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Ternette N, Adamopoulou E, Purcell AW. How mass spectrometric interrogation of MHC class I ligandomes has advanced our understanding of immune responses to viruses. Semin Immunol 2023; 68:101780. [PMID: 37276649 DOI: 10.1016/j.smim.2023.101780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Affiliation(s)
- Nicola Ternette
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX37BN, UK.
| | - Eleni Adamopoulou
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX37BN, UK
| | - Anthony W Purcell
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
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2
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Jiang N, Malone M, Chizari S. Antigen-specific and cross-reactive T cells in protection and disease. Immunol Rev 2023; 316:120-135. [PMID: 37209375 PMCID: PMC10524458 DOI: 10.1111/imr.13217] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/22/2023]
Abstract
Human T cells have a diverse T-cell receptor (TCR) repertoire that endows them with the ability to identify and defend against a broad spectrum of antigens. The universe of possible antigens that T cells may encounter, however, is even larger. To effectively surveil such a vast universe, the T-cell repertoire must adopt a high degree of cross-reactivity. Likewise, antigen-specific and cross-reactive T-cell responses play pivotal roles in both protective and pathological immune responses in numerous diseases. In this review, we explore the implications of these antigen-driven T-cell responses, with a particular focus on CD8+ T cells, using infection, neurodegeneration, and cancer as examples. We also summarize recent technological advances that facilitate high-throughput profiling of antigen-specific and cross-reactive T-cell responses experimentally, as well as computational biology approaches that predict these interactions.
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Affiliation(s)
- Ning Jiang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA, 19104
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA, 19104
- Institute for RNA Innovation, University of Pennsylvania, Philadelphia, PA, 19104
| | - Michael Malone
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
| | - Shahab Chizari
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
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3
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Shapiro IE, Bassani-Sternberg M. The impact of immunopeptidomics: From basic research to clinical implementation. Semin Immunol 2023; 66:101727. [PMID: 36764021 DOI: 10.1016/j.smim.2023.101727] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/10/2023]
Abstract
The immunopeptidome is the set of peptides presented by the major histocompatibility complex (MHC) molecules, in humans also known as the human leukocyte antigen (HLA), on the surface of cells that mediate T-cell immunosurveillance. The immunopeptidome is a sampling of the cellular proteome and hence it contains information about the health state of cells. The peptide repertoire is influenced by intra- and extra-cellular perturbations - such as in the case of drug exposure, infection, or oncogenic transformation. Immunopeptidomics is the bioanalytical method by which the presented peptides are extracted from biological samples and analyzed by high-performance liquid chromatography coupled to tandem mass spectrometry (MS), resulting in a deep qualitative and quantitative snapshot of the immunopeptidome. In this review, we discuss published immunopeptidomics studies from recent years, grouped into three main domains: i) basic, ii) pre-clinical and iii) clinical research and applications. We review selected fundamental immunopeptidomics studies on the antigen processing and presentation machinery, on HLA restriction and studies that advanced our understanding of various diseases, and how exploration of the antigenic landscape allowed immune targeting at the pre-clinical stage, paving the way to pioneering exploratory clinical trials where immunopeptidomics is directly implemented in the conception of innovative treatments for cancer patients.
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Affiliation(s)
- Ilja E Shapiro
- Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland; Agora Cancer Research Centre, 1011 Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland; Agora Cancer Research Centre, 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland.
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4
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Connelley T, Nicastri A, Sheldrake T, Vrettou C, Fisch A, Reynisson B, Buus S, Hill A, Morrison I, Nielsen M, Ternette N. Immunopeptidomic Analysis of BoLA-I and BoLA-DR Presented Peptides from Theileria parva Infected Cells. Vaccines (Basel) 2022; 10:vaccines10111907. [PMID: 36423003 PMCID: PMC9699068 DOI: 10.3390/vaccines10111907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
The apicomplexan parasite Theileria parva is the causative agent of East Coast fever, usually a fatal disease for cattle, which is prevalent in large areas of eastern, central, and southern Africa. Protective immunity against T. parva is mediated by CD8+ T cells, with CD4+ T-cells thought to be important in facilitating the full maturation and development of the CD8+ T-cell response. T. parva has a large proteome, with >4000 protein-coding genes, making T-cell antigen identification using conventional screening approaches laborious and expensive. To date, only a limited number of T-cell antigens have been described. Novel approaches for identifying candidate antigens for T. parva are required to replace and/or complement those currently employed. In this study, we report on the use of immunopeptidomics to study the repertoire of T. parva peptides presented by both BoLA-I and BoLA-DR molecules on infected cells. The study reports on peptides identified from the analysis of 13 BoLA-I and 6 BoLA-DR datasets covering a range of different BoLA genotypes. This represents the most comprehensive immunopeptidomic dataset available for any eukaryotic pathogen to date. Examination of the immunopeptidome data suggested the presence of a large number of coprecipitated and non-MHC-binding peptides. As part of the work, a pipeline to curate the datasets to remove these peptides was developed and used to generate a final list of 74 BoLA-I and 15 BoLA-DR-presented peptides. Together, the data demonstrated the utility of immunopeptidomics as a method to identify novel T-cell antigens for T. parva and the importance of careful curation and the application of high-quality immunoinformatics to parse the data generated.
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Affiliation(s)
- Timothy Connelley
- The Roslin Institute, The Royal (Dick) School of Veterinary Science, The University of Edinburgh, Edinburgh EH25 9RG, UK
- Correspondence:
| | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, The University of Oxford, Oxford OX3 7BN, UK
| | - Tara Sheldrake
- The Roslin Institute, The Royal (Dick) School of Veterinary Science, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Christina Vrettou
- The Roslin Institute, The Royal (Dick) School of Veterinary Science, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Andressa Fisch
- Ribeirão Preto College of Nursing, University of São Paulo, Av Bandeirantes, Ribeirão Preto 3900, Brazil
| | - Birkir Reynisson
- Department of Health Technology, Technical University of Denmark, DK-2800 Copenhagen, Denmark
| | - Soren Buus
- Laboratory of Experimental Immunology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Adrian Hill
- The Jenner Institute, Nuffield Department of Medicine, The University of Oxford, Oxford OX3 7BN, UK
| | - Ivan Morrison
- The Roslin Institute, The Royal (Dick) School of Veterinary Science, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, DK-2800 Copenhagen, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín CP1650, Argentina
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, The University of Oxford, Oxford OX3 7BN, UK
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5
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Thawornkuno C, Nogrado K, Adisakwattana P, Thiangtrongjit T, Reamtong O. Identification and profiling of Trichinella spiralis circulating antigens and proteins in sera of mice with trichinellosis. PLoS One 2022; 17:e0265013. [PMID: 35271623 PMCID: PMC8912135 DOI: 10.1371/journal.pone.0265013] [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: 10/27/2021] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Trichinellosis is a zoonotic disease caused by the ingestion of the Trichinella nematode. With a worldwide incidence of approximately 10,000 cases per year, Trichinella spiralis is responsible for most human infections. There are no specific signs or symptoms of this parasitic infection. Muscle biopsy is the gold diagnostic standard for trichinellosis, but the technique is invasive and unable to detect the early stage of infection. Although immunodiagnostics are also available, antibody detection usually occurs after 3 weeks and prolonged up to 19 years after the acute phase. Therefore, additional diagnostic biomarkers must be identified to improve trichinellosis diagnosis. This study aimed to measure concentration changes in mouse serum proteins prior to T. spiralis infection and 2, 4 and 8 weeks after infection, and to identify T. spiralis circulating proteins and antigens using mass spectrometry-based proteomics. Mouse muscle-related proteins including inter-alpha-trypsin inhibitor heavy chain H2, a protein involved in the response to muscle tissue damage, were up-regulated in mouse sera during the T. spiralis larvae invasion. Additionally, 33 circulatory parasite proteins were identified in infected mouse sera. Notably, T. spiralis long-chain fatty acid transport protein 1 could be detected in the early stage of infection and peroxidasin-like protein was identified 2, 4 and 8 weeks after infection. Seventeen T. spiralis circulating antigens were detected in mouse immune complexes, with PX domain protein being found 2, 4 and 8 weeks after infection. Because peroxidasin-like protein and PX domain protein were detected at all post-infection time points, sequence alignments of these proteins were performed, which showed they are conserved among Trichinella spp. and have less similarity to the human and murine sequences. Integrative analysis of T. spiralis biomarkers throughout the course of infection may reveal additional diagnostic targets to improve early diagnosis of trichinellosis.
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Affiliation(s)
- Charin Thawornkuno
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kathyleen Nogrado
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tipparat Thiangtrongjit
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- * E-mail:
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Abstract
T cells must recognize pathogen-derived peptides bound to major histocompatibility complexes (MHCs) in order to initiate a cell-mediated immune response against an infection, or to support the development of high-affinity antibody responses. Identifying antigens presented on MHCs by infected cells and professional antigen-presenting cells (APCs) during infection may therefore provide a route toward developing new vaccines. Peptides bound to MHCs can be identified at whole-proteome scale using mass spectrometry-a technique referred to as "immunopeptidomics." This technique has emerged as a powerful tool for identifying potential vaccine targets in the context of many infectious diseases. In this review, we discuss the contributions immunopeptidomic studies have made to understanding antigen presentation and T cell priming in the context of infection and the potential for immunopeptidomics to inform the development of vaccines to address pressing global health problems in infectious disease.
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7
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Hare J, Macharia G, Yue L, Streatfield CL, Hunter E, Purcell A, Ternette N, Gilmour J. Direct identification of HLA-presented CD8 T cell epitopes from transmitted founder HIV-1 variants. Proteomics 2021; 21:e2100142. [PMID: 34275180 DOI: 10.1002/pmic.202100142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 11/09/2022]
Abstract
Cytotoxic T lymphocytes (CTLs) are a critical arm of the immune response to viral infections. The activation and expansion of antigen specific CTL requires recognition of peptide antigens presented on class I major histocompatibility complex molecules (MHC-1) of infected cells. Methods to identify presented peptide antigens that do not rely on the pre-existence of antigen specific CTL are critical to the development of new vaccines. We infected activated CD4+ T cells with two HIV-1 transmitted founder (TF) isolates and used high-resolution mass spectrometry (MS) to identify HIV peptides bound on MHC-1. Using this approach, we identified 14 MHC-1 bound peptides from across the two TF isolates. Assessment of predicted binding thresholds revealed good association of the identified peptides to the shared HLA alleles between the HIV+ donors and the naïve PBMC sample with three peptides identified through peptide sequencing inducing a CD8 T-cell response (p < 0.05). Direct infection of naïve CD4 cells by HIV TF isolates and sequencing of MHC-I presented peptides by HPLC-MS/MS enables identification of novel peptides that may be missed by alternative epitope mapping strategies and can provide valuable insight in to the first peptides presented by an HIV-infected CD4 cell in the first few days post infection.
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Affiliation(s)
- Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College London, London, UK.,IAVI, New York, New York, USA
| | - Gladys Macharia
- IAVI Human Immunology Laboratory, Imperial College London, London, UK.,Department of Infectious Disease, Imperial College London, London, UK
| | - Ling Yue
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Claire L Streatfield
- IAVI Human Immunology Laboratory, Imperial College London, London, UK.,Department of Infectious Disease, Imperial College London, London, UK
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Anthony Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | | | - Jill Gilmour
- Department of Infectious Disease, Imperial College London, London, UK
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Bosch-Camós L, López E, Navas MJ, Pina-Pedrero S, Accensi F, Correa-Fiz F, Park C, Carrascal M, Domínguez J, Salas ML, Nikolin V, Collado J, Rodríguez F. Identification of Promiscuous African Swine Fever Virus T-Cell Determinants Using a Multiple Technical Approach. Vaccines (Basel) 2021; 9:29. [PMID: 33430316 PMCID: PMC7825812 DOI: 10.3390/vaccines9010029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 11/23/2022] Open
Abstract
The development of subunit vaccines against African swine fever (ASF) is mainly hindered by the lack of knowledge regarding the specific ASF virus (ASFV) antigens involved in protection. As a good example, the identity of ASFV-specific CD8+ T-cell determinants remains largely unknown, despite their protective role being established a long time ago. Aiming to identify them, we implemented the IFNγ ELISpot as readout assay, using as effector cells peripheral blood mononuclear cells (PBMCs) from pigs surviving experimental challenge with Georgia2007/1. As stimuli for the ELISpot, ASFV-specific peptides or full-length proteins identified by three complementary strategies were used. In silico prediction of specific CD8+ T-cell epitopes allowed identifying a 19-mer peptide from MGF100-1L, as frequently recognized by surviving pigs. Complementarily, the repertoire of SLA I-bound peptides identified in ASFV-infected porcine alveolar macrophages (PAMs), allowed the characterization of five additional SLA I-restricted ASFV-specific epitopes. Finally, in vitro stimulation studies using fibroblasts transfected with plasmids encoding full-length ASFV proteins, led to the identification of MGF505-7R, A238L and MGF100-1L as promiscuously recognized antigens. Interestingly, each one of these proteins contain individual peptides recognized by surviving pigs. Identification of the same ASFV determinants by means of such different approaches reinforce the results presented here.
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Affiliation(s)
- Laia Bosch-Camós
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (L.B.-C.); (E.L.); (M.J.N.); (S.P.-P.); (F.C.-F.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
| | - Elisabet López
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (L.B.-C.); (E.L.); (M.J.N.); (S.P.-P.); (F.C.-F.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
| | - María Jesús Navas
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (L.B.-C.); (E.L.); (M.J.N.); (S.P.-P.); (F.C.-F.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
| | - Sonia Pina-Pedrero
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (L.B.-C.); (E.L.); (M.J.N.); (S.P.-P.); (F.C.-F.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
| | - Francesc Accensi
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
- UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, 08193 Bellaterra, Spain
| | - Florencia Correa-Fiz
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (L.B.-C.); (E.L.); (M.J.N.); (S.P.-P.); (F.C.-F.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
| | - Chankyu Park
- Department of Stem Cells and Regenerative Biology, Konkuk University, Seoul 05029, Korea;
| | - Montserrat Carrascal
- Instituto de Investigaciones Biomédicas de Barcelona-Unidad de Espectrometría de Masas Biológica y Proteómica, Consejo Superior de Investigaciones Científicas (CSIC), 08193 Bellaterra, Spain;
| | - Javier Domínguez
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28049 Madrid, Spain;
| | - Maria Luisa Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autònoma de Madrid, 28049 Madrid, Spain;
| | - Veljko Nikolin
- Boehringer Ingelheim Veterinary Research Center (BIVRC) GmbH & Co. KG, 30559 Hannover, Germany;
| | - Javier Collado
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
| | - Fernando Rodríguez
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (L.B.-C.); (E.L.); (M.J.N.); (S.P.-P.); (F.C.-F.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
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Lee CH, Salio M, Napolitani G, Ogg G, Simmons A, Koohy H. Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors. Front Immunol 2020; 11:565096. [PMID: 33193332 PMCID: PMC7642207 DOI: 10.3389/fimmu.2020.565096] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
Adaptive immune recognition is mediated by specific interactions between heterodimeric T cell receptors (TCRs) and their cognate peptide-MHC (pMHC) ligands, and the methods to accurately predict TCR:pMHC interaction would have profound clinical, therapeutic and pharmaceutical applications. Herein, we review recent developments in predicting cross-reactivity and antigen specificity of TCR recognition. We discuss current experimental and computational approaches to investigate cross-reactivity and antigen-specificity of TCRs and highlight how integrating kinetic, biophysical and structural features may offer valuable insights in modeling immunogenicity. We further underscore the close inter-relationship of these two interconnected notions and the need to investigate each in the light of the other for a better understanding of T cell responsiveness for the effective clinical applications.
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Affiliation(s)
- Chloe H. Lee
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mariolina Salio
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Giorgio Napolitani
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Graham Ogg
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Alison Simmons
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, United Kingdom
| | - Hashem Koohy
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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10
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Venkatakrishnan AJ, Kayal N, Anand P, Badley AD, Church GM, Soundararajan V. Benchmarking evolutionary tinkering underlying human-viral molecular mimicry shows multiple host pulmonary-arterial peptides mimicked by SARS-CoV-2. Cell Death Discov 2020; 6:96. [PMID: 33024578 PMCID: PMC7529588 DOI: 10.1038/s41420-020-00321-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/01/2020] [Indexed: 12/14/2022] Open
Abstract
The hand of molecular mimicry in shaping SARS-CoV-2 evolution and immune evasion remains to be deciphered. Here, we report 33 distinct 8-mer/9-mer peptides that are identical between SARS-CoV-2 and the human reference proteome. We benchmark this observation against other viral-human 8-mer/9-mer peptide identity, which suggests generally similar extents of molecular mimicry for SARS-CoV-2 and many other human viruses. Interestingly, 20 novel human peptides mimicked by SARS-CoV-2 have not been observed in any previous coronavirus strains (HCoV, SARS-CoV, and MERS). Furthermore, four of the human 8-mer/9-mer peptides mimicked by SARS-CoV-2 map onto HLA-B*40:01, HLA-B*40:02, and HLA-B*35:01 binding peptides from human PAM, ANXA7, PGD, and ALOX5AP proteins. This mimicry of multiple human proteins by SARS-CoV-2 is made salient by single-cell RNA-seq (scRNA-seq) analysis that shows the targeted genes significantly expressed in human lungs and arteries; tissues implicated in COVID-19 pathogenesis. Finally, HLA-A*03 restricted 8-mer peptides are found to be shared broadly by human and coronaviridae helicases in functional hotspots, with potential implications for nucleic acid unwinding upon initial infection. This study presents the first scan of human peptide mimicry by SARS-CoV-2, and via its benchmarking against human-viral mimicry more broadly, presents a computational framework for follow-up studies to assay how evolutionary tinkering may relate to zoonosis and herd immunity.
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Affiliation(s)
| | | | | | - Andrew D. Badley
- Department of Infectious Diseases, Mayo Clinic, Rochester, MN USA
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In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementary ligand enrichment and data acquisition strategies. Mol Immunol 2020; 123:7-17. [PMID: 32387766 DOI: 10.1016/j.molimm.2020.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/07/2020] [Accepted: 04/12/2020] [Indexed: 12/15/2022]
Abstract
The identification of T cell epitopes derived from tumour specific antigens remains a significant challenge for the development of peptide-based vaccines and immunotherapies. The use of mass spectrometry-based approaches (immunopeptidomics) can provide powerful new avenues for the identification of such epitopes. In this study we report the use of complementary peptide antigen enrichment methods and a comprehensive mass spectrometric acquisition strategy to provide in-depth immunopeptidome data for the THP-1 cell line, a cell line used widely as a model of human leukaemia. To accomplish this, we combined robust experimental workflows that incorporated ultrafiltration or off-line reversed phase chromatography to enrich peptide ligand as well as a multifaceted data acquisition strategy using an Orbitrap Fusion LC-MS instrument. Using the combined datasets from the two ligand enrichment methods we gained significant depth in immunopeptidome coverage by identifying a total of 41,816 HLA class I peptides from THP-1 cells, including a significant number of peptides derived from different oncogenes or over expressed proteins associated with cancer. The physicochemical properties of the HLA-bound peptides dictated their recovery using the two ligand enrichment approaches and their distribution across the different precursor charge states considered in the data acquisition strategy. The data highlight the complementarity of the two enrichment procedures, and in cases where sample is not limiting, suggest that the combination of both approaches will yield the most comprehensive immunopeptidome information.
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12
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Solleder M, Guillaume P, Racle J, Michaux J, Pak HS, Müller M, Coukos G, Bassani-Sternberg M, Gfeller D. Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands. Mol Cell Proteomics 2020; 19:390-404. [PMID: 31848261 PMCID: PMC7000122 DOI: 10.1074/mcp.tir119.001641] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/06/2019] [Indexed: 12/19/2022] Open
Abstract
The presentation of peptides on class I human leukocyte antigen (HLA-I) molecules plays a central role in immune recognition of infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-specific alternative mRNA splicing or aberrant post-translational modifications. Identifying HLA-I ligands remains a challenging task that requires either heavy experimental work for in vivo identification or optimized bioinformatics tools for accurate predictions. To date, no HLA-I ligand predictor includes post-translational modifications. To fill this gap, we curated phosphorylated HLA-I ligands from several immunopeptidomics studies (including six newly measured samples) covering 72 HLA-I alleles and retrieved a total of 2,066 unique phosphorylated peptides. We then expanded our motif deconvolution tool to identify precise binding motifs of phosphorylated HLA-I ligands. Our results reveal a clear enrichment of phosphorylated peptides among HLA-C ligands and demonstrate a prevalent role of both HLA-I motifs and kinase motifs on the presentation of phosphorylated peptides. These data further enabled us to develop and validate the first predictor of interactions between HLA-I molecules and phosphorylated peptides.
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Affiliation(s)
- Marthe Solleder
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Philippe Guillaume
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Julien Racle
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Justine Michaux
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Hui-Song Pak
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Markus Müller
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland.
| | - David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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13
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Croft NP. Peptide Presentation to T Cells: Solving the Immunogenic Puzzle: Systems Immunology Profiling of Antigen Presentation for Prediction of CD8 + T Cell Immunogenicity. Bioessays 2020; 42:e1900200. [PMID: 31958157 DOI: 10.1002/bies.201900200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/18/2019] [Indexed: 02/02/2023]
Abstract
The vertebrate immune system uses an impressive arsenal of mechanisms to combat harmful cellular states such as infection. One way is via cells delivering real-time snapshots of their protein content to the cell surface in the form of short peptides. Specialized immune cells (T cells) sample these peptides and assess whether they are foreign, warranting an action such as destruction of the infected cell. The delivery of peptides to the cell surface is termed antigen processing and presentation, and decades of research have provided unprecedented understanding of this process. However, predicting the capacity for a given peptide to be immunogenic-to elicit a T cell response-has remained both enigmatic and a long sought-after goal. In the era of big data, a point is being approached where the steps of antigen processing and presentation can be quantified and assessed against peptide immunogenicity in order to build predictive models. This review presents new findings in this area and contemplates challenges ahead.
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Affiliation(s)
- Nathan P Croft
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
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14
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Vizcaíno JA, Kubiniok P, Kovalchik KA, Ma Q, Duquette JD, Mongrain I, Deutsch EW, Peters B, Sette A, Sirois I, Caron E. The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases. Mol Cell Proteomics 2020; 19:31-49. [PMID: 31744855 PMCID: PMC6944237 DOI: 10.1074/mcp.r119.001743] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/18/2019] [Indexed: 12/11/2022] Open
Abstract
The science that investigates the ensembles of all peptides associated to human leukocyte antigen (HLA) molecules is termed "immunopeptidomics" and is typically driven by mass spectrometry (MS) technologies. Recent advances in MS technologies, neoantigen discovery and cancer immunotherapy have catalyzed the launch of the Human Immunopeptidome Project (HIPP) with the goal of providing a complete map of the human immunopeptidome and making the technology so robust that it will be available in every clinic. Here, we provide a long-term perspective of the field and we use this framework to explore how we think the completion of the HIPP will truly impact the society in the future. In this context, we introduce the concept of immunopeptidome-wide association studies (IWAS). We highlight the importance of large cohort studies for the future and how applying quantitative immunopeptidomics at population scale may provide a new look at individual predisposition to common immune diseases as well as responsiveness to vaccines and immunotherapies. Through this vision, we aim to provide a fresh view of the field to stimulate new discussions within the community, and present what we see as the key challenges for the future for unlocking the full potential of immunopeptidomics in this era of precision medicine.
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Affiliation(s)
- Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Peter Kubiniok
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | | | - Qing Ma
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | | | - Ian Mongrain
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, QC, Canada; Montreal Heart Institute, Montreal, QC, Canada
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington, 98109
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, California, 92037
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California, 92037
| | - Isabelle Sirois
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, QC H3T 1J4, Canada.
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15
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Faridi P, Li C, Ramarathinam SH, Vivian JP, Illing PT, Mifsud NA, Ayala R, Song J, Gearing LJ, Hertzog PJ, Ternette N, Rossjohn J, Croft NP, Purcell AW. A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands. Sci Immunol 2019; 3:3/28/eaar3947. [PMID: 30315122 DOI: 10.1126/sciimmunol.aar3947] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 05/29/2018] [Accepted: 08/31/2018] [Indexed: 12/19/2022]
Abstract
The diversity of peptides displayed by class I human leukocyte antigen (HLA) plays an essential role in T cell immunity. The peptide repertoire is extended by various posttranslational modifications, including proteasomal splicing of peptide fragments from distinct regions of an antigen to form nongenomically templated cis-spliced sequences. Previously, it has been suggested that a fraction of the immunopeptidome constitutes such cis-spliced peptides; however, because of computational limitations, it has not been possible to assess whether trans-spliced peptides (i.e., the fusion of peptide segments from distinct antigens) are also bound and presented by HLA molecules, and if so, in what proportion. Here, we have developed and applied a bioinformatic workflow and demonstrated that trans-spliced peptides are presented by HLA-I, and their abundance challenges current models of proteasomal splicing that predict cis-splicing as the most probable outcome. These trans-spliced peptides display canonical HLA-binding sequence features and are as frequently identified as cis-spliced peptides found bound to a number of different HLA-A and HLA-B allotypes. Structural analysis reveals that the junction between spliced peptides is highly solvent exposed and likely to participate in T cell receptor interactions. These results highlight the unanticipated diversity of the immunopeptidome and have important implications for autoimmunity, vaccine design, and immunotherapy.
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Affiliation(s)
- Pouya Faridi
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Chen Li
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Biology, Institute of Molecular Systems Biology,ETH Zurich, Zurich 8093, Switzerland
| | - Sri H Ramarathinam
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Julian P Vivian
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Patricia T Illing
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Rochelle Ayala
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jiangning Song
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, Victoria 3800, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Science, School of Clinical Science, Monash University, Clayton, Victoria 3168, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Science, School of Clinical Science, Monash University, Clayton, Victoria 3168, Australia
| | | | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine,Heath Park, Cardiff CF14 4XN, UK
| | - Nathan P Croft
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
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16
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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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17
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Ternette N, Purcell AW. Immunopeptidomics Special Issue. Proteomics 2019; 18:e1800145. [PMID: 29949244 DOI: 10.1002/pmic.201800145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 06/04/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Nicola Ternette
- The Jenner Institute, Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, OX3, 7FZ, UK
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
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18
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Koutsakos M, Illing PT, Nguyen THO, Mifsud NA, Crawford JC, Rizzetto S, Eltahla AA, Clemens EB, Sant S, Chua BY, Wong CY, Allen EK, Teng D, Dash P, Boyd DF, Grzelak L, Zeng W, Hurt AC, Barr I, Rockman S, Jackson DC, Kotsimbos TC, Cheng AC, Richards M, Westall GP, Loudovaris T, Mannering SI, Elliott M, Tangye SG, Wakim LM, Rossjohn J, Vijaykrishna D, Luciani F, Thomas PG, Gras S, Purcell AW, Kedzierska K. Human CD8 + T cell cross-reactivity across influenza A, B and C viruses. Nat Immunol 2019; 20:613-625. [PMID: 30778243 DOI: 10.1038/s41590-019-0320-6] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/10/2019] [Indexed: 12/18/2022]
Abstract
Influenza A, B and C viruses (IAV, IBV and ICV, respectively) circulate globally and infect humans, with IAV and IBV causing the most severe disease. CD8+ T cells confer cross-protection against IAV strains, however the responses of CD8+ T cells to IBV and ICV are understudied. We investigated the breadth of CD8+ T cell cross-recognition and provide evidence of CD8+ T cell cross-reactivity across IAV, IBV and ICV. We identified immunodominant CD8+ T cell epitopes from IBVs that were protective in mice and found memory CD8+ T cells directed against universal and influenza-virus-type-specific epitopes in the blood and lungs of healthy humans. Lung-derived CD8+ T cells displayed tissue-resident memory phenotypes. Notably, CD38+Ki67+CD8+ effector T cells directed against novel epitopes were readily detected in IAV- or IBV-infected pediatric and adult subjects. Our study introduces a new paradigm whereby CD8+ T cells confer unprecedented cross-reactivity across all influenza viruses, a key finding for the design of universal vaccines.
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Affiliation(s)
- Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Patricia T Illing
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | | | - Simone Rizzetto
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Auda A Eltahla
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Sneha Sant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Brendon Y Chua
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Chinn Yi Wong
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - E Kaitlynn Allen
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Don Teng
- Infection and Immunity Program & Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Pradyot Dash
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - David F Boyd
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ludivine Grzelak
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Biology Department, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, Cachan, France
| | - Weiguang Zeng
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Aeron C Hurt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ian Barr
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- School of Applied Biomedical Sciences, Federation University, Churchill, Victoria, Australia
| | - Steve Rockman
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Seqirus, Parkville, Victoria, Australia
| | - David C Jackson
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Tom C Kotsimbos
- Department of Allergy, Immunology and Respiratory Medicine, The Alfred Hospital, Melbourne, Victoria, Australia
- Department of Medicine, Monash University, Central Clinical School, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Allen C Cheng
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Infection Prevention and Healthcare Epidemiology Unit, Alfred Health, Melbourne, Victoria, Australia
| | - Michael Richards
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Glen P Westall
- Lung Transplant Unit, Alfred Hospital, Melbourne, Victoria, Australia
| | - Thomas Loudovaris
- Immunology and Diabetes Unit, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | | | - Michael Elliott
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Chris O'Brien Lifehouse Cancer Centre, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Stuart G Tangye
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Dhanasekaran Vijaykrishna
- Infection and Immunity Program & Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Fabio Luciani
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephanie Gras
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Anthony W Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia.
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19
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Purcell AW, Sechi S, DiLorenzo TP. The Evolving Landscape of Autoantigen Discovery and Characterization in Type 1 Diabetes. Diabetes 2019; 68:879-886. [PMID: 31010879 PMCID: PMC6477901 DOI: 10.2337/dbi18-0066] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/29/2019] [Indexed: 12/20/2022]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease that is caused, in part, by T cell-mediated destruction of insulin-producing β-cells. High risk for disease, in those with genetic susceptibility, is predicted by the presence of two or more autoantibodies against insulin, the 65-kDa form of glutamic acid decarboxylase (GAD65), insulinoma-associated protein 2 (IA-2), and zinc transporter 8 (ZnT8). Despite this knowledge, we still do not know what leads to the breakdown of tolerance to these autoantigens, and we have an incomplete understanding of T1D etiology and pathophysiology. Several new autoantibodies have recently been discovered using innovative technologies, but neither their potential utility in monitoring disease development and treatment nor their role in the pathophysiology and etiology of T1D has been explored. Moreover, neoantigen generation (through posttranslational modification, the formation of hybrid peptides containing two distinct regions of an antigen or antigens, alternative open reading frame usage, and translation of RNA splicing variants) has been reported, and autoreactive T cells that target these neoantigens have been identified. Collectively, these new studies provide a conceptual framework to understand the breakdown of self-tolerance, if such modifications occur in a tissue- or disease-specific context. A recent workshop sponsored by the National Institute of Diabetes and Digestive and Kidney Diseases brought together investigators who are using new methods and technologies to identify autoantigens and characterize immune responses toward these proteins. Researchers with diverse expertise shared ideas and identified resources to accelerate antigen discovery and the detection of autoimmune responses in T1D. The application of this knowledge will direct strategies for the identification of improved biomarkers for disease progression and treatment response monitoring and, ultimately, will form the foundation for novel antigen-specific therapeutics. This Perspective highlights the key issues that were addressed at the workshop and identifies areas for future investigation.
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Affiliation(s)
- Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Salvatore Sechi
- Division of Diabetes, Endocrinology, and Metabolic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Teresa P DiLorenzo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY
- Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY
- Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
- Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, NY
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20
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4-Chloro-l-kynurenine as fluorescent amino acid in natural peptides. Amino Acids 2018; 50:1697-1705. [DOI: 10.1007/s00726-018-2642-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/27/2018] [Indexed: 11/26/2022]
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21
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Ramarathinam SH, Croft NP, Illing PT, Faridi P, Purcell AW. Employing proteomics in the study of antigen presentation: an update. Expert Rev Proteomics 2018; 15:637-645. [PMID: 30080115 DOI: 10.1080/14789450.2018.1509000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Our immune system discriminates self from non-self by examining the peptide cargo of human leukocyte antigen (HLA) molecules displayed on the cell surface. Successful recognition of HLA-bound non-self peptides can induce T cell responses leading to, for example, the destruction of infected cells. Today, largely due to advances in technology, we have an unprecedented capability to identify the nature of these presented peptides and unravel the true complexity of antigen presentation. Areas covered: In addition to conventional linear peptides, HLA molecules also present post-translationally modified sequences comprising a wealth of chemical and structural modifications, including a novel class of noncontiguous spliced peptides. This review focuses on these emerging themes in antigen presentation and how mass spectrometry in particular has contributed to a new view of the antigenic landscape that is presented to the immune system. Expert Commentary: Advances in the sensitivity of mass spectrometers and use of hybrid fragmentation technologies will provide more information-rich spectra of HLA bound peptides leading to more definitive identification of T cell epitopes. Coupled with improvements in sample preparation and new informatics workflows, studies will access novel classes of peptide antigen and allow interrogation of rare and clinically relevant samples.
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Affiliation(s)
- Sri H Ramarathinam
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Nathan P Croft
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Patricia T Illing
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Pouya Faridi
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Anthony W Purcell
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
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