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Adnane M, de Almeida AM, Chapwanya A. Unveiling the power of proteomics in advancing tropical animal health and production. Trop Anim Health Prod 2024; 56:182. [PMID: 38825622 DOI: 10.1007/s11250-024-04037-4] [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: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/04/2024]
Abstract
Proteomics, the large-scale study of proteins in biological systems has emerged as a pivotal tool in the field of animal and veterinary sciences, mainly for investigating local and rustic breeds. Proteomics provides valuable insights into biological processes underlying animal growth, reproduction, health, and disease. In this review, we highlight the key proteomics technologies, methodologies, and their applications in domestic animals, particularly in the tropical context. We also discuss advances in proteomics research, including integration of multi-omics data, single-cell proteomics, and proteogenomics, all of which are promising for improving animal health, adaptation, welfare, and productivity. However, proteomics research in domestic animals faces challenges, such as sample preparation variation, data quality control, privacy and ethical considerations relating to animal welfare. We also provide recommendations for overcoming these challenges, emphasizing the importance of following best practices in sample preparation, data quality control, and ethical compliance. We therefore aim for this review to harness the full potential of proteomics in advancing our understanding of animal biology and ultimately improve animal health and productivity in local breeds of diverse animal species in a tropical context.
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Affiliation(s)
- Mounir Adnane
- Department of Biomedicine, Institute of Veterinary Sciences, University of Tiaret, Tiaret, 14000, Algeria.
| | - André M de Almeida
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, 1349-017, Portugal
| | - Aspinas Chapwanya
- Department of Clinical Sciences, Ross University School of Veterinary Medicine, Basseterre, 00265, Saint Kitts and Nevis
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2
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Celis-Giraldo C, Ordoñez D, Díaz-Arévalo D, Bohórquez MD, Ibarrola N, Suárez CF, Rodríguez K, Yepes Y, Rodríguez A, Avendaño C, López-Abán J, Manzano-Román R, Patarroyo MA. Identifying major histocompatibility complex class II-DR molecules in bovine and swine peripheral blood monocyte-derived macrophages using mAb-L243. Vaccine 2024; 42:3445-3454. [PMID: 38631956 DOI: 10.1016/j.vaccine.2024.04.042] [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: 12/22/2023] [Revised: 04/04/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
Major histocompatibility complex class II (MHC-II) molecules are involved in immune responses against pathogens and vaccine candidates' immunogenicity. Immunopeptidomics for identifying cancer and infection-related antigens and epitopes have benefited from advances in immunopurification methods and mass spectrometry analysis. The mouse anti-MHC-II-DR monoclonal antibody L243 (mAb-L243) has been effective in recognising MHC-II-DR in both human and non-human primates. It has also been shown to cross-react with other animal species, although it has not been tested in livestock. This study used mAb-L243 to identify Staphylococcus aureus and Salmonella enterica serovar Typhimurium peptides binding to cattle and swine macrophage MHC-II-DR molecules using flow cytometry, mass spectrometry and two immunopurification techniques. Antibody cross-reactivity led to identifying expressed MHC-II-DR molecules, together with 10 Staphylococcus aureus peptides in cattle and 13 S. enterica serovar Typhimurium peptides in swine. Such data demonstrates that MHC-II-DR expression and immunocapture approaches using L243 mAb represents a viable strategy for flow cytometry and immunopeptidomics analysis of bovine and swine antigen-presenting cells.
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Affiliation(s)
- Carmen Celis-Giraldo
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia; PhD Programme in Tropical Health and Development, Doctoral School "Studii Salamantini", Universidad de Salamanca, Salamanca, Spain
| | - Diego Ordoñez
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia; PhD Programme in Tropical Health and Development, Doctoral School "Studii Salamantini", Universidad de Salamanca, Salamanca, Spain
| | - Diana Díaz-Arévalo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Michel D Bohórquez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia; MSc Programme in Microbiology, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Nieves Ibarrola
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (IBMCC), CSIC-University of Salamanca, Salamanca, Spain
| | - Carlos F Suárez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Kewin Rodríguez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Yoelis Yepes
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Alexander Rodríguez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Catalina Avendaño
- Department of Immunology and Theranostics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, National Medical Center, Duarte, CA, United States
| | - Julio López-Abán
- Infectious and Tropical Diseases Group (e-INTRO), IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca - Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca), Pharmacy Faculty, Universidad de Salamanca, C/ L. Méndez Nieto s/n, 37007 Salamanca, Spain
| | - Raúl Manzano-Román
- Infectious and Tropical Diseases Group (e-INTRO), IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca - Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca), Pharmacy Faculty, Universidad de Salamanca, C/ L. Méndez Nieto s/n, 37007 Salamanca, Spain
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia; Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia.
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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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Chen Y, Mason GH, Scourfield DO, Greenshields-Watson A, Haigh TA, Sewell AK, Long HM, Gallimore AM, Rizkallah P, MacLachlan BJ, Godkin A. Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity. Cell Rep 2023; 42:112827. [PMID: 37471227 PMCID: PMC10840515 DOI: 10.1016/j.celrep.2023.112827] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/21/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023] Open
Abstract
CD4+ T cells recognize a broad range of peptide epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which contribute to immune memory and limit COVID-19 disease. We demonstrate that the immunogenicity of SARS-CoV-2 peptides, in the context of the model allotype HLA-DR1, does not correlate with their binding affinity to the HLA heterodimer. Analyzing six epitopes, some with very low binding affinity, we solve X-ray crystallographic structures of each bound to HLA-DR1. Further structural definitions reveal the precise molecular impact of viral variant mutations on epitope presentation. Omicron escaped ancestral SARS-CoV-2 immunity to two epitopes through two distinct mechanisms: (1) mutations to TCR-facing epitope positions and (2) a mechanism whereby a single amino acid substitution caused a register shift within the HLA binding groove, completely altering the peptide-HLA structure. This HLA-II-specific paradigm of immune escape highlights how CD4+ T cell memory is finely poised at the level of peptide-HLA-II presentation.
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Affiliation(s)
- Yuan Chen
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Georgina H Mason
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - D Oliver Scourfield
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Alexander Greenshields-Watson
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Tracey A Haigh
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Heather M Long
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Awen M Gallimore
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Pierre Rizkallah
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Bruce J MacLachlan
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
| | - Andrew Godkin
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Department of Gastroenterology & Hepatology, University Hospital of Wales, Cardiff CF14 4XW, UK.
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5
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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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6
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Aran A, Peg V, Rabanal RM, Bernadó C, Zamora E, Molina E, Arribas YA, Arribas J, Pérez J, Roura-Mir C, Carrascal M, Cortés J, Martí M. Epstein-Barr Virus+ B Cells in Breast Cancer Immune Response: A Case Report. Front Immunol 2021; 12:761798. [PMID: 34868006 PMCID: PMC8637110 DOI: 10.3389/fimmu.2021.761798] [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: 08/20/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022] Open
Abstract
EBV-specific T cells have been recently described to be involved in fatal encephalitis and myocarditis in cancer patients after immune checkpoint therapies. Here, we report the study of a human triple-negative breast cancer tumor (TNBC) and EBV-transformed B cells obtained from a patient-derived xenograft (PDX) that progressed into a lymphocytic neoplasm named xenograft-associated B-cell lymphoma (XABCL). T-cell receptor (TCR) high-throughput sequencing was performed to monitor the T-cell clonotypes present in the different samples. Forty-three T-cell clonotypes were found infiltrating the XABCL tissue after three passes in mice along 6 months. Eighteen of these (42%) were also found in the TNBC biopsy. TCR infiltrating the XABCL tissue showed a very restricted T-cell repertoire as compared with the biopsy-infiltrating T cells. Consequently, T cells derived from the TNBC biopsy were expanded in the presence of the B-cell line obtained from the XABCL (XABCL-LCL), after which the TCR repertoire obtained was again very restricted, i.e., only certain clonotypes were selected by the B cells. A number of these TCRs had previously been reported as sequences involved in infection, cancer, and/or autoimmunity. We then analyzed the immunopeptidome from the XABCL-LCL, to identify putative B-cell-associated peptides that might have been expanding these T cells. The HLA class I and class II-associated peptides from XABCL-LCL were then compared with published repertoires from LCL of different HLA typing. Proteins from the antigen processing and presentation pathway remained significantly enriched in the XABCL-LCL repertoire. Interestingly, some class II-presented peptides were derived from cancer-related proteins. These results suggest that bystander tumor-infiltrating EBV+ B cells acting as APC may be able to interact with tumor-infiltrating T cells and influence the TCR repertoire in the tumor site.
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Affiliation(s)
- Andrea Aran
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Vicente Peg
- Translational Molecular Pathology, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Rosa Maria Rabanal
- Unitat de Patologia Murina i Comparada, Department of Animal Medicine and Surgery, Veterinary Faculty, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Cristina Bernadó
- Preclinical and Translational Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Esther Zamora
- Breast Cancer Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Elisa Molina
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Yago A Arribas
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Joaquín Arribas
- Preclinical and Translational Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - José Pérez
- International Breast Cancer Center (BCC), Quironsalud Group, Barcelona, Spain
| | - Carme Roura-Mir
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Montserrat Carrascal
- Biological and Environmental Proteomics, Institute of Biomedical Research of Barcelona, Spanish National Research Council, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IIBB-CSIC/IDIBAPS), Barcelona, Spain
| | - Javier Cortés
- Breast Cancer Unit, Vall d'Hebron Institute of Oncology (VHIO), Hospital Universitari Vall d'Hebron, Barcelona, Spain.,International Breast Cancer Center (BCC), Quironsalud Group, Barcelona, Spain
| | - Mercè Martí
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
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Stopfer L, D'Souza A, White F. 1,2,3, MHC: a review of mass-spectrometry-based immunopeptidomics methods for relative and absolute quantification of pMHCs. IMMUNO-ONCOLOGY TECHNOLOGY 2021; 11:100042. [PMID: 35756972 PMCID: PMC9216433 DOI: 10.1016/j.iotech.2021.100042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Quantitative mass-spectrometry-based methods to perform relative and absolute quantification of peptides in the immunopeptidome are growing in popularity as researchers aim to measure the dynamic nature of the peptide major histocompatibility complex repertoire and make copies-per-cell estimations of target antigens of interest. Multiple methods to carry out these experiments have been reported, each with unique advantages and limitations. This article describes existing methods and recent applications, offering guidance for improving quantitative accuracy and selecting an appropriate experimental set-up to maximize data quality and quantity.
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Affiliation(s)
- L.E. Stopfer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA,Koch Institute for Integrative Cancer Research, Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, USA
| | - A.D. D'Souza
- Koch Institute for Integrative Cancer Research, Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, USA,Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, USA
| | - F.M. White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA,Koch Institute for Integrative Cancer Research, Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, USA,Correspondence to: Prof. Forest M. White, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Tel: 617-258-8949
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8
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Marcu A, Bichmann L, Kuchenbecker L, Kowalewski DJ, Freudenmann LK, Backert L, Mühlenbruch L, Szolek A, Lübke M, Wagner P, Engler T, Matovina S, Wang J, Hauri-Hohl M, Martin R, Kapolou K, Walz JS, Velz J, Moch H, Regli L, Silginer M, Weller M, Löffler MW, Erhard F, Schlosser A, Kohlbacher O, Stevanović S, Rammensee HG, Neidert MC. HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy. J Immunother Cancer 2021; 9:e002071. [PMID: 33858848 PMCID: PMC8054196 DOI: 10.1136/jitc-2020-002071] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The human leucocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Understanding the benign HLA ligand repertoire is a prerequisite to define safe T-cell-based immunotherapies against cancer. Due to the poor availability of benign tissues, if available, normal tissue adjacent to the tumor has been used as a benign surrogate when defining tumor-associated antigens. However, this comparison has proven to be insufficient and even resulted in lethal outcomes. In order to match the tumor immunopeptidome with an equivalent counterpart, we created the HLA Ligand Atlas, the first extensive collection of paired HLA-I and HLA-II immunopeptidomes from 227 benign human tissue samples. This dataset facilitates a balanced comparison between tumor and benign tissues on HLA ligand level. METHODS Human tissue samples were obtained from 16 subjects at autopsy, five thymus samples and two ovary samples originating from living donors. HLA ligands were isolated via immunoaffinity purification and analyzed in over 1200 liquid chromatography mass spectrometry runs. Experimentally and computationally reproducible protocols were employed for data acquisition and processing. RESULTS The initial release covers 51 HLA-I and 86 HLA-II allotypes presenting 90,428 HLA-I- and 142,625 HLA-II ligands. The HLA allotypes are representative for the world population. We observe that immunopeptidomes differ considerably between tissues and individuals on source protein and HLA-ligand level. Moreover, we discover 1407 HLA-I ligands from non-canonical genomic regions. Such peptides were previously described in tumors, peripheral blood mononuclear cells (PBMCs), healthy lung tissues and cell lines. In a case study in glioblastoma, we show that potential on-target off-tumor adverse events in immunotherapy can be avoided by comparing tumor immunopeptidomes to the provided multi-tissue reference. CONCLUSION Given that T-cell-based immunotherapies, such as CAR-T cells, affinity-enhanced T cell transfer, cancer vaccines and immune checkpoint inhibition, have significant side effects, the HLA Ligand Atlas is the first step toward defining tumor-associated targets with an improved safety profile. The resource provides insights into basic and applied immune-associated questions in the context of cancer immunotherapy, infection, transplantation, allergy and autoimmunity. It is publicly available and can be browsed in an easy-to-use web interface at https://hla-ligand-atlas.org .
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Affiliation(s)
- Ana Marcu
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Leon Bichmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Leon Kuchenbecker
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Daniel Johannes Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Lena Katharina Freudenmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Linus Backert
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Lena Mühlenbruch
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - András Szolek
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Maren Lübke
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Philipp Wagner
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Tobias Engler
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Sabine Matovina
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Jian Wang
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mathias Hauri-Hohl
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich, Switzerland
| | - Roland Martin
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Konstantina Kapolou
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
| | - Juliane Sarah Walz
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital of Tübingen, Tübingen, Germany
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology (IKP) and Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany
| | - Julia Velz
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Luca Regli
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
| | - Manuela Silginer
- Clinical Neuroscience Center and Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Michael Weller
- Clinical Neuroscience Center and Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Markus W Löffler
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Department of General, Visceral and Transplant Surgery, University Hospital of Tübingen, Tübingen, Germany
- Department of Clinical Pharmacology, University of Hospital Tübingen, Tübingen, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Bayern, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center - Center for Integrative and Translational Bioimaging, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Cluster of Excellence Machine Learning in the Sciences (EXC 2064), University of Tübingen, Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Marian Christoph Neidert
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
- Department of Neurosurgery, Cantonal Hospital St.Gallen, St.Gallen, Switzerland
- Neuroscience Center Zurich (ZNZ), University of Zurich and ETH Zurich, Zurich, Switzerland
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9
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Khan F, Kumar A. Vaccine Design and Immunoinformatics. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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10
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Knierman MD, Lannan MB, Spindler LJ, McMillian CL, Konrad RJ, Siegel RW. The Human Leukocyte Antigen Class II Immunopeptidome of the SARS-CoV-2 Spike Glycoprotein. Cell Rep 2020; 33:108454. [PMID: 33220791 PMCID: PMC7664343 DOI: 10.1016/j.celrep.2020.108454] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/16/2020] [Accepted: 11/06/2020] [Indexed: 12/20/2022] Open
Abstract
Precise elucidation of the antigen sequences for T cell immunosurveillance greatly enhances our ability to understand and modulate humoral responses to viral infection or active immunization. Mass spectrometry is used to identify 526 unique sequences from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein extracellular domain in a complex with human leukocyte antigen class II molecules on antigen-presenting cells from a panel of healthy donors selected to represent a majority of allele usage from this highly polymorphic molecule. The identified sequences span the entire spike protein, and several sequences are isolated from a majority of the sampled donors, indicating promiscuous binding. Importantly, many peptides derived from the receptor binding domain used for cell entry are identified. This work represents a precise and comprehensive immunopeptidomic investigation with the SARS-CoV-2 spike glycoprotein and allows detailed analysis of features that may aid vaccine development to end the current coronavirus disease 2019 (COVID-19) pandemic.
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Affiliation(s)
- Michael D Knierman
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Megan B Lannan
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Laura J Spindler
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Carl L McMillian
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Robert J Konrad
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Robert W Siegel
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA.
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11
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Gutierrez-Hoffmann MG, O'Meally RN, Cole RN, Tiniakou E, Darrah E, Soloski MJ. Borrelia burgdorferi-Induced Changes in the Class II Self-Immunopeptidome Displayed on HLA-DR Molecules Expressed by Dendritic Cells. Front Med (Lausanne) 2020; 7:568. [PMID: 33043033 PMCID: PMC7524959 DOI: 10.3389/fmed.2020.00568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/11/2020] [Indexed: 01/19/2023] Open
Abstract
The MHC class II antigen processing and presentation pathway has evolved to derive short amino acid peptides from proteins that enter the endocytic pathway, load them onto MHC class II molecules and display them on the surface of antigen presenting cells for recognition by CD4+ T cells. Under normal circumstances, peptides bound to MHC class II molecules are derived from host (self) proteins and not recognized by T cells due to tolerance mechanisms. Pathogens induce significant changes in the biology of antigen presenting cells, including upregulation of MHC processing and presentation. We therefore hypothesized that exposure to pathogens may alter the repertoire of self-peptides bound to MHC class II molecules. To test this hypothesis, we isolated monocyte-derived dendritic cells from healthy subjects, exposed them to the TLR-2 agonist lipoteichoic acid or live Borrelia burgdorferi, the causative agent of Lyme disease, and isolated and characterized HLA-DR associated peptides using mass spectrometry. Our results show that lipoteichoic acid-stimulated, B. burgdorferi-stimulated and unstimulated monocyte-derived dendritic cells largely derive their self-peptides from similar overlapping sets of host proteins. However, lipoteichoic acid and B. burgdorferi stimulation promote the processing and presentation of new sets of HLA-DR associated self-peptides derived from unique protein sources. Examination of processes and compartments these proteins reside in, indicate that activation of monocyte-derived dendritic cells changes the range of host self-proteins available for processing and presentation on MHC class II molecules. These findings reveal that the HLA-DR-bound self-immunopeptidome presented by mo-DCs is dynamic in nature and changes with activation state reflective of cellular function. In addition, among the repertoire of self-peptides bound to HLA-DR are several epitopes known to be recognized by autoreactive T cells. These studies are relevant to our basic understanding of pathogen-induced changes in monocyte-derived dendritic cell function, and the mechanisms involved in infection-induced autoimmune illnesses such as Lyme arthritis.
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Affiliation(s)
- Maria G. Gutierrez-Hoffmann
- Lyme Disease Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Robert N. O'Meally
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Robert N. Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Eleni Tiniakou
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Erika Darrah
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Mark J. Soloski
- Lyme Disease Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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12
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Kardani K, Bolhassani A, Namvar A. An overview of in silico vaccine design against different pathogens and cancer. Expert Rev Vaccines 2020; 19:699-726. [PMID: 32648830 DOI: 10.1080/14760584.2020.1794832] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Due to overcome the hardness of the vaccine design, computational vaccinology is emerging widely. Prediction of T cell and B cell epitopes, antigen processing analysis, antigenicity analysis, population coverage, conservancy analysis, allergenicity assessment, toxicity prediction, and protein-peptide docking are important steps in the process of designing and developing potent vaccines against various viruses and cancers. In order to perform all of the analyses, several bioinformatics tools and online web servers have been developed. Scientists must take the decision to apply more suitable and precise servers for each part based on their accuracy. AREAS COVERED In this review, a wide-range list of different bioinformatics tools and online web servers has been provided. Moreover, some studies were proposed to show the importance of various bioinformatics tools for predicting and developing efficient vaccines against different pathogens including viruses, bacteria, parasites, and fungi as well as cancer. EXPERT OPINION Immunoinformatics is the best way to find potential vaccine candidates against different pathogens. Thus, the selection of the most accurate tools is necessary to predict and develop potent preventive and therapeutic vaccines. To further evaluation of the computational and in silico vaccine design, in vitro/in vivo analyses are required to develop vaccine candidates.
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Affiliation(s)
- Kimia Kardani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences , Tehran, Iran.,Department of Hepatitis and AIDS, Pasteur Institute of Iran , Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran , Tehran, Iran
| | - Ali Namvar
- Iranian Comprehensive Hemophilia Care Center , Tehran, Iran
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13
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James EA, Mallone R, Kent SC, DiLorenzo TP. T-Cell Epitopes and Neo-epitopes in Type 1 Diabetes: A Comprehensive Update and Reappraisal. Diabetes 2020; 69:1311-1335. [PMID: 32561620 PMCID: PMC7306130 DOI: 10.2337/dbi19-0022] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023]
Abstract
The autoimmune disease type 1 diabetes is characterized by effector T-cell responses to pancreatic β-cell-derived peptides presented by HLA class I and class II molecules, leading ultimately to β-cell demise and insulin insufficiency. Although a given HLA molecule presents a vast array of peptides, only those recognized by T cells are designated as epitopes. Given their intimate link to etiology, the discovery and characterization of T-cell epitopes is a critical aspect of type 1 diabetes research. Understanding epitope recognition is also crucial for the pursuit of antigen-specific immunotherapies and implementation of strategies for T-cell monitoring. For these reasons, a cataloging and appraisal of the T-cell epitopes targeted in type 1 diabetes was completed over a decade ago, providing an important resource for both the research and the clinical communities. Here we present a much needed update and reappraisal of this earlier work and include online supplementary material where we cross-index each epitope with its primary references and Immune Epitope Database (IEDB) identifier. Our analysis includes a grading scale to score the degree of evidence available for each epitope, which conveys our perspective on several useful criteria for epitope evaluation. While providing an efficient summary of the arguably impressive current state of knowledge, this work also brings to light several deficiencies. These include the need for improved epitope validation, as few epitopes score highly by the criteria employed, and the dearth of investigations of the epitopes recognized in the context of several understudied type 1 diabetes-associated HLA molecules.
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Affiliation(s)
- Eddie A James
- Department of Translational Research, Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - Roberto Mallone
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
- Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Hôpitaux Universitaires de Paris Centre-Université de Paris, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sally C Kent
- Diabetes Center of Excellence, Division of Diabetes, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Teresa P DiLorenzo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY
- Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY
- Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
- The Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, NY
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14
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Bettencourt P, Müller J, Nicastri A, Cantillon D, Madhavan M, Charles PD, Fotso CB, Wittenberg R, Bull N, Pinpathomrat N, Waddell SJ, Stylianou E, Hill AVS, Ternette N, McShane H. Identification of antigens presented by MHC for vaccines against tuberculosis. NPJ Vaccines 2020; 5:2. [PMID: 31908851 PMCID: PMC6941960 DOI: 10.1038/s41541-019-0148-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/25/2019] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium tuberculosis (M.tb) is responsible for more deaths globally than any other pathogen. The only available vaccine, bacillus Calmette-Guérin (BCG), has variable efficacy throughout the world. A more effective vaccine is urgently needed. The immune response against tuberculosis relies, at least in part, on CD4+ T cells. Protective vaccines require the induction of antigen-specific CD4+ T cells via mycobacterial peptides presented by MHC class-II in infected macrophages. In order to identify mycobacterial antigens bound to MHC, we have immunoprecipitated MHC class-I and class-II complexes from THP-1 macrophages infected with BCG, purified MHC class-I and MHC class-II peptides and analysed them by liquid chromatography tandem mass spectrometry. We have successfully identified 94 mycobacterial peptides presented by MHC-II and 43 presented by MHC-I, from 76 and 41 antigens, respectively. These antigens were found to be highly expressed in infected macrophages. Gene ontology analysis suggests most of these antigens are associated with membranes and involved in lipid biosynthesis and transport. The sequences of selected peptides were confirmed by spectral match validation and immunogenicity evaluated by IFN-gamma ELISpot against peripheral blood mononuclear cell from volunteers vaccinated with BCG, M.tb latently infected subjects or patients with tuberculosis disease. Three antigens were expressed in viral vectors, and evaluated as vaccine candidates alone or in combination in a murine aerosol M.tb challenge model. When delivered in combination, the three candidate vaccines conferred significant protection in the lungs and spleen compared with BCG alone, demonstrating proof-of-concept for this unbiased approach to identifying new candidate antigens. Protective vaccines against Mycobacterium tuberculosis (M.tb), such as bacillus Calmette-Guérin (BCG), trigger strong CD4 T-cell responses specific to mycobacterium peptides, but their efficacy is variable. Paulo Bettencourt and colleagues now identify a set of mycobacterium peptides presented by BCG-infected macrophages via major compatibility complexes (MHC), and show that three of these antigens can be combined to formulate a vaccine that confers improved protection to Mtb infection in mice. After identifying 94 MHC-II-associated and 43 MHC-I-associated mycobacterium peptides, the researchers performed immunogenicity assays with peripheral blood mononuclear cells from BCG-vaccinated donors, latent Mtb-infected patients and patients with tuberculosis, and show that a set of these peptides was recognised by the immune cells, validating their potential as possible components for new Mtb vaccine formulations. These findings further support the value of immunopeptidomics for the identification of new antigens for effective vaccine alternatives.
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Affiliation(s)
| | - Julius Müller
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
| | - Annalisa Nicastri
- 2Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Daire Cantillon
- 3Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX UK
| | - Meera Madhavan
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
| | - Philip D Charles
- 2Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Carine B Fotso
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
| | | | - Naomi Bull
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
| | | | - Simon J Waddell
- 3Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX UK
| | | | | | - Nicola Ternette
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK.,2Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Helen McShane
- 1Jenner Institute, University of Oxford, Oxford, OX3 7DQ UK
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15
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MacLachlan BJ, Dolton G, Papakyriakou A, Greenshields-Watson A, Mason GH, Schauenburg A, Besneux M, Szomolay B, Elliott T, Sewell AK, Gallimore A, Rizkallah P, Cole DK, Godkin A. Human leukocyte antigen (HLA) class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope. J Biol Chem 2019; 294:20246-20258. [PMID: 31619516 PMCID: PMC6937582 DOI: 10.1074/jbc.ra119.009437] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/18/2019] [Indexed: 01/03/2023] Open
Abstract
CD4+ T-cells recognize peptide antigens, in the context of human leukocyte antigen (HLA) class II molecules (HLA-II), which through peptide-flanking residues (PFRs) can extend beyond the limits of the HLA binding. The role of the PFRs during antigen recognition is not fully understood; however, recent studies have indicated that these regions can influence T-cell receptor (TCR) affinity and pHLA-II stability. Here, using various biochemical approaches including peptide sensitivity ELISA and ELISpot assays, peptide-binding assays and HLA-II tetramer staining, we focused on CD4+ T-cell responses against a tumor antigen, 5T4 oncofetal trophoblast glycoprotein (5T4), which have been associated with improved control of colorectal cancer. Despite their weak TCR-binding affinity, we found that anti-5T4 CD4+ T-cells are polyfunctional and that their PFRs are essential for TCR recognition of the core bound nonamer. The high-resolution (1.95 Å) crystal structure of HLA-DR1 presenting the immunodominant 20-mer peptide 5T4111-130, combined with molecular dynamic simulations, revealed how PFRs explore the HLA-proximal space to contribute to antigen reactivity. These findings advance our understanding of what constitutes an HLA-II epitope and indicate that PFRs can tune weak affinity TCR-pHLA-II interactions.
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Affiliation(s)
- Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Garry Dolton
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Athanasios Papakyriakou
- Institute of Biosciences and Applications, NCSR "Demokritos," Agia Paraskevi, 15341 Athens, Greece
| | - Alexander Greenshields-Watson
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Georgina H Mason
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Andrea Schauenburg
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Matthieu Besneux
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Barbara Szomolay
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Tim Elliott
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Centre for Cancer Immunology, University of Southampton, Faculty of Medicine, University Hospital, Southampton SO16 6YD, United Kingdom
| | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Awen Gallimore
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Pierre Rizkallah
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Andrew Godkin
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
- Department of Gastroenterology and Hepatology, University Hospital of Wales, CF14 4XN Cardiff, United Kingdom
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16
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Lorente E, Martín-Galiano AJ, Barnea E, Barriga A, Palomo C, García-Arriaza J, Mir C, Lauzurica P, Esteban M, Admon A, López D. Proteomics Analysis Reveals That Structural Proteins of the Virion Core and Involved in Gene Expression Are the Main Source for HLA Class II Ligands in Vaccinia Virus-Infected Cells. J Proteome Res 2019; 18:900-911. [PMID: 30629447 DOI: 10.1021/acs.jproteome.8b00595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protective cellular and humoral immune responses require previous recognition of viral antigenic peptides complexed with human leukocyte antigen (HLA) class II molecules on the surface of the antigen presenting cells. The HLA class II-restricted immune response is important for the control and the clearance of poxvirus infection including vaccinia virus (VACV), the vaccine used in the worldwide eradication of smallpox. In this study, a mass spectrometry analysis was used to identify VACV ligands bound to HLA-DR and -DP class II molecules present on the surface of VACV-infected cells. Twenty-six naturally processed viral ligands among the tens of thousands of cell peptides bound to HLA class II proteins were identified. These viral ligands arose from 19 parental VACV proteins: A4, A5, A18, A35, A38, B5, B13, D1, D5, D7, D12, D13, E3, E8, H5, I2, I3, J2, and K2. The majority of these VACV proteins yielded one HLA ligand and were generated mainly, but not exclusively, by the classical HLA class II antigen processing pathway. Medium-sized and abundant proteins from the virion core and/or involved in the viral gene expression were the major source of VACV ligands bound to HLA-DR and -DP class II molecules. These findings will help to understand the effectiveness of current poxvirus-based vaccines and will be important in the design of new ones.
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Affiliation(s)
| | | | - Eilon Barnea
- Department of Biology , Technion-Israel Institute of Technology , 32000 Haifa , Israel
| | | | | | - Juan García-Arriaza
- Department of Molecular and Cellular Biology , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid , Spain
| | | | | | - Mariano Esteban
- Department of Molecular and Cellular Biology , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid , Spain
| | - Arie Admon
- Department of Biology , Technion-Israel Institute of Technology , 32000 Haifa , Israel
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17
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Footprints of antigen processing boost MHC class II natural ligand predictions. Genome Med 2018; 10:84. [PMID: 30446001 PMCID: PMC6240193 DOI: 10.1186/s13073-018-0594-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/30/2018] [Indexed: 12/21/2022] Open
Abstract
Background Major histocompatibility complex class II (MHC-II) molecules present peptide fragments to T cells for immune recognition. Current predictors for peptide to MHC-II binding are trained on binding affinity data, generated in vitro and therefore lacking information about antigen processing. Methods We generate prediction models of peptide to MHC-II binding trained with naturally eluted ligands derived from mass spectrometry in addition to peptide binding affinity data sets. Results We show that integrated prediction models incorporate identifiable rules of antigen processing. In fact, we observed detectable signals of protease cleavage at defined positions of the ligands. We also hypothesize a role of the length of the terminal ligand protrusions for trimming the peptide to the MHC presented ligand. Conclusions The results of integrating binding affinity and eluted ligand data in a combined model demonstrate improved performance for the prediction of MHC-II ligands and T cell epitopes and foreshadow a new generation of improved peptide to MHC-II prediction tools accounting for the plurality of factors that determine natural presentation of antigens. Electronic supplementary material The online version of this article (10.1186/s13073-018-0594-6) contains supplementary material, which is available to authorized users.
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18
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Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes. Nat Med 2018; 24:1762-1772. [PMID: 30349087 DOI: 10.1038/s41591-018-0203-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/20/2018] [Indexed: 01/01/2023]
Abstract
Identifying immunodominant T cell epitopes remains a significant challenge in the context of infectious disease, autoimmunity, and immuno-oncology. To address the challenge of antigen discovery, we developed a quantitative proteomic approach that enabled unbiased identification of major histocompatibility complex class II (MHCII)-associated peptide epitopes and biochemical features of antigenicity. On the basis of these data, we trained a deep neural network model for genome-scale predictions of immunodominant MHCII-restricted epitopes. We named this model bacteria originated T cell antigen (BOTA) predictor. In validation studies, BOTA accurately predicted novel CD4 T cell epitopes derived from the model pathogen Listeria monocytogenes and the commensal microorganism Muribaculum intestinale. To conclusively define immunodominant T cell epitopes predicted by BOTA, we developed a high-throughput approach to screen DNA-encoded peptide-MHCII libraries for functional recognition by T cell receptors identified from single-cell RNA sequencing. Collectively, these studies provide a framework for defining the immunodominance landscape across a broad range of immune pathologies.
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19
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Quarmby V, Phung QT, Lill JR. MAPPs for the identification of immunogenic hotspots of biotherapeutics; an overview of the technology and its application to the biopharmaceutical arena. Expert Rev Proteomics 2018; 15:733-748. [DOI: 10.1080/14789450.2018.1521279] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Valerie Quarmby
- Department of BioAnalytical Sciences, Genentech Inc., San Francisco, CA, USA
| | - Qui T Phung
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc., San Francisco, CA, USA
| | - Jennie R Lill
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc., San Francisco, CA, USA
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20
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Álvaro-Benito M, Morrison E, Abualrous ET, Kuropka B, Freund C. Quantification of HLA-DM-Dependent Major Histocompatibility Complex of Class II Immunopeptidomes by the Peptide Landscape Antigenic Epitope Alignment Utility. Front Immunol 2018; 9:872. [PMID: 29774024 PMCID: PMC5943503 DOI: 10.3389/fimmu.2018.00872] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 04/09/2018] [Indexed: 01/19/2023] Open
Abstract
The major histocompatibility complex of class II (MHCII) immunopeptidome represents the repertoire of antigenic peptides with the potential to activate CD4+ T cells. An understanding of how the relative abundance of specific antigenic epitopes affects the outcome of T cell responses is an important aspect of adaptive immunity and offers a venue to more rationally tailor T cell activation in the context of disease. Recent advances in mass spectrometric instrumentation, computational power, labeling strategies, and software analysis have enabled an increasing number of stratified studies on HLA ligandomes, in the context of both basic and translational research. A key challenge in the case of MHCII immunopeptidomes, often determined for different samples at distinct conditions, is to derive quantitative information on consensus epitopes from antigenic peptides of variable lengths. Here, we present the design and benchmarking of a new algorithm [peptide landscape antigenic epitope alignment utility (PLAtEAU)] allowing the identification and label-free quantification (LFQ) of shared consensus epitopes arising from series of nested peptides. The algorithm simplifies the complexity of the dataset while allowing the identification of nested peptides within relatively short segments of protein sequences. Moreover, we apply this algorithm to the comparison of the ligandomes of cell lines with two different expression levels of the peptide-exchange catalyst HLA-DM. Direct comparison of LFQ intensities determined at the peptide level is inconclusive, as most of the peptides are not significantly enriched due to poor sampling. Applying the PLAtEAU algorithm for grouping of the peptides into consensus epitopes shows that more than half of the total number of epitopes is preferentially and significantly enriched for each condition. This simplification and deconvolution of the complex and ambiguous peptide-level dataset highlights the value of the PLAtEAU algorithm in facilitating robust and accessible quantitative analysis of immunopeptidomes across cellular contexts. In silico analysis of the peptides enriched for each HLA-DM expression conditions suggests a higher affinity of the pool of peptides isolated from the high DM expression samples. Interestingly, our analysis reveals that while for certain autoimmune-relevant epitopes their presentation increases upon DM expression others are clearly edited out from the peptidome.
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Affiliation(s)
- Miguel Álvaro-Benito
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Eliot Morrison
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Esam T Abualrous
- Computational Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Benno Kuropka
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Christian Freund
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
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21
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Zhou Z, Reyes-Vargas E, Escobar H, Chang KY, Barker AP, Rockwood AL, Delgado JC, He X, Jensen PE. Peptidomic analysis of type 1 diabetes associated HLA-DQ molecules and the impact of HLA-DM on peptide repertoire editing. Eur J Immunol 2016; 47:314-326. [PMID: 27861808 DOI: 10.1002/eji.201646656] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/21/2016] [Accepted: 11/10/2016] [Indexed: 11/08/2022]
Abstract
HLA-DM and class II associated invariant chain (Ii) are key cofactors in the MHC class II (MHCII) antigen processing pathway. We used tandem mass spectrometry sequencing to directly interrogate the global impact of DM and Ii on the repertoire of MHCII-bound peptides in human embryonic kidney 293T cells expressing HLA-DQ molecules in the absence or presence of these cofactors. We found that Ii and DM have a major impact on the repertoire of peptides presented by DQ1 and DQ6, with the caveat that this technology is not quantitative. The peptide repertoires of type 1 diabetes (T1D) associated DQ8, DQ2, and DQ8/2 are altered to a lesser degree by DM expression, and these molecules share overlapping features in their peptide binding motifs that are distinct from control DQ1 and DQ6 molecules. Peptides were categorized into DM-resistant, DM-dependent, or DM-sensitive groups based on the mass spectrometry data, and representative peptides were tested in competitive binding assays and peptide dissociation rate experiments with soluble DQ6. Our data support the conclusion that high intrinsic stability of DQ-peptide complexes is necessary but not sufficient to confer resistance to DM editing, and provide candidate parameters that may be useful in predicting the sensitivity of T-cell epitopes to DM editing.
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Affiliation(s)
- Zemin Zhou
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | | | | | - Kuan Y Chang
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Adam P Barker
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Alan L Rockwood
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Julio C Delgado
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Xiao He
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Peter E Jensen
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
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22
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Wang Q, Drouin EE, Yao C, Zhang J, Huang Y, Leon DR, Steere AC, Costello CE. Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis. J Proteome Res 2016; 16:122-136. [PMID: 27726376 DOI: 10.1021/acs.jproteome.6b00386] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Human leukocyte antigen-antigen D related (HLA-DR) molecules are highly expressed in synovial tissue (ST), the target of the immune response in chronic inflammatory forms of arthritis. Here, we used LC-MS/MS to identify HLA-DR-presented self-peptides in cells taken directly from clinical samples: ST, synovial fluid mononuclear cells (SFMC), or peripheral blood mononuclear cells (PBMC) from five patients with rheumatoid arthritis (RA) and eight with Lyme arthritis (LA). We identified 1593 non-redundant HLA-DR-presented peptides, derived from 870 source proteins. A total of 67% of the peptides identified in SFMC and 55% of those found in PBMC were found in ST, but analysis of SFMC/PBMC also revealed new antigen-presented peptides. Peptides were synthesized and examined for reactivity with the patients' PBMC. To date, three autoantigens in RA and four novel autoantigens in LA, presented in ST and/or PBMC, were shown to be targets of T- and B-cell responses in these diseases; ongoing analyses may add to this list. Thus, immunoprecipitation and LC-MS/MS can now identify hundreds of HLA-DR-presented self-peptides from individual patients' tissues or fluids with mixed cell populations. Importantly, identification of HLA-DR-presented peptides from SFMC or PBMC allows testing of more patients, including those early in the disease. Direct analysis of clinical samples facilitates identification of novel immunogenic T-cell epitopes.
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Affiliation(s)
- Qi Wang
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Elise E Drouin
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School , Boston, Massachusetts 02114, United States
| | - Chunxiang Yao
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Jiyang Zhang
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States.,National University of Defense Technology , Changsha, 410000 Hunan Province, China
| | - Yu Huang
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Deborah R Leon
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
| | - Allen C Steere
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School , Boston, Massachusetts 02114, United States
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine , Boston, Massachusetts 02118, United States
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23
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Malaker SA, Ferracane MJ, Depontieu FR, Zarling AL, Shabanowitz J, Bai DL, Topalian SL, Engelhard VH, Hunt DF. Identification and Characterization of Complex Glycosylated Peptides Presented by the MHC Class II Processing Pathway in Melanoma. J Proteome Res 2016; 16:228-237. [PMID: 27550523 DOI: 10.1021/acs.jproteome.6b00496] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The MHC class II (MHCII) processing pathway presents peptides derived from exogenous or membrane-bound proteins to CD4+ T cells. Several studies have shown that glycopeptides are necessary to modulate CD4+ T cell recognition, though glycopeptide structures in these cases are generally unknown. Here, we present a total of 93 glycopeptides from three melanoma cell lines and one matched EBV-transformed line with most found only in the melanoma cell lines. The glycosylation we detected was diverse and comprised 17 different glycoforms. We then used molecular modeling to demonstrate that complex glycopeptides are capable of binding the MHC and may interact with complementarity determining regions. Finally, we present the first evidence of disulfide-bonded peptides presented by MHCII. This is the first large scale study to sequence glyco- and disulfide bonded MHCII peptides from the surface of cancer cells and could represent a novel avenue of tumor activation and/or immunoevasion.
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Affiliation(s)
| | - Michael J Ferracane
- Department of Medicinal Chemistry, University of Florida , Gainesville, Florida 32610, United States
| | - Florence R Depontieu
- Department of Surgery, Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
| | | | | | | | - Suzanne L Topalian
- Department of Surgery, Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
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24
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Class II major histocompatibility complex mutant mice to study the germ-line bias of T-cell antigen receptors. Proc Natl Acad Sci U S A 2016; 113:E5608-17. [PMID: 27588903 DOI: 10.1073/pnas.1609717113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The interaction of αβ T-cell antigen receptors (TCRs) with peptides bound to MHC molecules lies at the center of adaptive immunity. Whether TCRs have evolved to react with MHC or, instead, processes in the thymus involving coreceptors and other molecules select MHC-specific TCRs de novo from a random repertoire is a longstanding immunological question. Here, using nuclease-targeted mutagenesis, we address this question in vivo by generating three independent lines of knockin mice with single-amino acid mutations of conserved class II MHC amino acids that often are involved in interactions with the germ-line-encoded portions of TCRs. Although the TCR repertoire generated in these mutants is similar in size and diversity to that in WT mice, the evolutionary bias of TCRs for MHC is suggested by a shift and preferential use of some TCR subfamilies over others in mice expressing the mutant class II MHCs. Furthermore, T cells educated on these mutant MHC molecules are alloreactive to each other and to WT cells, and vice versa, suggesting strong functional differences among these repertoires. Taken together, these results highlight both the flexibility of thymic selection and the evolutionary bias of TCRs for MHC.
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25
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Mou Z, Li J, Boussoffara T, Kishi H, Hamana H, Ezzati P, Hu C, Yi W, Liu D, Khadem F, Okwor I, Jia P, Shitaoka K, Wang S, Ndao M, Petersen C, Chen J, Rafati S, Louzir H, Muraguchi A, Wilkins JA, Uzonna JE. Identification of broadly conserved cross-species protective Leishmania antigen and its responding CD4+ T cells. Sci Transl Med 2016; 7:310ra167. [PMID: 26491077 DOI: 10.1126/scitranslmed.aac5477] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is currently no clinically effective vaccine against leishmaniasis because of poor understanding of the antigens that elicit dominant T cell immunity. Using proteomics and cellular immunology, we identified a dominant naturally processed peptide (PEPCK335-351) derived from Leishmania glycosomal phosphoenolpyruvate carboxykinase (PEPCK). PEPCK was conserved in all pathogenic Leishmania, expressed in glycosomes of promastigotes and amastigotes, and elicited strong CD4(+) T cell responses in infected mice and humans. I-A(b)-PEPCK335-351 tetramer identified protective Leishmania-specific CD4(+) T cells at a clonal level, which comprised ~20% of all Leishmania-reactive CD4(+) T cells at the peak of infection. PEPCK335-351-specific CD4(+) T cells were oligoclonal in their T cell receptor usage, produced polyfunctional cytokines (interleukin-2, interferon-γ, and tumor necrosis factor), and underwent expansion, effector activities, contraction, and stable maintenance after lesion resolution. Vaccination with PEPCK peptide, DNA expressing full-length PEPCK, or rPEPCK induced strong durable cross-species protection in both resistant and susceptible mice. The effectiveness and durability of protection in vaccinated mice support the development of a broadly cross-species protective vaccine against different forms of leishmaniasis by targeting PEPCK.
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Affiliation(s)
- Zhirong Mou
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada
| | - Jintao Li
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada. Institute of Tropical Medicine, Third Military Medical University, Chongqing 400038, China
| | - Thouraya Boussoffara
- Laboratory of Transmission, Control and Immunobiology of Infections, Pasteur Institute of Tunis, Tunis 1002, Tunisia
| | - Hiroyuki Kishi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Hiroshi Hamana
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Peyman Ezzati
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Health Sciences Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Chuanmin Hu
- Department of Clinical Biochemistry, Laboratory Sciences, Third Military Medical University, Chongqing 400038, China
| | - Weijing Yi
- Department of Clinical Biochemistry, Laboratory Sciences, Third Military Medical University, Chongqing 400038, China
| | - Dong Liu
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada
| | - Forough Khadem
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada
| | - Ifeoma Okwor
- Department of Medical Microbiology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Ping Jia
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada
| | - Kiyomi Shitaoka
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Shufeng Wang
- Department of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Momar Ndao
- National Reference Centre for Parasitology, Department of Medicine, Division of Infectious Diseases, McGill University, Montreal, Quebec H3G 1A4, Canada
| | | | - Jianping Chen
- Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610065, China
| | - Sima Rafati
- Molecular Immunology and Vaccine Research Laboratory, Pasteur Institute of Iran, Tehran 13164, Iran
| | - Hechmi Louzir
- Laboratory of Transmission, Control and Immunobiology of Infections, Pasteur Institute of Tunis, Tunis 1002, Tunisia
| | - Atsushi Muraguchi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - John A Wilkins
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Health Sciences Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Jude E Uzonna
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada. Department of Medical Microbiology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada.
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26
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Purcell AW, Croft NP, Tscharke DC. Immunology by numbers: quantitation of antigen presentation completes the quantitative milieu of systems immunology! Curr Opin Immunol 2016; 40:88-95. [PMID: 27060633 DOI: 10.1016/j.coi.2016.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/15/2016] [Accepted: 03/20/2016] [Indexed: 10/22/2022]
Abstract
We review approaches to quantitate antigen presentation using a variety of biological and biochemical readouts and highlight the emerging role of mass spectrometry (MS) in defining and quantifying MHC-bound peptides presented at the cell surface. The combination of high mass accuracy in the determination of the molecular weight of the intact peptide of interest and its signature pattern of fragmentation during tandem MS provide an unambiguous and definitive identification. This is in contrast to the potential receptor cross-reactivity towards closely related peptides and variable dose responsiveness seen in biological readouts. In addition, we gaze into the not too distant future where big data approaches in MS can be accommodated to quantify whole immunopeptidomes both in vitro and in vivo.
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Affiliation(s)
- Anthony W Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
| | - Nathan P Croft
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - David C Tscharke
- The John Curtin School of Medical Research, ANU College of Medicine, Biology & Environment, Australian National University, Acton, ACT 2601, Australia.
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27
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Mommen GPM, Marino F, Meiring HD, Poelen MCM, van Gaans-van den Brink JAM, Mohammed S, Heck AJR, van Els CACM. Sampling From the Proteome to the Human Leukocyte Antigen-DR (HLA-DR) Ligandome Proceeds Via High Specificity. Mol Cell Proteomics 2016; 15:1412-23. [PMID: 26764012 PMCID: PMC4824864 DOI: 10.1074/mcp.m115.055780] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Indexed: 12/12/2022] Open
Abstract
Comprehensive analysis of the complex nature of the Human Leukocyte Antigen (HLA) class II ligandome is of utmost importance to understand the basis for CD4+ T cell mediated immunity and tolerance. Here, we implemented important improvements in the analysis of the repertoire of HLA-DR-presented peptides, using hybrid mass spectrometry-based peptide fragmentation techniques on a ligandome sample isolated from matured human monocyte-derived dendritic cells (DC). The reported data set constitutes nearly 14 thousand unique high-confident peptides, i.e. the largest single inventory of human DC derived HLA-DR ligands to date. From a technical viewpoint the most prominent finding is that no single peptide fragmentation technique could elucidate the majority of HLA-DR ligands, because of the wide range of physical chemical properties displayed by the HLA-DR ligandome. Our in-depth profiling allowed us to reveal a strikingly poor correlation between the source proteins identified in the HLA class II ligandome and the DC cellular proteome. Important selective sieving from the sampled proteome to the ligandome was evidenced by specificity in the sequences of the core regions both at their N- and C- termini, hence not only reflecting binding motifs but also dominant protease activity associated to the endolysosomal compartments. Moreover, we demonstrate that the HLA-DR ligandome reflects a surface representation of cell-compartments specific for biological events linked to the maturation of monocytes into antigen presenting cells. Our results present new perspectives into the complex nature of the HLA class II system and will aid future immunological studies in characterizing the full breadth of potential CD4+ T cell epitopes relevant in health and disease.
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Affiliation(s)
- Geert P M Mommen
- From the ‡Institute for Translational Vaccinology, P.O. Box 450, 3720 AL Bilthoven, the Netherlands; §Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Fabio Marino
- §Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; ¶Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Hugo D Meiring
- From the ‡Institute for Translational Vaccinology, P.O. Box 450, 3720 AL Bilthoven, the Netherlands
| | - Martien C M Poelen
- ‖Centre for Infectious Disease Control, National Institute for Public Health and the Environment, P.O. Box 1, 3720 AL Bilthoven, the Netherlands
| | | | - Shabaz Mohammed
- §Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; ¶Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands; **Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, OX13TA, Oxford, United Kingdom; ‡‡Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, United Kingdom
| | - Albert J R Heck
- §Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; ¶Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Cécile A C M van Els
- ‖Centre for Infectious Disease Control, National Institute for Public Health and the Environment, P.O. Box 1, 3720 AL Bilthoven, the Netherlands;
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28
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Sofron A, Ritz D, Neri D, Fugmann T. High-resolution analysis of the murine MHC class II immunopeptidome. Eur J Immunol 2015; 46:319-28. [PMID: 26495903 DOI: 10.1002/eji.201545930] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/09/2015] [Accepted: 10/19/2015] [Indexed: 02/06/2023]
Abstract
The reliable identification of peptides bound to major histocompatibility complex (MHC) class II is fundamental for the study of the host immune response against pathogens and the pathogenesis of autoimmune conditions. Here, we describe an improved methodology combining immuno-affinity enrichment of MHC class II complexes, optimized elution conditions and quadrupole Orbitrap mass spectrometry-based characterization of the immunopeptidome. The methodology allowed the identification of over 1000 peptides with 1% false discovery rate from 10(8) murine A20 lymphoma cells. The study revealed the I-A(d) -specific motif in high resolution after multisequence alignment. The methodology was generally applied to the purification of MHC class II from cell lines and murine spleens. We identified 2963 peptides from BALB/c and 2712 from C57BL/6 mouse spleens. The identification of peptides bound to MHC class II in vitro and in vivo will facilitate the characterization of T-cell specificities, as well as the development of biotherapeutics and vaccines.
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Affiliation(s)
- Adriana Sofron
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Dario Neri
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
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29
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Bergseng E, Dørum S, Arntzen MØ, Nielsen M, Nygård S, Buus S, de Souza GA, Sollid LM. Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires. Immunogenetics 2014; 67:73-84. [PMID: 25502872 PMCID: PMC4297300 DOI: 10.1007/s00251-014-0819-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/28/2014] [Indexed: 02/07/2023]
Abstract
Celiac disease is caused by intolerance to cereal gluten proteins, and HLA-DQ molecules are involved in the disease pathogenesis by presentation of gluten peptides to CD4+ T cells. The α- or β-chain sharing HLA molecules DQ2.5, DQ2.2, and DQ7.5 display different risks for the disease. It was recently demonstrated that T cells of DQ2.5 and DQ2.2 patients recognize distinct sets of gluten epitopes, suggesting that these two DQ2 variants select different peptides for display. To explore whether this is the case, we performed a comprehensive comparison of the endogenous self-peptides bound to HLA-DQ molecules of B-lymphoblastoid cell lines. Peptides were eluted from affinity-purified HLA molecules of nine cell lines and subjected to quadrupole orbitrap mass spectrometry and MaxQuant software analysis. Altogether, 12,712 endogenous peptides were identified at very different relative abundances. Hierarchical clustering of normalized quantitative data demonstrated significant differences in repertoires of peptides between the three DQ variant molecules. The neural network-based method, NNAlign, was used to identify peptide-binding motifs. The binding motifs of DQ2.5 and DQ7.5 concurred with previously established binding motifs. The binding motif of DQ2.2 was strikingly different from that of DQ2.5 with position P3 being a major anchor having a preference for threonine and serine. This is notable as three recently identified epitopes of gluten recognized by T cells of DQ2.2 celiac patients harbor serine at position P3. This study demonstrates that relative quantitative comparison of endogenous peptides sampled from our protein metabolism by HLA molecules provides clues to understand HLA association with disease.
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Affiliation(s)
- Elin Bergseng
- Centre for Immune Regulation, Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
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30
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A mechanistic, multiscale mathematical model of immunogenicity for therapeutic proteins: part 2-model applications. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2014; 3:e134. [PMID: 25184734 PMCID: PMC4211264 DOI: 10.1038/psp.2014.31] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 05/12/2014] [Indexed: 01/09/2023]
Abstract
A mechanistic, multiscale mathematical model of immunogenicity for therapeutic proteins was built by recapitulating key underlying known biological processes for immunogenicity. The model is able to simulate immune responses based on protein-specific antigenic properties (e.g., number of T-epitopes and their major histocompatibility complex (MHC)-II binding affinities) and host-specific immunological/physiological characteristics (e.g., MHC-II allele genotype, drug clearance rate). Preliminary validation was performed using mouse studies with antigens such as ovalbumin (OVA) or OVA-derived peptide. Further, using adalimumab as an example therapeutic protein, the model is able to simulate immune responses against adalimumab in individual subjects and in a population, and also provides estimations of immunogenicity incidence and drug exposure reduction that can be validated experimentally. This is a first attempt at modeling immunogenicity of biologics, so the model simulations should be used to help understand the immunogenicity mechanisms and impacting factors, rather than making direct predictions. This prototype model needs to be subjected to extensive experimental validation and refinement before fulfilling its ultimate mission of predicting immunogenicity. Nevertheless, the current model could potentially set up the starting framework to integrate various in silico, in vitro, in vivo, and clinical immunogenicity assessment results to help meet the challenge of immunogenicity prediction.
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31
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de Jong H, Koffeman EC, Meerding JM, Scholman RC, Wieten L, de Jager W, Klein M, Otten H, van Wijk F, van der Zee R, Bijlsma JWJ, Broere F, van Eden W, Prakken BJ. T cell recognition of naturally presented epitopes of self-heat shock protein 70. Cell Stress Chaperones 2014; 19:569-78. [PMID: 24425585 PMCID: PMC4041940 DOI: 10.1007/s12192-013-0484-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 11/12/2013] [Accepted: 12/04/2013] [Indexed: 12/01/2022] Open
Abstract
Self-reactive T cells have shown to have a potential role as regulators of the immune system preventing or even suppressing autoimmunity. One of the most abundant proteins that can be eluted from human HLA molecules is heat shock protein 70 (HSP70). The aims of the current study are to identify HSP70 epitopes based on published HLA elution studies and to investigate whether T cells from healthy individuals may respond to such self-epitopes. A literature search and subsequent in silico binding prediction based on theoretical MHC binding motifs resulted in the identification of seven HSP70 epitopes. PBMCs of healthy controls proliferated after incubation with two of the seven peptides (H167 and H290). Furthermore H161, H290, and H443 induced CD69 expression or production of cytokines IFNγ or TNFα in healthy controls. The identification of these naturally presented epitopes and the response they elicit in the normal immune system make them potential candidates to study during inflammatory conditions as well as in autoimmune diseases.
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Affiliation(s)
- Huib de Jong
- />Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
- />Laboratory of Translational Immunology, Department of Pediatric Immunology, University Medical Center Utrecht, Huispostnummer KE 04.131.1, Postbus 85090, 3508 AB Utrecht, The Netherlands
| | - Eva C. Koffeman
- />Laboratory of Translational Immunology, Department of Pediatric Immunology, University Medical Center Utrecht, Huispostnummer KE 04.131.1, Postbus 85090, 3508 AB Utrecht, The Netherlands
| | - Jennifer M. Meerding
- />Laboratory of Translational Immunology, Department of Pediatric Immunology, University Medical Center Utrecht, Huispostnummer KE 04.131.1, Postbus 85090, 3508 AB Utrecht, The Netherlands
| | - Rianne C. Scholman
- />Laboratory of Translational Immunology, Department of Pediatric Immunology, University Medical Center Utrecht, Huispostnummer KE 04.131.1, Postbus 85090, 3508 AB Utrecht, The Netherlands
| | - Lotte Wieten
- />Department of Infectious Diseases and Immunology, Division of Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Wilco de Jager
- />Laboratory of Translational Immunology, Department of Pediatric Immunology, University Medical Center Utrecht, Huispostnummer KE 04.131.1, Postbus 85090, 3508 AB Utrecht, The Netherlands
| | - Mark Klein
- />Laboratory of Translational Immunology, Department of Pediatric Immunology, University Medical Center Utrecht, Huispostnummer KE 04.131.1, Postbus 85090, 3508 AB Utrecht, The Netherlands
| | - Henny Otten
- />Department of Immunology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
| | - Femke van Wijk
- />Laboratory of Translational Immunology, Department of Pediatric Immunology, University Medical Center Utrecht, Huispostnummer KE 04.131.1, Postbus 85090, 3508 AB Utrecht, The Netherlands
| | - Ruurd van der Zee
- />Department of Infectious Diseases and Immunology, Division of Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Johannes W. J. Bijlsma
- />Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Femke Broere
- />Department of Infectious Diseases and Immunology, Division of Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Willem van Eden
- />Department of Infectious Diseases and Immunology, Division of Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Berent J. Prakken
- />Laboratory of Translational Immunology, Department of Pediatric Immunology, University Medical Center Utrecht, Huispostnummer KE 04.131.1, Postbus 85090, 3508 AB Utrecht, The Netherlands
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Abstract
The mammalian immune system has evolved to display peptides derived from microbial antigens to immune effector cells. Liberated from the intact antigens through distinct proteolytic mechanisms, these peptides are subsequently transported to the cell surface while bound to chaperone-like receptors known as major histocompatibility complex molecules. These complexes are then scrutinized by T-cells that express receptors with specificity for specific major histocompatibility complex-peptide complexes. In normal uninfected cells, this process of antigen processing and presentation occurs continuously, with the resultant array of self-antigen-derived peptides displayed on the surface of these cells. Changes in this cellular peptide array alert the immune system to changes in the intracellular environment that may be associated with infection, oncogenesis or other abnormal cellular processes, resulting in a cascade of events that result in the elimination of the abnormal cell. Since peptides play such an essential role in informing the immune system of infection with viral or microbial pathogens and the transformation of cells in malignancy, the tools of proteomics, in particular mass spectrometry, are ideally suited to study these immune responses at a molecular level. Recent advances in studies of immune responses that have utilized mass spectrometry and associated technologies are reviewed. The authors gaze into the future and look at current challenges and where proteomics will impact in immunology over the next 5 years.
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Affiliation(s)
- Nicholas A Williamson
- The University of Melbourne, Department of Biochemistry & Molecular Biology, The Bio21 Molecular Science & Biotechnology Institute, 3010, Victoria, Australia.
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Ferrante A. For many but not for all: how the conformational flexibility of the peptide/MHCII complex shapes epitope selection. Immunol Res 2013; 56:85-95. [PMID: 22753017 DOI: 10.1007/s12026-012-8342-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The adaptive immune response starts when CD4+ T cells recognize peptide antigens presented by class II molecules of the Major Histocompatibility Complex (MHCII). Two outstanding features of MHCII molecules are their polymorphism and the ability of each allele to bind a large panoply of peptides. The ability of each MHCII molecule to interact with a limited, though broad, range of amino acid sequences, or "permissive specificity" of binding, is the result of structural flexibility. This flexibility has been identified through biochemical and biophysical studies, and molecular dynamic simulations have modeled the conformational rearrangements that the peptide and the MHCII undergo during interaction. Moreover, there is evidence that the structural flexibility of the peptide/MHCII complex correlates with the activity of the "peptide-editing" molecule DM. In light of the impact that these recent findings have on our ability to predict MHCII epitopes, a review of the structural and thermodynamic determinants of peptide binding to MHCII is proposed.
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Affiliation(s)
- Andrea Ferrante
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775-7000, USA.
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Holland CJ, Cole DK, Godkin A. Re-Directing CD4(+) T Cell Responses with the Flanking Residues of MHC Class II-Bound Peptides: The Core is Not Enough. Front Immunol 2013; 4:172. [PMID: 23847615 PMCID: PMC3696884 DOI: 10.3389/fimmu.2013.00172] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 06/14/2013] [Indexed: 11/17/2022] Open
Abstract
Recombinant αβ T cell receptors, expressed on T cell membranes, recognize short peptides presented at the cell surface in complex with MHC molecules. There are two main subsets of αβ T cells: CD8(+) T cells that recognize mainly cytosol-derived peptides in the context of MHC class I (pMHC-I), and CD4(+) T cells that recognize peptides usually derived from exogenous proteins presented by MHC class II (pMHC-II). Unlike the more uniform peptide lengths (usually 8-13mers) bound in the MHC-I closed groove, MHC-II presented peptides are of a highly variable length. The bound peptides consist of a core bound 9mer (reflecting the binding motif for the particular MHC-II type) but with variable peptide flanking residues (PFRs) that can extend from both the N- and C-terminus of the MHC-II binding groove. Although pMHC-I and pMHC-II play a virtually identical role during T cell responses (T cell antigen presentation) and are very similar in overall conformation, there exist a number of subtle but important differences that may govern the functional dichotomy observed between CD8(+) and CD4(+) T cells. Here, we provide an overview of the impact of structural differences between pMHC-I and pMHC-II and the molecular interactions with the T cell receptor including the functional importance of MHC-II PFRs. We consider how factors such as anatomical location, inflammatory milieu, and particular types of antigen presenting cell might, in theory, contribute to the quantitative (i.e., pMHC ligand frequency) as well as qualitative (i.e., variable PFR) nature of peptide epitopes, and hence offer a means of control and influence of a CD4(+) T cell response. Lastly, we review our recent findings showing how modifications to MHC-II PFRs can modify CD4(+) T cell antigen recognition. These findings may have novel applications for the development of CD4(+) T cell peptide vaccines and diagnostics.
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Affiliation(s)
| | - David K. Cole
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Andrew Godkin
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
- Department of Integrated Medicine, University Hospital of Wales, Cardiff, UK
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van Eden W, van Herwijnen M, Wagenaar J, van Kooten P, Broere F, van der Zee R. Stress proteins are used by the immune system for cognate interactions with anti-inflammatory regulatory T cells. FEBS Lett 2013; 587:1951-8. [PMID: 23707418 DOI: 10.1016/j.febslet.2013.05.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 05/07/2013] [Accepted: 05/07/2013] [Indexed: 01/21/2023]
Abstract
Since the initial discovery of the protective role of heat shock protein (HSP) 60 in arthritis, T cell recognition of endogenous HSP was found to be one of the possible underlying mechanisms. Recently we have uncovered potent disease-suppressive Tregs (anti-inflammatory immunosuppressive T cells) recognizing HSP70 self-antigens, and enabling selective targeting of such Tregs to inflamed tissues. HSP70 is a major contributor to the major histocompatibility complex (MHC) Class II ligandome and we have shown that a conserved HSP70-epitope (B29) is abundantly present in murine MHC Class II. Upon transfer, B29-induced CD4+CD25+Foxp3+T cells suppressed established proteoglycan-induced arthritis (PGIA) in mice. These self-antigen specific Tregs were activated in vivo and as little as 4.000 cells sufficed to fully inhibit arthritis. Furthermore, in vivo depletion of transferred Tregs abrogated disease suppression. Given that B29 can be presented by most human MHC class II molecules and that B29 inhibited arthritis in HLA-DQ8 (human MHC) transgenic mice, we feel that therapeutic vaccination with selected HSP peptides can be an effective route for induction of anti-inflammatory Tregs as a novel intervention in chronic inflammatory diseases.
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Affiliation(s)
- Willem van Eden
- Division of Immunology, Dept. Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Yalelaan 1, 3584 CL Utrecht, The Netherlands.
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Sauna ZE, Ameri A, Kim B, Yanover C, Viel KR, Rajalingam R, Cole SA, Howard TE. Observations regarding the immunogenicity of BDD-rFVIII derived from a mechanistic personalized medicine perspective. J Thromb Haemost 2012; 10:1961-5. [PMID: 22734827 DOI: 10.1111/j.1538-7836.2012.04830.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Marrack P, Kappler JW. Do MHCII-presented neoantigens drive type 1 diabetes and other autoimmune diseases? Cold Spring Harb Perspect Med 2012; 2:a007765. [PMID: 22951444 PMCID: PMC3426820 DOI: 10.1101/cshperspect.a007765] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The strong association between particular MHCII alleles and type 1 diabetes is not fully understood. Two ideas that have been considered for many years are that autoimmunity is driven by (1) low-affinity CD4(+) T cells that escape thymic negative selection and respond to certain autoantigen peptides that are particularly well presented by particular MHCII molecules, or (2) CD4(+) T cells responding to neoantigens that are absent in the thymus, but uniquely created in the target tissue in the periphery and presented by particular MHCII alleles. Here we discuss the recent structural data in favor of the second idea. We review studies suggesting that peptide antigens recognized by autoimmune T cells are uniquely proteolytically processed and/or posttranslationally modified in the target tissue, thus allowing these T cells to escape deletion in the thymus during T-cell development. We postulate that an encounter with these tissue-specific neoantigenic peptides presented by the particular susceptible MHCII alleles in the peripheral tissues when accompanied by the appropriate inflammatory milieu activates these T-cell escapees leading to the onset of autoimmune disease.
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Affiliation(s)
- Philippa Marrack
- Howard Hughes Medical Institute and Integrated Department of Immunology, National Jewish Health, University of Colorado Denver, School of Medicine, Denver, CO 80206, USA
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38
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Chornoguz O, Gapeev A, O'Neill MC, Ostrand-Rosenberg S. Major histocompatibility complex class II+ invariant chain negative breast cancer cells present unique peptides that activate tumor-specific T cells from breast cancer patients. Mol Cell Proteomics 2012; 11:1457-67. [PMID: 22942358 DOI: 10.1074/mcp.m112.019232] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The major histocompatibility complex (MHC) class II-associated Invariant chain (Ii) is present in professional antigen presenting cells where it regulates peptide loading onto MHC class II molecules and the peptidome presented to CD4+ T lymphocytes. Because Ii prevents peptide loading in neutral subcellular compartments, we reasoned that Ii- cells may present peptides not presented by Ii+ cells. Based on the hypothesis that patients are tolerant to MHC II-restricted tumor peptides presented by Ii+ cells, but will not be tolerant to novel peptides presented by Ii- cells, we generated MHC II vaccines to activate cancer patients' T cells. The vaccines are Ii- tumor cells expressing syngeneic HLA-DR and the costimulatory molecule CD80. We used liquid chromatography coupled with mass spectrometry to sequence MHC II-restricted peptides from Ii+ and Ii- MCF10 human breast cancer cells transfected with HLA-DR7 or the MHC Class II transactivator CIITA to determine if Ii- cells present novel peptides. Ii expression was induced in the HLA-DR7 transfectants by transfection of Ii, and inhibited in the CIITA transfectants by RNA interference. Peptides were analyzed and binding affinity predicted by artificial neural net analysis. HLA-DR7-restricted peptides from Ii- and Ii+ cells do not differ in size or in subcellular location of their source proteins; however, a subset of HLA-DR7-restricted peptides of Ii- cells are not presented by Ii+ cells, and are derived from source proteins not used by Ii+ cells. Peptides from Ii- cells with the highest predicted HLA-DR7 binding affinity were synthesized, and activated tumor-specific HLA-DR7+ human T cells from healthy donors and breast cancer patients, demonstrating that the MS-identified peptides are bonafide tumor antigens. These results demonstrate that Ii regulates the repertoire of tumor peptides presented by MHC class II+ breast cancer cells and identify novel immunogenic MHC II-restricted peptides that are potential therapeutic reagents for cancer patients.
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Affiliation(s)
- Olesya Chornoguz
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
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39
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Effect of MHC and non-MHC donor/recipient genetic disparity on the outcome of allogeneic HCT. Blood 2012; 120:2796-806. [PMID: 22859606 DOI: 10.1182/blood-2012-04-347286] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The outcome of allogeneic hematopoietic cell transplantation is influenced by donor/recipient genetic disparity at loci both inside and outside the MHC on chromosome 6p. Although disparity at loci within the MHC is the most important risk factor for the development of severe GVHD, disparity at loci outside the MHC that encode minor histocompatibility (H) antigens can elicit GVHD and GVL activity in donor/recipient pairs who are otherwise genetically identical across the MHC. Minor H antigens are created by sequence and structural variations within the genome. The enormous variation that characterizes the human genome suggests that the total number of minor H loci is probably large and ensures that all donor/recipient pairs, despite selection for identity at the MHC, will be mismatched for many minor H antigens. In addition to mismatch at minor H loci, unrelated donor/recipient pairs exhibit genetic disparity at numerous loci within the MHC, particularly HLA-DP, despite selection for identity at HLA-A, -B, -C, and -DRB1. Disparity at HLA-DP exists in 80% of unrelated pairs and clearly influences the outcome of unrelated hematopoietic cell transplantation; the magnitude of this effect probably exceeds that associated with disparity at any locus outside the MHC.
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Chaves FA, Lee AH, Nayak JL, Richards KA, Sant AJ. The utility and limitations of current Web-available algorithms to predict peptides recognized by CD4 T cells in response to pathogen infection. THE JOURNAL OF IMMUNOLOGY 2012; 188:4235-48. [PMID: 22467652 DOI: 10.4049/jimmunol.1103640] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The ability to track CD4 T cells elicited in response to pathogen infection or vaccination is critical because of the role these cells play in protective immunity. Coupled with advances in genome sequencing of pathogenic organisms, there is considerable appeal for implementation of computer-based algorithms to predict peptides that bind to the class II molecules, forming the complex recognized by CD4 T cells. Despite recent progress in this area, there is a paucity of data regarding the success of these algorithms in identifying actual pathogen-derived epitopes. In this study, we sought to rigorously evaluate the performance of multiple Web-available algorithms by comparing their predictions with our results--obtained by purely empirical methods for epitope discovery in influenza that used overlapping peptides and cytokine ELISPOTs--for three independent class II molecules. We analyzed the data in different ways, trying to anticipate how an investigator might use these computational tools for epitope discovery. We come to the conclusion that currently available algorithms can indeed facilitate epitope discovery, but all shared a high degree of false-positive and false-negative predictions. Therefore, efficiencies were low. We also found dramatic disparities among algorithms and between predicted IC(50) values and true dissociation rates of peptide-MHC class II complexes. We suggest that improved success of predictive algorithms will depend less on changes in computational methods or increased data sets and more on changes in parameters used to "train" the algorithms that factor in elements of T cell repertoire and peptide acquisition by class II molecules.
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Affiliation(s)
- Francisco A Chaves
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
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Bozzacco L, Yu H, Zebroski HA, Dengjel J, Deng H, Mojsov S, Steinman RM. Mass spectrometry analysis and quantitation of peptides presented on the MHC II molecules of mouse spleen dendritic cells. J Proteome Res 2011; 10:5016-30. [PMID: 21913724 PMCID: PMC3270889 DOI: 10.1021/pr200503g] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Major histocompatibility complex class II (MHC II) molecules are expressed on the surface of antigen-presenting cells and display short bound peptide fragments derived from self- and nonself antigens. These peptide-MHC complexes function to maintain immunological tolerance in the case of self-antigens and initiate the CD4(+) T cell response in the case of foreign proteins. Here we report the application of LC-MS/MS analysis to identify MHC II peptides derived from endogenous proteins expressed in freshly isolated murine splenic DCs. The cell number was enriched in vivo upon treatment with Flt3L-B16 melanoma cells. In a typical experiment, starting with about 5 × 10(8) splenic DCs, we were able to reliably identify a repertoire of over 100 MHC II peptides originating from about 55 proteins localized in membrane (23%), intracellular (26%), endolysosomal (12%), nuclear (14%), and extracellular (25%) compartments. Using synthetic isotopically labeled peptides corresponding to the sequences of representative bound MHC II peptides, we quantified by LC-MS relative peptide abundance. In a single experiment, peptides were detected in a wide concentration range spanning from 2.5 fmol/μL to 12 pmol/μL or from approximately 13 to 2 × 10(5) copies per DC. These peptides were found in similar amounts on B cells where we detected about 80 peptides originating from 55 proteins distributed homogenously within the same cellular compartments as in DCs. About 90 different binding motifs predicted by the epitope prediction algorithm were found within the sequences of the identified MHC II peptides. These results set a foundation for future studies to quantitatively investigate the MHC II repertoire on DCs generated under different immunization conditions.
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42
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Zhang L, Udaka K, Mamitsuka H, Zhu S. Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools. Brief Bioinform 2011; 13:350-64. [PMID: 21949215 DOI: 10.1093/bib/bbr060] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Binding of short antigenic peptides to major histocompatibility complex (MHC) molecules is a core step in adaptive immune response. Precise identification of MHC-restricted peptides is of great significance for understanding the mechanism of immune response and promoting the discovery of immunogenic epitopes. However, due to the extremely high MHC polymorphism and huge cost of biochemical experiments, there is no experimentally measured binding data for most MHC molecules. To address the problem of predicting peptides binding to these MHC molecules, recently computational approaches, called pan-specific methods, have received keen interest. Pan-specific methods make use of experimentally obtained binding data of multiple alleles, by which binding peptides (binders) of not only these alleles but also those alleles with no known binders can be predicted. To investigate the possibility of further improvement in performance and usability of pan-specific methods, this article extensively reviews existing pan-specific methods and their web servers. We first present a general framework of pan-specific methods. Then, the strategies and performance as well as utilities of web servers are compared. Finally, we discuss the future direction to improve pan-specific methods for MHC-peptide binding prediction.
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Affiliation(s)
- Lianming Zhang
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China
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43
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Delluc S, Ravot G, Maillere B. Quantitative analysis of the CD4 T‐cell repertoire specific to therapeutic antibodies in healthy donors. FASEB J 2011; 25:2040-8. [DOI: 10.1096/fj.10-173872] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Bernard Maillere
- Service d'Ingenierie Moleculaire des ProteinesInstitut de Biologie et de Technologies de SaclayCommissariat à l'E´nergie Atomique et aux Energies AlternativesGif Sur YvetteFrance
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44
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Egger M, Jürets A, Wallner M, Briza P, Ruzek S, Hainzl S, Pichler U, Kitzmüller C, Bohle B, Huber CG, Ferreira F. Assessing protein immunogenicity with a dendritic cell line-derived endolysosomal degradome. PLoS One 2011; 6:e17278. [PMID: 21359181 PMCID: PMC3040223 DOI: 10.1371/journal.pone.0017278] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 01/27/2011] [Indexed: 12/17/2022] Open
Abstract
Background The growing number of novel candidate molecules for the treatment of allergic diseases imposed a dramatic increase in the demand for animal experiments to select immunogenic vaccines, a pre-requisite for efficacy. Because no in vitro methods to predict the immunogenicity of a protein are currently available, we developed an in vitro assay that exploits the link between a protein's immunogenicity and its susceptibility to endolysosomal proteolysis. Methodology We compared protein composition and proteolytic activity of endolysosomal fractions isolated from murine bone marrow- and human blood- derived dendritic cells, and from the dendritic cell line JAWS II. Three groups of structurally related antigen variants differing in their ability to elicit immune responses in vivo (Bet v 1.0101 and Bet v 1.0401, RNases A and S, holo- and apo-HRP) were subjected to in vitro simulated endolysosomal degradation. Kinetics and patterns of generated proteolytic peptides were evaluated by gel electrophoresis and mass spectrometry. Results Antigens displaying weak capacity of T cell priming in vivo were highly susceptible to endolysosomal proteases in vitro. As proteolytic composition, activity, and specificity of endolysosomal fractions derived from human and murine dendritic cells were comparable, the JAWS II cell line could be used as a substitute for freshly isolated human or murine cells in in vitro degradation assays. Conclusions Endolysosomal fractions prepared from the JAWS II cell line provide a reliable tool for in vitro estimation of protein immunogenicity. The rapid and simple assay described here is very useful to study the immunogenic properties of a protein, and can help to replace, reduce, and refine animal experiments in allergy research and vaccine development in general.
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Affiliation(s)
- Matthias Egger
- Christian Doppler Laboratory for Allergy Diagnosis and Therapy, Department of Molecular Biology, University of Salzburg, Salzburg, Austria.
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45
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Seward RJ, Drouin EE, Steere AC, Costello CE. Peptides presented by HLA-DR molecules in synovia of patients with rheumatoid arthritis or antibiotic-refractory Lyme arthritis. Mol Cell Proteomics 2010; 10:M110.002477. [PMID: 21081667 DOI: 10.1074/mcp.m110.002477] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Disease-associated HLA-DR molecules, which may present autoantigens, constitute the greatest genetic risk factor for rheumatoid arthritis (RA) and antibiotic-refractory Lyme arthritis (LA). The peptides presented by HLA-DR molecules in synovia have not previously been defined. Using tandem mass spectrometry, rigorous database searches, and manual spectral interpretation, we identified 1,427 HLA-DR-presented peptides (220-464 per patient) from the synovia of four patients, two diagnosed with RA and two diagnosed with LA. The peptides were derived from 166 source proteins, including a wide range of intracellular and plasma proteins. A few epitopes were found only in RA or LA patients. However, two patients with different diseases who had the same HLA allele had the largest number of epitopes in common. In one RA patient, peptides were identified as originating from source proteins that have been reported to undergo citrullination under other circumstances, yet neither this post-translational modification nor anti-cyclic citrullinated peptide antibodies were detected. Instead, peptides with the post-translational modification of S-cysteinylation were identified. We conclude that a wide range of proteins enter the HLA-DR pathway of antigen-presenting cells in the patients' synovial tissue, and their HLA-DR genotype, not the disease type, appears to be the primary determinant of their HLA-DR-peptide repertoire. New insights into the naturally presented HLA-DR epitope repertoire in target tissues may allow the identification of pathogenic T cell epitopes, and this could lead to innovative therapeutic interventions.
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Affiliation(s)
- Robert J Seward
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, and Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, Massachusetts 02118, USA
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46
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Lippolis JD, Reinhardt TA. Utility, limitations, and promise of proteomics in animal science. Vet Immunol Immunopathol 2010; 138:241-51. [PMID: 21074277 DOI: 10.1016/j.vetimm.2010.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Proteomics experiments have the ability to simultaneously identify and quantify thousands of proteins in one experiment. The use of this technology in veterinary/animal science is still in its infancy, yet it holds significant promise as a method for advancing veterinary/animal science research. Examples of current experimental designs and capabilities of proteomic technology and basic principles of mass spectrometry are discussed. In addition, challenges and limitations of proteomics are presented, stressing those that are unique to veterinary/animal sciences.
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Affiliation(s)
- John D Lippolis
- Ruminant Diseases and Immunology Research Unit, USDA-ARS, National Animal Disease Center, 1920 Dayton Avenue, Ames, IA 50010, United States.
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47
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Stoeckle C, Tolosa E. Antigen processing and presentation in multiple sclerosis. Results Probl Cell Differ 2010; 51:149-72. [PMID: 19582405 DOI: 10.1007/400_2009_22] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
CD4(+) T cells play a central role in the pathogenesis of multiple sclerosis (MS). Generation, activation and effector function of these cells crucially depends on their interaction with MHC II-peptide complexes displayed by antigen presenting cells (APC). Processing and presentation of self antigens by different APC therefore influences the disease course at all stages. Selection by thymic APC leads to the generation of autoreactive T cells, which can be activated by peripheral APC. Reactivation by central nervous system APC leads to the initiation of the inflammatory response resulting in demyelination. In this review we will focus on how MHC class II antigenic epitopes are created by different APC from the thymus, the periphery and from the brain, and will discuss the relevance of the balance between creation and destruction of such epitopes in the context of MS. A solid understanding of these processes offers the possibility for designing future therapeutic strategies.
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Affiliation(s)
- Christina Stoeckle
- Department of General Neurology, Hertie Institute for Clinical Brain Research, Otfried-Mueller-Str. 27, 72076, Tuebingen, Germany.
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Mutschlechner S, Egger M, Briza P, Wallner M, Lackner P, Karle A, Vogt AB, Fischer GF, Bohle B, Ferreira F. Naturally processed T cell-activating peptides of the major birch pollen allergen. J Allergy Clin Immunol 2010; 125:711-8, 718.e1-718.e2. [PMID: 20132976 DOI: 10.1016/j.jaci.2009.10.052] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 10/06/2009] [Accepted: 10/29/2009] [Indexed: 11/29/2022]
Abstract
BACKGROUND Although antigen processing and presentation of allergens to CD4(+)T lymphocytes are key events in the pathophysiology of allergic disorders, they still remain poorly understood. OBJECTIVE To investigate allergen processing and presentation by dendritic cells using the major birch pollen allergen Bet v 1 as a model. METHODS Endolysosomal extracts of dendritic cells derived from patients with birch pollen allergy were used to digest Bet v 1. Dendritic cells were pulsed with Bet v 1, and peptides were eluted from MHC class II molecules. Peptides obtained by either approach were sequenced by tandem mass spectrometry. Bet v 1-specific T-cell cultures were stimulated with HLA-DR-eluted Bet v 1-derived peptides. Bet v 1-specific T-cell lines were generated from each patient and analyzed for epitope recognition. RESULTS A high proportion of Bet v 1 remained intact for a long period of endolysosomal degradation. The peptides that appeared early in the degradation process contained frequently recognized T-cell epitopes. Bet v 1-derived peptides eluted from MHC class II molecules corresponded to those generated by endolysosomal degradation, matched known T-cell epitopes, and showed T cell-activating capacity. The Bet v 1-specific T-cell line of each individual harbored T cells reactive with peptides located within the MHC class II-eluted Bet v 1-derived sequences demonstrating their occurrence in vivo. CONCLUSION We report for the first time how epitopes of allergens are generated and selected for presentation to T lymphocytes. The limited susceptibility of Bet v 1 to endolysosomal processing might contribute to its high allergenic potential.
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Affiliation(s)
- Sonja Mutschlechner
- Christian Doppler Laboratory for Allergy Diagnosis and Therapy, Department of Molecular Biology, University of Salzburg, Salzburg, Austria
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Abstract
It has previously been shown that a approximately 27 kDa serine protease of Schistosoma mansoni larvae, the cercarial elastase (CE), was a poor immunogen in as much as it failed to induce an antibody response. The CE has a critical role in enabling schistosome larvae to penetrate the skin of their definitive hosts, so the apparently poor immunogenicity of this enzyme is clearly of interest. To understand its lack of immunogenicity better and in particular to determine whether it is related to its proteolytic activity, we have measured antibody responses of mice to three different serine proteases. Groups of mice were immunized with porcine pancreatic trypsin (TRY), chymotrypsin (CHY) or elastase (ELA) and the resulting antibody response compared with antibody responses to two non-protease antigens, chicken egg albumin (OVA) and Schistosoma japonicum glutathione S-transferase (GST), all being administered with alum as an adjuvant. Of 12 mice that were injected five times at 14 day intervals with TRY, only one produced antibody reactive with this enzyme in ELISA. Immunizations with CHY or ELA induced somewhat better antibody responses than TRY, but the responses to the first and second injections of these two proteases nevertheless seemed comparatively lower than the responses to GST. Induction of antibody responses by OVA and GST was not affected when TRY was injected concomitantly. Thus, the antibody response to one of the serine proteases used in this study, mammalian trypsin, was anomalous.
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Affiliation(s)
- H Y Darani
- Department of Parasitology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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Identification of tumor-associated, MHC class II-restricted phosphopeptides as targets for immunotherapy. Proc Natl Acad Sci U S A 2009; 106:12073-8. [PMID: 19581576 DOI: 10.1073/pnas.0903852106] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The activation and recruitment of CD4(+) T cells are critical for the development of efficient antitumor immunity and may allow for the optimization of current cancer immunotherapy strategies. Searching for more optimal and selective targets for CD4(+) T cells, we have investigated phosphopeptides, a new category of tumor-derived epitopes linked to proteins with vital cellular functions. Although MHC I-restricted phosphopeptides have been identified, it was previously unknown whether human MHC II molecules present phosphopeptides for specific CD4(+) T cell recognition. We first demonstrated the fine specificity of human CD4(+) T cells to discriminate a phosphoresidue by using cells raised against the candidate melanoma antigen mutant B-Raf or its phosphorylated counterpart. Then, we assessed the presence and complexity of human MHC II-associated phosphopeptides by analyzing 2 autologous pairs of melanoma and EBV-transformed B lymphoblastoid lines. By using sequential affinity isolation, biochemical enrichment, mass spectrometric sequencing, and comparative analysis, a total of 175 HLA-DR-associated phosphopeptides were characterized. Many were derived from source proteins that may have roles in cancer development, growth, and metastasis. Most were expressed exclusively by either melanomas or transformed B cells, suggesting the potential to define cell type-specific phosphatome "fingerprints." We then generated HLA-DRbeta1*0101-restricted CD4(+) T cells specific for a phospho-MART-1 peptide identified in both melanoma cell lines. These T cells showed specificity for phosphopeptide-pulsed antigen-presenting cells as well as for intact melanoma cells. This previously undescribed demonstration of MHC II-restricted phosphopeptides recognizable by human CD4(+) T cells provides potential new targets for cancer immunotherapy.
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