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Hamza H, Ghosh M, Löffler MW, Rammensee HG, Planz O. Identification and relative abundance of naturally presented and cross-reactive influenza A virus MHC class I-restricted T cell epitopes. Emerg Microbes Infect 2024; 13:2306959. [PMID: 38240239 PMCID: PMC10854457 DOI: 10.1080/22221751.2024.2306959] [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: 12/13/2023] [Accepted: 01/14/2024] [Indexed: 02/10/2024]
Abstract
Cytotoxic T lymphocytes are key for controlling viral infection. Unravelling CD8+ T cell-mediated immunity to distinct influenza virus strains and subtypes across prominent HLA types is relevant for combating seasonal infections and emerging new variants. Using an immunopeptidomics approach, naturally presented influenza A virus-derived ligands restricted to HLA-A*24:02, HLA-A*68:01, HLA-B*07:02, and HLA-B*51:01 molecules were identified. Functional characterization revealed multifunctional memory CD8+ T cell responses for nine out of sixteen peptides. Peptide presentation kinetics was optimal around 12 h post infection and presentation of immunodominant epitopes shortly after infection was not always persistent. Assessment of immunogenic epitopes revealed that they are highly conserved across the major zoonotic reservoirs and may contain a single substitution in the vicinity of the anchor residues. These findings demonstrate how the identified epitopes promote T cell pools, possibly cross-protective in individuals and can be potential targets for vaccination.
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Affiliation(s)
- Hazem Hamza
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Virology Laboratory, Environmental Research Division, National Research Centre, Giza, Egypt
| | - Michael Ghosh
- Institute for Immunology, University of Tübingen, Tübingen, Germany
| | - Markus W Löffler
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Institute for Clinical and Experimental Transfusion Medicine, Medical Faculty of Tübingen, Tübingen, Germany
- Centre for Clinical Transfusion Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence CMFI (EXC2124) "Controlling Microbes to Fight Infections", University of Tübingen, Tübingen, Germany
| | - Oliver Planz
- Institute for Immunology, University of Tübingen, Tübingen, Germany
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2
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Vecchio F, Carré A, Korenkov D, Zhou Z, Apaolaza P, Tuomela S, Burgos-Morales O, Snowhite I, Perez-Hernandez J, Brandao B, Afonso G, Halliez C, Kaddis J, Kent SC, Nakayama M, Richardson SJ, Vinh J, Verdier Y, Laiho J, Scharfmann R, Solimena M, Marinicova Z, Bismuth E, Lucidarme N, Sanchez J, Bustamante C, Gomez P, Buus S, You S, Pugliese A, Hyoty H, Rodriguez-Calvo T, Flodstrom-Tullberg M, Mallone R. Coxsackievirus infection induces direct pancreatic β cell killing but poor antiviral CD8 + T cell responses. SCIENCE ADVANCES 2024; 10:eadl1122. [PMID: 38446892 PMCID: PMC10917340 DOI: 10.1126/sciadv.adl1122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Coxsackievirus B (CVB) infection of pancreatic β cells is associated with β cell autoimmunity and type 1 diabetes. We investigated how CVB affects human β cells and anti-CVB T cell responses. β cells were efficiently infected by CVB in vitro, down-regulated human leukocyte antigen (HLA) class I, and presented few, selected HLA-bound viral peptides. Circulating CD8+ T cells from CVB-seropositive individuals recognized a fraction of these peptides; only another subfraction was targeted by effector/memory T cells that expressed exhaustion marker PD-1. T cells recognizing a CVB epitope cross-reacted with β cell antigen GAD. Infected β cells, which formed filopodia to propagate infection, were more efficiently killed by CVB than by CVB-reactive T cells. Our in vitro and ex vivo data highlight limited CD8+ T cell responses to CVB, supporting the rationale for CVB vaccination trials for type 1 diabetes prevention. CD8+ T cells recognizing structural and nonstructural CVB epitopes provide biomarkers to differentially follow response to infection and vaccination.
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Affiliation(s)
- Federica Vecchio
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Alexia Carré
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Daniil Korenkov
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Zhicheng Zhou
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Paola Apaolaza
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Soile Tuomela
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | | | - Isaac Snowhite
- Diabetes Research Institute, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | | | - Barbara Brandao
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Georgia Afonso
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Clémentine Halliez
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
| | - John Kaddis
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sally C. Kent
- Diabetes Center of Excellence, Department of Medicine, University of Massachusetts Medical Chan School, Worcester, MA, USA
| | - Maki Nakayama
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sarah J. Richardson
- Islet Biology Exeter (IBEx), Exeter Centre of Excellence for Diabetes Research (EXCEED), Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Exeter, UK
| | - Joelle Vinh
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS UMR8249, Paris, France
| | - Yann Verdier
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS UMR8249, Paris, France
| | - Jutta Laiho
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Michele Solimena
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Paul Langerhans Institute Dresden (PLID), Helmholtz Munich, University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Zuzana Marinicova
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Paul Langerhans Institute Dresden (PLID), Helmholtz Munich, University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Elise Bismuth
- Assistance Publique Hôpitaux de Paris, Service d’Endocrinologie Pédiatrique, Robert Debré Hospital, Paris, France
| | - Nadine Lucidarme
- Assistance Publique Hôpitaux de Paris, Service de Pédiatrie, Jean Verdier Hospital, Bondy, France
| | - Janine Sanchez
- Department of Pediatrics, Division of Pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Carmen Bustamante
- Department of Pediatrics, Division of Pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Patricia Gomez
- Department of Pediatrics, Division of Pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Soren Buus
- Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - the nPOD-Virus Working Group
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Diabetes Research Institute, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Diabetes Center of Excellence, Department of Medicine, University of Massachusetts Medical Chan School, Worcester, MA, USA
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
- Islet Biology Exeter (IBEx), Exeter Centre of Excellence for Diabetes Research (EXCEED), Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Exeter, UK
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS UMR8249, Paris, France
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Paul Langerhans Institute Dresden (PLID), Helmholtz Munich, University Hospital and Faculty of Medicine, TU Dresden, Dresden, Germany
- Assistance Publique Hôpitaux de Paris, Service d’Endocrinologie Pédiatrique, Robert Debré Hospital, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Pédiatrie, Jean Verdier Hospital, Bondy, France
- Department of Pediatrics, Division of Pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
- Fimlab Laboratories, Tampere, Finland
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Sylvaine You
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Alberto Pugliese
- Diabetes Research Institute, Leonard Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Heikki Hyoty
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Teresa Rodriguez-Calvo
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Malin Flodstrom-Tullberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Roberto Mallone
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
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3
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Weingarten-Gabbay S, Chen DY, Sarkizova S, Taylor HB, Gentili M, Hernandez GM, Pearlman LR, Bauer MR, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. The HLA-II immunopeptidome of SARS-CoV-2. Cell Rep 2024; 43:113596. [PMID: 38117652 PMCID: PMC10860710 DOI: 10.1016/j.celrep.2023.113596] [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: 05/15/2023] [Revised: 11/08/2023] [Accepted: 12/01/2023] [Indexed: 12/22/2023] Open
Abstract
Targeted synthetic vaccines have the potential to transform our response to viral outbreaks, yet the design of these vaccines requires a comprehensive knowledge of viral immunogens. Here, we report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) peptides that are naturally processed and loaded onto human leukocyte antigen-II (HLA-II) complexes in infected cells. We identify over 500 unique viral peptides from canonical proteins as well as from overlapping internal open reading frames. Most HLA-II peptides colocalize with known CD4+ T cell epitopes in coronavirus disease 2019 patients, including 2 reported immunodominant regions in the SARS-CoV-2 membrane protein. Overall, our analyses show that HLA-I and HLA-II pathways target distinct viral proteins, with the structural proteins accounting for most of the HLA-II peptidome and nonstructural and noncanonical proteins accounting for the majority of the HLA-I peptidome. These findings highlight the need for a vaccine design that incorporates multiple viral elements harboring CD4+ and CD8+ T cell epitopes to maximize vaccine effectiveness.
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Affiliation(s)
- Shira Weingarten-Gabbay
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
| | - Da-Yuan Chen
- Department of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | | | - Hannah B Taylor
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Matteo Gentili
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | | | - Leah R Pearlman
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Matthew R Bauer
- Harvard Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard University Medical School, Boston, MA, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | | | - Mohsan Saeed
- Department of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA; Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
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4
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Zhao G, Bu G, Liu G, Kong X, Sun C, Li Z, Dai D, Sun H, Kang Y, Feng G, Zhong Q, Zeng M. mRNA-based Vaccines Targeting the T-cell Epitope-rich Domain of Epstein Barr Virus Latent Proteins Elicit Robust Anti-Tumor Immunity in Mice. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302116. [PMID: 37890462 PMCID: PMC10724410 DOI: 10.1002/advs.202302116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 09/04/2023] [Indexed: 10/29/2023]
Abstract
Epstein-Barr virus (EBV) is associated with various malignancies and infects >90% of the global population. EBV latent proteins are expressed in numerous EBV-associated cancers and contribute to carcinogenesis, making them critical therapeutic targets for these cancers. Thus, this study aims to develop mRNA-based therapeutic vaccines that express the T-cell-epitope-rich domain of truncated latent proteins of EBV, including truncatedlatent membrane protein 2A (Trunc-LMP2A), truncated EBV nuclear antigen 1 (Trunc-EBNA1), and Trunc-EBNA3A. The vaccines effectively activate both cellular and humoral immunity in mice and show promising results in suppressing tumor progression and improving survival time in tumor-bearing mice. Furthermore, it is observed that the truncated forms of the antigens, Trunc-LMP2A, Trunc-EBNA1, and Trunc-EBNA3A, are more effective than full-length antigens in activating antigen-specific immune responses. In summary, the findings demonstrate the effectiveness of mRNA-based therapeutic vaccines targeting the T-cell-epitope-rich domain of EBV latent proteins and providing new treatment options for EBV-associated cancers.
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Affiliation(s)
- Ge‐Xin Zhao
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer. MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma, Diagnosis, and TherapySun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Guo‐Long Bu
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer. MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma, Diagnosis, and TherapySun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Gang‐Feng Liu
- Department of Head and Neck Surgery Section IIThe Third Affiliated Hospital of Kunming Medical University/Yunnan Cancer Hospital519 Kunzhou RoadKunming650118China
| | - Xiang‐Wei Kong
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer. MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma, Diagnosis, and TherapySun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Cong Sun
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer. MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma, Diagnosis, and TherapySun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Zi‐Qian Li
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer. MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma, Diagnosis, and TherapySun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Dan‐Ling Dai
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer. MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma, Diagnosis, and TherapySun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Hai‐Xia Sun
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer. MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma, Diagnosis, and TherapySun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Yin‐Feng Kang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer. MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma, Diagnosis, and TherapySun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Guo‐Kai Feng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer. MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma, Diagnosis, and TherapySun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Qian Zhong
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer. MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma, Diagnosis, and TherapySun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Mu‐Sheng Zeng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer. MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma, Diagnosis, and TherapySun Yat‐sen University Cancer CenterGuangzhou510060China
- Guangdong‐Hong Kong Joint Laboratory for RNA MedicineSun Yat‐sen University Cancer CenterGuangzhou510060China
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5
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MacNabb BW, Kline J. MHC cross-dressing in antigen presentation. Adv Immunol 2023; 159:115-147. [PMID: 37996206 DOI: 10.1016/bs.ai.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Dendritic cells (DCs) orchestrate T cell responses by presenting antigenic peptides on major histocompatibility complex (MHC) and providing costimulation and other instructive signals. Professional antigen presenting cells (APCs), including DCs, are uniquely capable of generating and presenting peptide antigens derived from exogenous proteins. In addition to these canonical cross-presentation and MHC-II presentation pathways, APCs can also display exogenous peptide/MHC (p/MHC) acquired from neighboring cells and extracellular vesicles (EVs). This process, known as MHC cross-dressing, has been implicated in the regulation of T cell responses in a variety of in vivo contexts, including allogeneic solid organ transplantation, tumors, and viral infection. Although the occurrence of MHC cross-dressing has been clearly demonstrated, the importance of this antigen presentation mechanism continues to be elucidated. The contribution of MHC cross-dressing to overall antigen presentation has been obfuscated by the fact that DCs express the same MHC alleles as all other cells in the host, making it difficult to distinguish p/MHC generated within the DC from p/MHC acquired from another cell. As a result, much of what is known about MHC cross-dressing comes from studies using allogeneic organ transplantation and bone marrow chimeric mice, though recent development of mice bearing conditional knockout MHC and β2-microglobulin alleles should facilitate substantial progress in the coming years. In this review, we highlight recent advances in our understanding of MHC cross-dressing and its role in activating T cell responses in various contexts, as well as the experimental insights into the mechanism by which it occurs.
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Affiliation(s)
- Brendan W MacNabb
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States.
| | - Justin Kline
- Department of Medicine, Committee on Immunology, and Committee on Cancer Biology, University of Chicago, Chicago, IL, United States.
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6
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Dinh VT, Loaëc N, Quillévéré A, Le Sénéchal R, Keruzoré M, Martins RP, Granzhan A, Blondel M. The hide-and-seek game of the oncogenic Epstein-Barr virus-encoded EBNA1 protein with the immune system: An RNA G-quadruplex tale. Biochimie 2023; 214:57-68. [PMID: 37473831 DOI: 10.1016/j.biochi.2023.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023]
Abstract
The Epstein-Barr virus (EBV) is the first oncogenic virus described in human. EBV infects more than 90% of the human population worldwide, but most EBV infections are asymptomatic. After the primary infection, the virus persists lifelong in the memory B cells of the infected individuals. Under certain conditions the virus can cause several human cancers, that include lymphoproliferative disorders such as Burkitt and Hodgkin lymphomas and non-lymphoid malignancies such as 100% of nasopharyngeal carcinoma and 10% of gastric cancers. Each year, about 200,000 EBV-related cancers emerge, hence accounting for at least 1% of worldwide cancers. Like all gammaherpesviruses, EBV has evolved a strategy to escape the host immune system. This strategy is mainly based on the tight control of the expression of its Epstein-Barr nuclear antigen-1 (EBNA1) protein, the EBV-encoded genome maintenance protein. Indeed, EBNA1 is essential for viral genome replication and maintenance but, at the same time, is also highly antigenic and T cells raised against EBNA1 exist in infected individuals. For this reason, EBNA1 is considered as the Achilles heel of EBV and the virus has seemingly evolved a strategy that employs the binding of nucleolin, a host cell factor, to RNA G-quadruplex (rG4) within EBNA1 mRNA to limit its expression to the minimal level required for function while minimizing immune recognition. This review recapitulates in a historical way the knowledge accumulated on EBNA1 immune evasion and discusses how this rG4-dependent mechanism can be exploited as an intervention point to unveil EBV-related cancers to the immune system.
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Affiliation(s)
- Van-Trang Dinh
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France.
| | - Nadège Loaëc
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France
| | - Alicia Quillévéré
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France
| | - Ronan Le Sénéchal
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France
| | - Marc Keruzoré
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France
| | | | - Anton Granzhan
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Marc Blondel
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France.
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7
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Hogan MJ, Maheshwari N, Begg BE, Nicastri A, Hedgepeth EJ, Muramatsu H, Pardi N, Miller MA, Reilly SP, Brossay L, Lynch KW, Ternette N, Eisenlohr LC. Cryptic MHC-E epitope from influenza elicits a potent cytolytic T cell response. Nat Immunol 2023; 24:1933-1946. [PMID: 37828378 DOI: 10.1038/s41590-023-01644-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
The extent to which unconventional forms of antigen presentation drive T cell immunity is unknown. By convention, CD8 T cells recognize viral peptides, or epitopes, in association with classical major histocompatibility complex (MHC) class I, or MHC-Ia, but immune surveillance can, in some cases, be directed against peptides presented by nonclassical MHC-Ib, in particular the MHC-E proteins (Qa-1 in mice and HLA-E in humans); however, the overall importance of nonclassical responses in antiviral immunity remains unclear. Similarly uncertain is the importance of 'cryptic' viral epitopes, defined as those undetectable by conventional mapping techniques. Here we used an immunopeptidomic approach to search for unconventional epitopes that drive T cell responses in mice infected with influenza virus A/Puerto Rico/8/1934. We identified a nine amino acid epitope, termed M-SL9, that drives a co-immunodominant, cytolytic CD8 T cell response that is unconventional in two major ways: first, it is presented by Qa-1, and second, it has a cryptic origin, mapping to an unannotated alternative reading frame product of the influenza matrix gene segment. Presentation and immunogenicity of M-SL9 are dependent on the second AUG codon of the positive sense matrix RNA segment, suggesting translation initiation by leaky ribosomal scanning. During influenza virus A/Puerto Rico/8/1934 infection, M-SL9-specific T cells exhibit a low level of egress from the lungs and strong differentiation into tissue-resident memory cells. Importantly, we show that M-SL9/Qa-1-specific T cells can be strongly induced by messenger RNA vaccination and that they can mediate antigen-specific cytolysis in vivo. Our results demonstrate that noncanonical translation products can account for an important fraction of the T cell repertoire and add to a growing body of evidence that MHC-E-restricted T cells could have substantial therapeutic value.
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Affiliation(s)
- Michael J Hogan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Nikita Maheshwari
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Bridget E Begg
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Emma J Hedgepeth
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael A Miller
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA
- Century Therapeutics, Philadelphia, PA, USA
| | - Shanelle P Reilly
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Laurent Brossay
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Laurence C Eisenlohr
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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8
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Chen R, Fulton KM, Tran A, Duque D, Kovalchik K, Caron E, Twine SM, Li J. Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2-Infected Calu-3 Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen Presentation. Mol Cell Proteomics 2023; 22:100645. [PMID: 37709257 PMCID: PMC10580047 DOI: 10.1016/j.mcpro.2023.100645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023] Open
Abstract
We present an integrated immunopeptidomics and proteomics study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection to comprehensively decipher the changes in host cells in response to viral infection. Immunopeptidomics analysis identified viral antigens presented by host cells through both class I and class II MHC system for recognition by the adaptive immune system. The host proteome changes were characterized by quantitative proteomics and glycoproteomics and from these data, the activation of toll-like receptor 3-interferon pathway was identified. Glycosylation analysis of human leukocyte antigen (HLA) proteins from the elution and flow-through of immunoprecipitation revealed that SARS-CoV-2 infection changed the glycosylation pattern of certain HLA alleles with different HLA alleles, showing distinct dynamic changes in relative abundance. The difference in the glycosylation and abundance of HLA alleles changed the number of strong binding antigens each allele presented, suggesting the impact of SARS-CoV-2 infection on antigen presentation is allele-specific. These results could be further exploited to explain the imbalanced response from innate and adaptive immune system in coronavirus disease 2019 cases, which would be helpful for the development of therapeutics and vaccine for coronavirus disease 2019 and preparation for future pandemic.
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Affiliation(s)
- Rui Chen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada.
| | - Kelly M Fulton
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Anh Tran
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Diana Duque
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Kevin Kovalchik
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Quebec, Canada
| | - Susan M Twine
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Jianjun Li
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada.
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9
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Zhang B, Bassani-Sternberg M. Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery. J Immunother Cancer 2023; 11:e007073. [PMID: 37899131 PMCID: PMC10619091 DOI: 10.1136/jitc-2023-007073] [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] [Accepted: 07/21/2023] [Indexed: 10/31/2023] Open
Abstract
Identification of tumor antigens presented by the human leucocyte antigen (HLA) molecules is essential for the design of effective and safe cancer immunotherapies that rely on T cell recognition and killing of tumor cells. Mass spectrometry (MS)-based immunopeptidomics enables high-throughput, direct identification of HLA-bound peptides from a variety of cell lines, tumor tissues, and healthy tissues. It involves immunoaffinity purification of HLA complexes followed by MS profiling of the extracted peptides using data-dependent acquisition, data-independent acquisition, or targeted approaches. By incorporating DNA, RNA, and ribosome sequencing data into immunopeptidomics data analysis, the proteogenomic approach provides a powerful means for identifying tumor antigens encoded within the canonical open reading frames of annotated coding genes and non-canonical tumor antigens derived from presumably non-coding regions of our genome. We discuss emerging computational challenges in immunopeptidomics data analysis and tumor antigen identification, highlighting key considerations in the proteogenomics-based approach, including accurate DNA, RNA and ribosomal sequencing data analysis, careful incorporation of predicted novel protein sequences into reference protein database, special quality control in MS data analysis due to the expanded and heterogeneous search space, cancer-specificity determination, and immunogenicity prediction. The advancements in technology and computation is continually enabling us to identify tumor antigens with higher sensitivity and accuracy, paving the way toward the development of more effective cancer immunotherapies.
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Affiliation(s)
- Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
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10
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Witney MJ, Tscharke DC. BMX-A and BMX-S: Accessible cell-free methods to estimate peptide-MHC-I affinity and stability. Mol Immunol 2023; 161:1-10. [PMID: 37478775 DOI: 10.1016/j.molimm.2023.07.008] [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: 12/20/2022] [Revised: 06/12/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
The affinity and stability of peptide binding to Major Histocompatibility Complex Class I (MHC-I) molecules are fundamental parameters that underpin the specificity and magnitude of CD8+ T cell responses. These parameters can be estimated in some cases by computational tools, but experimental validation remains valuable, especially for stability. Methods to measure peptide binding can be broadly categorised into either cell-based assays using TAP-deficient cell lines such as RMA/S, or cell-free strategies, such as peptide competition-binding assays and surface plasmon resonance. Cell-based assays are subject to confounding biological activity, including peptide trimming by peptidases and dilution of peptide-loaded MHC-I on the surface of cells through cell division. Current cell-free methods require in-house production and purification of MHC-I. In this study, we present the development of new cell-free assays to estimate the relative affinity and dissociation kinetics of peptide binding to MHC-I. These assays, which we have called BMX-A (relative affinity) and BMX-S (kinetic stability), are reliable, scalable and accessible, in that they use off-the-shelf commercial reagents and standard flow cytometry techniques.
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Affiliation(s)
- Matthew J Witney
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
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11
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Vecchio F, Carré A, Korenkov D, Zhou Z, Apaolaza P, Tuomela S, Burgos-Morales O, Snowhite I, Perez-Hernandez J, Brandao B, Afonso G, Halliez C, Kaddis J, Kent SC, Nakayama M, Richardson SJ, Vinh J, Verdier Y, Laiho J, Scharfmann R, Solimena M, Marinicova Z, Bismuth E, Lucidarme N, Sanchez J, Bustamante C, Gomez P, Buus S, You S, Pugliese A, Hyoty H, Rodriguez-Calvo T, Flodstrom-Tullberg M, Mallone R. Coxsackievirus infection induces direct pancreatic β-cell killing but poor anti-viral CD8+ T-cell responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553954. [PMID: 37662376 PMCID: PMC10473604 DOI: 10.1101/2023.08.19.553954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Coxsackievirus B (CVB) infection of pancreatic β cells is associated with β-cell autoimmunity. We investigated how CVB impacts human β cells and anti-CVB T-cell responses. β cells were efficiently infected by CVB in vitro, downregulated HLA Class I and presented few, selected HLA-bound viral peptides. Circulating CD8+ T cells from CVB-seropositive individuals recognized only a fraction of these peptides, and only another sub-fraction was targeted by effector/memory T cells that expressed the exhaustion marker PD-1. T cells recognizing a CVB epitope cross-reacted with the β-cell antigen GAD. Infected β cells, which formed filopodia to propagate infection, were more efficiently killed by CVB than by CVB-reactive T cells. Thus, our in-vitro and ex-vivo data highlight limited T-cell responses to CVB, supporting the rationale for CVB vaccination trials for type 1 diabetes prevention. CD8+ T cells recognizing structural and non-structural CVB epitopes provide biomarkers to differentially follow response to infection and vaccination.
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Affiliation(s)
- Federica Vecchio
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Alexia Carré
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Daniil Korenkov
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Zhicheng Zhou
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Paola Apaolaza
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Soile Tuomela
- Center for Infectious Medicine, Department of medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | | | - Isaac Snowhite
- Diabetes Research Institute, Leonard Miller School of Medicine, University of Miami, FL, USA
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | | | - Barbara Brandao
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Georgia Afonso
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | | | - John Kaddis
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sally C. Kent
- University of Massachusetts Medical Chan School, Diabetes Center of Excellence, Department of Medicine, Worcester, MA, USA
| | - Maki Nakayama
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sarah J. Richardson
- Islet Biology Exeter (IBEx), Exeter Centre of Excellence for Diabetes Research (EXCEED), Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Exeter, UK
| | - Joelle Vinh
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS UMR8249, Paris, France
| | - Yann Verdier
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS UMR8249, Paris, France
| | - Jutta Laiho
- Tampere University, Faculty of Medicine and Health Technology and Fimlab Laboratories, Tampere, Finland
| | | | - Michele Solimena
- Paul Langerhans Institute, Technical University Dresden, Germany
| | | | - Elise Bismuth
- Assistance Publique Hôpitaux de Paris, Service d’Endocrinologie Pédiatrique, Robert Debré Hospital, Paris, France
| | - Nadine Lucidarme
- Assistance Publique Hôpitaux de Paris, Service de Pédiatrie, Jean Verdier Hospital, Bondy, France
| | - Janine Sanchez
- Department of Pediatrics, Division of pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, FL, USA
| | - Carmen Bustamante
- Department of Pediatrics, Division of pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, FL, USA
| | - Patricia Gomez
- Department of Pediatrics, Division of pediatric Endocrinology, Leonard Miller School of Medicine, University of Miami, FL, USA
| | - Soren Buus
- Panum Institute, Department of International Health, Immunology and Microbiology, Copenhagen, Denmark
| | | | - Sylvaine You
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Alberto Pugliese
- Diabetes Research Institute, Leonard Miller School of Medicine, University of Miami, FL, USA
- Department of Diabetes Immunology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Heikki Hyoty
- Tampere University, Faculty of Medicine and Health Technology and Fimlab Laboratories, Tampere, Finland
| | - Teresa Rodriguez-Calvo
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Malin Flodstrom-Tullberg
- Center for Infectious Medicine, Department of medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Roberto Mallone
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
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12
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Révész Á, Hevér H, Steckel A, Schlosser G, Szabó D, Vékey K, Drahos L. Collision energies: Optimization strategies for bottom-up proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:1261-1299. [PMID: 34859467 DOI: 10.1002/mas.21763] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 06/07/2023]
Abstract
Mass-spectrometry coupled to liquid chromatography is an indispensable tool in the field of proteomics. In the last decades, more and more complex and diverse biochemical and biomedical questions have arisen. Problems to be solved involve protein identification, quantitative analysis, screening of low abundance modifications, handling matrix effect, and concentrations differing by orders of magnitude. This led the development of more tailored protocols and problem centered proteomics workflows, including advanced choice of experimental parameters. In the most widespread bottom-up approach, the choice of collision energy in tandem mass spectrometric experiments has outstanding role. This review presents the collision energy optimization strategies in the field of proteomics which can help fully exploit the potential of MS based proteomics techniques. A systematic collection of use case studies is then presented to serve as a starting point for related further scientific work. Finally, this article discusses the issue of comparing results from different studies or obtained on different instruments, and it gives some hints on methodology transfer between laboratories based on measurement of reference species.
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Affiliation(s)
- Ágnes Révész
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Helga Hevér
- Chemical Works of Gedeon Richter Plc, Budapest, Hungary
| | - Arnold Steckel
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
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13
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Becerra-Artiles A, Nanaware PP, Muneeruddin K, Weaver GC, Shaffer SA, Calvo-Calle JM, Stern LJ. Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T-cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2. PLoS Pathog 2023; 19:e1011032. [PMID: 37498934 PMCID: PMC10409285 DOI: 10.1371/journal.ppat.1011032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/08/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023] Open
Abstract
Seasonal "common-cold" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but the T-cell response to seasonal coronaviruses remains largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal coronavirus OC43. We identified MHC-bound peptides derived from each of the viral structural proteins (spike, nucleoprotein, hemagglutinin-esterase, membrane, and envelope) as well as non-structural proteins nsp3, nsp5, nsp6, and nsp12. Eighty MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. Fewer and less abundant MHC-I bound OC43-derived peptides were observed, possibly due to MHC-I downregulation induced by OC43 infection. The MHC-II peptides elicited low-abundance recall T-cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T-cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T-cell lines. Among the validated epitopes, spike protein S903-917 presented by DPA1*01:03/DPB1*04:01 and S1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. Nucleoprotein N54-68 and hemagglutinin-esterase HE128-142 presented by DRB1*15:01 and HE259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow CD4 T-cell cross-reactivity after infection or vaccination, and to guide selection of epitopes for inclusion in pan-coronavirus vaccines.
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Affiliation(s)
- Aniuska Becerra-Artiles
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Padma P. Nanaware
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Khaja Muneeruddin
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury Massachusetts, United States of America
| | - Grant C. Weaver
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Scott A. Shaffer
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - J. Mauricio Calvo-Calle
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Lawrence J. Stern
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
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14
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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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15
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Eizirik DL, Szymczak F, Mallone R. Why does the immune system destroy pancreatic β-cells but not α-cells in type 1 diabetes? Nat Rev Endocrinol 2023; 19:425-434. [PMID: 37072614 DOI: 10.1038/s41574-023-00826-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/06/2023] [Indexed: 04/20/2023]
Abstract
A perplexing feature of type 1 diabetes (T1D) is that the immune system destroys pancreatic β-cells but not neighbouring α-cells, even though both β-cells and α-cells are dysfunctional. Dysfunction, however, progresses to death only for β-cells. Recent findings indicate important differences between these two cell types. First, expression of BCL2L1, a key antiapoptotic gene, is higher in α-cells than in β-cells. Second, endoplasmic reticulum (ER) stress-related genes are differentially expressed, with higher expression levels of pro-apoptotic CHOP in β-cells than in α-cells and higher expression levels of HSPA5 (which encodes the protective chaperone BiP) in α-cells than in β-cells. Third, expression of viral recognition and innate immune response genes is higher in α-cells than in β-cells, contributing to the enhanced resistance of α-cells to coxsackievirus infection. Fourth, expression of the immune-inhibitory HLA-E molecule is higher in α-cells than in β-cells. Of note, α-cells are less immunogenic than β-cells, and the CD8+ T cells invading the islets in T1D are reactive to pre-proinsulin but not to glucagon. We suggest that this finding is a result of the enhanced capacity of the α-cell to endure viral infections and ER stress, which enables them to better survive early stressors that can cause cell death and consequently amplify antigen presentation to the immune system. Moreover, the processing of the pre-proglucagon precursor in enteroendocrine cells might favour immune tolerance towards this potential self-antigen compared to pre-proinsulin.
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Affiliation(s)
- Decio L Eizirik
- Université Libre de Bruxelles (ULB) Center for Diabetes Research and Welbio, Medical Faculty, Brussels, Belgium.
| | - Florian Szymczak
- Université Libre de Bruxelles (ULB) Center for Diabetes Research and Welbio, Medical Faculty, Brussels, Belgium
| | - Roberto Mallone
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
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16
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Weingarten-Gabbay S, Chen DY, Sarkizova S, Taylor HB, Gentili M, Pearlman LR, Bauer MR, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. The HLA-II immunopeptidome of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542482. [PMID: 37398281 PMCID: PMC10312465 DOI: 10.1101/2023.05.26.542482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Targeted synthetic vaccines have the potential to transform our response to viral outbreaks; yet the design of these vaccines requires a comprehensive knowledge of viral immunogens, including T-cell epitopes. Having previously mapped the SARS-CoV-2 HLA-I landscape, here we report viral peptides that are naturally processed and loaded onto HLA-II complexes in infected cells. We identified over 500 unique viral peptides from canonical proteins, as well as from overlapping internal open reading frames (ORFs), revealing, for the first time, the contribution of internal ORFs to the HLA-II peptide repertoire. Most HLA-II peptides co-localized with the known CD4+ T cell epitopes in COVID-19 patients. We also observed that two reported immunodominant regions in the SARS-CoV-2 membrane protein are formed at the level of HLA-II presentation. Overall, our analyses show that HLA-I and HLA-II pathways target distinct viral proteins, with the structural proteins accounting for most of the HLA-II peptidome and non-structural and non-canonical proteins accounting for the majority of the HLA-I peptidome. These findings highlight the need for a vaccine design that incorporates multiple viral elements harboring CD4+ and CD8+ T cell epitopes to maximize the vaccine effectiveness.
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17
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Schroeder SM, Nelde A, Walz JS. Viral T-cell epitopes - Identification, characterization and clinical application. Semin Immunol 2023; 66:101725. [PMID: 36706520 DOI: 10.1016/j.smim.2023.101725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023]
Abstract
T-cell immunity, mediated by CD4+ and CD8+ T cells, represents a cornerstone in the control of viral infections. Virus-derived T-cell epitopes are represented by human leukocyte antigen (HLA)-presented viral peptides on the surface of virus-infected cells. They are the prerequisite for the recognition of infected cells by T cells. Knowledge of viral T-cell epitopes provides on the one hand a diagnostic tool to decipher protective T-cell immune responses in the human population and on the other hand various prophylactic and therapeutic options including vaccination approaches and the transfer of virus-specific T cells. Such approaches have already been proven to be effective against various viral infections, particularly in immunocompromised patients lacking sufficient humoral, antibody-based immune response. This review provides an overview on the state of the art as well as current studies regarding the identification and characterization of viral T-cell epitopes and approaches of clinical application. In the first chapter in silico prediction tools and direct, mass spectrometry-based identification of viral T-cell epitopes is compared. The second chapter provides an overview of commonly used assays for further characterization of T-cell responses and phenotypes. The final chapter presents an overview of clinical application of viral T-cell epitopes with a focus on human immunodeficiency virus (HIV), human cytomegalovirus (HCMV) and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), being representatives of relevant viruses.
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Affiliation(s)
- Sarah M Schroeder
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany; Department for Otorhinolaryngology, Head, and Neck Surgery, University Hospital Tübingen, Tübingen, Germany; Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany; Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany; Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany; Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.
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18
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Abd El-Baky N, Amara AA, Redwan EM. HLA-I and HLA-II Peptidomes of SARS-CoV-2: A Review. Vaccines (Basel) 2023; 11:548. [PMID: 36992131 PMCID: PMC10058130 DOI: 10.3390/vaccines11030548] [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: 01/29/2023] [Revised: 02/18/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
The adaptive (T-cell-mediated) immune response is a key player in determining the clinical outcome, in addition to neutralizing antibodies, after SARS-CoV-2 infection, as well as supporting the efficacy of vaccines. T cells recognize viral-derived peptides bound to major histocompatibility complexes (MHCs) so that they initiate cell-mediated immunity against SARS-CoV-2 infection or can support developing a high-affinity antibody response. SARS-CoV-2-derived peptides bound to MHCs are characterized via bioinformatics or mass spectrometry on the whole proteome scale, named immunopeptidomics. They can identify potential vaccine targets or therapeutic approaches for SARS-CoV-2 or else may reveal the heterogeneity of clinical outcomes. SARS-CoV-2 epitopes that are naturally processed and presented on the human leukocyte antigen class I (HLA-I) and class II (HLA-II) were identified for immunopeptidomics. Most of the identified SARS-CoV-2 epitopes were canonical and out-of-frame peptides derived from spike and nucleocapsid proteins, followed by membrane proteins, whereby many of which are not caught by existing vaccines and could elicit effective responses of T cells in vivo. This review addresses the detection of SARS-CoV-2 viral epitopes on HLA-I and HLA-II using bioinformatics prediction and mass spectrometry (HLA peptidomics). Profiling the HLA-I and HLA-II peptidomes of SARS-CoV-2 is also detailed.
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Affiliation(s)
- Nawal Abd El-Baky
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
| | - Amro A. Amara
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
| | - Elrashdy M. Redwan
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah P.O. Box 80203, Saudi Arabia
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19
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Lin F, Lin X, Fu B, Xiong Y, Zaky MY, Wu H. Functional studies of HLA and its role in SARS-CoV-2: Stimulating T cell response and vaccine development. Life Sci 2023; 315:121374. [PMID: 36621539 PMCID: PMC9815883 DOI: 10.1016/j.lfs.2023.121374] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
In the biological immune process, the major histocompatibility complex (MHC) plays an indispensable role in the expression of HLA molecules in the human body when viral infection activates the T-cell response to remove the virus. Since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in 2019, how to address and prevent SARS-CoV-2 has become a common problem facing all mankind. The T-cell immune response activated by MHC peptides is a way to construct a defense line and reduce the transmission and harm of the virus. Presentation of SARS-CoV-2 antigen is associated with different types of HLA phenotypes, and different HLA phenotypes induce different immune responses. The prediction of SARS-CoV-2 mutation information and the design of vaccines based on HLAs can effectively activate autoimmunity and cope with virus mutations, which can provide some references for the prevention and treatment of SARS-CoV-2.
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Affiliation(s)
- Feng Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Xiaoyuan Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Mohamed Y Zaky
- Molecular Physiology Division, Zoology Department, Faculty of Science, Beni-Suef University, P.O. Box 62521, Beni-Suef, Egypt; Department of Oncology and Department of Biomedical and Clinical Science, Faculty of Medicine, Linköping University, Sweden
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
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20
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Weingarten-Gabbay S, Pearlman LR, Chen DY, Klaeger S, Taylor HB, Welch NL, Keskin DB, Carr SA, Abelin JG, Saeed M, Sabeti PC. HLA-I immunopeptidome profiling of human cells infected with high-containment enveloped viruses. STAR Protoc 2022; 3:101910. [PMID: 36595954 PMCID: PMC9731565 DOI: 10.1016/j.xpro.2022.101910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/10/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
Immunopeptidome profiling of infected cells is a powerful technique for detecting viral peptides that are naturally processed and loaded onto class I human leukocyte antigens (HLAs-I). Here, we provide a protocol for preparing samples for immunopeptidome profiling that can inactivate enveloped viruses while still preserving the integrity of the HLA-I complex. We detail steps for lysate preparation of infected cells followed by HLA-I immunoprecipitation and virus inactivation. We further describe peptide purification for mass spectrometry outside a high-containment facility. For complete details on the use and execution of this protocol, please refer to Weingarten-Gabbay et al. (2021).1.
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Affiliation(s)
- Shira Weingarten-Gabbay
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA,Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA,Corresponding author
| | | | - Da-Yuan Chen
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nicole L. Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Derin B. Keskin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA,Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Howard Hughes Medical Institute, Chevy Chase, MD, USA
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21
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Becerra-Artiles A, Nanaware PP, Muneeruddin K, Weaver GC, Shaffer SA, Calvo-Calle JM, Stern LJ. Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.01.518643. [PMID: 36482973 PMCID: PMC9727760 DOI: 10.1101/2022.12.01.518643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Seasonal "common-cold" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but identification and characterization of the T cell response to seasonal human coronaviruses remain largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal human coronavirus OC43. We identified MHC-I and MHC-II bound peptides derived from the viral spike, nucleocapsid, hemagglutinin-esterase, 3C-like proteinase, and envelope proteins. Only three MHC-I bound OC43-derived peptides were observed, possibly due to the potent MHC-I downregulation induced by OC43 infection. By contrast, 80 MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. These peptides elicited low-abundance recall T cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T cell lines. Among the validated epitopes, S 903-917 presented by DPA1*01:03/DPB1*04:01 and S 1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. N 54-68 and HE 128-142 presented by DRB1*15:01 and HE 259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow T cell cross-reactivity after infection or vaccination and could aid in the selection of epitopes for inclusion in pan-coronavirus vaccines. Author Summary There is much current interest in cellular immune responses to seasonal common-cold coronaviruses because of their possible role in mediating protection against SARS-CoV-2 infection or pathology. However, identification of relevant T cell epitopes and systematic studies of the T cell responses responding to these viruses are scarce. We conducted a study to identify naturally processed and presented MHC-I and MHC-II epitopes from human cells infected with the seasonal coronavirus HCoV-OC43, and to characterize the T cell responses associated with these epitopes. We found epitopes specific to the seasonal coronaviruses, as well as epitopes cross-reactive between HCoV-OC43 and SARS-CoV-2. These epitopes should be useful in following immune responses to seasonal coronaviruses and identifying their roles in COVID-19 vaccination, infection, and pathogenesis.
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Affiliation(s)
- Aniuska Becerra-Artiles
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Padma P. Nanaware
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Khaja Muneeruddin
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury MA
| | - Grant C. Weaver
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Scott A. Shaffer
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury MA
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - J. Mauricio Calvo-Calle
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Lawrence J. Stern
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA 01655, USA
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22
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Meraviglia-Crivelli D, Zheleva A, Barainka M, Moreno B, Villanueva H, Pastor F. Therapeutic Strategies to Enhance Tumor Antigenicity: Making the Tumor Detectable by the Immune System. Biomedicines 2022; 10:biomedicines10081842. [PMID: 36009389 PMCID: PMC9405394 DOI: 10.3390/biomedicines10081842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/12/2022] [Accepted: 07/27/2022] [Indexed: 12/22/2022] Open
Abstract
Cancer immunotherapy has revolutionized the oncology field, but many patients still do not respond to current immunotherapy approaches. One of the main challenges in broadening the range of responses to this type of treatment is the limited source of tumor neoantigens. T cells constitute a main line of defense against cancer, and the decisive step to trigger their activation is mediated by antigen recognition. Antigens allow the immune system to differentiate between self and foreign, which constitutes a critical step in recognition of cancer cells and the consequent development or control of the malignancy. One of the keystones to achieving a successful antitumor response is the presence of potent tumor antigens, known as neoantigens. However, tumors develop strategies to evade the immune system and resist current immunotherapies, and many tumors present a low tumor mutation burden limiting the presence of tumor antigenicity. Therefore, new approaches must be taken into consideration to overcome these shortcomings. The possibility of making tumors more antigenic represents a promising front to further improve the success of immunotherapy in cancer. Throughout this review, we explored different state-of-the-art tools to induce the presentation of new tumor antigens by intervening at protein, mRNA or genomic levels in malignant cells.
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Affiliation(s)
- Daniel Meraviglia-Crivelli
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain; (D.M.-C.); (A.Z.); (M.B.); (B.M.); (H.V.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - Angelina Zheleva
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain; (D.M.-C.); (A.Z.); (M.B.); (B.M.); (H.V.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - Martin Barainka
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain; (D.M.-C.); (A.Z.); (M.B.); (B.M.); (H.V.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - Beatriz Moreno
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain; (D.M.-C.); (A.Z.); (M.B.); (B.M.); (H.V.)
| | - Helena Villanueva
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain; (D.M.-C.); (A.Z.); (M.B.); (B.M.); (H.V.)
| | - Fernando Pastor
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain; (D.M.-C.); (A.Z.); (M.B.); (B.M.); (H.V.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
- Correspondence:
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23
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Jin Q, Zuo C, Cui H, Li L, Yang Y, Dai H, Chen L. Single-cell entropy network detects the activity of immune cells based on ribosomal protein genes. Comput Struct Biotechnol J 2022; 20:3556-3566. [PMID: 35860411 PMCID: PMC9287362 DOI: 10.1016/j.csbj.2022.06.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 11/16/2022] Open
Abstract
We developed a new computational method, Single-Cell Entropy Network (SCEN) to analyze single-cell RNA-seq data, which used the information of gene-gene associations to discover new heterogeneity of immune cells as well as identify existing cell types. Based on SCEN, we defined association-entropy (AE) for each cell and each gene through single-cell gene co-expression networks to measure the strength of association between each gene and all other genes at a single-cell resolution. Analyses of public datasets indicated that the AE of ribosomal protein genes (RP genes) varied greatly even in the same cell type of immune cells and the average AE of RP genes of immune cells in each person was significantly associated with the healthy/disease state of this person. Based on existing research and theory, we inferred that the AE of RP genes represented the heterogeneity of ribosomes and reflected the activity of immune cells. We believe SCEN can provide more biological insights into the heterogeneity and diversity of immune cells, especially the change of immune cells in the diseases.
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Affiliation(s)
- Qiqi Jin
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunman Zuo
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haoyue Cui
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Li
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yiwen Yang
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Dai
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Guangdong Institute of Intelligence Science and Technology, Hengqin, Zhuhai, Guangdong 519031, China.,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
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24
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Boettcher M, Joechner A, Li Z, Yang SF, Schlegel P. Development of CAR T Cell Therapy in Children-A Comprehensive Overview. J Clin Med 2022; 11:jcm11082158. [PMID: 35456250 PMCID: PMC9024694 DOI: 10.3390/jcm11082158] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 01/27/2023] Open
Abstract
CAR T cell therapy has revolutionized immunotherapy in the last decade with the successful establishment of chimeric antigen receptor (CAR)-expressing cellular therapies as an alternative treatment in relapsed and refractory CD19-positive leukemias and lymphomas. There are fundamental reasons why CAR T cell therapy has been approved by the Food and Drug administration and the European Medicines Agency for pediatric and young adult patients first. Commonly, novel therapies are developed for adult patients and then adapted for pediatric use, due to regulatory and commercial reasons. Both strategic and biological factors have supported the success of CAR T cell therapy in children. Since there is an urgent need for more potent and specific therapies in childhood malignancies, efforts should also include the development of CAR therapeutics and expand applicability by introducing new technologies. Basic aspects, the evolution and the drawbacks of childhood CAR T cell therapy are discussed as along with the latest clinically relevant information.
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Affiliation(s)
- Michael Boettcher
- Department of Pediatric Surgery, University Medical Centre Mannheim, University of Heidelberg, 69117 Heidelberg, Germany;
| | - Alexander Joechner
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia;
- Cellular Cancer Therapeutics Unit, Children’s Medical Research Institute, Sydney 2145, Australia; (Z.L.); (S.F.Y.)
| | - Ziduo Li
- Cellular Cancer Therapeutics Unit, Children’s Medical Research Institute, Sydney 2145, Australia; (Z.L.); (S.F.Y.)
| | - Sile Fiona Yang
- Cellular Cancer Therapeutics Unit, Children’s Medical Research Institute, Sydney 2145, Australia; (Z.L.); (S.F.Y.)
| | - Patrick Schlegel
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia;
- Cellular Cancer Therapeutics Unit, Children’s Medical Research Institute, Sydney 2145, Australia; (Z.L.); (S.F.Y.)
- Department of Pediatric Hematology and Oncology, Westmead Children’s Hospital, Sydney 2145, Australia
- Correspondence:
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25
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Yewdell JW. MHC Class I Immunopeptidome: Past, Present, and Future. Mol Cell Proteomics 2022; 21:100230. [PMID: 35395404 PMCID: PMC9243166 DOI: 10.1016/j.mcpro.2022.100230] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 12/14/2022] Open
Abstract
In the 35 years since the revelation that short peptides bound to major histocompatibility complex class I and II molecules are the secret of the major histocompatibility complex–restricted nature of T-cell recognition, there has been enormous progress in characterizing the immunopeptidome, the repertoire of peptide presented for immunosurveillance. Here, the major milestones in the journey are marked, the contribution of proteasome-mediated splicing to the immunopeptidome is discussed, and exciting recent findings relating the immunopeptidome to the translatome revealed by ribosome profiling (RiboSeq) is detailed. Finally, what is needed for continued progress is opined about, which includes the infusion of talented young scientists into the antigen-processing field, currently undergoing a renaissance; thanks in part to the astounding success of T-cell–based cancer immunotherapy. Concise history of the discoveries leading to the molecular explanation for the phenomenon of the MHC class I–restricted nature of T-cell recognition. Historical review of how MS became a critical technique for defining MHC class I–associated peptides and understanding how peptides are generated from proteins biosynthesized by the antigen-presenting cell. Critical review of recent findings linking the translatome to the MHC class I immunopeptidome and the controversy regarding contribution of proteasome-mediated peptide splicing to the immunopeptidome. Speculative discussion of the future contributions of MS to understanding the generation of the MHC class I immunopeptidome.
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Affiliation(s)
- Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.
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26
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Martini V, Edmans M, Gubbins S, Jayaraman S, Paudyal B, Morgan S, McNee A, Morin T, Rijal P, Gerner W, Sewell AK, Inoue R, Bailey M, Connelley T, Charleston B, Townsend A, Beverley P, Tchilian E. Spatial, temporal and molecular dynamics of swine influenza virus-specific CD8 tissue resident memory T cells. Mucosal Immunol 2022; 15:428-442. [PMID: 35145208 PMCID: PMC9038527 DOI: 10.1038/s41385-021-00478-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/23/2021] [Accepted: 12/08/2021] [Indexed: 02/04/2023]
Abstract
For the first time we have defined naïve, central memory, effector memory and differentiated effector porcine CD8 T cells and analyzed their distribution in lymphoid and respiratory tissues after influenza infection or immunization, using peptide-MHC tetramers of three influenza nucleoprotein (NP) epitopes. The hierarchy of response to the three epitopes changes during the response in different tissues. Most NP-specific CD8 T cells in broncho-alveolar lavage (BAL) and lung are tissue resident memory cells (TRM) that express CD69 and downregulate CD45RA and CCR7. NP-specific cells isolated from BAL express genes characteristic of TRM, but gene expression differs at 7, 21 and 63 days post infection. In all tissues the frequency of NP-specific CD8 cells declines over 63 days almost to background levels but is best maintained in BAL. The kinetic of influenza specific memory CD8 T cell in this natural host species differs from that in small animal models.
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Affiliation(s)
- Veronica Martini
- The Pirbright Institute, Pirbright, UK.
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Institute for Research in Biomedicine, Bellinzona, Switzerland.
| | | | | | | | | | | | | | - Théo Morin
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Pramila Rijal
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Ryo Inoue
- Laboratory of Animal Science, Setsunan University, Osaka, Japan
| | - Mick Bailey
- Bristol Veterinary School, University of Bristol, Langford, UK
| | | | | | - Alain Townsend
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Peter Beverley
- National Heart and Lung Institute, St Mary's Campus, Imperial College, London, UK
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27
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Lu C, Chen H, Wang C, Yang F, Li J, Liu H, Chen G. An Emerging Role of TIM3 Expression on T Cells in Chronic Kidney Inflammation. Front Immunol 2022; 12:798683. [PMID: 35154075 PMCID: PMC8825483 DOI: 10.3389/fimmu.2021.798683] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/16/2021] [Indexed: 12/29/2022] Open
Abstract
T cell immunoglobulin domain and mucin domain 3 (TIM3) was initially identified as an inhibitory molecule on IFNγ-producing T cells. Further research discovered the broad expression of TIM3 on different immune cells binding to multiple ligands. Apart from its suppressive effects on the Th1 cells, recent compelling experiments highlighted the indispensable role of TIM3 in the myeloid cell-mediated inflammatory response, supporting that TIM3 exerts pleiotropic effects on both adaptive and innate immune cells in a context-dependent manner. A large number of studies have been conducted on TIM3 biology in the disease settings of infection, cancer, and autoimmunity. However, there is a lack of clinical evidence to closely evaluate the role of T cell-expressing TIM3 in the pathogenesis of chronic kidney disease (CKD). Here, we reported an intriguing case of Mycobacterium tuberculosis (Mtb) infection that was characterized by persistent overexpression of TIM3 on circulating T cells and ongoing kidney tubulointerstitial inflammation for a period of 12 months. In this case, multiple histopathological biopsies revealed a massive accumulation of recruited T cells and macrophages in the enlarged kidney and liver. After standard anti-Mtb treatment, repeated renal biopsy identified a dramatic remission of the infiltrated immune cells in the tubulointerstitial compartment. This is the first clinical report to reveal a time-course expression of TIM3 on the T cells, which is pathologically associated with the progression of severe kidney inflammation in a non-autoimmunity setting. Based on this case, we summarize the recent findings on TIM3 biology and propose a novel model of CKD progression due to the aberrant crosstalk among immune cells.
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Affiliation(s)
- Can Lu
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Huihui Chen
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China
- Clinical Immunology Research Center, Central South University, Changsha, China
| | - Chang Wang
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, China
| | - Fei Yang
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, China
| | - Jun Li
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, China
| | - Hong Liu
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, China
| | - Guochun Chen
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, China
- Clinical Immunology Research Center, Central South University, Changsha, China
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28
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Abstract
Immune principles formulated by Jenner, Pasteur, and early immunologists served as fundamental propositions for vaccine discovery against many dreadful pathogens. However, decisive success in the form of an efficacious vaccine still eludes for diseases such as tuberculosis, leishmaniasis, and trypanosomiasis. Several antileishmanial vaccine trials have been undertaken in past decades incorporating live, attenuated, killed, or subunit vaccination, but the goal remains unmet. In light of the above facts, we have to reassess the principles of vaccination by dissecting factors associated with the hosts' immune response. This chapter discusses the pathogen-associated perturbations at various junctures during the generation of the immune response which inhibits antigenic processing, presentation, or remodels memory T cell repertoire. This can lead to ineffective priming or inappropriate activation of memory T cells during challenge infection. Thus, despite a protective primary response, vaccine failure can occur due to altered immune environments in the presence of pathogens.
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Affiliation(s)
| | - Sunil Kumar
- National Centre for Cell Science, Pune, Maharashtra, India
| | | | - Bhaskar Saha
- National Centre for Cell Science, Pune, Maharashtra, India.
- Trident Academy of Creative Technology, Bhubaneswar, Odisha, India.
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29
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Son ET, Faridi P, Paul-Heng M, Leong ML, English K, Ramarathinam SH, Braun A, Dudek NL, Alexander IE, Lisowski L, Bertolino P, Bowen DG, Purcell AW, Mifsud NA, Sharland AF. The self-peptide repertoire plays a critical role in transplant tolerance induction. J Clin Invest 2021; 131:e146771. [PMID: 34428180 DOI: 10.1172/jci146771] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 08/18/2021] [Indexed: 11/17/2022] Open
Abstract
While direct allorecognition underpins both solid organ allograft rejection and tolerance induction, the specific molecular targets of most directly alloreactive CD8+ T cells have not been defined. In this study, we used a combination of genetically engineered major histocompatibility complex class I (MHC I) constructs, mice with a hepatocyte-specific mutation in the class I antigen-presentation pathway, and immunopeptidomic analysis to provide definitive evidence for the contribution of the peptide cargo of allogeneic MHC I molecules to transplant tolerance induction. We established a systematic approach for the discovery of directly recognized pMHC epitopes and identified 17 strongly immunogenic H-2Kb-associated peptides recognized by CD8+ T cells from B10.BR (H-2k) mice, 13 of which were also recognized by BALB/c (H-2d) mice. As few as 5 different tetramers used together were able to identify a high proportion of alloreactive T cells within a polyclonal population, suggesting that there are immunodominant allogeneic MHC-peptide complexes that can account for a large component of the alloresponse.
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Affiliation(s)
- Eric T Son
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Pouya Faridi
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Moumita Paul-Heng
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Mario L Leong
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Kieran English
- Liver Immunology Group and AW Morrow Gastroenterology and Liver Centre, The University of Sydney and Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Sri H Ramarathinam
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Asolina Braun
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Nadine L Dudek
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, The University of Sydney, Faculty of Medicine and Health and Sydney Children's Hospitals Network, Westmead, New South Wales, Australia.,The University of Sydney, Sydney Medical School, Discipline of Child and Adolescent Health, Westmead, New South Wales, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia.,Vector and Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia.,Military Institute of Medicine, Laboratory of Molecular Oncology and Innovative Therapies, Warsaw, Poland
| | - Patrick Bertolino
- Liver Immunology Group and AW Morrow Gastroenterology and Liver Centre, The University of Sydney and Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - David G Bowen
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, New South Wales, Australia.,Liver Immunology Group and AW Morrow Gastroenterology and Liver Centre, The University of Sydney and Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Anthony W Purcell
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Alexandra F Sharland
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, New South Wales, Australia
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30
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Daouda T, Dumont-Lagacé M, Feghaly A, Benslimane Y, Panes R, Courcelles M, Benhammadi M, Harrington L, Thibault P, Major F, Bengio Y, Gagnon É, Lemieux S, Perreault C. CAMAP: Artificial neural networks unveil the role of codon arrangement in modulating MHC-I peptides presentation. PLoS Comput Biol 2021; 17:e1009482. [PMID: 34679099 PMCID: PMC8577786 DOI: 10.1371/journal.pcbi.1009482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 11/09/2021] [Accepted: 09/27/2021] [Indexed: 12/02/2022] Open
Abstract
MHC-I associated peptides (MAPs) play a central role in the elimination of virus-infected and neoplastic cells by CD8 T cells. However, accurately predicting the MAP repertoire remains difficult, because only a fraction of the transcriptome generates MAPs. In this study, we investigated whether codon arrangement (usage and placement) regulates MAP biogenesis. We developed an artificial neural network called Codon Arrangement MAP Predictor (CAMAP), predicting MAP presentation solely from mRNA sequences flanking the MAP-coding codons (MCCs), while excluding the MCC per se. CAMAP predictions were significantly more accurate when using original codon sequences than shuffled codon sequences which reflect amino acid usage. Furthermore, predictions were independent of mRNA expression and MAP binding affinity to MHC-I molecules and applied to several cell types and species. Combining MAP ligand scores, transcript expression level and CAMAP scores was particularly useful to increase MAP prediction accuracy. Using an in vitro assay, we showed that varying the synonymous codons in the regions flanking the MCCs (without changing the amino acid sequence) resulted in significant modulation of MAP presentation at the cell surface. Taken together, our results demonstrate the role of codon arrangement in the regulation of MAP presentation and support integration of both translational and post-translational events in predictive algorithms to ameliorate modeling of the immunopeptidome. MHC-I associated peptides (MAPs) are small fragments of intracellular proteins presented at the surface of cells and used by the immune system to detect and eliminate cancerous or virus-infected cells. While it is theoretically possible to predict which portions of the intracellular proteins will be naturally processed by the cells to ultimately reach the surface, current methodologies have prohibitively high false discovery rates. Here we introduce an artificial neural network called Codon Arrangement MAP Predictor (CAMAP) which integrates information from mRNA-to-protein translation to other factors regulating MAP biogenesis (e.g. MAP ligand score and transcript expression levels) to improve MAP prediction accuracy. While most MAP predictive approaches focus on MAP sequences per se, CAMAP’s novelty is to analyze the MAP-flanking mRNA sequences, thereby providing completely independent information for MAP prediction. We show on several datasets that the integration of CAMAP scores with other known factors involved in MAP presentation (i.e. MAP ligand score and mRNA expression) significantly improves MAP prediction accuracy, and further validate CAMAP learned features using an in-vitro assay. These findings may have major implications for the design of vaccines against cancers and viruses, and in times of pandemics could accelerate the identification of relevant MAPs of viral origins.
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Affiliation(s)
- Tariq Daouda
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Biochemistry, Université de Montréal, Montréal, Canada
- * E-mail:
| | - Maude Dumont-Lagacé
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Medicine, Université de Montréal, Montréal, Canada
| | - Albert Feghaly
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Yahya Benslimane
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Medicine, Université de Montréal, Montréal, Canada
| | - Rébecca Panes
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, Canada
| | - Mathieu Courcelles
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Mohamed Benhammadi
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Medicine, Université de Montréal, Montréal, Canada
| | - Lea Harrington
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Medicine, Université de Montréal, Montréal, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Chemistry, Université de Montréal, Montréal, Canada
| | - François Major
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, Canada
| | - Yoshua Bengio
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, Canada
| | - Étienne Gagnon
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Biochemistry, Université de Montréal, Montréal, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Medicine, Université de Montréal, Montréal, Canada
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31
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Identification of tumor antigens with immunopeptidomics. Nat Biotechnol 2021; 40:175-188. [PMID: 34635837 DOI: 10.1038/s41587-021-01038-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 07/29/2021] [Indexed: 12/18/2022]
Abstract
The identification of actionable tumor antigens is indispensable for the development of several cancer immunotherapies, including T cell receptor-transduced T cells and patient-specific mRNA or peptide vaccines. Most known tumor antigens have been identified through extensive molecular characterization and are considered canonical if they derive from protein-coding regions of the genome. By eluting human leukocyte antigen-bound peptides from tumors and subjecting these to mass spectrometry analysis, the peptides can be identified by matching the resulting spectra against reference databases. Recently, mass-spectrometry-based immunopeptidomics has enabled the discovery of noncanonical antigens-antigens derived from sequences outside protein-coding regions or generated by noncanonical antigen-processing mechanisms. Coupled with transcriptomics and ribosome profiling, this method enables the identification of thousands of noncanonical peptides, of which a substantial fraction may be detected exclusively in tumors. Spectral matching against the immense noncanonical reference may generate false positives. However, sensitive mass spectrometry, analytical validation and advanced bioinformatics solutions are expected to uncover the full landscape of presented antigens and clinically relevant targets.
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32
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Bailey A, Nicholas B, Darley R, Parkinson E, Teo Y, Aleksic M, Maxwell G, Elliott T, Ardern-Jones M, Skipp P. Characterization of the Class I MHC Peptidome Resulting From DNCB Exposure of HaCaT Cells. Toxicol Sci 2021; 180:136-147. [PMID: 33372950 PMCID: PMC7916740 DOI: 10.1093/toxsci/kfaa184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Skin sensitization following the covalent modification of proteins by low molecular weight chemicals (haptenation) is mediated by cytotoxic T lymphocyte (CTL) recognition of human leukocyte antigen (HLA) molecules presented on the surface of almost all nucleated cells. There exist 3 nonmutually exclusive hypotheses for how haptens mediate CTL recognition: direct stimulation by haptenated peptides, hapten modification of HLA leading to an altered HLA-peptide repertoire, or a hapten altered proteome leading to an altered HLA-peptide repertoire. To shed light on the mechanism underpinning skin sensitization, we set out to utilize proteomic analysis of keratinocyte presented antigens following exposure to 2,4-dinitrochlorobenzene (DNCB). We show that the following DNCB exposure, cultured keratinocytes present cysteine haptenated (dinitrophenylated) peptides in multiple HLA molecules. In addition, we find that one of the DNCB modified peptides derives from the active site of cytosolic glutathione-S transferase-ω. These results support the current view that a key mechanism of skin sensitization is stimulation of CTLs by haptenated peptides. Data are available via ProteomeXchange with identifier PXD021373.
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Affiliation(s)
- Alistair Bailey
- Centre for Proteomic Research, Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Centre for Cancer Immunology and Institute for Life Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Ben Nicholas
- Centre for Proteomic Research, Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Centre for Cancer Immunology and Institute for Life Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Rachel Darley
- Centre for Cancer Immunology and Institute for Life Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Erika Parkinson
- Centre for Proteomic Research, Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Ying Teo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Maja Aleksic
- Safety & Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook MK44 1LQ, UK
| | - Gavin Maxwell
- Safety & Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook MK44 1LQ, UK
| | - Tim Elliott
- Centre for Cancer Immunology and Institute for Life Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Michael Ardern-Jones
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Paul Skipp
- Centre for Proteomic Research, Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
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33
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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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34
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Weingarten-Gabbay S, Klaeger S, Sarkizova S, Pearlman LR, Chen DY, Gallagher KME, Bauer MR, Taylor HB, Dunn WA, Tarr C, Sidney J, Rachimi S, Conway HL, Katsis K, Wang Y, Leistritz-Edwards D, Durkin MR, Tomkins-Tinch CH, Finkel Y, Nachshon A, Gentili M, Rivera KD, Carulli IP, Chea VA, Chandrashekar A, Bozkus CC, Carrington M, Bhardwaj N, Barouch DH, Sette A, Maus MV, Rice CM, Clauser KR, Keskin DB, Pregibon DC, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs. Cell 2021; 184:3962-3980.e17. [PMID: 34171305 PMCID: PMC8173604 DOI: 10.1016/j.cell.2021.05.046] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/21/2021] [Accepted: 05/27/2021] [Indexed: 01/23/2023]
Abstract
T cell-mediated immunity plays an important role in controlling SARS-CoV-2 infection, but the repertoire of naturally processed and presented viral epitopes on class I human leukocyte antigen (HLA-I) remains uncharacterized. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two cell lines at different times post infection using mass spectrometry. We found HLA-I peptides derived not only from canonical open reading frames (ORFs) but also from internal out-of-frame ORFs in spike and nucleocapsid not captured by current vaccines. Some peptides from out-of-frame ORFs elicited T cell responses in a humanized mouse model and individuals with COVID-19 that exceeded responses to canonical peptides, including some of the strongest epitopes reported to date. Whole-proteome analysis of infected cells revealed that early expressed viral proteins contribute more to HLA-I presentation and immunogenicity. These biological insights, as well as the discovery of out-of-frame ORF epitopes, will facilitate selection of peptides for immune monitoring and vaccine development.
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Affiliation(s)
- Shira Weingarten-Gabbay
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | | | - Leah R Pearlman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Da-Yuan Chen
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Kathleen M E Gallagher
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Matthew R Bauer
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah B Taylor
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Suzanna Rachimi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hasahn L Conway
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Katelin Katsis
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Yuntong Wang
- Repertoire Immune Medicines, Cambridge, MA 02139, USA
| | | | | | - Christopher H Tomkins-Tinch
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yaara Finkel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Matteo Gentili
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Keith D Rivera
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Isabel P Carulli
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vipheaviny A Chea
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Cansu Cimen Bozkus
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Nina Bhardwaj
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Dan H Barouch
- Harvard Medical School, Boston, MA 02115, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Marcela V Maus
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Derin B Keskin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA; Health Informatics Lab, Metropolitan College, Boston University, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA; Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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35
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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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36
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Komov L, Melamed Kadosh D, Barnea E, Admon A. The Effect of Interferons on Presentation of Defective Ribosomal Products as HLA Peptides. Mol Cell Proteomics 2021; 20:100105. [PMID: 34087483 PMCID: PMC8724922 DOI: 10.1016/j.mcpro.2021.100105] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/15/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
A subset of class I major histocompatibility complex (MHC)-bound peptides is produced from immature proteins that are rapidly degraded after synthesis. These defective ribosomal products (DRiPs) have been implicated in early alert of the immune system about impending infections. Interferons are important cytokines, produced in response to viral infection, that modulate cellular metabolism and gene expression patterns, increase the presentation of MHC molecules, and induce rapid degradation of proteins and cell-surface presentation of their derived MHC peptides, thereby contributing to the battle against pathogen infections. This study evaluated the role of interferons in the induction of rapid degradation of DRiPs to modulate the repertoire of DRiP-derived MHC peptides. Cultured human breast cancer cells were treated with interferons, and the rates of synthesis and degradation of cellular protein and their degradation products were determined by LC-MS/MS analysis, following the rates of incorporation of heavy stable isotope–labeled amino acids (dynamic stable isotope labeling by amino acids in cell culture, dynamic SILAC) at several time points after the interferon application. Large numbers of MHC peptides that incorporated the heavy amino acids faster than their source proteins indicated that DRiP peptides were abundant in the MHC peptidome; interferon treatment increased by about twofold their relative proportions in the peptidome. Such typical DRiP-derived MHC peptides were from the surplus subunits of the proteasome and ribosome, which are degraded because of the transition to immunoproteasomes and a new composition of ribosomes incorporating protein subunits that are induced by the interferon. We conclude that degradation of surplus subunits induced by the interferon is a major source for DRiP–MHC peptides, a phenomenon relevant to coping with viral infections, where a rapid presentation of MHC peptides derived from excess viral proteins may help alert the immune system about the impending infection. Degradation products of surplus subunits are often presented as HLA peptides. Interferons increase degradation and presentation of such defective products. Dynamic SILAC facilitates identification of such HLA peptides. This cellular pathway provides alert to the immune system about viral infections.
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Affiliation(s)
- Liran Komov
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Eilon Barnea
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
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37
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Lin LCW, Croft SN, Croft NP, Wong YC, Smith SA, Tang SS, Purcell AW, Tscharke DC. Direct Priming of CD8 + T Cells Persists in the Face of Cowpox Virus Inhibitors of Antigen Presentation. J Virol 2021; 95:JVI.00186-21. [PMID: 33692206 PMCID: PMC8139650 DOI: 10.1128/jvi.00186-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/27/2021] [Indexed: 11/30/2022] Open
Abstract
Vaccinia virus (VACV) was the vaccine used to eradicate smallpox and is being repurposed as a vaccine vector. CD8+ T cells are key anti-viral mediators, but require priming to become effector or memory cells. Priming requires an interaction with dendritic cells that are either infected (direct priming), or that have acquired virus proteins but remain uninfected (cross priming). To investigate CD8+ T cell priming pathways for VACV, we engineered the virus to express CPXV12 and CPXV203, two inhibitors of antigen presentation encoded by cowpox virus. These intracellular proteins would be expected to block direct but not cross priming. The inhibitors had diverse impacts on the size of anti-VACV CD8+ T cell responses across epitopes and by different infection routes in mice, superficially suggesting variable use of direct and cross priming. However, when we then tested a form of antigen that requires direct priming, we found surprisingly that CD8+ T cell responses were not diminished by co-expression with CPXV12 and CPXV203. We then directly quantified the impact of CPXV12 and CPXV203 on viral antigen presentation using mass spectrometry, which revealed strong, but incomplete inhibition of antigen presentation by the CPXV proteins. Therefore, direct priming of CD8+ T cells by poxviruses is robust enough to withstand highly potent viral inhibitors of antigen presentation. This is a reminder of the limits of viral immune evasion and shows that viral inhibitors of antigen presentation cannot be assumed to dissect cleanly direct and cross priming of anti-viral CD8+ T cells.ImportanceCD8+ T cells are key to anti-viral immunity, so it is important to understand how they are activated. Many viruses have proteins that protect infected cells from T cell attack by interfering with the process that allows virus infection to be recognised by CD8+ T cells. It is thought that these proteins would also stop infected cells from activating T cells in the first place. However, we show here that this is not the case for two very powerful inhibitory proteins from cowpox virus. This demonstrates the flexibility and robustness of immune processes that turn on the immune responses required to fight infection.
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Affiliation(s)
- Leon C. W. Lin
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Sarah N. Croft
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Nathan P. Croft
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Yik Chun Wong
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Stewart A. Smith
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Swee-Seong Tang
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Anthony W. Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - David C. Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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38
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Sturm T, Sautter B, Wörner TP, Stevanović S, Rammensee HG, Planz O, Heck AJR, Aebersold R. Mild Acid Elution and MHC Immunoaffinity Chromatography Reveal Similar Albeit Not Identical Profiles of the HLA Class I Immunopeptidome. J Proteome Res 2020; 20:289-304. [PMID: 33141586 PMCID: PMC7786382 DOI: 10.1021/acs.jproteome.0c00386] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
To
understand and treat immunology-related diseases, a comprehensive,
unbiased characterization of major histocompatibility complex (MHC)
peptide ligands is of key importance. Preceding the analysis by mass
spectrometry, MHC class I peptide ligands are typically isolated by
MHC immunoaffinity chromatography (MHC-IAC) and less often by mild
acid elution (MAE). MAE may provide a cheap alternative to MHC-IAC
for suspension cells but has been hampered by the high number of contaminating,
MHC-unrelated peptides. Here, we optimized MAE, yielding MHC peptide
ligand purities of more than 80%. When compared with MHC-IAC, obtained
peptides were similar in numbers, identities, and to a large extent
intensities, while the percentage of cysteinylated peptides was 5
times higher in MAE. The latter benefitted the discovery of MHC-allotype-specific,
distinct cysteinylation frequencies at individual positions of MHC
peptide ligands. MAE revealed many MHC ligands with unmodified, N-terminal
cysteine residues which get lost in MHC-IAC workflows. The results
support the idea that MAE might be particularly valuable for the high-confidence
analysis of post-translational modifications by avoiding the exposure
of the investigated peptides to enzymes and reactive molecules in
the cell lysate. Our improved and carefully documented MAE workflow
represents a high-quality, cost-effective alternative to MHC-IAC for
suspension cells.
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Affiliation(s)
- Theo Sturm
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands.,Philochem AG, 8112 Otelfingen, Switzerland
| | - Benedikt Sautter
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Tobias P Wörner
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Oliver Planz
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.,Faculty of Science, University of Zurich, 8057 Zürich, Switzerland
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39
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Weingarten-Gabbay S, Klaeger S, Sarkizova S, Pearlman LR, Chen DY, Bauer MR, Taylor HB, Conway HL, Tomkins-Tinch CH, Finkel Y, Nachshon A, Gentili M, Rivera KD, Keskin DB, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33024965 PMCID: PMC7536868 DOI: 10.1101/2020.10.02.324145] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
T cell-mediated immunity may play a critical role in controlling and establishing protective immunity against SARS-CoV-2 infection; yet the repertoire of viral epitopes responsible for T cell response activation remains mostly unknown. Identification of viral peptides presented on class I human leukocyte antigen (HLA-I) can reveal epitopes for recognition by cytotoxic T cells and potential incorporation into vaccines. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two human cell lines at different times post-infection using mass spectrometry. We found HLA-I peptides derived not only from canonical ORFs, but also from internal out-of-frame ORFs in Spike and Nucleoprotein not captured by current vaccines. Proteomics analyses of infected cells revealed that SARS-CoV-2 may interfere with antigen processing and immune signaling pathways. Based on the endogenously processed and presented viral peptides that we identified, we estimate that a pool of 24 peptides would provide one or more peptides for presentation by at least one HLA allele in 99% of the human population. These biological insights and the list of naturally presented SARS-CoV-2 peptides will facilitate data-driven selection of peptides for immune monitoring and vaccine development.
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40
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Croft S, Wong YC, Smith SA, Flesch IEA, Tscharke DC. Surprisingly Effective Priming of CD8 + T Cells by Heat-Inactivated Vaccinia Virus Virions. J Virol 2020; 94:e01486-20. [PMID: 32759313 PMCID: PMC7527048 DOI: 10.1128/jvi.01486-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 12/29/2022] Open
Abstract
Robust priming of CD8+ T cells by viruses is considered to require infection and de novo expression of viral antigens. A corollary of this is that inactivated viruses are thought of as being inevitably poor vaccines for eliciting these responses. In contrast to this dogma, we found that some antigens present in vaccinia virus (VACV) virions prime strong CD8+ T cell responses when the virus was rendered noninfectious by heat. More surprisingly, in some cases these responses were similar in magnitude to those primed by infectious virus administered at an equivalent dose. Next, we tested whether this was a special property of particular antigens and their epitopes and found that foreign epitopes tagged onto three different VACV virion proteins were able to elicit CD8+ T cell responses irrespective of whether the virus was viable or heat killed. Further, the polyfunctionality and cytotoxic ability of the CD8+ T cells primed by these VACVs was equivalent irrespective of whether they were administered to mice as inactivated or live viruses. Finally, we used these VACVs in prime-boost combinations of inactivated and live virus and found that priming with dead virus before a live booster was the most immunogenic regime. We conclude that VACV virions can be efficient vectors for targeting antigens to dendritic cells for effective priming of CD8+ T cells, even when rendered noninfectious and speculate that this might also be the case for other viruses.IMPORTANCE The design of viral vectored vaccines is often considered to require a trade-off between efficacy and safety. This is especially the case for vaccines that aim to induce killer (CD8+) T cells, where there is a well-established dogma that links infection in vaccinated individuals with effective induction of immunity. However, we found that some proteins of vaccinia virus generate strong CD8+ T cell responses even when the virus preparation was inactivated by heat prior to administration as a vaccine. We took advantage of this finding by engineering a new vaccine vector virus that could be used as an inactivated vaccine. These results suggest that vaccinia virus may be a more versatile vaccine vector than previously appreciated and that in some instances safety can be prioritized by the complete elimination of viral replication without a proportional loss of immunogenicity.
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Affiliation(s)
- Sarah Croft
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Yik Chun Wong
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Stewart A Smith
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Inge E A Flesch
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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41
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Faridi P, Woods K, Ostrouska S, Deceneux C, Aranha R, Duscharla D, Wong SQ, Chen W, Ramarathinam SH, Lim Kam Sian TCC, Croft NP, Li C, Ayala R, Cebon JS, Purcell AW, Schittenhelm RB, Behren A. Spliced Peptides and Cytokine-Driven Changes in the Immunopeptidome of Melanoma. Cancer Immunol Res 2020; 8:1322-1334. [PMID: 32938616 DOI: 10.1158/2326-6066.cir-19-0894] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/20/2020] [Accepted: 08/20/2020] [Indexed: 11/16/2022]
Abstract
Antigen recognition by CD8+ T cells is governed by the pool of peptide antigens presented on the cell surface in the context of HLA class I complexes. Studies have shown not only a high degree of plasticity in the immunopeptidome, but also that a considerable fraction of all presented peptides is generated through proteasome-mediated splicing of noncontiguous regions of proteins to form novel peptide antigens. Here, we used high-resolution mass spectrometry combined with new bioinformatic approaches to characterize the immunopeptidome of melanoma cells in the presence or absence of IFNγ. In total, we identified more than 60,000 peptides from a single patient-derived cell line (LM-MEL-44) and demonstrated that IFNγ induced changes in the peptidome, with an overlap of only approximately 50% between basal and treated cells. Around 6% to 8% of the peptides were identified as cis-spliced peptides, and 2,213 peptides (1,827 linear and 386 cis-spliced peptides) were derived from known melanoma-associated antigens. These peptide antigens were equally distributed between the constitutive- and IFNγ-induced peptidome. We next examined additional HLA-matched patient-derived cell lines to investigate how frequently these peptides were identified and found that a high proportion of both linear and spliced peptides was conserved between individual patient tumors, drawing on data amassing to more than 100,000 peptide sequences. Several of these peptides showed in vitro immunogenicity across multiple patients with melanoma. These observations highlight the breadth and complexity of the repertoire of immunogenic peptides that can be exploited therapeutically and suggest that spliced peptides are a major class of tumor antigens.
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Affiliation(s)
- Pouya Faridi
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Katherine Woods
- Cancer Immunobiology, Olivia Newton-John Cancer Research Institute, Austin Hospital, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Simone Ostrouska
- Cancer Immunobiology, Olivia Newton-John Cancer Research Institute, Austin Hospital, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Cyril Deceneux
- Cancer Immunobiology, Olivia Newton-John Cancer Research Institute, Austin Hospital, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Ritchlynn Aranha
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Divya Duscharla
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Stephen Q Wong
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Terry C C Lim Kam Sian
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Chen Li
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Rochelle Ayala
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jonathan S Cebon
- Cancer Immunobiology, Olivia Newton-John Cancer Research Institute, Austin Hospital, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,Monash Proteomics & Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Andreas Behren
- Cancer Immunobiology, Olivia Newton-John Cancer Research Institute, Austin Hospital, Heidelberg, Victoria, Australia. .,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
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42
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A few good peptides: MHC class I-based cancer immunosurveillance and immunoevasion. Nat Rev Immunol 2020; 21:116-128. [PMID: 32820267 DOI: 10.1038/s41577-020-0390-6] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2020] [Indexed: 12/25/2022]
Abstract
The remarkable success of immune checkpoint inhibitors demonstrates the potential of tumour-specific CD8+ T cells to prevent and treat cancer. Although the number of lives saved by immunotherapy mounts, only a relatively small fraction of patients are cured. Here, we review two of the factors that limit the application of CD8+ T cell immunotherapies: difficulties in identifying tumour-specific peptides presented by MHC class I molecules and the ability of tumour cells to impair antigen presentation as they evolve under T cell selection. We describe recent advances in understanding how peptides are generated from non-canonical translation of defective ribosomal products, relate this to the dysregulated translation that is a feature of carcinogenesis and propose dysregulated translation as an important new source of tumour-specific peptides. We discuss how the synthesis and function of components of the antigen-processing and presentation pathway, including the recently described immunoribosome, are manipulated by tumours for immunoevasion and point to common druggable targets that may enhance immunotherapy.
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43
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Zamora AE, Crawford JC, Allen EK, Guo XZJ, Bakke J, Carter RA, Abdelsamed HA, Moustaki A, Li Y, Chang TC, Awad W, Dallas MH, Mullighan CG, Downing JR, Geiger TL, Chen T, Green DR, Youngblood BA, Zhang J, Thomas PG. Pediatric patients with acute lymphoblastic leukemia generate abundant and functional neoantigen-specific CD8 + T cell responses. Sci Transl Med 2020; 11:11/498/eaat8549. [PMID: 31243155 DOI: 10.1126/scitranslmed.aat8549] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 11/16/2018] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
Abstract
Cancer arises from the accumulation of genetic alterations, which can lead to the production of mutant proteins not expressed by normal cells. These mutant proteins can be processed and presented on the cell surface by major histocompatibility complex molecules as neoepitopes, allowing CD8+ T cells to mount responses against them. For solid tumors, only an average 2% of neoepitopes predicted by algorithms have detectable endogenous antitumor T cell responses. This suggests that low mutation burden tumors, which include many pediatric tumors, are poorly immunogenic. Here, we report that pediatric patients with acute lymphoblastic leukemia (ALL) have tumor-associated neoepitope-specific CD8+ T cells, responding to 86% of tested neoantigens and recognizing 68% of the tested neoepitopes. These responses include a public neoantigen from the ETV6-RUNX1 fusion that is targeted in seven of nine tested patients. We characterized phenotypic and transcriptional profiles of CD8+ tumor-infiltrating lymphocytes (TILs) at the single-cell level and found a heterogeneous population that included highly functional effectors. Moreover, we observed immunodominance hierarchies among the CD8+ TILs restricted to one or two putative neoepitopes. Our results indicate that robust antitumor immune responses are induced in pediatric ALL despite their low mutation burdens and emphasize the importance of immunodominance in shaping cellular immune responses. Furthermore, these data suggest that pediatric cancers may be amenable to immunotherapies aimed at enhancing immune recognition of tumor-specific neoantigens.
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Affiliation(s)
- Anthony E Zamora
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xi-Zhi J Guo
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jesse Bakke
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Department of Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, MI 48858, USA
| | - Robert A Carter
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hossam A Abdelsamed
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ardiana Moustaki
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yongjin Li
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ti-Cheng Chang
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Walid Awad
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mari H Dallas
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Terrence L Geiger
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Benjamin A Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA. .,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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44
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Abstract
The defective ribosomal product (DRiP) hypothesis was proposed nearly 25 years ago to account for the rapid generation of peptides from otherwise metabolically stable viral proteins. It posits that errors in converting genetic information into stable proteins accounts for a sizeable fraction of the immunopeptidome. Here, we review recent studies that provide insight into the importance of DRiPs for immunosurveillance and the myriad mechanisms that give rise to DRiPs.
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45
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Reguzova A, Ghosh M, Müller M, Rziha HJ, Amann R. Orf Virus-Based Vaccine Vector D1701-V Induces Strong CD8+ T Cell Response against the Transgene but Not against ORFV-Derived Epitopes. Vaccines (Basel) 2020; 8:E295. [PMID: 32531997 PMCID: PMC7349966 DOI: 10.3390/vaccines8020295] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/03/2020] [Accepted: 06/06/2020] [Indexed: 01/14/2023] Open
Abstract
The potency of viral vector-based vaccines depends on their ability to induce strong transgene-specific immune response without triggering anti-vector immunity. Previously, Orf virus (ORFV, Parapoxvirus) strain D1701-V was reported as a novel vector mediating protection against viral infections. The short-lived ORFV-specific immune response and the absence of virus neutralizing antibodies enables repeated immunizations and enhancement of humoral immune responses against the inserted antigens. However, only limited information exists about the D1701-V induced cellular immunity. In this study we employed major histocompatibility complex (MHC) ligandomics and immunogenicity analysis to identify ORFV-specific epitopes. Using liquid chromatography-tandem mass spectrometry we detected 36 ORFV-derived MHC I peptides, originating from various proteins. Stimulated splenocytes from ORFV-immunized mice did not exhibit specific CD8+ T cell responses against the tested peptides. In contrast, immunization with ovalbumin-expressing ORFV recombinant elicited strong SIINFEKL-specific CD8+ T lymphocyte response. In conclusion, our data indicate that cellular immunity to the ORFV vector is negligible, while strong CD8+ T cell response is induced against the inserted transgene. These results further emphasize the ORFV strain D1701-V as an attractive vector for vaccine development. Moreover, the presented experiments describe prerequisites for the selection of T cell epitopes exploitable for generation of ORFV-based vaccines by reverse genetics.
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Affiliation(s)
| | | | | | | | - Ralf Amann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.G.); (M.M.); (H.-J.R.)
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46
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Han KC, Park D, Ju S, Lee YE, Heo SH, Kim YA, Lee JE, Lee Y, Park KH, Park SH, Lee HJ, Lee C, Jang M. Streamlined selection of cancer antigens for vaccine development through integrative multi-omics and high-content cell imaging. Sci Rep 2020; 10:5885. [PMID: 32245999 PMCID: PMC7125174 DOI: 10.1038/s41598-020-62244-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/09/2020] [Indexed: 11/18/2022] Open
Abstract
Identification of tumor antigens that induce cytotoxic T lymphocytes (CTLs) is crucial for cancer-vaccine development. Despite their predictive ability, current algorithmic approaches and human leukocyte antigen (HLA)-peptidomic analysis allow limited selectivity. Here, we optimized a method to rapidly screen and identify highly immunogenic epitopes that trigger CTL responses. We used a combined application of this method involving immune-specific signature analysis and HLA-associated peptidomics using samples from six patients with triple-negative breast cancer (TNBC) in order to select immunogenic HLA epitopes for in vitro testing. Additionally, we applied high-throughput imaging at the single-cell level in order to confirm the immunoreactivity of the selected peptides. The results indicated that this method enabled identification of promising CTL peptides capable of inducing antitumor immunity. This platform combining high-resolution computational analysis, HLA-peptidomics, and high-throughput immunogenicity testing allowed rapid and robust identification of highly immunogenic epitopes and represents a powerful technique for cancer-vaccine development.
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Affiliation(s)
- Ki-Cheol Han
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-Gu, Seoul, 02792, Republic of Korea.
| | - Daechan Park
- Department of Biological Sciences, College of Natural Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Shinyeong Ju
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-Gu, Seoul, 02792, Republic of Korea
| | - Young Eun Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-Gu, Seoul, 02792, Republic of Korea.,College of Life Science and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Sun-Hee Heo
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea.,Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Young-Ae Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Ji Eun Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-Gu, Seoul, 02792, Republic of Korea
| | - Yuna Lee
- College of Life Science and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Kyong Hwa Park
- Oncology/Hematology, Department of Internal medicine, Korea University College of medicine, Seongbuk-Gu, Seoul, 02841, Republic of Korea
| | - Se-Ho Park
- College of Life Science and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hee Jin Lee
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea.,Asan Center for Cancer Genome Discovery, Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-Gu, Seoul, 02792, Republic of Korea. .,Department of Converging Science and Technology, KHU-KIST, Kyung Hee University, Seoul, 02447, Republic of Korea.
| | - Mihue Jang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-Gu, Seoul, 02792, Republic of Korea. .,Department of Converging Science and Technology, KHU-KIST, Kyung Hee University, Seoul, 02447, Republic of Korea.
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47
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Boucau J, Das J, Joshi N, Le Gall S. Latency reversal agents modulate HIV antigen processing and presentation to CD8 T cells. PLoS Pathog 2020; 16:e1008442. [PMID: 32196533 PMCID: PMC7112239 DOI: 10.1371/journal.ppat.1008442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 04/01/2020] [Accepted: 02/28/2020] [Indexed: 01/03/2023] Open
Abstract
Latency reversal agents (LRA) variably induce HIV re-expression in CD4 T cells but reservoirs are not cleared. Whether HIV epitope presentation is similar between latency reversal and initial infection of CD4 T cells is unknown yet crucial to define immune responses able to detect HIV-infected CD4 T cells after latency reversal. HIV peptides displayed by MHC comes from the intracellular degradation of proteins by proteasomes and post-proteasomal peptidases but the impact of LRAs on antigen processing is not known. Here we show that HDAC inhibitors (HDCAi) reduced cytosolic proteolytic activities while PKC agonists (PKCa) increased them to a lesser extent than that induced by TCR activation. During the cytosolic degradation of long HIV peptides in LRA-treated CD4 T cells extracts, HDACi and PKCa modulated degradation patterns of peptides and altered the production of HIV epitopes in often opposite ways. Beyond known HIV epitopes, HDACi narrowed the coverage of HIV antigenic fragments by 8-11aa degradation peptides while PKCa broadened it. LRAs altered HIV infection kinetics and modulated CD8 T cell activation in an epitope- and time-dependent manner. Interestingly the efficiency of endogenous epitope processing and presentation to CD8 T cells was increased by PKCa Ingenol at early time points despite low levels of antigens. LRA-induced modulations of antigen processing should be considered and exploited to enhance and broaden HIV peptide presentation by CD4 T cells and to improve immune recognition after latency reversal. This property of LRAs, if confirmed with other antigens, might be exploited to improve immune detection of diseased cells beyond HIV. Latently HIV-infected CD4 T cells persist and remain invisible to the immune system. Strategies to flush out HIV reservoirs propose to re-express HIV with latency reversal agents (LRAs), leading to CD4 T cell death or clearance by HIV-specific immune responses. LRAs tested so far variably induced HIV re-expression but did not eliminate reservoirs. The activation of HIV-specific immune responses is triggered by HIV peptides displayed by infected cells after HIV intracellular degradation. Whether HIV antigens are similarly degraded and displayed by CD4 T cells after latency reversal or during initial infection is unknown. We showed that LRAs altered the activities of the degradation machinery and changed the degradation patterns of HIV into peptides. LRA-treated HIV-infected CD4 T cells were variably recognized by immune cells in a time- and peptide-dependent manner. Some LRAs increased the efficiency of HIV peptide presentation despite low levels of HIV antigens inside CD4 T cells. The modulation of HIV peptide presentation by current or future LRAs should be accounted for and exploited to improve HIV peptide presentation and enhance immune detection of HIV-infected CD4 T cells after latency reversal.
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Affiliation(s)
- Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Neelambari Joshi
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital and Harvard Medical School, Cambridge, Massachusetts, United States of America
- * E-mail:
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48
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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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49
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Samreen B, Tao S, Tischer K, Adler H, Drexler I. ORF6 and ORF61 Expressing MVA Vaccines Impair Early but Not Late Latency in Murine Gammaherpesvirus MHV-68 Infection. Front Immunol 2019; 10:2984. [PMID: 31921215 PMCID: PMC6930802 DOI: 10.3389/fimmu.2019.02984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/05/2019] [Indexed: 01/02/2023] Open
Abstract
Gammaherpesviruses (γHV) are important pathogens causing persistent infections which lead to several malignancies in immunocompromised patients. Murine γHV 68 (MHV-68), a homolog to human EBV and KSHV, has been employed as a classical pathogen to investigate the molecular pathogenicity of γHV infections. γHV express distinct antigens during lytic or latent infection and antigen-specific T cells have a significant role in controlling the acute and latent viral infection, although the quality of anti-viral T cell responses required for protective immunity is not well-understood. We have generated recombinant modified vaccinia virus Ankara (recMVA) vaccines via MVA-BAC homologous recombination technology expressing MHV-68 ORF6 and ORF61 antigens encoding both MHC class I and II-restricted epitopes. After vaccination, we examined T cell responses before and after MHV-68 infection to determine their involvement in latent virus control. We show recognition of recMVA- and MHV-68-infected APC by ORF6 and ORF61 epitope-specific T cell lines in vitro. The recMVA vaccines efficiently induced MHV-68-specific CD8+ and CD4+ T cell responses after a single immunization and more pronounced after homologous prime/boost vaccination in mice. Moreover, we exhibit protective capacity of prophylactic recMVA vaccination during early latency at day 17 after intranasal challenge with MHV-68, but failed to protect from latency at day 45. Further T cell analysis indicated that T cell exhaustion was not responsible for the lack of protection by recMVA vaccination in long-term latency at day 45. The data support further efforts aiming at improved vaccine development against γHV infections with special focus on targeting protective CD4+ T cell responses.
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Affiliation(s)
- Baila Samreen
- Institute for Virology, Düsseldorf University Hospital, Heinrich-Heine-University, Düsseldorf, Germany.,Department of Oncology-Pathology, Science for Life Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Sha Tao
- Institute for Virology, Düsseldorf University Hospital, Heinrich-Heine-University, Düsseldorf, Germany
| | - Karsten Tischer
- Fachbereich Veterinärmedizin, Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Heiko Adler
- Comprehensive Pneumology Center, Research Unit Lung Repair and Regeneration, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health (GmbH), Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Ingo Drexler
- Institute for Virology, Düsseldorf University Hospital, Heinrich-Heine-University, Düsseldorf, Germany
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50
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Yewdell JW, Dersh D, Fåhraeus R. Peptide Channeling: The Key to MHC Class I Immunosurveillance? Trends Cell Biol 2019; 29:929-939. [PMID: 31662235 DOI: 10.1016/j.tcb.2019.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022]
Abstract
MHC class I presentation of short peptides enables CD8+ T cell (TCD8+) immunosurveillance of tumors and intracellular pathogens. A key feature of the class I pathway is that the immunopeptidome is highly skewed from the cellular degradome, indicating high selectivity of the access of protease-generated peptides to class I molecules. Similarly, in professional antigen-presenting cells, peptides from minute amounts of proteins introduced into the cytosol outcompete an overwhelming supply of constitutively generated peptides. Here, we propose that antigen processing is based on substrate channeling and review recent studies from the antigen processing and cell biology fields that provide a starting point for testing this hypothesis.
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Affiliation(s)
- Jonathan W Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, MD 20892, USA.
| | - Devin Dersh
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, MD 20892, USA
| | - Robin Fåhraeus
- Inserm, 27 rue Juliette Dodu, 750 10 Paris, France; International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland; Department of Medical Biosciences, Umeå University, 90187 Umeå, Sweden; RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653 Brno, Czech Republic
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