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Gibson Hughes TA, Dona MSI, Sobey CG, Pinto AR, Drummond GR, Vinh A, Jelinic M. Aortic Cellular Heterogeneity in Health and Disease: Novel Insights Into Aortic Diseases From Single-Cell RNA Transcriptomic Data Sets. Hypertension 2024; 81:738-751. [PMID: 38318714 DOI: 10.1161/hypertensionaha.123.20597] [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: 02/07/2024]
Abstract
Aortic diseases such as atherosclerosis, aortic aneurysms, and aortic stiffening are significant complications that can have significant impact on end-stage cardiovascular disease. With limited pharmacological therapeutic strategies that target the structural changes in the aorta, surgical intervention remains the only option for some patients with these diseases. Although there have been significant contributions to our understanding of the cellular architecture of the diseased aorta, particularly in the context of atherosclerosis, furthering our insight into the cellular drivers of disease is required. The major cell types of the aorta are well defined; however, the advent of single-cell RNA sequencing provides unrivaled insights into the cellular heterogeneity of each aortic cell type and the inferred biological processes associated with each cell in health and disease. This review discusses previous concepts that have now been enhanced with recent advances made by single-cell RNA sequencing with a focus on aortic cellular heterogeneity.
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Affiliation(s)
- Tayla A Gibson Hughes
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia (T.A.G.H., C.G.S., A.R.P., G.R.D., A.V., M.J.)
| | - Malathi S I Dona
- Baker Heart and Diabetes Research Institute, Melbourne, Victoria, Australia (M.S.I.D., A.R.P.)
| | - Christopher G Sobey
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia (T.A.G.H., C.G.S., A.R.P., G.R.D., A.V., M.J.)
| | - Alexander R Pinto
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia (T.A.G.H., C.G.S., A.R.P., G.R.D., A.V., M.J.)
- Baker Heart and Diabetes Research Institute, Melbourne, Victoria, Australia (M.S.I.D., A.R.P.)
| | - Grant R Drummond
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia (T.A.G.H., C.G.S., A.R.P., G.R.D., A.V., M.J.)
| | - Antony Vinh
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia (T.A.G.H., C.G.S., A.R.P., G.R.D., A.V., M.J.)
| | - Maria Jelinic
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia (T.A.G.H., C.G.S., A.R.P., G.R.D., A.V., M.J.)
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2
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Liu L, Yoon CW, Yuan Z, Guo T, Qu Y, He P, Yu X, Zhu Z, Limsakul P, Wang Y. Cellular and molecular imaging of CAR-T cell-based immunotherapy. Adv Drug Deliv Rev 2023; 203:115135. [PMID: 37931847 PMCID: PMC11052581 DOI: 10.1016/j.addr.2023.115135] [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] [Received: 08/15/2023] [Revised: 10/18/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Chimeric Antigen Receptor T cell (CAR-T) therapy has emerged as a transformative therapeutic strategy for hematological malignancies. However, its efficacy in treating solid tumors remains limited. An in-depth and comprehensive understanding of CAR-T cell signaling pathways and the ability to track CAR-T cell biodistribution and activation in real-time within the tumor microenvironment will be instrumental in designing the next generation of CAR-T cells for solid tumor therapy. This review summarizes the signaling network and the cellular and molecular imaging tools and platforms that are utilized in CAR-T cell-based immune therapies, covering both in vitro and in vivo studies. Firstly, we provide an overview of the existing understanding of the activation and cytotoxic mechanisms of CAR-T cells, compared to the mechanism of T cell receptor (TCR) signaling pathways. We further describe the commonly employed tools for live cell imaging, coupled with recent research progress, with a focus on genetically encoded fluorescent proteins (FPs) and biosensors. We then discuss the utility of diverse in vivo imaging modalities, including fluorescence and bioluminescence imaging, Magnetic Resonance Imaging (MRI), Positron Emission Tomography (PET), and photoacoustic (PA) imaging, for noninvasive monitoring of CAR-T cell dynamics within tumor tissues, thereby providing critical insights into therapy's strengths and weaknesses. Lastly, we discuss the current challenges and future directions of CAR-T cell therapy from the imaging perspective. We foresee that a comprehensive and integrative approach to CAR-T cell imaging will enable the development of more effective treatments for solid tumors in the future.
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Affiliation(s)
- Longwei Liu
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Chi Woo Yoon
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Zhou Yuan
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Tianze Guo
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Yunjia Qu
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Peixiang He
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Xi Yu
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Ziyue Zhu
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Praopim Limsakul
- Division of Physical Science, Faculty of Science and Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Yingxiao Wang
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
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Ponziani FR, Coppola G, Rio P, Caldarelli M, Borriello R, Gambassi G, Gasbarrini A, Cianci R. Factors Influencing Microbiota in Modulating Vaccine Immune Response: A Long Way to Go. Vaccines (Basel) 2023; 11:1609. [PMID: 37897011 PMCID: PMC10611107 DOI: 10.3390/vaccines11101609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Vaccine immunogenicity still represents an unmet need in specific populations, such as people from developing countries and "edge populations". Both intrinsic and extrinsic factors, such as the environment, age, and dietary habits, influence cellular and humoral immune responses. The human microbiota represents a potential key to understanding how these factors impact the immune response to vaccination, with its modulation being a potential step to address vaccine immunogenicity. The aim of this narrative review is to explore the intricate interactions between the microbiota and the immune system in response to vaccines, highlighting the state of the art in gut microbiota modulation as a novel therapeutic approach to enhancing vaccine immunogenicity and laying the foundation for future, more solid data for its translation to the clinical practice.
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Affiliation(s)
| | | | | | | | | | | | | | - Rossella Cianci
- Department of Translational Medicine and Surgery, Catholic University, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy (G.C.); (P.R.); (M.C.); (R.B.); (G.G.); (A.G.)
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Kalinina AA, Khromykh LM, Kazansky DB. T Cell Receptor Chain Centricity: The Phenomenon and Potential Applications in Cancer Immunotherapy. Int J Mol Sci 2023; 24:15211. [PMID: 37894892 PMCID: PMC10607890 DOI: 10.3390/ijms242015211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
T cells are crucial players in adaptive anti-cancer immunity. The gene modification of T cells with tumor antigen-specific T cell receptors (TCRs) was a milestone in personalized cancer immunotherapy. TCR is a heterodimer (either α/β or γ/δ) able to recognize a peptide antigen in a complex with self-MHC molecules. Although traditional concepts assume that an α- and β-chain contribute equally to antigen recognition, mounting data reveal that certain receptors possess chain centricity, i.e., one hemi-chain TCR dominates antigen recognition and dictates its specificity. Chain-centric TCRs are currently poorly understood in terms of their origin and the functional T cell subsets that express them. In addition, the ratio of α- and β-chain-centric TCRs, as well as the exact proportion of chain-centric TCRs in the native repertoire, is generally still unknown today. In this review, we provide a retrospective analysis of studies that evidence chain-centric TCRs, propose patterns of their generation, and discuss the potential applications of such receptors in T cell gene modification for adoptive cancer immunotherapy.
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Affiliation(s)
| | | | - Dmitry B. Kazansky
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, 115478 Moscow, Russia
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Yao M, Liu X, Qian Z, Fan D, Sun X, Zhong L, Wu P. Research progress of nanovaccine in anti-tumor immunotherapy. Front Oncol 2023; 13:1211262. [PMID: 37692854 PMCID: PMC10484753 DOI: 10.3389/fonc.2023.1211262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
Tumor vaccines aim to activate dormant or unresponsive tumor-specific T lymphocytes by using tumor-specific or tumor-associated antigens, thus enhancing the body's natural defense against cancer. However, the effectiveness of tumor vaccines is limited by the presence of tumor heterogeneity, low immunogenicity, and immune evasion mechanisms. Fortunately, multifunctional nanoparticles offer a unique chance to address these issues. With the advantages of their small size, high stability, efficient drug delivery, and controlled surface chemistry, nanomaterials can precisely target tumor sites, improve the delivery of tumor antigens and immune adjuvants, reshape the immunosuppressive tumor microenvironment, and enhance the body's anti-tumor immune response, resulting in improved efficacy and reduced side effects. Nanovaccine, a type of vaccine that uses nanotechnology to deliver antigens and adjuvants to immune cells, has emerged as a promising strategy for cancer immunotherapy due to its ability to stimulate immune responses and induce tumor-specific immunity. In this review, we discussed the compositions and types of nanovaccine, and the mechanisms behind their anti-tumor effects based on the latest research. We hope that this will provide a more scientific basis for designing tumor vaccines and enhancing the effectiveness of tumor immunotherapy.
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Affiliation(s)
- Min Yao
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiyu Liu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, China
| | - Zhangbo Qian
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, China
| | - Dianfa Fan
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, China
| | - Xinjun Sun
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, China
| | - Liping Zhong
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, China
| | - Pan Wu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi, China
- Pharmaceutical College, Guangxi Medical University, Nanning, Guangxi, China
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Hartout P, Počuča B, Méndez-García C, Schleberger C. Investigating the human and nonobese diabetic mouse MHC class II immunopeptidome using protein language modeling. Bioinformatics 2023; 39:btad469. [PMID: 37527005 PMCID: PMC10421966 DOI: 10.1093/bioinformatics/btad469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 06/17/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023] Open
Abstract
MOTIVATION Identifying peptides associated with the major histocompability complex class II (MHCII) is a central task in the evaluation of the immunoregulatory function of therapeutics and drug prototypes. MHCII-peptide presentation prediction has multiple biopharmaceutical applications, including the safety assessment of biologics and engineered derivatives in silico, or the fast progression of antigen-specific immunomodulatory drug discovery programs in immune disease and cancer. This has resulted in the collection of large-scale datasets on adaptive immune receptor antigenic responses and MHC-associated peptide proteomics. In parallel, recent deep learning algorithmic advances in protein language modeling have shown potential in leveraging large collections of sequence data and improve MHC presentation prediction. RESULTS Here, we train a compact transformer model (AEGIS) on human and mouse MHCII immunopeptidome data, including a preclinical murine model, and evaluate its performance on the peptide presentation prediction task. We show that the transformer performs on par with existing deep learning algorithms and that combining datasets from multiple organisms increases model performance. We trained variants of the model with and without MHCII information. In both alternatives, the inclusion of peptides presented by the I-Ag7 MHC class II molecule expressed by nonobese diabetic mice enabled for the first time the accurate in silico prediction of presented peptides in a preclinical type 1 diabetes model organism, which has promising therapeutic applications. AVAILABILITY AND IMPLEMENTATION The source code is available at https://github.com/Novartis/AEGIS.
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Affiliation(s)
- Philip Hartout
- Discovery Sciences, Novartis Institutes for Biomedical Research, Basel 4056, Switzerland
| | - Bojana Počuča
- NIBR Research Informatics, Novartis Institutes for Biomedical Research, Basel 4056, Switzerland
| | - Celia Méndez-García
- Discovery Sciences, Novartis Institutes for Biomedical Research, Basel 4056, Switzerland
| | - Christian Schleberger
- Discovery Sciences, Novartis Institutes for Biomedical Research, Basel 4056, Switzerland
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Afroz S, Bartolo L, Su LF. Pre-existing T Cell Memory to Novel Pathogens. Immunohorizons 2023; 7:543-553. [PMID: 37436166 PMCID: PMC10587503 DOI: 10.4049/immunohorizons.2200003] [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: 05/12/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
Immunological experiences lead to the development of specific T and B cell memory, which readies the host for a later pathogen rechallenge. Currently, immunological memory is best understood as a linear process whereby memory responses are generated by and directed against the same pathogen. However, numerous studies have identified memory cells that target pathogens in unexposed individuals. How "pre-existing memory" forms and impacts the outcome of infection remains unclear. In this review, we discuss differences in the composition of baseline T cell repertoire in mice and humans, factors that influence pre-existing immune states, and recent literature on their functional significance. We summarize current knowledge on the roles of pre-existing T cells in homeostasis and perturbation and their impacts on health and disease.
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Affiliation(s)
- Sumbul Afroz
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
| | - Laurent Bartolo
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
| | - Laura F. Su
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
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8
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Bartolo L, Afroz S, Pan YG, Xu R, Williams L, Lin CF, Tanes C, Bittinger K, Friedman ES, Gimotty PA, Wu GD, Su LF. SARS-CoV-2-specific T cells in unexposed adults display broad trafficking potential and cross-react with commensal antigens. Sci Immunol 2022; 7:eabn3127. [PMID: 35857619 PMCID: PMC9348748 DOI: 10.1126/sciimmunol.abn3127] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/30/2022] [Indexed: 01/18/2023]
Abstract
The baseline composition of T cells directly affects later response to pathogens, but the complexity of precursor states remains poorly defined. Here, we examined the baseline state of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cells in unexposed individuals. SARS-CoV-2-specific CD4+ T cells were identified in prepandemic blood samples by major histocompatibility complex (MHC) class II tetramer staining and enrichment. Our data revealed a substantial number of SARS-CoV-2-specific T cells that expressed memory phenotype markers. Integrated phenotypic analyses demonstrated diverse preexisting memory states that included cells with distinct polarization features and trafficking potential to barrier tissues. T cell clones generated from tetramer-labeled cells cross-reacted with antigens from commensal bacteria in the skin and gastrointestinal tract. Direct ex vivo tetramer staining for one spike-specific population showed a similar level of cross-reactivity to sequences from endemic coronavirus and commensal bacteria. These data highlight the complexity of precursor T cell repertoire and implicate noninfectious exposures to common microbes as a key factor that shapes human preexisting immunity to SARS-CoV-2.
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Affiliation(s)
- Laurent Bartolo
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sumbul Afroz
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi-Gen Pan
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ruozhang Xu
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Lea Williams
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Chin-Fang Lin
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Phyllis A. Gimotty
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laura F. Su
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
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Erausquin E, Serra P, Parras D, Santamaria P, López-Sagaseta J. Structural plasticity in I-Ag7 links autoreactivity to hybrid insulin peptides in type I diabetes. Front Immunol 2022; 13:924311. [PMID: 35967292 PMCID: PMC9365947 DOI: 10.3389/fimmu.2022.924311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
We recently provided evidence for promiscuous recognition of several different hybrid insulin peptides (HIPs) by the highly diabetogenic, I-Ag7-restricted 4.1-T cell receptor (TCR). To understand the structural determinants of this phenomenon, we solved the structure of an agonistic HIP/I-Ag7 complex, both in isolation as well as bound to the 4.1-TCR. We find that HIP promiscuity of the 4.1-TCR is dictated, on the one hand, by an amino acid sequence pattern that ensures I-Ag7 binding and, on the other hand, by the presence of three acidic residues at positions P5, P7 and P8 that favor an optimal engagement by the 4.1-TCR’s complementary determining regions. Surprisingly, comparison of the TCR-bound and unbound HIP/I-Ag7 structures reveals that 4.1-TCR binding triggers several novel and unique structural motions in both the I-Ag7 molecule and the peptide that are essential for docking. This observation indicates that the type 1 diabetes-associated I-Ag7 molecule is structurally malleable and that this plasticity allows the recognition of multiple peptides by individual TCRs that would otherwise be unable to do so.
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Affiliation(s)
- Elena Erausquin
- Unit of Protein Crystallography and Structural Immunology, Navarrabiomed, Navarra, Spain
- Public University of Navarra (UPNA), Pamplona, Spain
- Navarra University Hospital, Pamplona, Spain
| | - Pau Serra
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Daniel Parras
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Pere Santamaria
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- *Correspondence: Jacinto López-Sagaseta, ; Pere Santamaria,
| | - Jacinto López-Sagaseta
- Unit of Protein Crystallography and Structural Immunology, Navarrabiomed, Navarra, Spain
- Public University of Navarra (UPNA), Pamplona, Spain
- Navarra University Hospital, Pamplona, Spain
- *Correspondence: Jacinto López-Sagaseta, ; Pere Santamaria,
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Hopkins JR, MacLachlan BJ, Harper S, Sewell AK, Cole DK. Unconventional modes of peptide-HLA-I presentation change the rules of TCR engagement. DISCOVERY IMMUNOLOGY 2022; 1:kyac001. [PMID: 38566908 PMCID: PMC10917088 DOI: 10.1093/discim/kyac001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 04/04/2024]
Abstract
The intracellular proteome of virtually every nucleated cell in the body is continuously presented at the cell surface via the human leukocyte antigen class I (HLA-I) antigen processing pathway. This pathway classically involves proteasomal degradation of intracellular proteins into short peptides that can be presented by HLA-I molecules for interrogation by T-cell receptors (TCRs) expressed on the surface of CD8+ T cells. During the initiation of a T-cell immune response, the TCR acts as the T cell's primary sensor, using flexible loops to mould around the surface of the pHLA-I molecule to identify foreign or dysregulated antigens. Recent findings demonstrate that pHLA-I molecules can also be highly flexible and dynamic, altering their shape according to minor polymorphisms between different HLA-I alleles, or interactions with different peptides. These flexible presentation modes have important biological consequences that can, for example, explain why some HLA-I alleles offer greater protection against HIV, or why some cancer vaccine approaches have been ineffective. This review explores how these recent findings redefine the rules for peptide presentation by HLA-I molecules and extend our understanding of the molecular mechanisms that govern TCR-mediated antigen discrimination.
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Affiliation(s)
- Jade R Hopkins
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | | | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
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11
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Sun Y, Li X, Wang T, Li W. Core Fucosylation Regulates the Function of Pre-BCR, BCR and IgG in Humoral Immunity. Front Immunol 2022; 13:844427. [PMID: 35401499 PMCID: PMC8990897 DOI: 10.3389/fimmu.2022.844427] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/25/2022] [Indexed: 11/20/2022] Open
Abstract
Most of the membrane molecules involved in immune response are glycosylated. N-glycans linked to asparagine (Asn) of immune molecules contribute to the protein conformation, surface expression, stability, and antigenicity. Core fucosylation catalyzed by core fucosyltransferase (FUT8) is the most common post-translational modification. Core fucosylation is essential for evoking a proper immune response, which this review aims to communicate. First, FUT8 deficiency suppressed the interaction between μHC and λ5 during pre-BCR assembly is given. Second, we described the effects of core fucosylation in B cell signal transduction via BCR. Third, we investigated the role of core fucosylation in the interaction between helper T (TH) cells and B cells. Finally, we showed the role of FUT8 on the biological function of IgG. In this review, we discussed recent insights into the sites where core fucosylation is critical for humoral immune responses.
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Affiliation(s)
- Yuhan Sun
- College of Basic Medical Science, Dalian Medical University, Dalian, China
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Pharmaceutical University, Sendai, Japan
| | - Xueying Li
- Research Institute for Microbial Diseases and World Premier International Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Tiantong Wang
- College of Basic Medical Science, Dalian Medical University, Dalian, China
| | - Wenzhe Li
- College of Basic Medical Science, Dalian Medical University, Dalian, China
- *Correspondence: Wenzhe Li,
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Bartolo L, Afroz S, Pan YG, Xu R, Williams L, Lin CF, Friedman ES, Gimotty PA, Wu GD, Su LF. SARS-CoV-2-specific T cells in unexposed adults display broad trafficking potential and cross-react with commensal antigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.11.29.470421. [PMID: 34873598 PMCID: PMC8647649 DOI: 10.1101/2021.11.29.470421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The baseline composition of T cells directly impacts later response to a pathogen, but the complexity of precursor states remains poorly defined. Here we examined the baseline state of SARS-CoV-2 specific T cells in unexposed individuals. SARS-CoV-2 specific CD4 + T cells were identified in pre-pandemic blood samples by class II peptide-MHC tetramer staining and enrichment. Our data revealed a substantial number of SARS-CoV-2 specific T cells that expressed memory phenotype markers, including memory cells with gut homing receptors. T cell clones generated from tetramer-labeled cells cross-reacted with bacterial peptides and responded to stool lysates in a MHC-dependent manner. Integrated phenotypic analyses revealed additional precursor diversity that included T cells with distinct polarized states and trafficking potential to other barrier tissues. Our findings illustrate a complex pre-existing memory pool poised for immunologic challenges and implicate non-infectious stimuli from commensal colonization as a factor that shapes pre-existing immunity. ONE SENTENCE SUMMARY Pre-existing immunity to SARS-CoV-2 contains a complex pool of precursor lymphocytes that include differentiated cells with broad tissue tropism and the potential to cross-react with commensal antigens.
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Affiliation(s)
- Laurent Bartolo
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sumbul Afroz
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi-Gen Pan
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ruozhang Xu
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Lea Williams
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Chin-Fang Lin
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Phyllis A. Gimotty
- Department of Biostatistics, Informatics, and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laura F. Su
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
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13
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Edholm ES, Fenton CG, Mondot S, Paulssen RH, Lefranc MP, Boudinot P, Magadan S. Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids. Front Immunol 2021; 12:753960. [PMID: 34733285 PMCID: PMC8559430 DOI: 10.3389/fimmu.2021.753960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/28/2021] [Indexed: 12/17/2022] Open
Abstract
In jawed vertebrates, two major T cell populations have been characterized. They are defined as α/β or γ/δ T cells, based on the expressed T cell receptor. Salmonids (family Salmonidae) include two key teleost species for aquaculture, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) which constitute important models for fish immunology and important targets for vaccine development. The growing interest to decipher the dynamics of adaptive immune responses against pathogens or vaccines has resulted in recent efforts to sequence the immunoglobulin (IG) or antibodies and T cell receptor (TR) repertoire in these species. In this context, establishing a comprehensive and coherent locus annotation is the fundamental basis for the analysis of high-throughput repertoire sequencing data. We therefore decided to revisit the description and annotation of TRA/TRD locus in Atlantic salmon and two strains of rainbow trout (Swanson and Arlee) using the now available high-quality genome assemblies. Phylogenetic analysis of functional TRA/TRD V genes from these three genomes led to the definition of 25 subgroups shared by both species, some with particular feature. A total of 128 TRAJ genes were identified in Salmo, the majority with a close counterpart in Oncorhynchus. Analysis of expressed TRA repertoire indicates that most TRAV gene subgroups are expressed at mucosal and systemic level. The present work on TRA/TRD locus annotation along with the analysis of TRA repertoire sequencing data show the feasibility and advantages of a common salmonid TRA/TRD nomenclature that allows an accurate annotation and analysis of high-throughput sequencing results, across salmonid T cell subsets.
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Affiliation(s)
- Eva-Stina Edholm
- Faculty of Biosciences, Fisheries & Economics, Norwegian College of Fishery Science, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Christopher Graham Fenton
- Clinical Bioinformatics Research Group, Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Stanislas Mondot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.,GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ruth H Paulssen
- Clinical Bioinformatics Research Group, Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System (IMGT), Laboratoire d´ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier Cedex, France
| | - Pierre Boudinot
- Université Paris Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Susana Magadan
- Immunology Laboratory, Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain.,Galicia Sur Health Research Institute (IIS-GS), Hospital Alvaro Cunqueiro, Vigo, Spain
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14
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Milighetti M, Shawe-Taylor J, Chain B. Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes. Front Physiol 2021; 12:730908. [PMID: 34566692 PMCID: PMC8456106 DOI: 10.3389/fphys.2021.730908] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
The physical interaction between the T cell receptor (TCR) and its cognate antigen causes T cells to activate and participate in the immune response. Understanding this physical interaction is important in predicting TCR binding to a target epitope, as well as potential cross-reactivity. Here, we propose a way of collecting informative features of the binding interface from homology models of T cell receptor-peptide-major histocompatibility complex (TCR-pMHC) complexes. The information collected from these structures is sufficient to discriminate binding from non-binding TCR-pMHC pairs in multiple independent datasets. The classifier is limited by the number of crystal structures available for the homology modelling and by the size of the training set. However, the classifier shows comparable performance to sequence-based classifiers requiring much larger training sets.
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Affiliation(s)
- Martina Milighetti
- Division of Infection and Immunity, University College London, London, United Kingdom
- Cancer Institute, University College London, London, United Kingdom
| | - John Shawe-Taylor
- Department of Computer Science, University College London, London, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
- Department of Computer Science, University College London, London, United Kingdom
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15
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New peptides with immunomodulatory activity identified from rice proteins through peptidomic and in silico analysis. Food Chem 2021; 364:130357. [PMID: 34174647 DOI: 10.1016/j.foodchem.2021.130357] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 12/22/2022]
Abstract
The new food-derived bio-functional peptides are urgently needed globally, but the separation and purification process for obtaining the immunopeptides from food is low efficiency and highly time-consuming. In the present study, rice proteins were extracted and identified by using liquid chromatography/tandem mass spectrometry (LC-MS/MS). Furthermore, a strategy combining immuno-prediction and in silico simulation was used to screen for peptides showing immunomodulatory activity, including inhibition of the release of nitric oxide, tumor necrosis factor-α, and the interleukins IL-6 and IL-1β in lipopolysaccharide-induced RAW264.7 mouse macrophages. This LC-MS/MS identification and immuno-prediction method may provide insights for the potential identification of more food-derived immunopeptides.
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16
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Affiliation(s)
- Pirooz Zareie
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Carine Farenc
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Nicole L La Gruta
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
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17
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Zhang L, Liu Y, Meng G, Liang R, Zhang B, Xia C. Structural and Biophysical Insights into the TCRαβ Complex in Chickens. iScience 2020; 23:101828. [PMID: 33305184 PMCID: PMC7711287 DOI: 10.1016/j.isci.2020.101828] [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: 07/09/2020] [Revised: 09/16/2020] [Accepted: 11/16/2020] [Indexed: 10/25/2022] Open
Abstract
In this work, chicken HPAIV H5N1 epitope-specific TCRαβ (ch-TCRαβ) was isolated and its structure was determined. The Cα domain of ch-TCRαβ does not exhibit the typical structure of human TCRαβ, and the DE loop extends outward, resulting in close proximity between the Cα domain of ch-TCRαβ and CD3εδ/γ. The FG loop of the Cβ domain of ch-TCRαβ is shorter. The changes in the C domains of ch-TCRαβ and the difference in chicken CD3εδ/γ confirm that the complexes formed by TCRαβ and CD3εδ/γ differ from those in humans. In the chicken complex, a positively charged cleft is formed between the two CDR3 loops that might accommodate the acidic side chains of the chicken pMHC-I-bound HPAIV epitope intermediate portion oriented toward ch-TCRαβ. This is the first reported structure of chicken TCRαβ, and it provides a structural model of the ancestral TCR system in the immune synapses between T cells and antigen-presenting cells in lower vertebrates.
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Affiliation(s)
- Lijie Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China.,Joint National Laboratory for Antibody Drug Engineering, Key Laboratory of Cell and Molecular Immunology, School of Medical Sciences, Henan University, Kaifeng 475004, China
| | - Yanjie Liu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Geng Meng
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Ruiying Liang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Bing Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
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18
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Repertoire-scale determination of class II MHC peptide binding via yeast display improves antigen prediction. Nat Commun 2020; 11:4414. [PMID: 32887877 PMCID: PMC7473865 DOI: 10.1038/s41467-020-18204-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/12/2020] [Indexed: 02/03/2023] Open
Abstract
CD4+ helper T cells contribute important functions to the immune response during pathogen infection and tumor formation by recognizing antigenic peptides presented by class II major histocompatibility complexes (MHC-II). While many computational algorithms for predicting peptide binding to MHC-II proteins have been reported, their performance varies greatly. Here we present a yeast-display-based platform that allows the identification of over an order of magnitude more unique MHC-II binders than comparable approaches. These peptides contain previously identified motifs, but also reveal new motifs that are validated by in vitro binding assays. Training of prediction algorithms with yeast-display library data improves the prediction of peptide-binding affinity and the identification of pathogen-associated and tumor-associated peptides. In summary, our yeast-display-based platform yields high-quality MHC-II-binding peptide datasets that can be used to improve the accuracy of MHC-II binding prediction algorithms, and potentially enhance our understanding of CD4+ T cell recognition. Identifying peptides that can bind major histocompatibility complex II (MHC-II) is important for our understanding of T cell immunity and specificity. Here the authors present a yeast-display library screening approach that identifies more potential binders than various reported algorithms to help expand our understanding for antigen presentation.
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19
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Wang JH. T cell receptors, mechanosensors, catch bonds and immunotherapy. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 153:23-27. [DOI: 10.1016/j.pbiomolbio.2020.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 01/15/2020] [Indexed: 12/28/2022]
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20
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Singh NK, Abualrous ET, Ayres CM, Noé F, Gowthaman R, Pierce BG, Baker BM. Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen. Proteins 2020; 88:503-513. [PMID: 31589793 PMCID: PMC6982585 DOI: 10.1002/prot.25829] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/08/2019] [Accepted: 09/17/2019] [Indexed: 11/11/2022]
Abstract
Recognition of antigenic peptides bound to major histocompatibility complex (MHC) proteins by αβ T cell receptors (TCRs) is a hallmark of T cell mediated immunity. Recent data suggest that variations in TCR binding geometry may influence T cell signaling, which could help explain outliers in relationships between physical parameters such as TCR-pMHC binding affinity and T cell function. Traditionally, TCR binding geometry has been described with simple descriptors such as the crossing angle, which quantifies what has become known as the TCR's diagonal binding mode. However, these descriptors often fail to reveal distinctions in binding geometry that are apparent through visual inspection. To provide a better framework for relating TCR structure to T cell function, we developed a comprehensive system for quantifying the geometries of how TCRs bind peptide/MHC complexes. We show that our system can discern differences not clearly revealed by more common methods. As an example of its potential to impact biology, we used it to reveal differences in how TCRs bind class I and class II peptide/MHC complexes, which we show allow the TCR to maximize access to and "read out" the peptide antigen. We anticipate our system will be of use in not only exploring these and other details of TCR-peptide/MHC binding interactions, but also addressing questions about how TCR binding geometry relates to T cell function, as well as modeling structural properties of class I and class II TCR-peptide/MHC complexes from sequence information. The system is available at https://tcr3d.ibbr.umd.edu/tcr_com or for download as a script.
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MESH Headings
- Binding Sites
- Crystallography, X-Ray
- Histocompatibility Antigens Class I/chemistry
- Histocompatibility Antigens Class I/immunology
- Histocompatibility Antigens Class I/metabolism
- Histocompatibility Antigens Class II/chemistry
- Histocompatibility Antigens Class II/immunology
- Histocompatibility Antigens Class II/metabolism
- Humans
- Models, Molecular
- Principal Component Analysis
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocytes/chemistry
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Thermodynamics
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Affiliation(s)
- Nishant K. Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Esam T. Abualrous
- Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Frank Noé
- Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Ragul Gowthaman
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Brian G. Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
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21
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Agrawal B. Heterologous Immunity: Role in Natural and Vaccine-Induced Resistance to Infections. Front Immunol 2019; 10:2631. [PMID: 31781118 PMCID: PMC6856678 DOI: 10.3389/fimmu.2019.02631] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/23/2019] [Indexed: 12/11/2022] Open
Abstract
The central paradigm of vaccination is to generate resistance to infection by a specific pathogen when the vacinee is re-exposed to that pathogen. This paradigm is based on two fundamental characteristics of the adaptive immune system, specificity and memory. These characteristics come from the clonal specificity of T and B cells and the long-term survival of previously-encountered memory cells which can rapidly and specifically expand upon re-exposure to the same specific antigen. However, there is an increasing awareness of the concept, as well as experimental documentation of, heterologous immunity and cross-reactivity of adaptive immune lymphocytes in protection from infection. This awareness is supported by a number of human epidemiological studies in vaccine recipients and/or individuals naturally-resistant to certain infections, as well as studies in mouse models of infections, and indeed theoretical considerations regarding the disproportional repertoire of available T and B cell clonotypes compared to antigenic epitopes found on pathogens. Heterologous immunity can broaden the protective outcomes of vaccinations, and natural resistance to infections. Besides exogenous microbes/pathogens and/or vaccines, endogenous microbiota can also impact the outcomes of an infection and/or vaccination through heterologous immunity. Moreover, utilization of viral and/or bacterial vaccine vectors, capable of inducing heterologous immunity may also influence the natural course of many infections/diseases. This review article will briefly discuss these implications and redress the central dogma of specificity in the immune system.
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Affiliation(s)
- Babita Agrawal
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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22
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Bentzen AK, Hadrup SR. T-cell-receptor cross-recognition and strategies to select safe T-cell receptors for clinical translation. IMMUNO-ONCOLOGY AND TECHNOLOGY 2019; 2:1-10. [PMID: 35036898 PMCID: PMC8741623 DOI: 10.1016/j.iotech.2019.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Adoptive transfer of T-cell-receptor (TCR)-transduced T cells has shown promising results for cancer treatment, but has also produced severe immunotoxicities caused by on-target as well as off-target TCR recognition. Off-target toxicities are related to the ability of a single T cell to cross-recognize and respond to several different peptide–major histocompatibility complex (pMHC) antigens; a property that is essential for providing broad antigenic coverage despite a confined number of unique TCRs in the human body. However, this degeneracy makes it incredibly difficult to account for the range of targets that any TCR might recognize, which represents a major challenge for the clinical development of therapeutic TCRs. The prospect of using affinity-optimized TCRs has been impeded due to observations that affinity enhancement might alter the specificity of a TCR, thereby increasing the risk that it will cross-recognize endogenous tissue. Strategies for selecting safe TCRs for the clinic have included functional assessment after individual incubations with tissue-derived primary cells or with peptides substituted with single amino acids. However, these strategies have not been able to predict cross-recognition sufficiently, leading to fatal cross-reactivity in clinical trials. Novel technologies have emerged that enable extensive characterization of the exact interaction points of a TCR with pMHC, which provides a foundation from which to make predictions of the cross-recognition potential of individual TCRs. This review describes current advances in strategies for dissecting the molecular interaction points of TCRs, focusing on their potential as tools for predicting cross-recognition of TCRs in clinical development. T-cell-receptor (TCR) degeneracy plays a fundamental role in the capacity of our immune systems to recognize foreign antigens. TCR cross-reactivity provides an inherent risk in TCR–gene transfer cell therapies. Advances in description of TCR cross-recognition can guide the selection process for TCRs into clinical use.
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23
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Lu S, White JV, Judy RI, Merritt LL, Lin WL, Zhang X, Solomides C, Nwaneshiudu I, Gaughan J, Monos DS, Oleszak EL, Platsoucas CD. Clonally expanded alpha-chain T-cell receptor (TCR) transcripts are present in aneurysmal lesions of patients with Abdominal Aortic Aneurysm (AAA). PLoS One 2019; 14:e0218990. [PMID: 31310631 PMCID: PMC6634378 DOI: 10.1371/journal.pone.0218990] [Citation(s) in RCA: 4] [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: 11/05/2018] [Accepted: 06/14/2019] [Indexed: 01/25/2023] Open
Abstract
Abdominal aortic aneurysm (AAA) is a life-threatening immunological disease responsible for 1 to 2% of all deaths in 65 year old or older individuals. Although mononuclear cell infiltrates have been demonstrated in AAA lesions and autoimmunity may be responsible for the initiation and account for the propagation of the disease, the information available about the pathogenesis of AAA is limited. To examine whether AAA lesions from patients with AAA contain clonally expanded α-chain TCR transcripts, we amplified by the non-palindromic adaptor-PCR (NPA-PCR)/Vα-specific PCR and/or the Vα-specific PCR these α-chain TCR transcripts. The amplified transcripts were cloned and sequenced. Substantial proportions of identical α-chain TCR transcripts were identified in AAA lesions of 4 of 5 patients, demonstrating that clonally expanded T cells are present in these AAA lesions. These results were statistically significant by the bimodal distribution. Three of 5 of these patients were typed by DNA-based HLA-typing and all three expressed DRB1 alleles containing the DRβGln70 amino acid residue that has been demonstrated to be associated with AAA. All three patients exhibited clonally expanded T cells in AAA lesions. Four of the 5 patients with AAA who exhibited clonal expansions of α-chain TCR transcripts, also exhibited clonal expansions of β-chain TCR transcripts in AAA lesions, as we have demonstrated previously (J Immunol 192:4897, 2014). αβ TCR-expressing T cells infiltrating AAA lesions contain T-cell clones which have undergone proliferation and clonal expansion in vivo in response to as yet unidentified specific antigens that may be self or nonself. These results provide additional evidence supporting the hypothesis that AAA is a specific antigen-driven T-cell autoimmune disease.
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MESH Headings
- Aged
- Aged, 80 and over
- Amino Acid Sequence/genetics
- Antigens/genetics
- Antigens/immunology
- Aortic Aneurysm, Abdominal/genetics
- Aortic Aneurysm, Abdominal/immunology
- Aortic Aneurysm, Abdominal/pathology
- Cells, Cultured
- Clone Cells/immunology
- Humans
- Male
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Sequence Analysis, RNA
- T-Lymphocytes/immunology
- T-Lymphocytes/pathology
- Transcription, Genetic
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Affiliation(s)
- Song Lu
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - John V. White
- Department of Surgery, Advocate Lutheran General Hospital and University of Illinois School of Medicine, Park Ridge, IL, United States of America
| | - Raquel I. Judy
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States of America
| | - Lisa L. Merritt
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States of America
| | - Wan Lu Lin
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - Xiaoying Zhang
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - Charalambos Solomides
- Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - Ifeyinwa Nwaneshiudu
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - John Gaughan
- Biostatistics Consulting Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - Dimitri S. Monos
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Emilia L. Oleszak
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States of America
- Department of Anatomy and Cell Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
- Center for Molecular Medicine, Old Dominion University, Norfolk, VA, United States of America
| | - Chris D. Platsoucas
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States of America
- Center for Molecular Medicine, Old Dominion University, Norfolk, VA, United States of America
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24
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Mallis RJ, Brazin KN, Duke-Cohan JS, Hwang W, Wang JH, Wagner G, Arthanari H, Lang MJ, Reinherz EL. NMR: an essential structural tool for integrative studies of T cell development, pMHC ligand recognition and TCR mechanobiology. JOURNAL OF BIOMOLECULAR NMR 2019; 73:319-332. [PMID: 30815789 PMCID: PMC6693947 DOI: 10.1007/s10858-019-00234-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 02/06/2019] [Indexed: 05/05/2023]
Abstract
Early studies of T cell structural biology using X-ray crystallography, surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) focused on a picture of the αβT cell receptor (αβTCR) component domains and their cognate ligands (peptides bound to MHC molecules, i.e. pMHCs) as static interaction partners. Moving forward requires integrating this corpus of data with dynamic technologies such as NMR, molecular dynamics (MD) simulations and real-time single molecule (SM) studies exemplified by optical tweezers (OT). NMR bridges relevant timescales and provides the potential for an all-atom dynamic description of αβTCR components prior to and during interactions with binding partners. SM techniques have opened up vistas in understanding the non-equilibrium nature of T cell signaling through the introduction of force-mediated binding measurements into the paradigm for T cell function. In this regard, bioforces consequent to T-lineage cell motility are now perceived as placing piconewton (pN)-level loads on single receptor-pMHC bonds to impact structural change and αβT-lineage biology, including peptide discrimination, cellular activation, and developmental progression. We discuss herein essential NMR technologies in illuminating the role of ligand binding in the preT cell receptor (preTCR), the αβTCR developmental precursor, and convergence of NMR, SM and MD data in advancing our comprehension of T cell development. More broadly we review the central hypothesis that the αβTCR is a mechanosensor, fostered by breakthrough NMR-based structural insights. Collectively, elucidating dynamic aspects through the integrative use of NMR, SM, and MD shall advance fundamental appreciation of the mechanism of T cell signaling as well as inform translational efforts in αβTCR and chimeric T cell (CAR-T) immunotherapies and T cell vaccinology.
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Affiliation(s)
- Robert J Mallis
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Dermatology, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Kristine N Brazin
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Jonathan S Duke-Cohan
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
- Department of Materials Science & Engineering, Texas A&M University, College Station, TX, 77843, USA
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, 02455, Republic of Korea
| | - Jia-Huai Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA.
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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25
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Yokoyama H, Mizutani R, Noguchi S, Hayashida N. Structures of the antibody 64M-5 Fab and its complex with dT(6-4)T indicate induced-fit and high-affinity mechanisms. Acta Crystallogr F Struct Biol Commun 2019; 75:80-88. [PMID: 30713158 PMCID: PMC6360445 DOI: 10.1107/s2053230x18017661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/13/2018] [Indexed: 12/20/2022] Open
Abstract
DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts produced by ultraviolet light are mutagenic and carcinogenic. The crystal structures of the anti-(6-4) photoproduct antibody 64M-5 Fab and of its complex with dT(6-4)T were determined at 2.5 and 2.0 Å resolution, respectively. A comparison between the dT(6-4)T-liganded and unliganded structures indicates that the side chain of His93L is greatly rotated and shifted on binding to dT(6-4)T, leading to the formation of an electrostatic interaction with the phosphate moiety of dT(6-4)T, which shows a remarkable induced fit. Based on a comparison of the dT(6-4)T-liganded structures of the 64M-5 and 64M-2 Fabs, the electrostatic interaction between the side chain of His93L in 64M-5 and the phosphate moiety of dT(6-4)T is lost for Leu93L in 64M-2, while Arg90L in 64M-5 instead of Gln90L in 64M-2 stabilizes the conformation of complementarity-determining region (CDR) L3. These differences contribute to the higher affinity of 64M-5 for dT(6-4)T compared with that of 64M-2.
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Affiliation(s)
- Hideshi Yokoyama
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Ryuta Mizutani
- Graduate School of Engineering, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan
| | - Shuji Noguchi
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Naoki Hayashida
- Division of Molecular Gerontology and Anti-Ageing Medicine, Department of Biochemistry and Molecular Biology, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan
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26
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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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27
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Yokoyama H, Sawada JI, Sato K, Ogo N, Kamei N, Ishikawa Y, Hara K, Asai A, Hashimoto H. Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors. ACS OMEGA 2018; 3:12284-12294. [PMID: 31459302 PMCID: PMC6644766 DOI: 10.1021/acsomega.8b00778] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/22/2018] [Indexed: 06/10/2023]
Abstract
For a better understanding of protein-inhibitor interactions, we report structural, thermodynamic, and biological analyses of the interactions between S-trityl-l-cysteine (STLC) derivatives and the motor domain of kinesin spindle protein Eg5. Binding of STLC-type inhibitors to Eg5 was enthalpically driven and entropically unfavorable. The introduction of a para-methoxy substituent in one phenyl ring of STLC enhances its inhibitory activity resulting from a larger enthalpy gain possibly due to the increased shape complementarity. The substituent fits to a recess in the binding pocket. To avoid steric hindrance, the substituted STLC is nudged toward the side opposite to the recess, which enhances the interaction of Eg5 with the remaining part of the inhibitor. Further introduction of an ethylene linkage between two phenyl rings enhances Eg5 inhibitory activity by reducing the loss of entropy in forming the complex. This study provides valuable examples of enhancing protein-inhibitor interactions without forming additional hydrogen bonds.
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Affiliation(s)
- Hideshi Yokoyama
- Faculty
of Pharmaceutical Sciences, Tokyo University
of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Jun-ichi Sawada
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kohei Sato
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Naohisa Ogo
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Nanami Kamei
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yoshinobu Ishikawa
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kodai Hara
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Akira Asai
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroshi Hashimoto
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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Abstract
PURPOSE OF REVIEW A successful human immunodeficiency virus-type 1 (HIV-1) vaccine will require immunogens that induce protective immune responses. However, recent studies suggest that the response to HIV-1 and perhaps other viruses may be altered by immune system exposure to intestinal microbiota-antigens. This review will discuss select aspects of these studies. RECENT FINDINGS Naïve CD4 T and B cell repertoires can be imprinted by intestinal microbiota-antigens to respond to virus epitopes prior to virus infection. A multiclade envelope (Env) gp145 DNA prime, recombinant adenovirus type 5 boost vaccine tested in a HIV Vaccine Trials Network (HVTN) phase IIb human vaccine efficacy trial (HVTN 505) induced a dominant gp41-reactive antibody response that was non-neutralizing and cross-reactive with intestinal microbiota. This vaccine regimen also induced a dominant gp41-reactive, intestinal microbiota-cross-reactive gp41 antibody response in neonatal and adult Rhesus macaques. Studies of naïve CD4 T cells have demonstrated cross-reactivity to both HIV-1 and influenza peptides. SUMMARY HIV-1 Env vaccine-induced CD4 T and B cell responses can originate from a pool of intestinal microbiota-cross-reactive immune cells. Moreover, intestinal microbiota-cross-reactive HIV-1 Env antibodies are ineffective in protection against HIV-1 infection. Thus, intestinal microbiota-imprinting of the B cell repertoire may be one of several roadblocks to the induction of protective HIV-1 antibodies.
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29
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Ott JA, Castro CD, Deiss TC, Ohta Y, Flajnik MF, Criscitiello MF. Somatic hypermutation of T cell receptor α chain contributes to selection in nurse shark thymus. eLife 2018; 7:28477. [PMID: 29664399 PMCID: PMC5931798 DOI: 10.7554/elife.28477] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 04/16/2018] [Indexed: 12/17/2022] Open
Abstract
Since the discovery of the T cell receptor (TcR), immunologists have assigned somatic hypermutation (SHM) as a mechanism employed solely by B cells to diversify their antigen receptors. Remarkably, we found SHM acting in the thymus on α chain locus of shark TcR. SHM in developing shark T cells likely is catalyzed by activation-induced cytidine deaminase (AID) and results in both point and tandem mutations that accumulate non-conservative amino acid replacements within complementarity-determining regions (CDRs). Mutation frequency at TcRα was as high as that seen at B cell receptor loci (BcR) in sharks and mammals, and the mechanism of SHM shares unique characteristics first detected at shark BcR loci. Additionally, fluorescence in situ hybridization showed the strongest AID expression in thymic corticomedullary junction and medulla. We suggest that TcRα utilizes SHM to broaden diversification of the primary αβ T cell repertoire in sharks, the first reported use in vertebrates.
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Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas, United States
| | - Caitlin D Castro
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, United States
| | - Thaddeus C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas, United States
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, United States
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, United States
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas, United States.,Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Texas, United States
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30
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31
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Liang W, Mao S, Sun S, Li M, Li Z, Yu R, Ma T, Gu J, Zhang J, Taniguchi N, Li W. Core Fucosylation of the T Cell Receptor Is Required for T Cell Activation. Front Immunol 2018; 9:78. [PMID: 29434598 PMCID: PMC5796888 DOI: 10.3389/fimmu.2018.00078] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/11/2018] [Indexed: 12/05/2022] Open
Abstract
CD4+ T cell activation promotes the pathogenic process of systemic lupus erythematosus (SLE). T cell receptor (TCR) complex are highly core fucosylated glycoproteins, which play important roles in T cell activation. In this study, we found that the core fucosylation of CD4+ T cells was significantly increased in SLE patients. Loss of core fucosyltransferase (Fut8), the sole enzyme for catalyzing the core fucosylation of N-glycan, significantly reduced CD4+ T cell activation and ameliorated the experimental autoimmune encephalomyelitis-induced syndrome in Fut8−/− mice. T cell activation with OVA323–339 loaded major histocompatibility complex II (pMHC-II) on B cell was dramatically attenuated in Fut8−/−OT-II CD4+ T cells compared with Fut8+/+OT-II CD4+ T cells. Moreover, the phosphorylation of ZAP-70 was significantly reduced in Fut8+/+OT-II CD4+ T cells by the treatment of fucosidase. Our results suggest that core fucosylation is required for efficient TCR–pMHC-II contacts in CD4+ T cell activation, and hyper core fucosylation may serve as a potential novel biomarker in the sera from SLE patients.
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Affiliation(s)
- Wei Liang
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Shanshan Mao
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Shijie Sun
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Ming Li
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Zhi Li
- Clinical Laboratory, Dalian Municipal Central Hospital, Dalian, China
| | - Rui Yu
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Tonghui Ma
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Jianguo Gu
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Jianing Zhang
- School of Life Science and Medicine, Dalian University of Technology, Panjin, China
| | - Naoyuki Taniguchi
- Systems Glycobiology Research Group, Advanced Science Institute, RIKEN, Saitama, Japan
| | - Wenzhe Li
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
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32
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Marrack P, Krovi SH, Silberman D, White J, Kushnir E, Nakayama M, Crooks J, Danhorn T, Leach S, Anselment R, Scott-Browne J, Gapin L, Kappler J. The somatically generated portion of T cell receptor CDR3α contributes to the MHC allele specificity of the T cell receptor. eLife 2017; 6:30918. [PMID: 29148973 PMCID: PMC5701794 DOI: 10.7554/elife.30918] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/16/2017] [Indexed: 01/24/2023] Open
Abstract
Mature T cells bearing αβ T cell receptors react with foreign antigens bound to alleles of major histocompatibility complex proteins (MHC) that they were exposed to during their development in the thymus, a phenomenon known as positive selection. The structural basis for positive selection has long been debated. Here, using mice expressing one of two different T cell receptor β chains and various MHC alleles, we show that positive selection-induced MHC bias of T cell receptors is affected both by the germline encoded elements of the T cell receptor α and β chain and, surprisingly, dramatically affected by the non germ line encoded portions of CDR3 of the T cell receptor α chain. Thus, in addition to determining specificity for antigen, the non germline encoded elements of T cell receptors may help the proteins cope with the extremely polymorphic nature of major histocompatibility complex products within the species.
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Affiliation(s)
- Philippa Marrack
- Howard Hughes Medical Institute, Denver, United States.,Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Sai Harsha Krovi
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Daniel Silberman
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Janice White
- Department of Biomedical Research, National Jewish Health, Denver, United States
| | - Eleanor Kushnir
- Department of Biomedical Research, National Jewish Health, Denver, United States
| | - Maki Nakayama
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States.,Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, United States
| | - James Crooks
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Thomas Danhorn
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Sonia Leach
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Randy Anselment
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | | | - Laurent Gapin
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - John Kappler
- Howard Hughes Medical Institute, Denver, United States.,Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
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33
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Cortés A, Coral J, McLachlan C, Benítez R. The Use of Planar Electromagnetic Fields in Effective Vaccine Design. Vaccines (Basel) 2017. [DOI: 10.5772/intechopen.69546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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34
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Cortés A, Coral J, McLachlan C, Benítez R, Pinilla L. Planar molecular arrangements aid the design of MHC class II binding peptides. Mol Biol 2017. [DOI: 10.1134/s002689331702008x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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35
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Kovrigina EA, Galiakhmetov AR, Kovrigin EL. The Ras G Domain Lacks the Intrinsic Propensity to Form Dimers. Biophys J 2016; 109:1000-8. [PMID: 26331257 DOI: 10.1016/j.bpj.2015.07.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 05/27/2015] [Accepted: 07/07/2015] [Indexed: 12/24/2022] Open
Abstract
Ras GTPase is a molecular switch controlling a number of cellular pathways including growth, proliferation, differentiation, and apoptosis. Recent reports indicated that Ras undergoes dimerization at the membrane surface through protein-protein interactions. If firmly established this property of Ras would require profound reassessment of a large amount of published data and modification of the Ras signaling paradigm. One proposed mechanism of dimerization involves formation of salt bridges between the two GTPase domains (G domains) leading to formation of a compact dimer as observed in Ras crystal structures. In this work, we interrogated the intrinsic ability of Ras to self-associate in solution by creating conditions of high local concentration through irreversibly tethering the two G domains together at their unstructured C-terminal tails. We evaluated possible self-association in this inverted tandem conjugate via analysis of the time-domain fluorescence anisotropy and NMR chemical shift perturbations. We did not observe the increased rotational correlation time expected for the G domain dimer. Variation of the ionic strength (to modulate stability of the salt bridges) did not affect the rotational correlation time in the tandem further supporting independent rotational diffusion of two G domains. In a parallel line of experiments to detect and map weak self-association of the G domains, we analyzed NMR chemical shifts perturbations at a number of sites near the crystallographic dimer interface. The nearly complete lack of chemical shift perturbations in the tandem construct supported a simple model with the independent G domains repelled from each other by their overall negative charge. These results lead us to the conclusion that self-association of the G domains cannot be responsible for homodimerization of Ras reported in the literature.
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36
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How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire. Proc Natl Acad Sci U S A 2016; 113:E1276-85. [PMID: 26884163 DOI: 10.1073/pnas.1522069113] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining αβ TCR sequences and structures for evidence of physicochemical compatibility with MHC proteins. We found that human TCRs are enriched in the capacity to engage a polymorphic, positively charged "hot-spot" region that is almost exclusive to the α1-helix of the common human class I MHC protein, HLA-A*0201 (HLA-A2). TCR binding necessitates hot-spot burial, yielding high energetic penalties that must be offset via complementary electrostatic interactions. Enrichment of negative charges in TCR binding loops, particularly the germ-line loops encoded by the TCR Vα and Vβ genes, provides this capacity and is correlated with restricted positioning of TCRs over HLA-A2. Notably, this enrichment is absent from antibody genes. The data suggest a built-in TCR compatibility with HLA-A2 that biases receptors toward, but does not compel, particular binding modes. Our findings provide an instructional example for how structurally pliant MHC biases can be encoded within TCRs.
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37
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Reinherz EL. αβ TCR-mediated recognition: relevance to tumor-antigen discovery and cancer immunotherapy. Cancer Immunol Res 2016; 3:305-12. [PMID: 25847967 DOI: 10.1158/2326-6066.cir-15-0042] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
αβ T lymphocytes sense perturbations in host cellular body components induced by infectious pathogens, oncogenic transformation, or chemical or physical damage. Millions to billions of these lymphocytes are generated through T-lineage development in the thymus, each endowed with a clonally restricted surface T-cell receptor (TCR). An individual TCR has the capacity to recognize a distinct "foreign" peptide among the myriad of antigens that the mammalian host must be capable of detecting. TCRs explicitly distinguish foreign from self-peptides bound to major histocompatibility complex (MHC) molecules. This is a daunting challenge, given that the MHC-linked peptidome consists of thousands of distinct peptides with a relevant nonself target antigen often embedded at low number, among orders of magnitude higher frequency self-peptides. In this Masters of Immunology article, I review how TCR structure and attendant mechanobiology involving nonlinear responses affect sensitivity as well as specificity to meet this requirement. Assessment of human tumor-cell display using state-of-the-art mass spectrometry physical detection methods that quantify epitope copy number can help to provide information about requisite T-cell functional avidity affording protection and/or therapeutic immunity. Future rational CD8 cytotoxic T-cell-based vaccines may follow, targeting virally induced cancers, other nonviral immunogenic tumors, and potentially even nonimmunogenic tumors whose peptide display can be purposely altered by MHC-binding drugs to stimulate immune attack.
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Affiliation(s)
- Ellis L Reinherz
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts.
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38
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Evolution of V genes from the TRV loci of mammals. Immunogenetics 2015; 67:371-84. [PMID: 26024913 DOI: 10.1007/s00251-015-0850-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/22/2015] [Indexed: 10/23/2022]
Abstract
Information concerning the evolution of T lymphocyte receptors (TCR) can be deciphered from that part of the molecule that recognizes antigen presented by major histocompatibility complex (MHC), namely the variable (V) regions. The genes that code for these variable regions are found within the TCR loci. Here, we describe a study of the evolutionary origin of V genes that code for the α and β chains of the TCR loci of mammals. In particular, we demonstrate that most of the 35 TRAV and 25 TRBV conserved genes found in Primates are also found in other Eutheria, while in Marsupials, Monotremes, and Reptiles, these genes diversified in a different manner. We also show that in mammals, all TRAV genes are derived from five ancestral genes, while all TRBV genes originate from four such genes. In Reptiles, the five TRAV and three out of the four TRBV ancestral genes exist, as well as other V genes not found in mammals. We also studied the TRGV and TRDV loci from all mammals, and we show a relationship of the TRDV to the TRAV locus throughout evolutionary time.
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Williams SJ, Ve T, Kobe B. A linker strategy for the production and crystallization of Toll/interleukin-1 receptor/resistance protein domain complexes. Protein Eng Des Sel 2015; 28:137-45. [PMID: 25777769 DOI: 10.1093/protein/gzv013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/11/2015] [Indexed: 02/02/2023] Open
Abstract
Structural characterization of protein-protein complexes is required to fully understand biological processes. However, such studies can be difficult, particularly when the interactions are transient. In some cases, the covalent linking of weakly interacting binding partners has been shown to facilitate structural studies. Here, we used this approach to investigate, by X-ray crystallography, the interactions between TIR (Toll/interleukin-1 receptor/resistance protein) domains from proteins involved in plant and animal innate immunity. Combinations of TIR domains known to interact were covalently attached using short glycine- and serine-rich linkers. This approach enabled the production of a number of TIR-TIR domain complexes in soluble form, facilitating crystallization studies. Crystallization of two of the tested combinations was achieved. Furthermore, production in soluble form was achieved for another two combinations, where this was not possible for individual proteins. Our results demonstrate that the linker strategy can aid in the structural studies of TIR domains. Similarly, this approach has potential for improving protein production and facilitating structural studies of other protein-protein interaction domains.
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Affiliation(s)
- Simon J Williams
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas Ve
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
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40
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Rana A, Rub A, Akhter Y. Proteome-wide B and T cell epitope repertoires in outer membrane proteins of Mycobacterium avium subsp. paratuberculosis have vaccine and diagnostic relevance: a holistic approach. J Mol Recognit 2015; 28:506-20. [PMID: 25727233 DOI: 10.1002/jmr.2458] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/05/2014] [Accepted: 12/16/2014] [Indexed: 11/11/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is an etiological agent of chronic inflammation of the intestine among ruminants and humans. Currently, there are no effective vaccines and sensitive diagnostic tests available for its control and detection. For this, it is of paramount importance to identify the MAP antigens, which may be immunologically recognized by the host immune system. To address this challenge, we performed identification of the immunogenic epitopes in the MAP outer membrane proteins (OMPs). We have previously identified 57 MAP proteins as OMPs [Rana A, Rub A, Akhter Y. 2014. Molecular BioSystems, 10:2329-2337] and have evaluated them for the epitope selection and analysis employing a computational approach. Thirty-five MAP OMPs are reported with nine-mer peptides showing high binding affinity to major histocompatibility complex (MHC) class I molecules and 28 MAP OMPs with 15-mer peptides of high binding affinity for MHC class II molecules. The presence of MHC binding epitopes indicates the potential cell-mediated immune response inducing capacity of these MAP OMPs in infected host. To further investigate the humoral response inducing properties of OMPs of MAP, we report potential B cell epitopes based on the sequences of peptide antigens and their molecular structures. We also report 10 proteins having epitopes for both B and T cells representing potential candidates which may invoke both humoral and cellular immune responses in the host. These findings will greatly accelerate and expedite the formulation of effective and cost-efficient vaccines and diagnostic tests against MAP infection.
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Affiliation(s)
- Aarti Rana
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, Kangra, Himachal Pradesh, 176206, India
| | - Abdur Rub
- Infection and Immunity Laboratory, Department of Biotechnology, Jamia Millia Islamia (A Central University), New Delhi,, 110025, India
| | - Yusuf Akhter
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, Kangra, Himachal Pradesh, 176206, India
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Rechavi E, Lev A, Lee YN, Simon AJ, Yinon Y, Lipitz S, Amariglio N, Weisz B, Notarangelo LD, Somech R. Timely and spatially regulated maturation of B and T cell repertoire during human fetal development. Sci Transl Med 2015; 7:276ra25. [DOI: 10.1126/scitranslmed.aaa0072] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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TANIGUCHI M, HARADA M, DASHTSOODOL N, KOJO S. Discovery of NKT cells and development of NKT cell-targeted anti-tumor immunotherapy. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2015; 91:292-304. [PMID: 26194854 PMCID: PMC4631895 DOI: 10.2183/pjab.91.292] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 04/20/2015] [Indexed: 06/08/2023]
Abstract
Natural Killer T (NKT) cells are unique lymphocytes characterized by their expression of a single invariant antigen receptor encoded by Vα14Jα18 in mice and Vα24Jα18 in humans, which recognizes glycolipid antigens in association with the monomorphic CD1d molecule. NKT cells mediate adjuvant activity to activate both CD8T cells to kill MHC-positive tumor cells and NK cells to eliminate MHC-negative tumor at the same time in patients, resulting in the complete eradication of tumors without relapse. Therefore, the NKT cell-targeted therapy can be applied to any type of tumor and also to anyone individual, regardless of HLA type.Phase IIa clinical trials on advanced lung cancers and head and neck tumors have been completed and showed significantly prolonged median survival times with only the primary treatment. Another potential treatment option for the future is to use induced pluripotent stem cell (iPS)-derived NKT cells, which induced adjuvant effects on anti-tumor responses, inhibiting in vivo tumor growth in a mouse model.
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Affiliation(s)
- Masaru TANIGUCHI
- Laboratory of Immune Regulation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Michishige HARADA
- Laboratory of Immune Regulation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Nyambayar DASHTSOODOL
- Laboratory of Immune Regulation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Satoshi KOJO
- Laboratory of Immune Regulation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
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43
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Rossjohn J, Gras S, Miles JJ, Turner SJ, Godfrey DI, McCluskey J. T cell antigen receptor recognition of antigen-presenting molecules. Annu Rev Immunol 2014; 33:169-200. [PMID: 25493333 DOI: 10.1146/annurev-immunol-032414-112334] [Citation(s) in RCA: 489] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Major Histocompatibility Complex (MHC) locus encodes classical MHC class I and MHC class II molecules and nonclassical MHC-I molecules. The architecture of these molecules is ideally suited to capture and present an array of peptide antigens (Ags). In addition, the CD1 family members and MR1 are MHC class I-like molecules that bind lipid-based Ags and vitamin B precursors, respectively. These Ag-bound molecules are subsequently recognized by T cell antigen receptors (TCRs) expressed on the surface of T lymphocytes. Structural and associated functional studies have been highly informative in providing insight into these interactions, which are crucial to immunity, and how they can lead to aberrant T cell reactivity. Investigators have determined over thirty unique TCR-peptide-MHC-I complex structures and twenty unique TCR-peptide-MHC-II complex structures. These investigations have shown a broad consensus in docking geometry and provided insight into MHC restriction. Structural studies on TCR-mediated recognition of lipid and metabolite Ags have been mostly confined to TCRs from innate-like natural killer T cells and mucosal-associated invariant T cells, respectively. These studies revealed clear differences between TCR-lipid-CD1, TCR-metabolite-MR1, and TCR-peptide-MHC recognition. Accordingly, TCRs show remarkable structural and biological versatility in engaging different classes of Ag that are presented by polymorphic and monomorphic Ag-presenting molecules of the immune system.
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Affiliation(s)
- Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia; ,
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44
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Olsen LR, Campos B, Barnkob MS, Winther O, Brusic V, Andersen MH. Bioinformatics for cancer immunotherapy target discovery. Cancer Immunol Immunother 2014; 63:1235-49. [PMID: 25344903 PMCID: PMC11029190 DOI: 10.1007/s00262-014-1627-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 10/08/2014] [Indexed: 12/13/2022]
Abstract
The mechanisms of immune response to cancer have been studied extensively and great effort has been invested into harnessing the therapeutic potential of the immune system. Immunotherapies have seen significant advances in the past 20 years, but the full potential of protective and therapeutic cancer immunotherapies has yet to be fulfilled. The insufficient efficacy of existing treatments can be attributed to a number of biological and technical issues. In this review, we detail the current limitations of immunotherapy target selection and design, and review computational methods to streamline therapy target discovery in a bioinformatics analysis pipeline. We describe specialized bioinformatics tools and databases for three main bottlenecks in immunotherapy target discovery: the cataloging of potentially antigenic proteins, the identification of potential HLA binders, and the selection epitopes and co-targets for single-epitope and multi-epitope strategies. We provide examples of application to the well-known tumor antigen HER2 and suggest bioinformatics methods to ameliorate therapy resistance and ensure efficient and lasting control of tumors.
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Affiliation(s)
- Lars Rønn Olsen
- Department of Biology, Bioinformatics Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark,
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45
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Understanding the structural dynamics of TCR-pMHC interactions. Trends Immunol 2014; 35:604-612. [DOI: 10.1016/j.it.2014.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/20/2014] [Accepted: 10/20/2014] [Indexed: 12/23/2022]
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46
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Revisiting thymic positive selection and the mature T cell repertoire for antigen. Immunity 2014; 41:181-90. [PMID: 25148022 DOI: 10.1016/j.immuni.2014.07.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Indexed: 12/11/2022]
Abstract
To support effective host defense, the T cell repertoire must balance breadth of recognition with sensitivity for antigen. The concept that T lymphocytes are positively selected in the thymus is well established, but how this selection achieves such a repertoire has not been resolved. Here we suggest that it is direct linkage between self and foreign antigen recognition that produces the necessary blend of TCR diversity and specificity in the mature peripheral repertoire, enabling responses to a broad universe of unpredictable antigens while maintaining an adequate number of highly sensitive T cells in a population of limited size. Our analysis also helps to explain how diversity and frequency of antigen-reactive cells in a T cell repertoire are adjusted in animals of vastly different size scale to enable effective antipathogen responses and suggests a possible binary architecture in the TCR repertoire that is divided between germline-related optimal binding and diverse recognition.
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47
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Law SC, Benham H, Reid HH, Rossjohn J, Thomas R. Identification of Self-antigen–specific T Cells Reflecting Loss of Tolerance in Autoimmune Disease Underpins Preventative Immunotherapeutic Strategies in Rheumatoid Arthritis. Rheum Dis Clin North Am 2014; 40:735-52. [DOI: 10.1016/j.rdc.2014.07.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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48
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The immunology connection--my first T cell receptor structure projects. Protein Cell 2014; 5:649-52. [PMID: 25087847 PMCID: PMC4145086 DOI: 10.1007/s13238-014-0091-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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49
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Abstract
Molecular interactions at the interface between helper T cells and antigen-presenting B cells govern the ability to produce specific antibodies, which is a central event in protective immunity generated by natural infection or man-made vaccines. In order for a T cell to deliver effective help to a B cell and guide affinity maturation, it needs to provide feedback that is proportional to the amount of antigen the B cell collects with its surface antibody. This review focuses on mechanisms by which T and B cells manage to count the products of antigen capture and encourage B cells with the best receptors to dominate the response and make antibody-producing plasma cells. We discuss what is known about the proportionality of T cells responses to presented antigens and consider the mechanisms that B cells may use to keep count of positive feedback from T cells.
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Affiliation(s)
- Michael L Dustin
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, The University of Oxford, Roosevelt Drive, Headington OX3 7FY, UK; Skirball Institute of Biomolecular Medicine, Department of Pathology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
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50
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Stadinski BD, Trenh P, Duke B, Huseby PG, Li G, Stern LJ, Huseby ES. Effect of CDR3 sequences and distal V gene residues in regulating TCR-MHC contacts and ligand specificity. THE JOURNAL OF IMMUNOLOGY 2014; 192:6071-82. [PMID: 24813203 DOI: 10.4049/jimmunol.1303209] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mature T cell repertoire has the ability to orchestrate immunity to a wide range of potential pathogen challenges. This ability stems from thymic development producing individual T cell clonotypes that express TCRs with unique patterns of Ag reactivity. The Ag specificity of TCRs is created from the combinatorial pairing of one of a set of germline encoded TCR Vα and Vβ gene segments with randomly created CDR3 sequences. How the amalgamation of germline encoded and randomly created TCR sequences results in Ag receptors with unique patterns of ligand specificity is not fully understood. Using cellular, biophysical, and structural analyses, we show that CDR3α residues can modulate the geometry in which TCRs bind peptide-MHC (pMHC), governing whether and how germline encoded TCR Vα and Vβ residues interact with MHC. In addition, a CDR1α residue that is positioned distal to the TCR-pMHC binding interface is shown to contribute to the peptide specificity of T cells. These findings demonstrate that the specificity of individual T cell clonotypes arises not only from TCR residues that create direct contacts with the pMHC, but also from a collection of indirect effects that modulate how TCR residues are used to bind pMHC.
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Affiliation(s)
- Brian D Stadinski
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Peter Trenh
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Brian Duke
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Priya G Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Guoqi Li
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Eric S Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
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