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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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2
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Hammond S, Thomson P, Meng X, Naisbitt D. In-Vitro Approaches to Predict and Study T-Cell Mediated Hypersensitivity to Drugs. Front Immunol 2021; 12:630530. [PMID: 33927714 PMCID: PMC8076677 DOI: 10.3389/fimmu.2021.630530] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/17/2021] [Indexed: 01/11/2023] Open
Abstract
Mitigating the risk of drug hypersensitivity reactions is an important facet of a given pharmaceutical, with poor performance in this area of safety often leading to warnings, restrictions and withdrawals. In the last 50 years, efforts to diagnose, manage, and circumvent these obscure, iatrogenic diseases have resulted in the development of assays at all stages of a drugs lifespan. Indeed, this begins with intelligent lead compound selection/design to minimize the existence of deleterious chemical reactivity through exclusion of ominous structural moieties. Preclinical studies then investigate how compounds interact with biological systems, with emphasis placed on modeling immunological/toxicological liabilities. During clinical use, competent and accurate diagnoses are sought to effectively manage patients with such ailments, and pharmacovigilance datasets can be used for stratification of patient populations in order to optimise safety profiles. Herein, an overview of some of the in-vitro approaches to predict intrinsic immunogenicity of drugs and diagnose culprit drugs in allergic patients after exposure is detailed, with current perspectives and opportunities provided.
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Affiliation(s)
- Sean Hammond
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
- ApconiX, Alderley Park, Alderley Edge, United Kingdom
| | - Paul Thomson
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Xiaoli Meng
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Dean Naisbitt
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
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3
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Pak H, Michaux J, Huber F, Chong C, Stevenson BJ, Müller M, Coukos G, Bassani-Sternberg M. Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction. Mol Cell Proteomics 2021; 20:100080. [PMID: 33845167 PMCID: PMC8724634 DOI: 10.1016/j.mcpro.2021.100080] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/18/2021] [Accepted: 04/05/2021] [Indexed: 12/15/2022] Open
Abstract
Mass spectrometry (MS) is the state-of-the-art methodology for capturing the breadth and depth of the immunopeptidome across human leukocyte antigen (HLA) allotypes and cell types. The majority of studies in the immunopeptidomics field are discovery driven. Hence, data-dependent tandem MS (MS/MS) acquisition (DDA) is widely used, as it generates high-quality references of peptide fingerprints. However, DDA suffers from the stochastic selection of abundant ions that impairs sensitivity and reproducibility. In contrast, in data-independent acquisition (DIA), the systematic fragmentation and acquisition of all fragment ions within given isolation m/z windows yield a comprehensive map for a given sample. However, many DIA approaches commonly require generating comprehensive DDA-based spectrum libraries, which can become impractical for studying noncanonical and personalized neoantigens. Because the amount of HLA peptides eluted from biological samples such as small tissue biopsies is typically not sufficient for acquiring both meaningful DDA data necessary for generating comprehensive spectral libraries and DIA MS measurements, the implementation of DIA in the immunopeptidomics translational research domain has remained limited. We implemented a DIA immunopeptidomics workflow and assessed its sensitivity and accuracy by matching DIA data against libraries with growing complexity-from sample-specific libraries to libraries combining 2 to 40 different immunopeptidomics samples. Analyzing DIA immunopeptidomics data against a complex multi-HLA spectral library resulted in a two-fold increase in peptide identification compared with sample-specific library and in a three-fold increase compared with DDA measurements, yet with no detrimental effect on the specificity. Furthermore, we demonstrated the implementation of DIA for sensitive personalized neoantigen discovery through the analysis of DIA data with predicted MS/MS spectra of clinically relevant HLA ligands. We conclude that a comprehensive multi-HLA library for DIA approach in combination with MS/MS prediction is highly advantageous for clinical immunopeptidomics, especially when low amounts of biological samples are available.
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Affiliation(s)
- HuiSong Pak
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland
| | - Justine Michaux
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland
| | - Florian Huber
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland
| | - Chloe Chong
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland
| | | | - Markus Müller
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland.
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4
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Transcriptomic analysis reveals the role of a peptide derived from CRYAB on the CoCl 2-induced hypoxic HL-1 cardiomyocytes. J Thromb Thrombolysis 2020; 51:265-276. [PMID: 32621152 DOI: 10.1007/s11239-020-02117-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Acute myocardial infarction (AMI) is a life-threatening disease that often results in heart failure. CRYAB, a small heat shock protein, has been shown to have cardioprotective effects against oxidative stress-induced apoptosis in AMI. Previously, we purified a peptide derived from CRYAB (LEDQFFGEH), which we named PDFC. In this study, we determined the function of PDFC on HL-1 cardiomyocytes and explored the mechanism underlying its function. A hypoxic myocardiocyte cell line was generated by stimulation of HL-1 mouse cardiac muscle cells with different concentrations of CoCl2. Then, the hypoxic HL-1 cells were treated with the synthetic PDFC peptide, and cell proliferation, migration, and apoptosis were assessed to examine the effects of PDFC on HL-1 and hypoxic HL-1 cells. To examine the mechanism underlying the effects of PDFC on hypoxic cells, PDFC-treated hypoxic HL-1 cells were submitted for deep RNA sequencing. Finally, several differentially expressed genes in different pathways were selected for confirmation by RT-qPCR. Hypoxic myocardiocytes were generated by stimulating HL-1 cells with 800 µM CoCl2 for 24 h, which significantly upregulated HIF-1α. PDFC at 200 µg/ml showed the most positive effects on cell viability. Although hypoxic HL-1 cells and PDFC-treated hypoxic HL-1 cells both showed lower viability and migration and higher levels of apoptosis than untreated HL-1 cells, compared to hypoxic HL-1 cells, PDFC-treated hypoxic HL-1 cells showed higher viability and migration and lower apoptosis. The deep sequencing showed that 812 genes were upregulated and 1946 genes were downregulated. Among these differentially expressed genes, 699 of the upregulated genes and 1488 of the downregulated genes were protein-coding genes. Gene ontology and pathway enrichment analysis showed that the downregulated genes were dominant and that the PI3K-Akt pathway was located in the center of the network. A protein-protein interaction network was constructed, and 892 nodes were determined. In PDFC-treated hypoxic HL-1 cells, Fn1, Pik3r5, and Creb5 were downregulated, while Insr, Bcl2, Mapk14, and Pten were upregulated when compared to the levels in hypoxic HL-1 cells. In conclusion, this study reveals the significant bioactive effect of the CRYAB-derived peptide, PDFC on cardiomyocytes and the underlying mechanism.
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5
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Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E. The SysteMHC Atlas project. Nucleic Acids Res 2019; 46:D1237-D1247. [PMID: 28985418 PMCID: PMC5753376 DOI: 10.1093/nar/gkx664] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/21/2017] [Indexed: 11/25/2022] Open
Abstract
Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets. Here we present the SysteMHC Atlas (https://systemhcatlas.org), a public database that aims at collecting, organizing, sharing, visualizing and exploring immunopeptidomic data generated by MS. The Atlas includes raw mass spectrometer output files collected from several laboratories around the globe, a catalog of context-specific datasets of MHC class I and class II peptides, standardized MHC allele-specific peptide spectral libraries consisting of consensus spectra calculated from repeat measurements of the same peptide sequence, and links to other proteomics and immunology databases. The SysteMHC Atlas project was created and will be further expanded using a uniform and open computational pipeline that controls the quality of peptide identifications and peptide annotations. Thus, the SysteMHC Atlas disseminates quality controlled immunopeptidomic information to the public domain and serves as a community resource toward the generation of a high-quality comprehensive map of the human immunopeptidome and the support of consistent measurement of immunopeptidomic sample cohorts.
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Affiliation(s)
- Wenguang Shao
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Patrick G A Pedrioli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Witold Wolski
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | | | - Emanuel Schmid
- Scientific IT Services (SIS), ETH Zurich, Zurich 8093, Switzerland
| | - Juan A Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Mathieu Courcelles
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, H3T 1J4, Canada
| | - Heiko Schuster
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, 72076, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, 72076, Germany
| | - Daniel Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, 72076, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, 72076, Germany
| | - Fabio Marino
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne 1011, Switzerland.,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, The Netherlands.,Netherlands Proteomics Centre, Utrecht, 3584 CH, The Netherlands
| | | | - Kerrie Vaughan
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Krista E Meijgaarden
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Natalie Nieuwenhuizen
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin 10117, Germany
| | - Stefan H E Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin 10117, Germany
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | - John C Castle
- Vaccine Research and Translational Medicine, Agenus Switzerland Inc., 4157 Basel, Switzerland
| | - Alexey I Nesvizhskii
- Department of Pathology, BRCF Metabolomics Core, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Morten Nielsen
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, 1650, Argentina.,Department of Bio and Health Informatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | | | | | | | - Roman A Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Anders Jimmy Ytterberg
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-171 77, Sweden.,Rheumatology Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Anthony W Purcell
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, Australia
| | - Miguel Marcilla
- Proteomics Unit, Spanish National Biotechnology Centre, Madrid 28049, Spain
| | - Alberto Paradela
- Proteomics Unit, Spanish National Biotechnology Centre, Madrid 28049, Spain
| | - Qi Wang
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Nicola Ternette
- The Jenner Institute, Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, OX3 7FZ, UK
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Cécile A C M van Els
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3720 BA, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, The Netherlands.,Netherlands Proteomics Centre, Utrecht, 3584 CH, The Netherlands
| | - Gustavo A de Souza
- Centre for Immune Regulation, Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo 0372, Norway.,The Brain Institute, Universidade Federal do Rio Grande do Norte, 59056-450, Natal-RN, Brazil
| | - Ludvig M Sollid
- Centre for Immune Regulation, Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo 0372, Norway
| | - Arie Admon
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, 72076, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, 72076, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, 72076, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, 72076, Germany
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, H3T 1J4, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, H3T 1J4, Canada
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne 1011, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland.,Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
| | - Etienne Caron
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
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6
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Maes E, Oeyen E, Boonen K, Schildermans K, Mertens I, Pauwels P, Valkenborg D, Baggerman G. The challenges of peptidomics in complementing proteomics in a clinical context. MASS SPECTROMETRY REVIEWS 2019; 38:253-264. [PMID: 30372792 DOI: 10.1002/mas.21581] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
Naturally occurring peptides, including growth factors, hormones, and neurotransmitters, represent an important class of biomolecules and have crucial roles in human physiology. The study of these peptides in clinical samples is therefore as relevant as ever. Compared to more routine proteomics applications in clinical research, peptidomics research questions are more challenging and have special requirements with regard to sample handling, experimental design, and bioinformatics. In this review, we describe the issues that confront peptidomics in a clinical context. After these hurdles are (partially) overcome, peptidomics will be ready for a successful translation into medical practice.
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Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Food and Bio-Based Products, AgResearch Ltd., Lincoln, New Zealand
| | - Eline Oeyen
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Kurt Boonen
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Karin Schildermans
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Inge Mertens
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Patrick Pauwels
- Molecular Pathology Unit, Department of Pathology, Antwerp University Hospital, Edegem, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Center for Statistics, Hasselt University, Diepenbeek, Belgium
| | - Geert Baggerman
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
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7
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A tissue-based draft map of the murine MHC class I immunopeptidome. Sci Data 2018; 5:180157. [PMID: 30084848 PMCID: PMC6080492 DOI: 10.1038/sdata.2018.157] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/18/2018] [Indexed: 11/24/2022] Open
Abstract
The large array of peptides presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC class I immunopeptidome. Although the MHC class I immunopeptidome is ubiquitous in mammals and represents a critical component of the immune system, very little is known, in any species, about its composition across most tissues and organs in vivo. We applied mass spectrometry (MS) technologies to draft the first tissue-based atlas of the murine MHC class I immunopeptidome in health. Peptides were extracted from 19 normal tissues from C57BL/6 mice and prepared for MS injections, resulting in a total number of 28,448 high-confidence H2Db/Kb-associated peptides identified and annotated in the atlas. This atlas provides initial qualitative data to explore the tissue-specificity of the immunopeptidome and serves as a guide to identify potential tumor-associated antigens from various cancer models. Our data were shared via PRIDE (PXD008733), SysteMHC Atlas (SYSMHC00018) and SWATH Atlas. We anticipate that this unique dataset will be expanded in the future and will find wide applications in basic and translational immunology.
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8
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Zhu B, Dockrell HM, Ottenhoff THM, Evans TG, Zhang Y. Tuberculosis vaccines: Opportunities and challenges. Respirology 2018; 23:359-368. [PMID: 29341430 DOI: 10.1111/resp.13245] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/12/2017] [Accepted: 12/04/2017] [Indexed: 12/11/2022]
Abstract
Tuberculosis (TB) is a serious disease around the world. Bacillus Calmette-Guérin (BCG) is the only TB vaccine licensed for use in human beings, and is effective in protecting infants and children against severe miliary and meningeal TB. However, BCG's protective efficacy is variable in adults. Novel TB vaccine candidates being developed include whole-cell vaccines (recombinant BCG (rBCG), attenuated Mycobacterium tuberculosis, killed M. tuberculosis or Mycobacterium vaccae), adjuvanted protein subunit vaccines, viral vector-delivered subunit vaccines, plasmid DNA vaccines, RNA-based vaccines etc. At least 12 novel TB vaccine candidates are now in clinical trials, including killed M. vaccae, rBCG ΔureC::hly, adjuvanted fusion proteins M72 and H56 and viral vectored MVA85A. Unfortunately, in TB, there are no correlates of vaccine-induced protection, although cell-mediated immune responses such as interferon-gamma (IFN-γ) production are widely used to assess vaccine's immunogenicity. Recent studies suggested that central memory T cells and local secreted IgA correlated with protection against TB disease. Clinical TB vaccine efficacy trials should invest in identifying correlates of protection, and evaluate new TB biomarkers emerging from human and animal studies. Accumulating new knowledge on M. tuberculosis antigens and immune profiles correlating with protection or disease risk will be of great help in designing next generation of TB vaccines.
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Affiliation(s)
- Bingdong Zhu
- Lanzhou Center for Tuberculosis Research and Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Hazel M Dockrell
- Department of Immunology and Infection and Tuberculosis Centre, London School of Hygiene and Tropical Medicine, London, UK
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Ying Zhang
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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9
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Murphy JP, Konda P, Kowalewski DJ, Schuster H, Clements D, Kim Y, Cohen AM, Sharif T, Nielsen M, Stevanovic S, Lee PW, Gujar S. MHC-I Ligand Discovery Using Targeted Database Searches of Mass Spectrometry Data: Implications for T-Cell Immunotherapies. J Proteome Res 2017; 16:1806-1816. [PMID: 28244318 DOI: 10.1021/acs.jproteome.6b00971] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Class I major histocompatibility complex (MHC-I)-bound peptide ligands dictate the activation and specificity of CD8+ T cells and thus are important for devising T-cell immunotherapies. In recent times, advances in mass spectrometry (MS) have enabled the precise identification of these MHC-I peptides, wherein MS spectra are compared against a reference proteome. Unfortunately, matching these spectra to reference proteome databases is hindered by inflated search spaces attributed to a lack of enzyme restriction in the searches, limiting the efficiency with which MHC ligands are discovered. Here we offer a solution to this problem whereby we developed a targeted database search approach and accompanying tool SpectMHC, that is based on a priori-predicted MHC-I peptides. We first validated the approach using MS data from two different allotype-specific immunoprecipitates for the C57BL/6 mouse background. We then developed allotype-specific HLA databases to search previously published MS data sets of human peripheral blood mononuclear cells (PBMCs). This targeted search strategy improved peptide identifications for both mouse and human ligandomes by greater than 2-fold and is superior to traditional "no enzyme" searches of reference proteomes. Our targeted database search promises to uncover otherwise missed novel T-cell epitopes of therapeutic potential.
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Affiliation(s)
- J Patrick Murphy
- Department of Microbiology and Immunology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Prathyusha Konda
- Department of Microbiology and Immunology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Daniel J Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen , 72076 Tübingen, Germany.,Immatics Biotechnologies GmbH , 72076 Tübingen, Germany
| | - Heiko Schuster
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen , 72076 Tübingen, Germany.,Immatics Biotechnologies GmbH , 72076 Tübingen, Germany
| | - Derek Clements
- Department of Pathology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Youra Kim
- Department of Pathology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Alejandro M Cohen
- Proteomics Core Facility, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Tanveer Sharif
- Department of Microbiology and Immunology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark , 2800 Kongens Lyngby, Denmark
| | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen , 72076 Tübingen, Germany
| | - Patrick W Lee
- Department of Microbiology and Immunology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada.,Department of Pathology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Shashi Gujar
- Department of Microbiology and Immunology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada.,Department of Pathology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada.,Centre for Innovative and Collaborative Health Services Research, IWK Health Centre , Halifax, Nova Scotia B3K 6R8, Canada
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