1
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Rojas M, Acosta-Ampudia Y, Heuer LS, Zang W, M Monsalve D, Ramírez-Santana C, Anaya JM, M Ridgway W, A Ansari A, Gershwin ME. Antigen-specific T cells and autoimmunity. J Autoimmun 2024; 148:103303. [PMID: 39141985 DOI: 10.1016/j.jaut.2024.103303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/31/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024]
Abstract
Autoimmune diseases (ADs) showcase the intricate balance between the immune system's protective functions and its potential for self-inflicted damage. These disorders arise from the immune system's erroneous targeting of the body's tissues, resulting in damage and disease. The ability of T cells to distinguish between self and non-self-antigens is pivotal to averting autoimmune reactions. Perturbations in this process contribute to AD development. Autoreactive T cells that elude thymic elimination are activated by mimics of self-antigens or are erroneously activated by self-antigens can trigger autoimmune responses. Various mechanisms, including molecular mimicry and bystander activation, contribute to AD initiation, with specific triggers and processes varying across the different ADs. In addition, the formation of neo-epitopes could also be implicated in the emergence of autoreactivity. The specificity of T cell responses centers on the antigen recognition sequences expressed by T cell receptors (TCRs), which recognize peptide fragments displayed by major histocompatibility complex (MHC) molecules. The assortment of TCR gene combinations yields a diverse array of T cell populations, each with distinct affinities for self and non-self antigens. However, new evidence challenges the traditional notion that clonal expansion solely steers the selection of higher-affinity T cells. Lower-affinity T cells also play a substantial role, prompting the "two-hit" hypothesis. High-affinity T cells incite initial responses, while their lower-affinity counterparts perpetuate autoimmunity. Precision treatments that target antigen-specific T cells hold promise for avoiding widespread immunosuppression. Nevertheless, detection of such antigen-specific T cells remains a challenge, and multiple technologies have been developed with different sensitivities while still harboring several drawbacks. In addition, elements such as human leukocyte antigen (HLA) haplotypes and validation through animal models are pivotal for advancing these strategies. In brief, this review delves into the intricate mechanisms contributing to ADs, accentuating the pivotal role(s) of antigen-specific T cells in steering immune responses and disease progression, as well as the novel strategies for the identification of antigen-specific cells and their possible future use in humans. Grasping the mechanisms behind ADs paves the way for targeted therapeutic interventions, potentially enhancing treatment choices while minimizing the risk of systemic immunosuppression.
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Affiliation(s)
- Manuel Rojas
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA; Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia.
| | - Yeny Acosta-Ampudia
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia
| | - Luke S Heuer
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA
| | - Weici Zang
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA
| | - Diana M Monsalve
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia
| | - Carolina Ramírez-Santana
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia
| | | | - William M Ridgway
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA
| | - Aftab A Ansari
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA
| | - M Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA.
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2
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Bloodworth N, Chen W, Hunter K, Patrick D, Palubinsky A, Phillips E, Roeth D, Kalkum M, Mallal S, Davies S, Ao M, Moretti R, Meiler J, Harrison DG. Posttranslationally modified self-peptides promote hypertension in mouse models. J Clin Invest 2024; 134:e174374. [PMID: 39145457 PMCID: PMC11324298 DOI: 10.1172/jci174374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 06/13/2024] [Indexed: 08/16/2024] Open
Abstract
Posttranslational modifications can enhance immunogenicity of self-proteins. In several conditions, including hypertension, systemic lupus erythematosus, and heart failure, isolevuglandins (IsoLGs) are formed by lipid peroxidation and covalently bond with protein lysine residues. Here, we show that the murine class I major histocompatibility complex (MHC-I) variant H-2Db uniquely presents isoLG-modified peptides and developed a computational pipeline that identifies structural features for MHC-I accommodation of such peptides. We identified isoLG-adducted peptides from renal proteins, including sodium glucose transporter 2, cadherin 16, Kelch domain-containing protein 7A, and solute carrier family 23, that are recognized by CD8+ T cells in tissues of hypertensive mice, induce T cell proliferation in vitro, and prime hypertension after adoptive transfer. Finally, we find patterns of isoLG-adducted antigen restriction in class I human leukocyte antigens that are similar to those in murine analogs. Thus, we have used a combined computational and experimental approach to define likely antigenic peptides in hypertension.
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Affiliation(s)
| | - Wei Chen
- Division of Clinical Pharmacology, Department of Medicine
| | - Kuniko Hunter
- Division of Clinical Pharmacology, Department of Medicine
| | - David Patrick
- Division of Clinical Pharmacology, Department of Medicine
| | | | - Elizabeth Phillips
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Center for Drug Safety and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Daniel Roeth
- Department of Immunology and Theranostics, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Markus Kalkum
- Department of Immunology and Theranostics, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Simon Mallal
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Sean Davies
- Division of Clinical Pharmacology, Department of Medicine
| | - Mingfang Ao
- Division of Clinical Pharmacology, Department of Medicine
| | | | - Jens Meiler
- Center for Structural Biology, and
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Institute for Drug Discovery, Universität Leipzig Medical School, Leipzig, Germany
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3
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Loh TJ, Lim JJ, Jones CM, Dao HT, Tran MT, Baker DG, La Gruta NL, Reid HH, Rossjohn J. The molecular basis underlying T cell specificity towards citrullinated epitopes presented by HLA-DR4. Nat Commun 2024; 15:6201. [PMID: 39043656 PMCID: PMC11266596 DOI: 10.1038/s41467-024-50511-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 07/12/2024] [Indexed: 07/25/2024] Open
Abstract
CD4+ T cells recognising citrullinated self-epitopes presented by HLA-DRB1 bearing the shared susceptibility epitope (SE) are implicated in rheumatoid arthritis (RA). However, the underlying T cell receptor (TCR) determinants of epitope specificity towards distinct citrullinated peptide antigens, including vimentin-64cit59-71 and α-enolase-15cit10-22 remain unclear. Using HLA-DR4-tetramers, we examine the T cell repertoire in HLA-DR4 transgenic mice and observe biased TRAV6 TCR gene usage across these two citrullinated epitopes which matches with TCR bias previously observed towards the fibrinogen β-74cit69-81 epitope. Moreover, shared TRAV26-1 gene usage is evident in four α-enolase-15cit10-22 reactive T cells in three human samples. Crystal structures of mouse TRAV6+ and human TRAV26-1+ TCR-HLA-DR4 complexes presenting vimentin-64cit59-71 and α-enolase-15cit10-22, respectively, show three-way interactions between the TCR, SE, citrulline, and the basis for the biased selection of TRAV genes. Position 2 of the citrullinated epitope is a key determinant underpinning TCR specificity. Accordingly, we provide a molecular basis of TCR specificity towards citrullinated epitopes.
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MESH Headings
- Humans
- Mice, Transgenic
- HLA-DR4 Antigen/immunology
- HLA-DR4 Antigen/genetics
- Arthritis, Rheumatoid/immunology
- Arthritis, Rheumatoid/genetics
- Mice
- Animals
- Vimentin/immunology
- Vimentin/metabolism
- Vimentin/genetics
- CD4-Positive T-Lymphocytes/immunology
- Citrullination
- Phosphopyruvate Hydratase/immunology
- Phosphopyruvate Hydratase/genetics
- Phosphopyruvate Hydratase/metabolism
- Epitopes, T-Lymphocyte/immunology
- Citrulline/metabolism
- Citrulline/immunology
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Epitopes/immunology
- Crystallography, X-Ray
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
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Affiliation(s)
- Tiing Jen Loh
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Jia Jia Lim
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Claerwen M Jones
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Hien Thy Dao
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Mai T Tran
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Daniel G Baker
- Janssen Research & Development, LLC, Horsham, Philadelphia, PA, USA
| | - Nicole L La Gruta
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Hugh H Reid
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK.
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4
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Hu Y, Huang J, Wang S, Sun X, Wang X, Yu H. Deciphering Autoimmune Diseases: Unveiling the Diagnostic, Therapeutic, and Prognostic Potential of Immune Repertoire Sequencing. Inflammation 2024:10.1007/s10753-024-02079-2. [PMID: 38914737 DOI: 10.1007/s10753-024-02079-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/08/2024] [Indexed: 06/26/2024]
Abstract
Autoimmune diseases (AIDs) are immune system disorders where the body exhibits an immune response to its own antigens, causing damage to its own tissues and organs. The pathogenesis of AIDs is incompletely understood. However, recent advances in immune repertoire sequencing (IR-seq) technology have opened-up a new avenue to study the IR. These studies have revealed the prevalence in IR alterations, potentially inducing AIDs by disrupting immune tolerance and thereby contributing to our comprehension of AIDs. IR-seq harbors significant potential for the clinical diagnosis, personalized treatment, and prognosis of AIDs. This article reviews the application and progress of IR-seq in diseases, such as multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, and type 1 diabetes, to enhance our understanding of the pathogenesis of AIDs and offer valuable references for the diagnosis and treatment of AIDs.
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Affiliation(s)
- Yuelin Hu
- Department of Immunology, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Jialing Huang
- Department of Immunology, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Shuqing Wang
- Department of Immunology, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Xin Sun
- School of Basic Medical Sciences, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Xin Wang
- School of Basic Medical Sciences, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Hongsong Yu
- Department of Immunology, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China.
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5
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Bhattacharya D, Theodoropoulos J, Nurmi K, Juutilainen T, Eklund KK, Koivuniemi R, Kelkka T, Mustjoki S, Lönnberg T. Single-cell characterisation of tissue homing CD4 + and CD8 + T cell clones in immune-mediated refractory arthritis. Mol Med 2024; 30:48. [PMID: 38594612 PMCID: PMC11005137 DOI: 10.1186/s10020-024-00802-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 02/21/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Immune-mediated arthritis is a group of autoinflammatory diseases, where the patient's own immune system attacks and destroys synovial joints. Sustained remission is not always achieved with available immunosuppressive treatments, warranting more detailed studies of T cell responses that perpetuate synovial inflammation in treatment-refractory patients. METHODS In this study, we investigated CD4 + and CD8 + T lymphocytes from the synovial tissue and peripheral blood of patients with treatment-resistant immune-mediated arthritis using paired single-cell RNA and TCR-sequencing. To gain insights into the trafficking of clonal families, we compared the phenotypes of clones with the exact same TCRß amino acid sequence between the two tissues. RESULTS Our results show that both CD4 + and CD8 + T cells display a more activated and inflamed phenotype in the synovial tissue compared to peripheral blood both at the population level and within individual T cell families. Furthermore, we found that both cell subtypes exhibited clonal expansion in the synovial tissue. CONCLUSIONS Our findings suggest that the local environment in the synovium drives the proliferation of activated cytotoxic T cells, and both CD4 + and CD8 + T cells may contribute to tissue destruction and disease pathogenesis.
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Affiliation(s)
- Dipabarna Bhattacharya
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Jason Theodoropoulos
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Katariina Nurmi
- Translational Immunology Research Program, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Faculty of Medicine, Clinicum, Translational Immunology Program, University of Helsinki, Helsinki, Finland
| | | | - Kari K Eklund
- Translational Immunology Research Program, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Faculty of Medicine, Clinicum, Translational Immunology Program, University of Helsinki, Helsinki, Finland
- Department of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Riitta Koivuniemi
- Department of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tiina Kelkka
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.
- Translational Immunology Research Program, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
- Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- InFlames Flagship Center, University of Turku, Turku, Finland.
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6
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Klareskog L. Rheumatology tolerance for cure (RTCure) - an IMI project aimed at prevention and cure of RA. Semin Arthritis Rheum 2024; 64S:152322. [PMID: 38007362 DOI: 10.1016/j.semarthrit.2023.152322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/23/2023] [Indexed: 11/27/2023]
Abstract
The RT Cure project, supported from the Innovative Medicines Initiative (IMI) has been active for 6 years and involved several European and one Australian rheumatology institutions, six major pharma companies and a few small companies. The present report describes the major aims and results of the project which include new understanding of specificity and regulation a of adaptive immunity that precedes RA and is active in established disease. use this understanding to predict risk for RA and establish registers of at risk for RA cohorts. support for clinical trials aimed at prevention of RA with knowledge and tools for immune surveillance. The progress in these areas, including the support to successful clinical trials for prevention will provide a basis for further development of prevention of RA using increasingly specific immunotherapies.
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Affiliation(s)
- Lars Klareskog
- Department of Medicine, Rheumatology Division, Karolinska Institutet, Stockholm Sweden.
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7
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Bardwell B, Bay J, Colburn Z. The clinical applications of immunosequencing. Curr Res Transl Med 2024; 72:103439. [PMID: 38447267 DOI: 10.1016/j.retram.2024.103439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/20/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024]
Abstract
Technological advances in high-throughput sequencing have opened the door for the interrogation of adaptive immune responses at unprecedented scale. It is now possible to determine the sequences of antibodies or T-cell receptors produced by individual B and T cells in a sample. This capability, termed immunosequencing, has transformed the study of both infectious and non-infectious diseases by allowing the tracking of dynamic changes in B and T cell clonal populations over time. This has improved our understanding of the pathology of cancers, autoimmune diseases, and infectious diseases. However, to date there has been only limited clinical adoption of the technology. Advances over the last decade and on the horizon that reduce costs and improve interpretability could enable widespread clinical use. Many clinical applications have been proposed and, while most are still undergoing research and development, some methods relying on immunosequencing data have been implemented, the most widespread of which is the detection of measurable residual disease. Here, we review the diagnostic, prognostic, and therapeutic applications of immunosequencing for both infectious and non-infectious diseases.
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Affiliation(s)
- B Bardwell
- Department of Clinical Investigation, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA
| | - J Bay
- Department of Medicine, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA
| | - Z Colburn
- Department of Clinical Investigation, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA.
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8
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Anang DC, Walter HAW, Lim J, Niewold ITG, van der Weele L, Aronica E, Eftimov F, Raaphorst J, van Schaik BDC, van Kampen AHC, van der Kooi AJ, de Vries N. TCRβ clones in muscle tissue share structural features in patients with idiopathic inflammatory myopathy and are associated with disease activity. Front Immunol 2024; 14:1279055. [PMID: 38268914 PMCID: PMC10806010 DOI: 10.3389/fimmu.2023.1279055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024] Open
Abstract
Objectives To characterize the T cell receptor (TCRβ) repertoire in peripheral blood and muscle tissues of treatment naïve patients with newly diagnosed idiopathic inflammatory myopathies (IIMs). Methods High throughput RNA sequencing of the TCRβ chain was performed in peripheral blood and muscle tissue in twenty newly-diagnosed treatment-naïve IIM patients (9 DM, 5 NM/OM, 5 IMNM and 1 ASyS) and healthy controls. Results thereof were correlated with markers of disease activity. Results Muscle tissue of IIM patients shows more expansion of TCRβ clones and decreased diversity when compared to peripheral blood of IIM as well as healthy controls (both p=0.0001). Several expanded TCRβ clones in muscle are tissue restricted and cannot be retrieved in peripheral blood. These clones have significantly longer CDR3 regions when compared to clones (also) found in circulation (p=0.0002), while their CDR3 region is more hydrophobic (p<0.01). Network analysis shows that clonal TCRβ signatures are shared between patients. Increased clonal expansion in muscle tissue is significantly correlated with increased CK levels (p=0.03), while it tends to correlate with decreased muscle strength (p=0.08). Conclusion Network analysis of clones in muscle of IIM patients shows shared clusters of sequences across patients. Muscle-restricted CDR3 TCRβ clones show specific structural features in their T cell receptor. Our results indicate that clonal TCRβ expansion in muscle tissue might be associated with disease activity. Collectively, these findings support a role for specific clonal T cell responses in muscle tissue in the pathogenesis of the IIM subtypes studied.
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Affiliation(s)
- Dornatien C. Anang
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Genome Analysis, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Hannah A. W. Walter
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Johan Lim
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Ilse T. G. Niewold
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Genome Analysis, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Linda van der Weele
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Filip Eftimov
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Joost Raaphorst
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Barbera D. C. van Schaik
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Institute, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Antoine H. C. van Kampen
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Institute, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Anneke J. van der Kooi
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Niek de Vries
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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9
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Moustakas AK, Nguyen H, James EA, Papadopoulos GK. Autoimmune susceptible HLA class II motifs facilitate the presentation of modified neoepitopes to potentially autoreactive T cells. Cell Immunol 2023; 390:104729. [PMID: 37301094 DOI: 10.1016/j.cellimm.2023.104729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/27/2023] [Accepted: 05/11/2023] [Indexed: 06/12/2023]
Abstract
Rheumatoid arthritis (RA), multiple sclerosis (MS), type 1 diabetes (T1D), and celiac disease (CD), are strongly associated with susceptible HLA class II haplotypes. The peptide-binding pockets of these molecules are polymorphic, thus each HLA class II protein presents a distinct set of peptides to CD4+ T cells. Peptide diversity is increased through post-translational modifications, generating non-templated sequences that enhance HLA binding and/or T cell recognition. The high-risk HLA-DR alleles that confer susceptibility to RA are notable for their ability to accommodate citrulline, promoting responses to citrullinated self-antigens. Likewise, HLA-DQ alleles associated with T1D and CD favor the binding of deamidated peptides. In this review, we discuss structural features that promote modified self-epitope presentation, provide evidence supporting the relevance of T cell recognition of such antigens in disease processes, and make a case that interrupting the pathways that generate such epitopes and reprogramming neoepitope-specific T cells are key strategies for effective therapeutic intervention.
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Affiliation(s)
- Antonis K Moustakas
- Department of Food Science and Technology, Faculty of Environmental Sciences, Ionian University, GR26100 Argostoli, Cephalonia, Greece
| | - Hai Nguyen
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Eddie A James
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA.
| | - George K Papadopoulos
- Laboratory of Biophysics, Biochemistry, Bioprocessing and Bioproducts, Faculty of Agricultural Technology, Technological Educational Institute of Epirus, GR47100 Arta, Greece
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10
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Carlé C, Degboe Y, Ruyssen-Witrand A, Arleevskaya MI, Clavel C, Renaudineau Y. Characteristics of the (Auto)Reactive T Cells in Rheumatoid Arthritis According to the Immune Epitope Database. Int J Mol Sci 2023; 24:ijms24054296. [PMID: 36901730 PMCID: PMC10001542 DOI: 10.3390/ijms24054296] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
T cells are known to be involved in the pathogenesis of rheumatoid arthritis (RA). Accordingly, and to better understand T cells' contribution to RA, a comprehensive review based on an analysis of the Immune Epitope Database (IEDB) was conducted. An immune CD8+ T cell senescence response is reported in RA and inflammatory diseases, which is driven by active viral antigens from latent viruses and cryptic self-apoptotic peptides. RA-associated pro-inflammatory CD4+ T cells are selected by MHC class II and immunodominant peptides, which are derived from molecular chaperones, host extra-cellular and cellular peptides that could be post-translationally modified (PTM), and bacterial cross-reactive peptides. A large panel of techniques have been used to characterize (auto)reactive T cells and RA-associated peptides with regards to their interaction with the MHC and TCR, capacity to enter the docking site of the shared epitope (DRB1-SE), capacity to induce T cell proliferation, capacity to select T cell subsets (Th1/Th17, Treg), and clinical contribution. Among docking DRB1-SE peptides, those with PTM expand autoreactive and high-affinity CD4+ memory T cells in RA patients with an active disease. Considering original therapeutic options in RA, mutated, or altered peptide ligands (APL) have been developed and are tested in clinical trials.
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Affiliation(s)
- Caroline Carlé
- Referral Medical Biology Laboratory, Immunology Department, Institut Fédératif de Biologie, Toulouse University Hospital Center, 31300 Toulouse, France
- Laboratory of Cell Biology and Cytology, Institut Fédératif de Biologie, Toulouse University Hospital Center, 31300 Toulouse, France
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM U1291, CNRS U5051, University Toulouse III, 31062 Toulouse, France
| | - Yannick Degboe
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM U1291, CNRS U5051, University Toulouse III, 31062 Toulouse, France
- Rheumatology Department, Toulouse University Hospital Center, 31300 Toulouse, France
| | | | - Marina I. Arleevskaya
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Cyril Clavel
- Laboratory of Cell Biology and Cytology, Institut Fédératif de Biologie, Toulouse University Hospital Center, 31300 Toulouse, France
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM U1291, CNRS U5051, University Toulouse III, 31062 Toulouse, France
| | - Yves Renaudineau
- Referral Medical Biology Laboratory, Immunology Department, Institut Fédératif de Biologie, Toulouse University Hospital Center, 31300 Toulouse, France
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM U1291, CNRS U5051, University Toulouse III, 31062 Toulouse, France
- Correspondence: ; Tel.: +33-561-776-245
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11
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Identification of proteinase 3 autoreactive CD4 +T cells and their T-cell receptor repertoires in antineutrophil cytoplasmic antibody-associated vasculitis. Kidney Int 2023; 103:973-985. [PMID: 36804380 DOI: 10.1016/j.kint.2023.01.023] [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: 06/09/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 02/17/2023]
Abstract
Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is an autoimmune disease involving autoreactivity to proteinase 3 (PR3) as demonstrated by presence of ANCAs. While autoantibodies are screened for diagnosis, autoreactive T cells and their features are less well-studied. Here, we investigated PR3-specific CD4+T cell responses and features of autoreactive T cells in patients with PR3-AAV, using a cohort of 72 patients with either active or inactive disease. Autoreactive PR3-specific CD4+T cells producing interferon γ in response to protein stimulation were found to express the G-protein coupled receptor 56 (GPR56), a cell surface marker that distinguishes T cells with cytotoxic capacity. GPR56+CD4+T cells were significantly more prominent in the blood of patients with inactive as compared to active disease, suggesting that these cells were affected by immunosuppression and/or that they migrated from the circulation to sites of organ involvement. Indeed, GPR56+CD4+T cells were identified in T-cell infiltrates of affected kidneys and an association with immunosuppressive therapy was found. Moreover, distinct TCR gene segment usage and shared (public) T cell clones were found for the PR3-reactive TCRs. Shared T cell clones were found in different patients with AAV carrying the disease-associated HLA-DP allele, demonstrating convergence of the autoreactive T cell repertoire. Thus, we identified a CD4+T cell signature in blood and in affected kidneys that display PR3 autoreactivity and associates with T cell cytotoxicity. Our data provide a basis for novel rationales for both immune monitoring and future therapeutic intervention in PR3-AAV.
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12
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Turcinov S, Af Klint E, Van Schoubroeck B, Kouwenhoven A, Mia S, Chemin K, Wils H, Van Hove C, De Bondt A, Keustermans K, Van Houdt J, Reumers J, Felix N, Rao NL, Peeters P, Stevenaert F, Klareskog L, McKinnon M, Baker D, Suri A, Malmström V. Diversity and Clonality of T Cell Receptor Repertoire and Antigen Specificities in Small Joints of Early Rheumatoid Arthritis. Arthritis Rheumatol 2022; 75:673-684. [PMID: 36409582 DOI: 10.1002/art.42407] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 07/17/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
OBJECTIVE CD4+ T cells are implicated in rheumatoid arthritis (RA) pathology from the strong association between RA and certain HLA class II gene variants. This study was undertaken to examine the synovial T cell receptor (TCR) repertoire, T cell phenotypes, and T cell specificities in small joints of RA patients at time of diagnosis before therapeutic intervention. METHODS Sixteen patients, of whom 11 patients were anti-citrullinated protein antibody (ACPA)-positive and 5 patients were ACPA-, underwent ultrasound-guided synovial biopsy of a small joint (n = 13) or arthroscopic synovial biopsy of a large joint (n = 3), followed by direct sorting of single T cells for paired sequencing of the αβ TCR together with flow cytometry analysis. TCRs from expanded CD4+ T cell clones of 4 patients carrying an HLA-DRB1*04:01 allele were artificially reexpressed to study antigen specificity. RESULTS T cell analysis demonstrated CD4+ dominance and the presence of peripheral helper T-like cells in both patient groups. We identified >4,000 unique TCR sequences, as well as 225 clonal expansions. Additionally, T cells with double α-chains were a recurring feature. We identified a biased gene usage of the Vβ chain segment TRBV20-1 in CD4+ cells from ACPA+ patients. In vitro stimulation of T cell lines expressing selected TCRs with an extensive panel of citrullinated and viral peptides identified several different virus-specific TCRs (e.g., human cytomegalovirus and human herpesvirus 2). Still, the majority of clones remained orphans with unknown specificity. CONCLUSION Minimally invasive biopsies of the RA synovium allow for single-cell TCR sequencing and phenotyping. Clonally expanded, viral-reactive T cells account for part of the diverse CD4+ T cell repertoire. TRBV20-1 bias in ACPA+ patients suggests recognition of common antigens.
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Affiliation(s)
- Sara Turcinov
- Division of Rheumatology, Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, and Theme of Inflammation and Ageing, Medical Unit Gastro, Derma, Rheuma, Karolinska University Hospital, Solna, Sweden
| | - Erik Af Klint
- Theme of Inflammation and Ageing, Medical Unit Gastro, Derma, Rheuma, Karolinska University Hospital, Solna, Sweden
| | | | | | - Sohel Mia
- Division of Rheumatology, Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Solna, Sweden
| | - Karine Chemin
- Division of Rheumatology, Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Solna, Sweden
| | - Hans Wils
- Janssen Research and Development, Beerse, Belgium
| | | | - An De Bondt
- Janssen Research and Development, Beerse, Belgium
| | | | | | - Joke Reumers
- Janssen Research and Development, Beerse, Belgium
| | - Nathan Felix
- Janssen Research and Development, Spring House, Pennsylvania
| | - Navin L Rao
- Janssen Research and Development, Horsham, Pennsylvania
| | | | | | - Lars Klareskog
- Division of Rheumatology, Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Solna, Sweden
| | | | - Daniel Baker
- Janssen Research and Development, Spring House, Pennsylvania
| | - Anish Suri
- Janssen Research and Development, Beerse, Belgium
| | - Vivianne Malmström
- Division of Rheumatology, Department of Medicine Solna, Center for Molecular Medicine, Karolinska University Hospital and Karolinska Institutet, Solna, Sweden
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13
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Kasmani MY, Ciecko AE, Brown AK, Petrova G, Gorski J, Chen YG, Cui W. Autoreactive CD8 T cells in NOD mice exhibit phenotypic heterogeneity but restricted TCR gene usage. Life Sci Alliance 2022; 5:5/10/e202201503. [PMID: 35667687 PMCID: PMC9170949 DOI: 10.26508/lsa.202201503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/27/2022] Open
Abstract
Paired scRNA-seq and scTCR-seq reveals that diabetogenic CD8 T cells in the islets and spleens of NOD mice exhibit phenotypic and clonal heterogeneity despite restricted TCR gene usage. Expression of certain TCR genes correlates with clonal proliferation and effector phenotype. Type 1 diabetes (T1D) is an autoimmune disorder defined by CD8 T cell–mediated destruction of pancreatic β cells. We have previously shown that diabetogenic CD8 T cells in the islets of non-obese diabetic mice are phenotypically heterogeneous, but clonal heterogeneity remains relatively unexplored. Here, we use paired single-cell RNA and T-cell receptor sequencing (scRNA-seq and scTCR-seq) to characterize autoreactive CD8 T cells from the islets and spleens of non-obese diabetic mice. scTCR-seq demonstrates that CD8 T cells targeting the immunodominant β-cell epitope IGRP206-214 exhibit restricted TCR gene usage. scRNA-seq identifies six clusters of autoreactive CD8 T cells in the islets and six in the spleen, including memory and exhausted cells. Clonal overlap between IGRP206-214–reactive CD8 T cells in the islets and spleen suggests these cells may circulate between the islets and periphery. Finally, we identify correlations between TCR genes and T-cell clonal expansion and effector fate. Collectively, our work demonstrates that IGRP206-214–specific CD8 T cells are phenotypically heterogeneous but clonally restricted, raising the possibility of selectively targeting these TCR structures for therapeutic benefit.
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Affiliation(s)
- Moujtaba Y Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Ashley E Ciecko
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ashley K Brown
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Galina Petrova
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jack Gorski
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Yi-Guang Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA .,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA .,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
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14
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Open label safety and efficacy pilot to study mitigation of equine recurrent uveitis through topical suppressor of cytokine signaling-1 mimetic peptide. Sci Rep 2022; 12:7177. [PMID: 35505065 PMCID: PMC9065145 DOI: 10.1038/s41598-022-11338-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 04/19/2022] [Indexed: 02/07/2023] Open
Abstract
Equine recurrent uveitis (ERU) is a painful and debilitating autoimmune disease and represents the only spontaneous model of human recurrent uveitis (RU). Despite the efficacy of existing treatments, RU remains a leading cause of visual handicap in horses and humans. Cytokines, which utilize Janus kinase 2 (Jak2) for signaling, drive the inflammatory processes in ERU that promote blindness. Notably, suppressor of cytokine signaling 1 (SOCS1), which naturally limits the activation of Jak2 through binding interactions, is often deficient in autoimmune disease patients. Significantly, we previously showed that topical administration of a SOCS1 peptide mimic (SOCS1-KIR) mitigated induced rodent uveitis. In this pilot study, we test the potential to translate the therapeutic efficacy observed in experimental rodent uveitis to equine patient disease. Through bioinformatics and peptide binding assays we demonstrate putative binding of the SOCS1-KIR peptide to equine Jak2. We also show that topical, or intravitreal injection of SOCS1-KIR was well tolerated within the equine eye through physical and ophthalmic examinations. Finally, we show that topical SOCS1-KIR administration was associated with significant clinical ERU improvement. Together, these results provide a scientific rationale, and supporting experimental evidence for the therapeutic use of a SOCS1 mimetic peptide in RU.
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