietic factors such as FGF-7, IGF-1, BMP-4, VEGF-A, IL-7, IL-21, RANKL, LTβ, IL-22R, RANK, LTβR, SDF-1, CCL21, CCL25, CXCL5, Dll1, Dll4, Wnt4, CD40, CD80, CD86, ICAM-1, VCAM-1, FoxN1, leptin, cathepsin L, CK5, and CK8 through the NF-κB signal transduction pathway. Furthermore, our study also revealed the cytoprotective effects of FCPs on TECs against cyclophosphamide-induced cellular injury through the NF-κB signaling pathway. Importantly, FCPs exhibited a significant capability to facilitate thymic regeneration in mice after cyclophosphamide-induced damage via the NF-κB pathway. Taken together, this study sheds light on the role of FCPs in TEC function, thymopoiesis, and thymic regeneration, providing greater insight into the development of novel therapeutic strategies for effective thymus repopulation for numerous clinical conditions in which immune reconstitution is required.
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Affiliation(s)
- Do Young Lee
- Department of Anatomy and Convergence Medical Sciences, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
- Immune Reconstitution Research Center of Medical Research Institute, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
| | - Won Hoon Song
- Immune Reconstitution Research Center of Medical Research Institute, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
- Department of Urology, Pusan National University Yangsan Hospital and Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
| | - Ye Seon Lim
- Department of Anatomy and Convergence Medical Sciences, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
- Immune Reconstitution Research Center of Medical Research Institute, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
| | - Changyong Lee
- Department of Anatomy and Convergence Medical Sciences, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
- Immune Reconstitution Research Center of Medical Research Institute, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
| | - Lata Rajbongshi
- Department of Anatomy and Convergence Medical Sciences, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
- Immune Reconstitution Research Center of Medical Research Institute, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
| | - Seon Yeong Hwang
- Department of Anatomy and Convergence Medical Sciences, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
- Immune Reconstitution Research Center of Medical Research Institute, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
| | - Byoung Soo Kim
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan 626-870, Republic of Korea
| | - Dongjun Lee
- Department of Convergence Medicine, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
| | - Yong Jung Song
- Immune Reconstitution Research Center of Medical Research Institute, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
- Department of Obstetrics and Gynecology, Pusan National University Yangsan Hospital and Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
| | - Hwi-Gon Kim
- Immune Reconstitution Research Center of Medical Research Institute, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
- Department of Obstetrics and Gynecology, Pusan National University Yangsan Hospital and Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
| | - Sik Yoon
- Department of Anatomy and Convergence Medical Sciences, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
- Immune Reconstitution Research Center of Medical Research Institute, Pusan National University College of Medicine, Yangsan 626-870, Republic of Korea
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Quach DH, Lulla P, Rooney CM. Banking on virus-specific T cells to fulfill the need for off-the-shelf cell therapies. Blood 2023; 141:877-885. [PMID: 36574622 PMCID: PMC10023738 DOI: 10.1182/blood.2022016202] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/28/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
Adoptively transferred virus-specific T cells (VSTs) have shown remarkable safety and efficacy for the treatment of virus-associated diseases and malignancies in hematopoietic stem cell transplant (HSCT) recipients, for whom VSTs are derived from the HSCT donor. Autologous VSTs have also shown promise for the treatment of virus-driven malignancies outside the HSCT setting. In both cases, VSTs are manufactured as patient-specific products, and the time required for procurement, manufacture, and release testing precludes their use in acutely ill patients. Further, Good Manufacturing Practices-compliant products are expensive, and failures are common in virus-naive HSCT donors and patient-derived VSTs that are rendered anergic by immunosuppressive tumors. Hence, highly characterized, banked VSTs (B-VSTs) that can be used for multiple unrelated recipients are highly desirable. The major challenges facing B-VSTs result from the inevitable mismatches in the highly polymorphic and immunogenic human leukocyte antigens (HLA) that present internally processed antigens to the T-cell receptor, leading to the requirement for partial HLA matching between the B-VST and recipient. HLA mismatches lead to rapid rejection of allogeneic T-cell products and graft-versus-host disease induced by alloreactive T cells in the infusion product. Here, we summarize the clinical outcomes to date of trials of B-VSTs used for the treatment of viral infections and malignancies and their potential as a platform for chimeric antigen receptors targeting nonviral tumors. We will highlight the properties of VSTs that make them attractive off-the-shelf cell therapies, as well as the challenges that must be overcome before they can become mainstream.
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Affiliation(s)
- David H. Quach
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Premal Lulla
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Cliona M. Rooney
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children's Hospital, Houston, TX
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
- Department of Molecular Virology and Immunology, Baylor College of Medicine, Houston, TX
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Vidard L. 4-1BB and cytokines trigger human NK, γδ T, and CD8 + T cell proliferation and activation, but are not required for their effector functions. Immun Inflamm Dis 2023; 11:e749. [PMID: 36705415 PMCID: PMC9753824 DOI: 10.1002/iid3.749] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 10/11/2022] [Accepted: 10/17/2022] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION This study was designed to compare the costimulatory molecules and cytokines required to trigger the proliferation and activation of natural killer (NK), γδ T, and CD8+ T cells, and gain in-depth insight into the mechanisms shifting tolerance to immunity. METHODS K562-derived artificial antigen-presenting cells (aAPCs); that is, K562 forced to express CD86 and 4-1BBL costimulatory receptors, in the presence of cytokines, were used to mimic dendritic cells (DCs) and provide signals to support the proliferation and activation of NK, γδ T, and CD8+ T cells. RESULTS Three signals are required to trigger optimal proliferation in MART-1-specific CD8+ T cells: activation of T-cell receptors (TCRs) by the major histocompatibility complex (MHC) I/peptide complexes (signal 1); 4-1BB engagement (signal 2); and IL-15 and IL-21 receptor co-signaling (signal 3). NK and γδ T cell proliferation also require three signals, but the precise nature of signal 1 involving cell-to-cell contact was not determined. Once they become effectors, only signal 1 determines the sensitivity or resistance of the target cells to cytolysis by killer lymphocytes. When freshly purified, none had effector functions, except the NK cells, which could be activated by CD16 engagement. CONCLUSIONS Therefore, lymphocytes committed to kill are produced as inactive precursors, and the license to kill is delivered by three signals, allowing for extensive proliferation and effector function acquisition. This data challenges the paradigm of anergy and supports the danger signal theory originally proposed by Polly Matzinger, which states that killer cells are tolerant by default, thereby protecting the mammalian body from autoimmunity.
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Affiliation(s)
- Laurent Vidard
- Department of Immuno‐OncologySanofiVitry‐sur‐SeineFrance
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12
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Mehta NM, Li Y, Patel V, Li W, Morningstar-Kywi N, Pospiech M, Alachkar H, Haworth IS. Prediction of Peptide and TCR CDR3 Loops in Formation of Class I MHC-Peptide-TCR Complexes Using Molecular Models with Solvation. Methods Mol Biol 2023; 2673:273-287. [PMID: 37258921 PMCID: PMC11059237 DOI: 10.1007/978-1-0716-3239-0_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Formation of major histocompatibility (MHC)-peptide-T cell receptor (TCR) complexes is central to initiation of an adaptive immune response. These complexes form through initial stabilization of the MHC fold via binding of a short peptide, and subsequent interaction of the TCR to form a ternary complex, with contacts made predominantly through the complementarity-determining region (CDR) loops of the TCR. Stimulation of an immune response is central to cancer immunotherapy. This approach depends on identification of the appropriate combinations of MHC molecules, peptides, and TCRs to elicit an antitumor immune response. This prediction is a current challenge in computational biochemistry. In this chapter, we introduce a predictive method that involves generation of multiple peptides and TCR CDR 3 loop conformations, solvation of these conformers in the context of the MHC-peptide-TCR ternary complex, extraction of parameters from the generated complexes, and use of an AI model to evaluate the potential for the assembled ternary complex to support an immune response.
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Affiliation(s)
- Nairuti Milan Mehta
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yuhui Li
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Vini Patel
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Wanning Li
- Titus Family Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Noam Morningstar-Kywi
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Mateusz Pospiech
- Titus Family Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Houda Alachkar
- Titus Family Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ian S Haworth
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA.
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13
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Shevyrev DV, Tereshchenko VP, Sennikov SV. The Enigmatic Nature of the TCR-pMHC Interaction: Implications for CAR-T and TCR-T Engineering. Int J Mol Sci 2022; 23:ijms232314728. [PMID: 36499057 PMCID: PMC9740949 DOI: 10.3390/ijms232314728] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
The interaction of the T-cell receptor (TCR) with a peptide in the major histocompatibility complex (pMHC) plays a central role in the adaptive immunity of higher chordates. Due to the high specificity and sensitivity of this process, the immune system quickly recognizes and efficiently responds to the appearance of foreign and altered self-antigens. This is important for ensuring anti-infectious and antitumor immunity, in addition to maintaining self-tolerance. The most common parameter used for assessing the specificity of TCR-pMHC interaction is affinity. This thermodynamic characteristic is widely used not only in various theoretical aspects, but also in practice, for example, in the engineering of various T-cell products with a chimeric (CAR-T) or artificial (TCR-engineered T-cell) antigen receptor. However, increasing data reveal the fact that, in addition to the thermodynamic component, the specificity of antigen recognition is based on the kinetics and mechanics of the process, having even greater influence on the selectivity of the process and T lymphocyte activation than affinity. Therefore, the kinetic and mechanical aspects of antigen recognition should be taken into account when designing artificial antigen receptors, especially those that recognize antigens in the MHC complex. This review describes the current understanding of the nature of the TCR-pMHC interaction, in addition to the thermodynamic, kinetic, and mechanical principles underlying the specificity and high sensitivity of this interaction.
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Affiliation(s)
- D. V. Shevyrev
- Laboratory of molecular Immunology, Research Institute for Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
- Center for Cell Technology and Immunology, Sirius University of Science and Technology, 354340 Sochi, Russia
- Correspondence: ; Tel.: +7-9231345505
| | - V. P. Tereshchenko
- Laboratory of molecular Immunology, Research Institute for Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
- Center for Cell Technology and Immunology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - S. V. Sennikov
- Laboratory of molecular Immunology, Research Institute for Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
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14
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Sonigra A, Nel HJ, Wehr P, Ramnoruth N, Patel S, van Schie KA, Bladen MW, Mehdi AM, Tesiram J, Talekar M, Rossjohn J, Reid HH, Stuurman FE, Roberts H, Vecchio P, Gourley I, Rigby M, Becart S, Toes RE, Scherer HU, Lê Cao KA, Campbell K, Thomas R. Randomized phase I trial of antigen-specific tolerizing immunotherapy with peptide/calcitriol liposomes in ACPA+ rheumatoid arthritis. JCI Insight 2022; 7:e160964. [PMID: 36278483 PMCID: PMC9714780 DOI: 10.1172/jci.insight.160964] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/12/2022] [Indexed: 10/11/2023] Open
Abstract
BACKGROUNDAntigen-specific regulation of autoimmune disease is a major goal. In seropositive rheumatoid arthritis (RA), T cell help to autoreactive B cells matures the citrullinated (Cit) antigen-specific immune response, generating RA-specific V domain glycosylated anti-Cit protein antibodies (ACPA VDG) before arthritis onset. Low or escalating antigen administration under "sub-immunogenic" conditions favors tolerance. We explored safety, pharmacokinetics, and immunological and clinical effects of s.c. DEN-181, comprising liposomes encapsulating self-peptide collagen II259-273 (CII) and NF-κB inhibitor 1,25-dihydroxycholecalciferol.METHODSA double-blind, placebo-controlled, exploratory, single-ascending-dose, phase I trial assessed the impact of low, medium, and high DEN-181 doses on peripheral blood CII-specific and bystander Cit64vimentin59-71-specific (Cit-Vim-specific) autoreactive T cell responses, cytokines, and ACPA in 17 HLA-DRB1*04:01+ or *01:01+ ACPA+ RA patients on methotrexate.RESULTSDEN-181 was well tolerated. Relative to placebo and normalized to baseline values, Cit-Vim-specific T cells decreased in patients administered medium and high doses of DEN-181. Relative to placebo, percentage of CII-specific programmed cell death 1+ T cells increased within 28 days of DEN-181. Exploratory analysis in DEN-181-treated patients suggested improved RA disease activity was associated with expansion of CII-specific and Cit-Vim-specific T cells; reduction in ACPA VDG, memory B cells, and inflammatory myeloid populations; and enrichment in CCR7+ and naive T cells. Single-cell sequencing identified T cell transcripts associated with tolerogenic TCR signaling and exhaustion after low or medium doses of DEN-181.CONCLUSIONThe safety and immunomodulatory activity of low/medium DEN-181 doses provide rationale to further assess antigen-specific immunomodulatory therapy in ACPA+ RA.TRIAL REGISTRATIONAnzctr.org.au identifier ACTRN12617001482358, updated September 8, 2022.FUNDINGInnovative Medicines Initiative 2 Joint Undertaking (grant agreement 777357), supported by European Union's Horizon 2020 research and innovation programme and European Federation of Pharmaceutical Industries and Associations; Arthritis Queensland; National Health and Medical Research Council (NHMRC) Senior Research Fellowship; and NHMRC grant 2008287.
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Affiliation(s)
- Amee Sonigra
- Department of Rheumatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Hendrik J Nel
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Pascale Wehr
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Nishta Ramnoruth
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Swati Patel
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Karin A van Schie
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Maxwell W Bladen
- Melbourne Integrative Genomics and School of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia
| | - Ahmed M Mehdi
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Joanne Tesiram
- Department of Rheumatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Meghna Talekar
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Hugh H Reid
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Frederik E Stuurman
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
| | - Helen Roberts
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
- Dendright Pty Ltd, Brisbane, Queensland, Australia
| | - Phillip Vecchio
- Department of Rheumatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Ian Gourley
- Immunology Clinical Development, Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Mark Rigby
- Immunology Clinical Development, Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Stephane Becart
- Discovery Immunology, Janssen Research & Development, LLC, La Jolla, California, USA
| | - Rene Em Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Hans Ulrich Scherer
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics and School of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia
| | - Kim Campbell
- Immunology Translational Medicine, Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Ranjeny Thomas
- University of Queensland Diamantina Institute, the University of Queensland, Woolloongabba, Queensland, Australia
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15
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T. RR, Smith JC. Structural patterns in class 1 major histocompatibility complex‐restricted nonamer peptide binding to T‐cell receptors. Proteins 2022; 90:1645-1654. [DOI: 10.1002/prot.26343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/12/2022] [Accepted: 03/27/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Rajitha Rajeshwar T.
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville Tennessee USA
- UT/ORNL Center for Molecular Biophysics Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Jeremy C. Smith
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville Tennessee USA
- UT/ORNL Center for Molecular Biophysics Oak Ridge National Laboratory Oak Ridge Tennessee USA
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16
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Abstract
Exosomes are a type of extracellular vesicles secreted by cells in normal or pathological conditions for cell-cell communication. With immunomodulatory characteristics and potential therapeutic properties, immune-cell-derived exosomes play an important role in cancer therapy. They express various antigens on their surface, which can be employed for antigen presentation, immunological activation, and metabolic regulation, leading to the killing of cancerous cells. In addition, immune-cell-derived exosomes have received extensive attention as a drug delivery platform in effective antitumor therapy due to their excellent biocompatibility, low immunogenicity, and high loading capacity. In this review, the biological and therapeutic characteristics of immune-cell-derived exosomes are comprehensively outlined. The antitumor mechanism of exosomes secreted by immune cells, including macrophages, dendritic cells, T cells, B cells, and natural killer cells, are systematically summarized. Moreover, the applications of immune-cell-derived exosomes as nanocarriers to transport antitumor agents (chemotherapeutic drugs, genes, proteins, etc.) are discussed. More importantly, the existing challenges of immune-cell-derived exosomes are pointed out, and their antitumor potentials are also discussed.
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Affiliation(s)
- Yongmei Zhao
- School of Pharmacy, Nantong University, Nantong 226019, China
| | - Tianqing Liu
- NICM Health Research Institute, Western Sydney University, Westmead, New South Wales 2145, Australia
| | - Mengjiao Zhou
- School of Pharmacy, Nantong University, Nantong 226019, China
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17
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Kästle M, Merten C, Hartig R, Plaza-Sirvent C, Schmitz I, Bommhardt U, Schraven B, Simeoni L. Type of PaperY192 within the SH2 Domain of Lck Regulates TCR Signaling Downstream of PLC-γ1 and Thymic Selection. Int J Mol Sci 2022; 23:ijms23137271. [PMID: 35806279 PMCID: PMC9267008 DOI: 10.3390/ijms23137271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023] Open
Abstract
Signaling via the TCR, which is initiated by the Src-family tyrosine kinase Lck, is crucial for the determination of cell fates in the thymus. Because of its pivotal role, ablation of Lck results in a profound block of T-cell development. Here, we show that, in addition to its well-known function in the initiation of TCR signaling, Lck also acts at a more downstream level. This novel function of Lck is determined by the tyrosine residue (Y192) located in its SH2 domain. Thymocytes from knock-in mice expressing a phosphomimetic Y192E mutant of Lck initiate TCR signaling upon CD3 cross-linking up to the level of PLC-γ1 phosphorylation. However, the activation of downstream pathways including Ca2+ influx and phosphorylation of Erk1/2 are impaired. Accordingly, positive and negative selections are blocked in LckY192E knock-in mice. Collectively, our data indicate that Lck has a novel function downstream of PLCγ-1 in the regulation of thymocyte differentiation and selection.
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Affiliation(s)
- Matthias Kästle
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (M.K.); (C.M.); (R.H.); (C.P.-S.); (I.S.); (U.B.)
| | - Camilla Merten
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (M.K.); (C.M.); (R.H.); (C.P.-S.); (I.S.); (U.B.)
| | - Roland Hartig
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (M.K.); (C.M.); (R.H.); (C.P.-S.); (I.S.); (U.B.)
| | - Carlos Plaza-Sirvent
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (M.K.); (C.M.); (R.H.); (C.P.-S.); (I.S.); (U.B.)
- Department of Molecular Immunology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Ingo Schmitz
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (M.K.); (C.M.); (R.H.); (C.P.-S.); (I.S.); (U.B.)
- Department of Molecular Immunology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Ursula Bommhardt
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (M.K.); (C.M.); (R.H.); (C.P.-S.); (I.S.); (U.B.)
- Health Campus Immunology, Infectiology and Inflammation (GC-I3), Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Burkhart Schraven
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (M.K.); (C.M.); (R.H.); (C.P.-S.); (I.S.); (U.B.)
- Health Campus Immunology, Infectiology and Inflammation (GC-I3), Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Correspondence: (B.S.); (L.S.)
| | - Luca Simeoni
- Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany; (M.K.); (C.M.); (R.H.); (C.P.-S.); (I.S.); (U.B.)
- Health Campus Immunology, Infectiology and Inflammation (GC-I3), Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Correspondence: (B.S.); (L.S.)
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18
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Tseng CY, Wang WX, Douglas TR, Chou LYT. Engineering DNA Nanostructures to Manipulate Immune Receptor Signaling and Immune Cell Fates. Adv Healthc Mater 2022; 11:e2101844. [PMID: 34716686 DOI: 10.1002/adhm.202101844] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/14/2021] [Indexed: 12/19/2022]
Abstract
Immune cells sense, communicate, and logically integrate a multitude of environmental signals to make important cell-fate decisions and fulfill their effector functions. These processes are initiated and regulated by a diverse array of immune receptors and via their dynamic spatiotemporal organization upon ligand binding. Given the widespread relevance of the immune system to health and disease, there have been significant efforts toward understanding the biophysical principles governing immune receptor signaling and activation, as well as the development of biomaterials which exploit these principles for therapeutic immune engineering. Here, how advances in the field of DNA nanotechnology constitute a growing toolbox for further pursuit of these endeavors is discussed. Key cellular players involved in the induction of immunity against pathogens or diseased cells are first summarized. How the ability to design DNA nanostructures with custom shapes, dynamics, and with site-specific incorporation of diverse guests can be leveraged to manipulate the signaling pathways that regulate these processes is then presented. It is followed by highlighting emerging applications of DNA nanotechnology at the crossroads of immune engineering, such as in vitro reconstitution platforms, vaccines, and adjuvant delivery systems. Finally, outstanding questions that remain for further advancing immune-modulatory DNA nanodevices are outlined.
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Affiliation(s)
- Chung Yi Tseng
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Wendy Xueyi Wang
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Travis Robert Douglas
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Leo Y. T. Chou
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
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19
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Liang W, Wang F. Characterization of Mouse CD4 TCR and Its Targeting Antigen. Methods Mol Biol 2022; 2574:221-232. [PMID: 36087204 DOI: 10.1007/978-1-0716-2712-9_10] [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] [Indexed: 06/15/2023]
Abstract
The initial step of activation and differentiation of naïve CD4+ T cells is the TCR-antigenic stimulation. The specific antigen peptides (>11 residues) are presented by the class II MHC (MHC II) protein which expresses professional antigen-presenting cells (APCs). To recognize various peptides and highly polymorphic MHC molecules, a diverse TCR repertoire is achieved through random V(D)J rearrangement. Following TCR initiation, naive CD4+ T cells proliferate and differentiate into one of the lineages of T helper (Th) cells, including Th1, Th2, Th17, iTreg, and some new subsets, as defined by the signatures of functional cytokines. In this chapter, we provide a series of methods to identify antigens for a specific TCR in vitro and also track the dynamics of the specific TCR-expressing T cell in vivo.
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Affiliation(s)
- Wenhua Liang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Research Center of Translational Medicine, Shanghai Children's Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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20
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Ashouri JF, Lo W, Nguyen TTT, Shen L, Weiss A. ZAP70, too little, too much can lead to autoimmunity*. Immunol Rev 2021; 307:145-160. [PMID: 34923645 PMCID: PMC8986586 DOI: 10.1111/imr.13058] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/05/2021] [Indexed: 12/21/2022]
Abstract
Establishing both central and peripheral tolerance requires the appropriate TCR signaling strength to discriminate self‐ from agonist‐peptide bound to self MHC molecules. ZAP70, a cytoplasmic tyrosine kinase, directly interacts with the TCR complex and plays a central and requisite role in TCR signaling in both thymocytes and peripheral T cells. By studying ZAP70 hypomorphic mutations in mice and humans with a spectrum of hypoactive or hyperactive activities, we have gained insights into mechanisms of central and peripheral tolerance. Interestingly, both hypoactive and hyperactive ZAP70 can lead to the development of autoimmune diseases, albeit through distinct mechanisms. Immature thymocytes and mature T cells rely on normal ZAP70 function to complete their development in the thymus and to modulate T cell responses in the periphery. Hypoactive ZAP70 function compromises key developmental checkpoints required to establish central tolerance, allowing thymocytes with potentially self‐reactive TCRs a greater chance to escape negative selection. Such ‘forbidden clones’ may escape into the periphery and may pose a greater risk for autoimmune disease development since they may not engage negative regulatory mechanisms as effectively. Hyperactive ZAP70 enhances thymic negative selection but some thymocytes will, nonetheless, escape negative selection and have greater sensitivity to weak and self‐ligands. Such cells must be controlled by mechanisms involved in anergy, expansion of Tregs, and upregulation of inhibitory receptors or signaling molecules. However, such potentially autoreactive cells may still be able to escape control by peripheral negative regulatory constraints. Consistent with findings in Zap70 mutants, the signaling defects in at least one ZAP70 substrate, LAT, can also lead to autoimmune disease. By dissecting the similarities and differences among mouse models of patient disease or mutations in ZAP70 that affect TCR signaling strength, we have gained insights into how perturbed ZAP70 function can lead to autoimmunity. Because of our work and that of others on ZAP70, it is likely that perturbations in other molecules affecting TCR signaling strength will be identified that also overcome tolerance mechanisms and cause autoimmunity. Delineating these molecular pathways could lead to the development of much needed new therapeutic targets in these complex diseases.
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Affiliation(s)
- Judith F. Ashouri
- Department of Medicine Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center University of California, San Francisco San Francisco California USA
| | - Wan‐Lin Lo
- Division of Microbiology and Immunology Department of Pathology University of Utah Salt Lake City Utah USA
| | - Trang T. T. Nguyen
- Department of Medicine Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center University of California, San Francisco San Francisco California USA
| | - Lin Shen
- Department of Medicine Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center University of California, San Francisco San Francisco California USA
| | - Arthur Weiss
- Department of Medicine Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center University of California, San Francisco San Francisco California USA
- Howard Hughes Medical Institute University of California, San Francisco San Francisco California USA
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21
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Patarroyo ME, Patarroyo MA, Alba MP, Pabon L, Rugeles MT, Aguilar-Jimenez W, Florez L, Bermudez A, Rout AK, Griesinger C, Suarez CF, Aza-Conde J, Reyes C, Avendaño C, Samacá J, Camargo A, Silva Y, Forero M, Gonzalez E. The First Chemically-Synthesised, Highly Immunogenic Anti-SARS-CoV-2 Peptides in DNA Genotyped Aotus Monkeys for Human Use. Front Immunol 2021; 12:724060. [PMID: 34539660 PMCID: PMC8446425 DOI: 10.3389/fimmu.2021.724060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Thirty-five peptides selected from functionally-relevant SARS-CoV-2 spike (S), membrane (M), and envelope (E) proteins were suitably modified for immunising MHC class II (MHCII) DNA-genotyped Aotus monkeys and matched with HLA-DRβ1* molecules for use in humans. This was aimed at producing the first minimal subunit-based, chemically-synthesised, immunogenic molecules (COLSARSPROT) covering several HLA alleles. They were predicted to cover 48.25% of the world’s population for 6 weeks (short-term) and 33.65% for 15 weeks (long-lasting) as they induced very high immunofluorescent antibody (IFA) and ELISA titres against S, M and E parental native peptides, SARS-CoV-2 neutralising antibodies and host cell infection. The same immunological methods that led to identifying new peptides for inclusion in the COLSARSPROT mixture were used for antigenicity studies. Peptides were analysed with serum samples from patients suffering mild or severe SARS-CoV-2 infection, thereby increasing chemically-synthesised peptides’ potential coverage for the world populations up to 62.9%. These peptides’ 3D structural analysis (by 1H-NMR acquired at 600 to 900 MHz) suggested structural-functional immunological association. This first multi-protein, multi-epitope, minimal subunit-based, chemically-synthesised, highly immunogenic peptide mixture highlights such chemical synthesis methodology’s potential for rapidly obtaining very pure, highly reproducible, stable, cheap, easily-modifiable peptides for inducing immune protection against COVID-19, covering a substantial percentage of the human population.
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Affiliation(s)
- Manuel E Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,Universidad Santo Tomás, Bogotá, Colombia
| | - Manuel A Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha P Alba
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Laura Pabon
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - María T Rugeles
- Grupo Inmunovirología, Universidad de Antioquia, Medellín, Colombia
| | | | - Lizdany Florez
- Grupo Inmunovirología, Universidad de Antioquia, Medellín, Colombia
| | - Adriana Bermudez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Ashok K Rout
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carlos F Suarez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jorge Aza-Conde
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - César Reyes
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Catalina Avendaño
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia
| | - Jhoan Samacá
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Anny Camargo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Yolanda Silva
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha Forero
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Edgardo Gonzalez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
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22
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Joyce S, Ternette N. Know thy immune self and non-self: Proteomics informs on the expanse of self and non-self, and how and where they arise. Proteomics 2021; 21:e2000143. [PMID: 34310018 PMCID: PMC8865197 DOI: 10.1002/pmic.202000143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022]
Abstract
T cells play an important role in the adaptive immune response to a variety of infections and cancers. Initiation of a T cell mediated immune response requires antigen recognition in a process termed MHC (major histocompatibility complex) restri ction. A T cell antigen is a composite structure made up of a peptide fragment bound within the antigen‐binding groove of an MHC‐encoded class I or class II molecule. Insight into the precise composition and biology of self and non‐self immunopeptidomes is essential to harness T cell mediated immunity to prevent, treat, or cure infectious diseases and cancers. T cell antigen discovery is an arduous task! The pioneering work in the early 1990s has made large‐scale T cell antigen discovery possible. Thus, advancements in mass spectrometry coupled with proteomics and genomics technologies make possible T cell antigen discovery with ease, accuracy, and sensitivity. Yet we have only begun to understand the breadth and the depth of self and non‐self immunopeptidomes because the molecular biology of the cell continues to surprise us with new secrets directly related to the source, and the processing and presentation of MHC ligands. Focused on MHC class I molecules, this review, therefore, provides a brief historic account of T cell antigen discovery and, against a backdrop of key advances in molecular cell biologic processes, elaborates on how proteogenomics approaches have revolutionised the field.
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Affiliation(s)
- Sebastian Joyce
- Department of Veterans Affairs, Tennessee Valley Healthcare System and the Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nicola Ternette
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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23
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Baxter-Lowe LA. The changing landscape of HLA typing: Understanding how and when HLA typing data can be used with confidence from bench to bedside. Hum Immunol 2021; 82:466-477. [PMID: 34030895 DOI: 10.1016/j.humimm.2021.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022]
Abstract
Human leukocyte antigen (HLA) genes are extraordinary for their extreme diversity and widespread impact on human health and disease. More than 30,000 HLA alleles have been officially named and more alleles continue to be discovered at a rapid pace. HLA typing systems which have been developed to detect HLA diversity have advanced rapidly and are revolutionizing our understanding of HLA's clinical importance. However, continuous improvements in knowledge and technology have created challenges for clinicians and scientists. This review explains how differences in HLA typing systems can impact the HLA types that are assigned. The consequences of differences in laboratory testing methods and reference databases are described. The challenges of using HLA types that are not equivalent are illustrated. A fundamental understanding of the continual expansion of our understanding of HLA diversity and limitations in some of the typing data is essential for using typing data appropriately in clinical and research settings.
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Affiliation(s)
- Lee Ann Baxter-Lowe
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, USA; Department of Pathology, University of Southern California, USA.
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24
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Froimchuk E, Oakes RS, Kapnick SM, Yanes AA, Jewell CM. Biophysical Properties of Self-Assembled Immune Signals Impact Signal Processing and the Nature of Regulatory Immune Function. NANO LETTERS 2021; 21:3762-3771. [PMID: 33881872 PMCID: PMC8119350 DOI: 10.1021/acs.nanolett.0c05118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Outcomes during immunotherapy are impacted not only by the specific therapeutic signals and pharmacodynamics, but also by the biophysical forms in which signals are delivered. This integration is determinative in autoimmunity because the disease is caused by immune dysregulation and inflammation. Unfortunately, the links between nanomaterial design, biophysical properties, and immune regulation are poorly defined. Here we designed cationic peptide antigens with defined charge distributions and then used electrostatics to assemble these peptides into complexes with anionic regulatory cues. We first show complexes induce antigen-specific tolerance during myelin-driven autoimmunity. We next show the affinity between these immune cues is controlled by charge balance and that affinity confers distinct biophysical properties important in immunological processing, including antigen availability. The underlying binding affinities between the self-assembled signals influences inflammatory gene expression in dendritic cells and antigen-specific regulatory outcomes in self-reactive transgenic T cells. This granular understanding of nanomaterial-immune interactions contributes to a more rational immunotherapy design.
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Affiliation(s)
- Eugene Froimchuk
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742
| | - Robert S. Oakes
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742
- United States Department of Veterans Affairs, VA Maryland Health Care System, Baltimore, MD, 21202
| | - Senta M. Kapnick
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742
| | - Alexis A. Yanes
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742
| | - Christopher M. Jewell
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742
- United States Department of Veterans Affairs, VA Maryland Health Care System, Baltimore, MD, 21202
- Robert E. Fischell Institute for Biomedical Devices, College Park, MD, 20742
- Department of Microbiology and Immunology, University of Maryland Medical School, Baltimore, MD, 21201
- Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD, 21201
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25
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Lo WL, Weiss A. Adapting T Cell Receptor Ligand Discrimination Capability via LAT. Front Immunol 2021; 12:673196. [PMID: 33936119 PMCID: PMC8085316 DOI: 10.3389/fimmu.2021.673196] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022] Open
Abstract
Self- and non-self ligand discrimination is a core principle underlying T cell-mediated immunity. Mature αβ T cells can respond to a foreign peptide ligand presented by major histocompatibility complex molecules (pMHCs) on antigen presenting cells, on a background of continuously sensed self-pMHCs. How αβ T cells can properly balance high sensitivity and high specificity to foreign pMHCs, while surrounded by a sea of self-peptide ligands is not well understood. Such discrimination cannot be explained solely by the affinity parameters of T cell antigen receptor (TCR) and pMHC interaction. In this review, we will discuss how T cell ligand discrimination may be molecularly defined by events downstream of the TCR-pMHC interaction. We will discuss new evidence in support of the kinetic proofreading model of TCR ligand discrimination, and in particular how the kinetics of specific phosphorylation sites within the adaptor protein linker for activation of T cells (LAT) determine the outcome of TCR signaling. In addition, we will discuss emerging data regarding how some kinases, including ZAP-70 and LCK, may possess scaffolding functions to more efficiently direct their kinase activities.
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Affiliation(s)
- Wan-Lin Lo
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Arthur Weiss
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, United States
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26
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Tamouza R, Krishnamoorthy R, Leboyer M. Understanding the genetic contribution of the human leukocyte antigen system to common major psychiatric disorders in a world pandemic context. Brain Behav Immun 2021; 91:731-739. [PMID: 33031918 PMCID: PMC7534661 DOI: 10.1016/j.bbi.2020.09.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/01/2020] [Accepted: 09/30/2020] [Indexed: 12/20/2022] Open
Abstract
The human leukocyte antigen (HLA) is a complex genetic system that encodes proteins which predominantly regulate immune/inflammatory processes. It can be involved in a variety of immuno-inflammatory disorders ranging from infections to autoimmunity and cancers. The HLA system is also suggested to be involved in neurodevelopment and neuroplasticity, especially through microglia regulation and synaptic pruning. Consequently, this highly polymorphic gene region has recently emerged as a major player in the etiology of several major psychiatric disorders, such as schizophrenia, autism spectrum disorder and bipolar disorder and with less evidence for major depressive disorders and attention deficit hyperactivity disorder. We thus review here the role of HLA genes in particular subgroups of psychiatric disorders and foresee their potential implication in future research. In particular, given the prominent role that the HLA system plays in the regulation of viral infection, this review is particularly timely in the context of the Covid-19 pandemic.
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Affiliation(s)
- Ryad Tamouza
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie Translationnelle, F-94010 Creteil, France; AP-HP, Hopital Henri Mondor, Département Medico-Universitaire de Psychiatrie et d'Addictologie (DMU ADAPT), F-94010, France; Fondation FondaMental, Créteil, France.
| | | | - Marion Leboyer
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie Translationnelle, F-94010 Creteil, France; AP-HP, Hopital Henri Mondor, Département Medico-Universitaire de Psychiatrie et d'Addictologie (DMU ADAPT), F-94010, France; Fondation FondaMental, Créteil, France
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27
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TCRα reporter mice reveal contribution of dual TCRα expression to T cell repertoire and function. Proc Natl Acad Sci U S A 2020; 117:32574-32583. [PMID: 33288689 DOI: 10.1073/pnas.2013188117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
It is known that a subpopulation of T cells expresses two T cell receptor (TCR) clonotypes, though the extent and functional significance of this is not established. To definitively evaluate dual TCRα cells, we generated mice with green fluorescent protein and red fluorescent protein reporters linked to TCRα, revealing that ∼16% of T cells express dual TCRs, notably higher than prior estimates. Importantly, dual TCR expression has functional consequences, as dual TCR cells predominated response to lymphocytic choriomeningitis virus infection, comprising up to 60% of virus-specific CD4+ and CD8+ T cells during acute responses. Dual receptor expression selectively influenced immune memory, as postinfection memory CD4+ populations contained significantly increased frequencies of dual TCR cells. These data reveal a previously unappreciated contribution of dual TCR cells to the immune repertoire and highlight their potential effects on immune responses.
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28
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Wong WK, Marks C, Leem J, Lewis AP, Shi J, Deane CM. TCRBuilder: multi-state T-cell receptor structure prediction. Bioinformatics 2020; 36:3580-3581. [PMID: 32181809 DOI: 10.1093/bioinformatics/btaa194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/21/2020] [Accepted: 03/13/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION T-cell receptors (TCRs) are immune proteins that primarily target peptide antigens presented by the major histocompatibility complex. They tend to have lower specificity and affinity than their antibody counterparts, and their binding sites have been shown to adopt multiple conformations, which is potentially an important factor for their polyspecificity. None of the current TCR-modelling tools predict this variability which limits our ability to accurately predict TCR binding. RESULTS We present TCRBuilder, a multi-state TCR structure prediction tool. Given a paired αβTCR sequence, TCRBuilder returns a model or an ensemble of models covering the potential conformations of the binding site. This enables the analysis of structurally driven polyspecificity in TCRs, which is not possible with existing tools. AVAILABILITY AND IMPLEMENTATION http://opig.stats.ox.ac.uk/resources. CONTACT deane@stats.ox.ac.uk. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wing Ki Wong
- Department of Statistics, University of Oxford, Oxford OX1 3LB, UK
| | - Claire Marks
- Department of Statistics, University of Oxford, Oxford OX1 3LB, UK
| | - Jinwoo Leem
- Department of Statistics, University of Oxford, Oxford OX1 3LB, UK
| | - Alan P Lewis
- Data and Computational Sciences, GlaxoSmithKline Research and Development, Stevenage SG1 2NY, UK
| | - Jiye Shi
- Department of Chemistry, UCB Pharma, Slough SL1 3WE, UK
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29
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Guzella TS, Barreto VM, Carneiro J. Partitioning stable and unstable expression level variation in cell populations: A theoretical framework and its application to the T cell receptor. PLoS Comput Biol 2020; 16:e1007910. [PMID: 32841238 PMCID: PMC7498022 DOI: 10.1371/journal.pcbi.1007910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/17/2020] [Accepted: 04/24/2020] [Indexed: 11/19/2022] Open
Abstract
Phenotypic variation in the copy number of gene products expressed by cells or tissues has been the focus of intense investigation. To what extent the observed differences in cellular expression levels are persistent or transient is an intriguing question. Here, we develop a quantitative framework that resolves the expression variation into stable and unstable components. The difference between the expression means in two cohorts isolated from any cell population is shown to converge to an asymptotic value, with a characteristic time, τT, that measures the timescale of the unstable dynamics. The asymptotic difference in the means, relative to the initial value, measures the stable proportion of the original population variance Rα2. Empowered by this insight, we analysed the T-cell receptor (TCR) expression variation in CD4 T cells. About 70% of TCR expression variance is stable in a diverse polyclonal population, while over 80% of the variance in an isogenic TCR transgenic population is volatile. In both populations the TCR levels fluctuate with a characteristic time of 32 hours. This systematic characterisation of the expression variation dynamics, relying on time series of cohorts’ means, can be combined with technologies that measure gene or protein expression in single cells or in bulk. No two cells are identical. Even isogenic cells, living in the same environment and expressing the same set of genes display measurable differences or variation in the expression level of any of these genes. How much of the differences in expression levels are permanent and how much of these differences vanish in time has intrigued us for generations. We develop a theoretical framework based on a stochastic model and put it to work in the analysis of T cell receptor expression level in CD4 T cells. We show that T cell populations with genetically diverse receptors display stable variation in receptor expression but, surprisingly, we detect persistent differences in receptor levels among uniform transgenic T cells. The analysis, being based on the mean cohort expression levels logarithm, can be applied to techniques that measure expression at single-cell level and also to the myriad of genomics and proteomics techniques that measure expression in bulk populations.
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Affiliation(s)
| | - Vasco M. Barreto
- CEDOC - Chronic Diseases Research Center, NOVA Medical School, Universidade Nova de Lisboa, Lisboa, Portugal
- * E-mail: (VMB); (JC)
| | - Jorge Carneiro
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail: (VMB); (JC)
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30
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Junghans V, Chouliara M, Santos AM, Hatherley D, Petersen J, Dam T, Svensson LM, Rossjohn J, Davis SJ, Jönsson P. Effects of a local auxiliary protein on the two-dimensional affinity of a TCR-peptide MHC interaction. J Cell Sci 2020; 133:jcs245985. [PMID: 32591485 DOI: 10.1242/jcs.245985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022] Open
Abstract
The affinity of T-cell receptors (TCRs) for major histocompatibility complex molecules (MHCs) presenting cognate antigens likely determines whether T cells initiate immune responses, or not. There exist few measurements of two-dimensional (2D) TCR-MHC interactions, and the effect of auxiliary proteins on binding is unexplored. Here, Jurkat T-cells expressing the MHC molecule HLA-DQ8-glia-α1 and the ligand of an adhesion protein (rat CD2) were allowed to bind supported lipid bilayers (SLBs) presenting fluorescently labelled L3-12 TCR and rat CD2, allowing measurements of binding unconfounded by cell signaling effects or co-receptor binding. The 2D Kd for L3-12 TCR binding to HLA-DQ8-glia-α1, of 14±5 molecules/μm2 (mean±s.d.), was only marginally influenced by including CD2 up to ∼200 bound molecules/μm2 but higher CD2 densities reduced the affinity up to 1.9-fold. Cell-SLB contact size increased steadily with ligand density without affecting binding for contacts at up to ∼20% of total cell area, but beyond this lamellipodia appeared, giving an apparent increase in bound receptors of up to 50%. Our findings show how parameters other than the specific protein-protein interaction can influence binding behavior at cell-cell contacts.
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Affiliation(s)
| | - Manto Chouliara
- Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Ana Mafalda Santos
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford; and Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, UK
| | - Deborah Hatherley
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford; and Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, UK
| | - Jan Petersen
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Tommy Dam
- Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Lena M Svensson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; and School of Medical Sciences, Örebro University, 701 82 Örebro, Sweden
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Simon J Davis
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford; and Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, UK
| | - Peter Jönsson
- Department of Chemistry, Lund University, 221 00 Lund, Sweden
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31
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CD5 dynamically calibrates basal NF-κB signaling in T cells during thymic development and peripheral activation. Proc Natl Acad Sci U S A 2020; 117:14342-14353. [PMID: 32513716 PMCID: PMC7322041 DOI: 10.1073/pnas.1922525117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Immature T cells undergo a process of positive selection in the thymus when their new T cell receptor (TCR) engages and signals in response to self-peptides. As the T cell matures, a slew of negative regulatory molecules, including the inhibitory surface glycoprotein CD5, are up-regulated in proportion to the strength of the self-peptide signal. Together these regulators dampen TCR-proximal signaling and help avoid any subsequent peripheral activation of T cells by self-peptides. Paradoxically, antigen-specific T cells initially expressing more CD5 (CD5hi) have been found to better persist as effector/memory cells after a peripheral challenge. The molecular mechanisms underlying such a duality in CD5 function is not clear. We found that CD5 alters the basal activity of the NF-κB signaling in resting peripheral T cells. When CD5 was conditionally ablated, T cells were unable to maintain higher expression of the cytoplasmic NF-κB inhibitor IκBα. Consistent with this, resting CD5hi T cells expressed more of the NF-κB p65 protein than CD5lo cells, without significant increases in transcript levels, in the absence of TCR signals. This posttranslationally stabilized cellular NF-κB depot potentially confers a survival advantage to CD5hi T cells over CD5lo ones. Taken together, these data suggest a two-step model whereby the strength of self-peptide-induced TCR signal lead to the up-regulation of CD5, which subsequently maintains a proportional reserve of NF-κB in peripheral T cells poised for responding to agonistic antigen-driven T cell activation.
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32
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Van Laethem F, Saba I, Lu J, Bhattacharya A, Tai X, Guinter TI, Engelhardt B, Alag A, Rojano M, Ashe JM, Hanada KI, Yang JC, Sun PD, Singer A. Novel MHC-Independent αβTCRs Specific for CD48, CD102, and CD155 Self-Proteins and Their Selection in the Thymus. Front Immunol 2020; 11:1216. [PMID: 32612609 PMCID: PMC7308553 DOI: 10.3389/fimmu.2020.01216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
MHC-independent αβTCRs (TCRs) recognize conformational epitopes on native self-proteins and arise in mice lacking both MHC and CD4/CD8 coreceptor proteins. Although naturally generated in the thymus, these TCRs resemble re-engineered therapeutic chimeric antigen receptor (CAR) T cells in their specificity for MHC-independent ligands. Here we identify naturally arising MHC-independent TCRs reactive to three native self-proteins (CD48, CD102, and CD155) involved in cell adhesion. We report that naturally arising MHC-independent TCRs require high affinity TCR-ligand engagements in the thymus to signal positive selection and that high affinity positive selection generates a peripheral TCR repertoire with limited diversity and increased self-reactivity. We conclude that the affinity of TCR-ligand engagements required to signal positive selection in the thymus inversely determines the diversity and self-tolerance of the mature TCR repertoire that is selected.
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Affiliation(s)
- François Van Laethem
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Ingrid Saba
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Jinghua Lu
- Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Abhisek Bhattacharya
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Xuguang Tai
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Terry I Guinter
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Britta Engelhardt
- Theodor Kocher Institute, Faculty of Bern, Universität Bern, Bern, Switzerland
| | - Amala Alag
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Mirelle Rojano
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Jennifer M Ashe
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Ken-Ichi Hanada
- Surgery Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - James C Yang
- Surgery Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Peter D Sun
- Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Alfred Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
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33
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Impact of T-cell receptor and B-cell receptor repertoire on the recurrence of early stage lung adenocarcinoma. Exp Cell Res 2020; 394:112134. [PMID: 32540399 DOI: 10.1016/j.yexcr.2020.112134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 12/25/2022]
Abstract
Surgical resection is the only curative treatment for patients with early stage non-small cell lung cancer. However, approximately 33% of non-small cell lung cancer patients recur with the stage I disease, which may be attributed to a deficiency in antitumor immunity. In the present study, for early stage lung adenocarcinoma patients with early recurrence and early non-recurrence, we investigated the quantity of tumor-infiltrating T and B cells by immunohistochemistry, as well as the genes in the complementarity determining region 3 of the T-cell receptor β chain and the B-cell receptor immunoglobulin heavy chain. A decreased number of tumor-infiltrating lymphocytes cells (CD3+, CD4+, CD8+ and CD20+) was present in early recurrence patients. A significant increase in oligoclones and a reduction in T-cell receptor diversity were observed in the early recurrence group. Furthermore, there was a preference for V, J gene, and VJ gene combinations in patients with early recurrence versus non-recurrence, suggesting that this may be a new biomarker for the recurrence of early stage lung adenocarcinoma. These data indicate that T and B cell receptor repertoires influence the depth of human adaptive immune responses, and in addition to the quantity of tumor infiltrating T and B cells, may contribute to the prevention of early stage lung adenocarcinoma recurrence after surgical resection. Our study illustrates the potential value of the immune repertoire for predicting clinical efficacy and patient outcomes.
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Huang H, Long L, Zhou P, Chapman NM, Chi H. mTOR signaling at the crossroads of environmental signals and T-cell fate decisions. Immunol Rev 2020; 295:15-38. [PMID: 32212344 PMCID: PMC8101438 DOI: 10.1111/imr.12845] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/19/2020] [Indexed: 12/28/2022]
Abstract
The evolutionarily conserved serine/threonine kinase mTOR (mechanistic target of rapamycin) forms the distinct protein complexes mTORC1 and mTORC2 and integrates signals from the environment to coordinate downstream signaling events and various cellular processes. T cells rely on mTOR activity for their development and to establish their homeostasis and functional fitness. Here, we review recent progress in our understanding of the upstream signaling and downstream targets of mTOR. We also provide an updated overview of the roles of mTOR in T-cell development, homeostasis, activation, and effector-cell fate decisions, as well as its important impacts on the suppressive activity of regulatory T cells. Moreover, we summarize the emerging roles of mTOR in T-cell exhaustion and transdifferentiation. A better understanding of the contribution of mTOR to T-cell fate decisions will ultimately aid in the therapeutic targeting of mTOR in human disease.
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Affiliation(s)
- Hongling Huang
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Lingyun Long
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Equal contribution
| | - Peipei Zhou
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Equal contribution
| | - Nicole M. Chapman
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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35
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Neier SC, Ferrer A, Wilton KM, Smith SEP, Kelcher AMH, Pavelko KD, Canfield JM, Davis TR, Stiles RJ, Chen Z, McCluskey J, Burrows SR, Rossjohn J, Hebrink DM, Carmona EM, Limper AH, Kappes DJ, Wettstein PJ, Johnson AJ, Pease LR, Daniels MA, Neuhauser C, Gil D, Schrum AG. The early proximal αβ TCR signalosome specifies thymic selection outcome through a quantitative protein interaction network. Sci Immunol 2020; 4:4/32/eaal2201. [PMID: 30770409 DOI: 10.1126/sciimmunol.aal2201] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/17/2019] [Indexed: 12/18/2022]
Abstract
During αβ T cell development, T cell antigen receptor (TCR) engagement transduces biochemical signals through a protein-protein interaction (PPI) network that dictates dichotomous cell fate decisions. It remains unclear how signal specificity is communicated, instructing either positive selection to advance cell differentiation or death by negative selection. Early signal discrimination might occur by PPI signatures differing qualitatively (customized, unique PPI combinations for each signal), quantitatively (graded amounts of a single PPI series), or kinetically (speed of PPI pathway progression). Using a novel PPI network analysis, we found that early TCR-proximal signals distinguishing positive from negative selection appeared to be primarily quantitative in nature. Furthermore, the signal intensity of this PPI network was used to find an antigen dose that caused a classic negative selection ligand to induce positive selection of conventional αβ T cells, suggesting that the quantity of TCR triggering was sufficient to program selection outcome. Because previous work had suggested that positive selection might involve a qualitatively unique signal through CD3δ, we reexamined the block in positive selection observed in CD3δ0 mice. We found that CD3δ0 thymocytes were inhibited but capable of signaling positive selection, generating low numbers of MHC-dependent αβ T cells that expressed diverse TCR repertoires and participated in immune responses against infection. We conclude that the major role for CD3δ in positive selection is to quantitatively boost the signal for maximal generation of αβ T cells. Together, these data indicate that a quantitative network signaling mechanism through the early proximal TCR signalosome determines thymic selection outcome.
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Affiliation(s)
- Steven C Neier
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA.,Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Alejandro Ferrer
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Katelynn M Wilton
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA.,Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN, USA.,Medical Scientist Training Program, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Stephen E P Smith
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - April M H Kelcher
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA.,Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN, USA.,Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Kevin D Pavelko
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jenna M Canfield
- Molecular Pathogenesis and Therapeutics PhD Graduate Program, University of Missouri, Columbia, MO, USA
| | - Tessa R Davis
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Robert J Stiles
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Zhenjun Chen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Scott R Burrows
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,School of Medicine, University of Queensland, Brisbane, Queensland 4006, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Deanne M Hebrink
- Thoracic Diseases Research Unit, Division of Pulmonary Critical Care and Internal Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Eva M Carmona
- Thoracic Diseases Research Unit, Division of Pulmonary Critical Care and Internal Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Andrew H Limper
- Thoracic Diseases Research Unit, Division of Pulmonary Critical Care and Internal Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Dietmar J Kappes
- Blood Cell Development and Cancer Keystone, Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Peter J Wettstein
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA.,Department of Surgery, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Aaron J Johnson
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA.,Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Larry R Pease
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Mark A Daniels
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.,Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA
| | | | - Diana Gil
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA. .,Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA.,Department of Bioengineering, College of Engineering, University of Missouri, Columbia, MO, USA
| | - Adam G Schrum
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA. .,Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA.,Department of Bioengineering, College of Engineering, University of Missouri, Columbia, MO, USA
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36
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ASK1 Mediates Nur77 Expression in T-Cell Receptor Mediated Thymocyte Apoptosis. Cells 2020; 9:cells9030585. [PMID: 32121597 PMCID: PMC7140521 DOI: 10.3390/cells9030585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/19/2020] [Accepted: 02/27/2020] [Indexed: 12/11/2022] Open
Abstract
: Apoptosis signal-regulating kinase 1 (ASK1) is a mitogen-activated protein kinase kinase kinase (MAPKKK) that activates downstream JNK and p38 mitogen-activated protein kinase (MAPK) to relay death signals into cells in response to various environmental stress. However, whether ASK1 plays a role in T cell receptor (TCR)-mediated apoptosis of thymocytes is unclear. Here, we show that ASK1 is activated upon TCR stimulation and plays an important role in TCR-mediated apoptosis of thymocytes by triggering downstream JNK and p38 signaling cascades. Mechanistically, ASK1-JNK/p38 signaling leads to the upregulation of neuron-derived clone 77 (Nur77), a critical pro-apoptotic protein involved in TCR-mediated apoptosis of thymocytes. Furthermore, we demonstrate that the activation of ASK1 is negatively modulated by Akt upon TCR stimulation. Thus, our results identify a previously unappreciated signaling mechanism involving ASK1 in TCR-mediated apoptosis of thymocytes.
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37
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Toshima K, Nagafuku M, Okazaki T, Kobayashi T, Inokuchi JI. Plasma membrane sphingomyelin modulates thymocyte development by inhibiting TCR-induced apoptosis. Int Immunol 2020; 31:211-223. [PMID: 30561621 DOI: 10.1093/intimm/dxy082] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/12/2019] [Indexed: 12/18/2022] Open
Abstract
Sphingomyelin (SM) in combination with cholesterol forms specialized membrane lipid microdomains in which specific receptors and signaling molecules are localized or recruited to mediate intracellular signaling. SM-microdomain levels in mouse thymus were low in the early CD4+CD8+ double-positive (DP) stage prior to thymic selection and increased >10-fold during late selection. T-cell receptor (TCR) signal strength is a key factor determining whether DP thymocytes undergo positive or negative selection. We examined the role of SM-microdomains in thymocyte development and related TCR signaling, using SM synthase 1 (SMS1)-deficient (SMS1-/-) mice which display low SM expression in all thymocyte populations. SMS1 deficiency caused reduced cell numbers after late DP stages in TCR transgenic models. TCR-dependent apoptosis induced by anti-CD3 treatment was enhanced in SMS1-/- DP thymocytes both in vivo and in vitro. SMS1-/- DP thymocytes, relative to controls, showed increased phosphorylation of TCR-proximal kinase ZAP-70 and increased expression of Bim and Nur77 proteins involved in negative selection following TCR stimulation. Addition of SM to cultured normal DP thymocytes led to greatly increased surface expression of SM-microdomains, with associated reduction of TCR signaling and TCR-induced apoptosis. Our findings indicate that SM-microdomains are increased in late DP stages, function as negative regulators of TCR signaling and modulate the efficiency of TCR-proximal signaling to promote thymic selection events leading to subsequent developmental stages.
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Affiliation(s)
- Kaoru Toshima
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Aoba-ku, Sendai, Miyagi, Japan
| | - Masakazu Nagafuku
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Aoba-ku, Sendai, Miyagi, Japan
| | - Toshiro Okazaki
- Department of Hematology and Immunology, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | | | - Jin-Ichi Inokuchi
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Aoba-ku, Sendai, Miyagi, Japan
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38
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Rushdi M, Li K, Yuan Z, Travaglino S, Grakoui A, Zhu C. Mechanotransduction in T Cell Development, Differentiation and Function. Cells 2020; 9:E364. [PMID: 32033255 PMCID: PMC7072571 DOI: 10.3390/cells9020364] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 02/07/2023] Open
Abstract
Cells in the body are actively engaging with their environments that include both biochemical and biophysical aspects. The process by which cells convert mechanical stimuli from their environment to intracellular biochemical signals is known as mechanotransduction. Exemplifying the reliance on mechanotransduction for their development, differentiation and function are T cells, which are central to adaptive immune responses. T cell mechanoimmunology is an emerging field that studies how T cells sense, respond and adapt to the mechanical cues that they encounter throughout their life cycle. Here we review different stages of the T cell's life cycle where existing studies have shown important effects of mechanical force or matrix stiffness on a T cell as sensed through its surface molecules, including modulating receptor-ligand interactions, inducing protein conformational changes, triggering signal transduction, amplifying antigen discrimination and ensuring directed targeted cell killing. We suggest that including mechanical considerations in the immunological studies of T cells would inform a more holistic understanding of their development, differentiation and function.
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Affiliation(s)
- Muaz Rushdi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.R.); (K.L.); (S.T.)
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Kaitao Li
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.R.); (K.L.); (S.T.)
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Zhou Yuan
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30313, USA
| | - Stefano Travaglino
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.R.); (K.L.); (S.T.)
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Arash Grakoui
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes Research Primate Center, Emory University School of Medicine, Atlanta, GA 30329, USA;
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.R.); (K.L.); (S.T.)
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30313, USA
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39
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Leem J, de Oliveira SHP, Krawczyk K, Deane CM. STCRDab: the structural T-cell receptor database. Nucleic Acids Res 2019; 46:D406-D412. [PMID: 29087479 PMCID: PMC5753249 DOI: 10.1093/nar/gkx971] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/09/2017] [Indexed: 01/16/2023] Open
Abstract
The Structural T–cell Receptor Database (STCRDab; http://opig.stats.ox.ac.uk/webapps/stcrdab) is an online resource that automatically collects and curates TCR structural data from the Protein Data Bank. For each entry, the database provides annotations, such as the α/β or γ/δ chain pairings, major histocompatibility complex details, and where available, antigen binding affinities. In addition, the orientation between the variable domains and the canonical forms of the complementarity-determining region loops are also provided. Users can select, view, and download individual or bulk sets of structures based on these criteria. Where available, STCRDab also finds antibody structures that are similar to TCRs, helping users explore the relationship between TCRs and antibodies.
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Affiliation(s)
- Jinwoo Leem
- Department of Statistics, University of Oxford, 24-29 St Giles, Oxford, OX1 3LB, UK
| | | | - Konrad Krawczyk
- Department of Statistics, University of Oxford, 24-29 St Giles, Oxford, OX1 3LB, UK
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, 24-29 St Giles, Oxford, OX1 3LB, UK
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40
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Quantitative characterization of T-cell repertoire alteration in Chinese patients with B-cell acute lymphocyte leukemia after CAR-T therapy. Bone Marrow Transplant 2019; 54:2072-2080. [PMID: 31383996 DOI: 10.1038/s41409-019-0625-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/27/2019] [Accepted: 05/18/2019] [Indexed: 01/08/2023]
Abstract
Chimeric antigen receptor (CAR) T-cell therapy has displayed potent anti-leukemia activity in acute lymphocytic leukemia (ALL), acting as a new ray of hope to refractory/relapsed patients. However, the influence of CAR-T therapy on host immune system has not been well elucidated. Thus, We applied high-throughput T cell receptor β chain sequencing to track the dynamic change of T-cell repertoire induced by CAR-T therapy in B-cell ALL patients. Six Chinese patients achieving complete remission were under observation, whose blood samples, bone marrow samples and infused CAR-T samples were collected at serial time points before and after CAR-T therapy. We observed decreased TCR diversity and increased clonality of T-cell repertoire in both peripheral blood and bone marrow after CAR-T administration. The persistent T cell clones in blood and bone marrow expanded following leukemic cell destruction and were barely detected in CAR T-cell pool. For the first time, our results demonstrated CAR-T therapy could stimulate the clonal proliferation of CAR-negative T cells in patients. Considering other groups' animal results indicating that CAR-T therapy could facilitate the proliferation of tumor antigen-specific T cells and that the emergence of these T cell clones followed the destruction of leukemic cells, they are most likely tumor antigen-specific.
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41
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Yablonski D. Bridging the Gap: Modulatory Roles of the Grb2-Family Adaptor, Gads, in Cellular and Allergic Immune Responses. Front Immunol 2019; 10:1704. [PMID: 31402911 PMCID: PMC6669380 DOI: 10.3389/fimmu.2019.01704] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/08/2019] [Indexed: 01/07/2023] Open
Abstract
Antigen receptor signaling pathways are organized by adaptor proteins. Three adaptors, LAT, Gads, and SLP-76, form a heterotrimeric complex that mediates signaling by the T cell antigen receptor (TCR) and by the mast cell high affinity receptor for IgE (FcεRI). In both pathways, antigen recognition triggers tyrosine phosphorylation of LAT and SLP-76. The recruitment of SLP-76 to phospho-LAT is bridged by Gads, a Grb2 family adaptor composed of two SH3 domains flanking a central SH2 domain and an unstructured linker region. The LAT-Gads-SLP-76 complex is further incorporated into larger microclusters that mediate antigen receptor signaling. Gads is positively regulated by dimerization, which promotes its cooperative binding to LAT. Negative regulation occurs via phosphorylation or caspase-mediated cleavage of the linker region of Gads. FcεRI-mediated mast cell activation is profoundly impaired in LAT- Gads- or SLP-76-deficient mice. Unexpectedly, the thymic developmental phenotype of Gads-deficient mice is much milder than the phenotype of LAT- or SLP-76-deficient mice. This distinction suggests that Gads is not absolutely required for TCR signaling, but may modulate its sensitivity, or regulate a particular branch of the TCR signaling pathway; indeed, the phenotypic similarity of Gads- and Itk-deficient mice suggests a functional connection between Gads and Itk. Additional Gads binding partners include costimulatory proteins such as CD28 and CD6, adaptors such as Shc, ubiquitin regulatory proteins such as USP8 and AMSH, and kinases such as HPK1 and BCR-ABL, but the functional implications of these interactions are not yet fully understood. No interacting proteins or function have been ascribed to the evolutionarily conserved N-terminal SH3 of Gads. Here we explore the biochemical and functional properties of Gads, and its role in regulating allergy, T cell development and T-cell mediated immunity.
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Affiliation(s)
- Deborah Yablonski
- The Immune Cell Signaling Lab, Department of Immunology, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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42
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Fernandes RA, Ganzinger KA, Tzou JC, Jönsson P, Lee SF, Palayret M, Santos AM, Carr AR, Ponjavic A, Chang VT, Macleod C, Lagerholm BC, Lindsay AE, Dushek O, Tilevik A, Davis SJ, Klenerman D. A cell topography-based mechanism for ligand discrimination by the T cell receptor. Proc Natl Acad Sci U S A 2019; 116:14002-14010. [PMID: 31221762 PMCID: PMC6628812 DOI: 10.1073/pnas.1817255116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The T cell receptor (TCR) initiates the elimination of pathogens and tumors by T cells. To avoid damage to the host, the receptor must be capable of discriminating between wild-type and mutated self and nonself peptide ligands presented by host cells. Exactly how the TCR does this is unknown. In resting T cells, the TCR is largely unphosphorylated due to the dominance of phosphatases over the kinases expressed at the cell surface. However, when agonist peptides are presented to the TCR by major histocompatibility complex proteins expressed by antigen-presenting cells (APCs), very fast receptor triggering, i.e., TCR phosphorylation, occurs. Recent work suggests that this depends on the local exclusion of the phosphatases from regions of contact of the T cells with the APCs. Here, we developed and tested a quantitative treatment of receptor triggering reliant only on TCR dwell time in phosphatase-depleted cell contacts constrained in area by cell topography. Using the model and experimentally derived parameters, we found that ligand discrimination likely depends crucially on individual contacts being ∼200 nm in radius, matching the dimensions of the surface protrusions used by T cells to interrogate their targets. The model not only correctly predicted the relative signaling potencies of known agonists and nonagonists but also achieved this in the absence of kinetic proofreading. Our work provides a simple, quantitative, and predictive molecular framework for understanding why TCR triggering is so selective and fast and reveals that, for some receptors, cell topography likely influences signaling outcomes.
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Affiliation(s)
- Ricardo A Fernandes
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, United Kingdom
- Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Kristina A Ganzinger
- Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Justin C Tzou
- Department of Applied & Computational Mathematics & Statistics, University of Notre Dame, Notre Dame, IN 46556
| | - Peter Jönsson
- Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Matthieu Palayret
- Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Ana Mafalda Santos
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, United Kingdom
- Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Alexander R Carr
- Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Aleks Ponjavic
- Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - Veronica T Chang
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, United Kingdom
- Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Charlotte Macleod
- Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom
| | - B Christoffer Lagerholm
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Alan E Lindsay
- Mathematics Department, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, United Kingdom
- Wolfson Centre for Mathematical Biology, University of Oxford, OX1 3RE Oxford, United Kingdom
| | - Andreas Tilevik
- School of Bioscience, University of Skövde, 541 28 Skövde, Sweden
| | - Simon J Davis
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, United Kingdom;
- Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - David Klenerman
- Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom;
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43
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Rodríguez-Jorge O, Kempis-Calanis LA, Abou-Jaoudé W, Gutiérrez-Reyna DY, Hernandez C, Ramirez-Pliego O, Thomas-Chollier M, Spicuglia S, Santana MA, Thieffry D. Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4 + T cell activation. Sci Signal 2019; 12:12/577/eaar3641. [PMID: 30992399 DOI: 10.1126/scisignal.aar3641] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
CD4+ T cells recognize antigens through their T cell receptors (TCRs); however, additional signals involving costimulatory receptors, for example, CD28, are required for proper T cell activation. Alternative costimulatory receptors have been proposed, including members of the Toll-like receptor (TLR) family, such as TLR5 and TLR2. To understand the molecular mechanism underlying a potential costimulatory role for TLR5, we generated detailed molecular maps and logical models for the TCR and TLR5 signaling pathways and a merged model for cross-interactions between the two pathways. Furthermore, we validated the resulting model by analyzing how T cells responded to the activation of these pathways alone or in combination, in terms of the activation of the transcriptional regulators CREB, AP-1 (c-Jun), and NF-κB (p65). Our merged model accurately predicted the experimental results, showing that the activation of TLR5 can play a similar role to that of CD28 activation with respect to AP-1, CREB, and NF-κB activation, thereby providing insights regarding the cross-regulation of these pathways in CD4+ T cells.
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Affiliation(s)
- Otoniel Rodríguez-Jorge
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, 62210 Cuernavaca, México.,Escuela de Estudios Superiores de Axochiapan, Universidad Autónoma del Estado de Morelos, 62951 Axochiapan, México
| | - Linda A Kempis-Calanis
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, 62210 Cuernavaca, México
| | - Wassim Abou-Jaoudé
- Computational System Biology Team, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, École Normale Supérieure, Université PSL, 75005 Paris, France
| | - Darely Y Gutiérrez-Reyna
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, 62210 Cuernavaca, México
| | - Céline Hernandez
- Computational System Biology Team, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, École Normale Supérieure, Université PSL, 75005 Paris, France
| | - Oscar Ramirez-Pliego
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, 62210 Cuernavaca, México
| | - Morgane Thomas-Chollier
- Computational System Biology Team, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, École Normale Supérieure, Université PSL, 75005 Paris, France
| | | | - Maria A Santana
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, 62210 Cuernavaca, México.
| | - Denis Thieffry
- Computational System Biology Team, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, École Normale Supérieure, Université PSL, 75005 Paris, France.
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44
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Sant AJ, DiPiazza AT, Nayak JL, Rattan A, Richards KA. CD4 T cells in protection from influenza virus: Viral antigen specificity and functional potential. Immunol Rev 2019; 284:91-105. [PMID: 29944766 DOI: 10.1111/imr.12662] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
CD4 T cells convey a number of discrete functions to protective immunity to influenza, a complexity that distinguishes this arm of adaptive immunity from B cells and CD8 T cells. Although the most well recognized function of CD4 T cells is provision of help for antibody production, CD4 T cells are important in many aspects of protective immunity. Our studies have revealed that viral antigen specificity is a key determinant of CD4 T cell function, as illustrated both by mouse models of infection and human vaccine responses, a factor whose importance is due at least in part to events in viral antigen handling. We discuss research that has provided insight into the diverse viral epitope specificity of CD4 T cells elicited after infection, how this primary response is modified as CD4 T cells home to the lung, establish memory, and after challenge with a secondary and distinct influenza virus strain. Our studies in human subjects point out the challenges facing vaccine efforts to facilitate responses to novel and avian strains of influenza, as well as strategies that enhance the ability of CD4 T cells to promote protective antibody responses to both seasonal and potentially pandemic strains of influenza.
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Affiliation(s)
- Andrea J Sant
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Anthony T DiPiazza
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Jennifer L Nayak
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA.,Division of Infectious Diseases, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Ajitanuj Rattan
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Katherine A Richards
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
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45
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Goyette J, Nieves DJ, Ma Y, Gaus K. How does T cell receptor clustering impact on signal transduction? J Cell Sci 2019; 132:132/4/jcs226423. [DOI: 10.1242/jcs.226423] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
ABSTRACT
The essential function of the T cell receptor (TCR) is to translate the engagement of peptides on the major histocompatibility complex (pMHC) into appropriate intracellular signals through the associated cluster of differentiation 3 (CD3) complex. The spatial organization of the TCR–CD3 complex in the membrane is thought to be a key regulatory element of signal transduction, raising the question of how receptor clustering impacts on TCR triggering. How signal transduction at the TCR–CD3 complex encodes the quality and quantity of pMHC molecules is not fully understood. This question can be approached by reconstituting T cell signaling in model and cell membranes and addressed by single-molecule imaging of endogenous proteins in T cells. We highlight such methods and further discuss how TCR clustering could affect pMHC rebinding rates, the local balance between kinase and phosphatase activity and/or the lipid environment to regulate the signal efficiency of the TCR–CD3 complex. We also examine whether clustering could affect the conformation of cytoplasmic CD3 tails through a biophysical mechanism. Taken together, we highlight how the spatial organization of the TCR–CD3 complex – addressed by reconstitution approaches – has emerged as a key regulatory element in signal transduction of this archetypal immune receptor.
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Affiliation(s)
- Jesse Goyette
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia
- ARC Centre of Excellence in Advanced Molecular imaging, University of New South Wales, Sydney 2052, Australia
| | - Daniel J. Nieves
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia
- ARC Centre of Excellence in Advanced Molecular imaging, University of New South Wales, Sydney 2052, Australia
| | - Yuanqing Ma
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia
- ARC Centre of Excellence in Advanced Molecular imaging, University of New South Wales, Sydney 2052, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia
- ARC Centre of Excellence in Advanced Molecular imaging, University of New South Wales, Sydney 2052, Australia
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46
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Goossens S, Wang J, Tremblay CS, De Medts J, T'Sas S, Nguyen T, Saw J, Haigh K, Curtis DJ, Van Vlierberghe P, Berx G, Taghon T, Haigh JJ. ZEB2 and LMO2 drive immature T-cell lymphoblastic leukemia via distinct oncogenic mechanisms. Haematologica 2019; 104:1608-1616. [PMID: 30679322 PMCID: PMC6669144 DOI: 10.3324/haematol.2018.207837] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/18/2019] [Indexed: 12/29/2022] Open
Abstract
ZEB1 and ZEB2 are structurally related E-box binding homeobox transcription factors that induce epithelial to mesenchymal transitions during development and disease. As such, they regulate cancer cell invasion, dissemination and metastasis of solid tumors. In addition, their expression is associated with the gain of cancer stem cell properties and resistance to therapy. Using conditional loss-of-function mice, we previously demonstrated that Zeb2 also plays pivotal roles in hematopoiesis, controlling important cell fate decisions, lineage commitment and fidelity. In addition, upon Zeb2 overexpression, mice spontaneously develop immature T-cell lymphoblastic leukemia. Here we show that pre-leukemic Zeb2-overexpressing thymocytes are characterized by a differentiation delay at beta-selection due to aberrant activation of the interleukin-7 receptor signaling pathway. Notably, and in contrast to Lmo2-overexpressing thymocytes, these pre-leukemic Zeb2-overexpressing T-cell progenitors display no acquired self-renewal properties. Finally, Zeb2 activation in more differentiated T-cell precursor cells can also drive malignant T-cell development, suggesting that the early T-cell differentiation delay is not essential for Zeb2-mediated leukemic transformation. Altogether, our data suggest that Zeb2 and Lmo2 drive malignant transformation of immature T-cell progenitors via distinct molecular mechanisms.
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Affiliation(s)
- Steven Goossens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium .,Department for Biomedical Molecular Biology, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jueqiong Wang
- Mammalian Functional Genetics Group, Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Cedric S Tremblay
- Stem Cell Research Group, Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Jelle De Medts
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Sara T'Sas
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Department for Biomedical Molecular Biology, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Thao Nguyen
- Mammalian Functional Genetics Group, Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Jesslyn Saw
- Stem Cell Research Group, Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Katharina Haigh
- Mammalian Functional Genetics Group, Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - David J Curtis
- Stem Cell Research Group, Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Geert Berx
- Department for Biomedical Molecular Biology, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jody J Haigh
- Mammalian Functional Genetics Group, Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia.,Department of Pharmacology and Therapeutics, Rady Faulty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.,Research Institute in Oncology and Hematology (RIOH), Cancer Care Manitoba, Winnipeg, Manitoba, Canada
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47
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Hart M, Walch-Rückheim B, Friedmann KS, Rheinheimer S, Tänzer T, Glombitza B, Sester M, Lenhof HP, Hoth M, Schwarz EC, Keller A, Meese E. miR-34a: a new player in the regulation of T cell function by modulation of NF-κB signaling. Cell Death Dis 2019; 10:46. [PMID: 30718475 PMCID: PMC6362007 DOI: 10.1038/s41419-018-1295-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/13/2018] [Accepted: 12/18/2018] [Indexed: 12/15/2022]
Abstract
NF-κB functions as modulator of T cell receptor-mediated signaling and transcriptional regulator of miR-34a. Our in silico analysis revealed that miR-34a impacts the NF-κB signalosome with miR-34a binding sites in 14 key members of the NF-κB signaling pathway. Functional analysis identified five target genes of miR-34a including PLCG1, CD3E, PIK3CB, TAB2, and NFΚBIA. Overexpression of miR-34a in CD4+ and CD8+ T cells led to a significant decrease of NFΚBIA as the most downstream cytoplasmic NF-κB member, a reduced cell surface abundance of TCRA and CD3E, and to a reduction of T cell killing capacity. Inhibition of miR-34a caused an increase of NFΚBIA, TCRA, and CD3E. Notably, activation of CD4+ and CD8+ T cells entrails a gradual increase of miR-34a. Our results lend further support to a model with miR-34a as a central NF-κB regulator in T cells.
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Affiliation(s)
- Martin Hart
- Institute of Human Genetics, Saarland University, 66421, Homburg, Germany.
| | - Barbara Walch-Rückheim
- Institute of Virology and Center of Human and Molecular Biology, Saarland University Medical School, 66421, Homburg, Germany
| | - Kim S Friedmann
- Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, 66421, Homburg, Germany
| | | | - Tanja Tänzer
- Institute of Virology and Center of Human and Molecular Biology, Saarland University Medical School, 66421, Homburg, Germany
| | - Birgit Glombitza
- Institute of Virology and Center of Human and Molecular Biology, Saarland University Medical School, 66421, Homburg, Germany
| | - Martina Sester
- Department of Transplant and Infection Immunology, Saarland University, 66421, Homburg, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Markus Hoth
- Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, 66421, Homburg, Germany
| | - Eva C Schwarz
- Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, 66421, Homburg, Germany
| | | | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421, Homburg, Germany
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48
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Yablonski D. Bridging the Gap: Modulatory Roles of the Grb2-Family Adaptor, Gads, in Cellular and Allergic Immune Responses. Front Immunol 2019; 10:1704. [PMID: 31402911 DOI: 10.3389/fimmu.2019.01704/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/08/2019] [Indexed: 05/22/2023] Open
Abstract
Antigen receptor signaling pathways are organized by adaptor proteins. Three adaptors, LAT, Gads, and SLP-76, form a heterotrimeric complex that mediates signaling by the T cell antigen receptor (TCR) and by the mast cell high affinity receptor for IgE (FcεRI). In both pathways, antigen recognition triggers tyrosine phosphorylation of LAT and SLP-76. The recruitment of SLP-76 to phospho-LAT is bridged by Gads, a Grb2 family adaptor composed of two SH3 domains flanking a central SH2 domain and an unstructured linker region. The LAT-Gads-SLP-76 complex is further incorporated into larger microclusters that mediate antigen receptor signaling. Gads is positively regulated by dimerization, which promotes its cooperative binding to LAT. Negative regulation occurs via phosphorylation or caspase-mediated cleavage of the linker region of Gads. FcεRI-mediated mast cell activation is profoundly impaired in LAT- Gads- or SLP-76-deficient mice. Unexpectedly, the thymic developmental phenotype of Gads-deficient mice is much milder than the phenotype of LAT- or SLP-76-deficient mice. This distinction suggests that Gads is not absolutely required for TCR signaling, but may modulate its sensitivity, or regulate a particular branch of the TCR signaling pathway; indeed, the phenotypic similarity of Gads- and Itk-deficient mice suggests a functional connection between Gads and Itk. Additional Gads binding partners include costimulatory proteins such as CD28 and CD6, adaptors such as Shc, ubiquitin regulatory proteins such as USP8 and AMSH, and kinases such as HPK1 and BCR-ABL, but the functional implications of these interactions are not yet fully understood. No interacting proteins or function have been ascribed to the evolutionarily conserved N-terminal SH3 of Gads. Here we explore the biochemical and functional properties of Gads, and its role in regulating allergy, T cell development and T-cell mediated immunity.
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Affiliation(s)
- Deborah Yablonski
- The Immune Cell Signaling Lab, Department of Immunology, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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49
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Abstract
Positive selection of T cells in the thymus is induced by low-affinity TCR recognition of self-peptide-MHC complexes expressed by cortical thymic epithelial cells (cTECs). cTECs express a specialized type of proteasomes, the thymoproteasome, which generates a unique spectrum of MHC class I-associated peptides and plays a critical role in thymic positive selection of CD8+ T cells. However, it remains unclear how the thymoproteasome contributes to the thymic positive selection. More than 30 years ago, the "peptidic self" hypothesis proposed that TCRs recognize MHC-presented peptides only, without interacting with MHC molecules, which turned out to be incorrect. Interestingly, however, by implying that a set of MHC-associated peptides forms immunological self, this hypothesis also predicted that positive selection in the thymus is the primary immune response to "foreign epitope" peptides during T cell development. The thymoproteasome-dependent unique self-peptides may create those foreign epitope peptides displayed in the thymus for positive selection of T cells.
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50
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Balamurugan A, Ng HL, Yang OO. Cross-Reactivity against Multiple HIV-1 Epitopes Is Characteristic of HIV-1-Specific Cytotoxic T Lymphocyte Clones. J Virol 2018; 92:e00617-18. [PMID: 29899094 PMCID: PMC6069174 DOI: 10.1128/jvi.00617-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/05/2018] [Indexed: 11/20/2022] Open
Abstract
Although a high level of promiscuity for heterologous epitopes is believed to exist for cellular immunity, limited data explore this issue for human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T lymphocyte (CTL) responses. Here, we found an unexpected degree of heterologous cross-reactivity against HIV-1 epitopes, in addition to the targeted index epitope. Most CTL clones screened cross-reacted against other known HIV-1 epitopes of the same major histocompatibility complex type I (MHC-I) restriction, up to 40% of tested nonindex epitopes in some cases. The observed cross-reactivity was universally lower avidity than recognition of the index epitope when examined for several A*02- and B*57-restricted CTL clones, demonstrating that the high concentrations of exogenous epitope typically used for screening of CTL responses are prone to detect such cross-reactivity spuriously. In agreement with this, we found that these cross-reactive responses do not appear to mediate CTL activity against HIV-1-infected cells. Overall, our data indicate that low-level cross-reactivity is remarkably common for HIV-1-specific CTLs. The role of this phenomenon is unclear, but low-avidity interactions have been shown to foster homeostatic proliferation of memory T cells.IMPORTANCE This study raises two issues related to HIV-1-specific CTL responses. These are key immune responses that retard disease progression in infected persons that are highly relevant to immunotherapies and vaccines for HIV-1. First, we make the novel observation that these responses are promiscuous and that CTLs targeting one epitope may cross-recognize other, completely distinct epitopes in the virus. While these are low-avidity interactions that do not appear to contribute directly to the antiviral activity of CTLs, this raises interesting biologic implications regarding the purpose of the phenomenon, such as providing a stimulus for these responses to persist long term. Second, the data raise a technical caveat to detection of CTL responses against particular epitopes, suggesting that some methodologies may unintentionally detect cross-reactivity and overestimate responses against an epitope.
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Affiliation(s)
- Arumugam Balamurugan
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California USA
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Hwee L Ng
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California USA
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Otto O Yang
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California USA
- UCLA AIDS Institute, University of California, Los Angeles, Los Angeles, California, USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- AIDS Healthcare Foundation, Los Angeles, California, USA
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