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Lorente E, Martín-Galiano AJ, Kadosh DM, Barriga A, García-Arriaza J, Mir C, Esteban M, Admon A, López D. Abundance, Betweenness Centrality, Hydrophobicity, and Isoelectric Points Are Relevant Factors in the Processing of Parental Proteins of the HLA Class II Ligandome. J Proteome Res 2021; 21:164-171. [PMID: 34937342 DOI: 10.1021/acs.jproteome.1c00662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adaptive cellular and humoral immune responses to infectious agents require previous recognition of pathogenic peptides bound to human leukocyte antigen (HLA) class II molecules exposed on the surface of the professional antigen-presenting cells. Knowledge of how these peptide ligands are generated is essential to understand the basis for CD4+ T-cell-mediated immunity and tolerance. In this study, a high-throughput mass spectrometry analysis was used to identify more than 16,000 cell peptides bound to several HLA-DR and -DP class II molecules isolated from large amounts of uninfected and virus-infected human cells (ProteomeXchange accession: PXD028006). The analysis of the 1808 parental proteins containing HLA class II ligands revealed that these cell proteins were more acidic, abundant, and highly connected but less hydrophilic than non-parental proteomes. Therefore, the percentage of acidic residues was increased and hydroxyl and polar residues were decreased in the parental proteins for the HLA class II ligandomes versus the non-parental proteomes. This definition of the properties shared by parental proteins that constitute the source of the HLA class II ligandomes can serve as the basis for the development of bioinformatics tools to predict proteins that are most likely recognized by the immune system through the CD4+ helper T lymphocytes in both autoimmunity and infection.
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Affiliation(s)
- Elena Lorente
- Unidad de Presentación y Regulación Inmunes, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Antonio J Martín-Galiano
- Unidad de Infecciones Intrahospitalarias, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | | | - Alejandro Barriga
- Unidad de Presentación y Regulación Inmunes, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Juan García-Arriaza
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Carmen Mir
- Unidad de Presentación y Regulación Inmunes, Instituto de Salud Carlos III, Majadahonda, 28220 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
| | - Daniel López
- Unidad de Presentación y Regulación Inmunes, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
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Acid Stripping after Infection Improves the Detection of Viral HLA Class I Natural Ligands Identified by Mass Spectrometry. Int J Mol Sci 2021; 22:ijms221910503. [PMID: 34638844 PMCID: PMC8508920 DOI: 10.3390/ijms221910503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/23/2021] [Accepted: 09/26/2021] [Indexed: 12/26/2022] Open
Abstract
Identification of a natural human leukocyte antigen (HLA) ligandome is a key element to understand the cellular immune response. Advanced high throughput mass spectrometry analyses identify a relevant, but not complete, fraction of the many tens of thousands of self-peptides generated by antigen processing in live cells. In infected cells, in addition to this complex HLA ligandome, a minority of peptides from degradation of the few proteins encoded by the viral genome are also bound to HLA class I molecules. In this study, the standard immunopeptidomics strategy was modified to include the classical acid stripping treatment after virus infection to enrich the HLA ligandome in virus ligands. Complexes of HLA-B*27:05-bound peptide pools were isolated from vaccinia virus (VACV)-infected cells treated with acid stripping after virus infection. The HLA class I ligandome was identified using high throughput mass spectrometry analyses, yielding 37 and 51 natural peptides processed and presented untreated and after acid stripping treatment VACV-infected human cells, respectively. Most of these virus ligands were identified in both conditions, but exclusive VACV ligands detected by mass spectrometry detected on acid stripping treatment doubled the number of those identified in the untreated VACV-infected condition. Theoretical binding affinity prediction of the VACV HLA-B*27:05 ligands and acute antiviral T cell response characterization in the HLA transgenic mice model showed no differences between HLA ligands identified under the two conditions: untreated and under acid stripping condition. These findings indicated that acid stripping treatment could be useful to identify HLA class I ligands from virus-infected cells.
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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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Milewska A, Ner‐Kluza J, Dabrowska A, Bodzon‐Kulakowska A, Pyrc K, Suder P. MASS SPECTROMETRY IN VIROLOGICAL SCIENCES. MASS SPECTROMETRY REVIEWS 2020; 39:499-522. [PMID: 31876329 PMCID: PMC7228374 DOI: 10.1002/mas.21617] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/15/2019] [Indexed: 05/24/2023]
Abstract
Virology, as a branch of the life sciences, discovered mass spectrometry (MS) to be the pivotal tool around two decades ago. The technique unveiled the complex network of interactions between the living world of pro- and eukaryotes and viruses, which delivered "a piece of bad news wrapped in protein" as defined by Peter Medawar, Nobel Prize Laureate, in 1960. However, MS is constantly evolving, and novel approaches allow for a better understanding of interactions in this micro- and nanoworld. Currently, we can investigate the interplay between the virus and the cell by analyzing proteomes, interactomes, virus-cell interactions, and search for the compounds that build viral structures. In addition, by using MS, it is possible to look at the cell from the broader perspective and determine the role of viral infection on the scale of the organism, for example, monitoring the crosstalk between infected tissues and the immune system. In such a way, MS became one of the major tools for the modern virology, allowing us to see the infection in the context of the whole cell or the organism. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Aleksandra Milewska
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakowPoland
| | - Joanna Ner‐Kluza
- Department of Biochemistry and Neurobiology, Faculty of Materials Sciences and CeramicsAGH University of Science and TechnologyMickiewicza 30 Ave.30‐059KrakowPoland
| | - Agnieszka Dabrowska
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakowPoland
- Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian UniversityGronostajowa 730‐387KrakowPoland
| | - Anna Bodzon‐Kulakowska
- Department of Biochemistry and Neurobiology, Faculty of Materials Sciences and CeramicsAGH University of Science and TechnologyMickiewicza 30 Ave.30‐059KrakowPoland
| | - Krzysztof Pyrc
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakowPoland
| | - Piotr Suder
- Department of Biochemistry and Neurobiology, Faculty of Materials Sciences and CeramicsAGH University of Science and TechnologyMickiewicza 30 Ave.30‐059KrakowPoland
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Lorente E, Barnea E, Mir C, Admon A, López D. The HLA-DP peptide repertoire from human respiratory syncytial virus is focused on major structural proteins with the exception of the viral polymerase. J Proteomics 2020; 221:103759. [PMID: 32244010 DOI: 10.1016/j.jprot.2020.103759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/12/2020] [Accepted: 03/23/2020] [Indexed: 01/09/2023]
Abstract
The recognition by specific T helper cells of viral antigenic peptides complexed with HLA class II molecules exposed on the surface of antigen presenting cells is the first step of the complex cascade of immunological events that generates the protective cellular and humoral immune responses. The HLA class II-restricted helper immune response is critical in the control and the clearance of human respiratory syncytial virus (HRSV) infection, a pathogen with severe health risk in pediatric, immunocompromised and elderly populations. In this study, a mass spectrometry analysis was used to identify HRSV ligands bound to HLA-DP class II molecules present on the surface of HRSV-infected cells. Among the thousands of cellular peptides bound to HLA class II proteins in the virus-infected cells, sixty-four naturally processed viral ligands, most of them included in complex nested set of peptides, were identified bound to HLA-DP molecules. These viral ligands arose from five of six major structural HRSV proteins: attachment, fusion, matrix, nucleoprotein, and phosphoprotein. In contrast, no HLA-DP ligands were identified from polymerase protein, the largest HRSV protein that includes half of the viral proteome. These findings have important implications for analysis of the helper immune response as for antiviral vaccine design. SIGNIFICANCE: The existence of a supertype including five alleles that bind a peptide repertoire very similar make HLA-DP class II molecules an interesting target for the design of vaccines. Here, we analyze the HLA-DP-restricted peptide repertoire against the human respiratory syncytial virus, a pathogen that represents a high health risk in infected pediatric, immunocompromised and elderly populations. This repertoire is focused on major structural proteins with the exception of the viral polymerase.
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Affiliation(s)
- Elena Lorente
- Unidad de Presentación y Regulación Inmunes, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda (Madrid) 28220, Spain
| | - Eilon Barnea
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Carmen Mir
- Unidad de Presentación y Regulación Inmunes, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda (Madrid) 28220, Spain
| | - Arie Admon
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Daniel López
- Unidad de Presentación y Regulación Inmunes, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda (Madrid) 28220, Spain.
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Chen B, Khodadoust MS, Olsson N, Wagar LE, Fast E, Liu CL, Muftuoglu Y, Sworder BJ, Diehn M, Levy R, Davis MM, Elias JE, Altman RB, Alizadeh AA. Predicting HLA class II antigen presentation through integrated deep learning. Nat Biotechnol 2019; 37:1332-1343. [PMID: 31611695 PMCID: PMC7075463 DOI: 10.1038/s41587-019-0280-2] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/09/2019] [Indexed: 12/21/2022]
Abstract
Accurate prediction of antigen presentation by human leukocyte antigen (HLA) class II molecules would be valuable for vaccine development and cancer immunotherapies. Current computational methods trained on in vitro binding data are limited by insufficient training data and algorithmic constraints. Here we describe MARIA (major histocompatibility complex analysis with recurrent integrated architecture; https://maria.stanford.edu/ ), a multimodal recurrent neural network for predicting the likelihood of antigen presentation from a gene of interest in the context of specific HLA class II alleles. In addition to in vitro binding measurements, MARIA is trained on peptide HLA ligand sequences identified by mass spectrometry, expression levels of antigen genes and protease cleavage signatures. Because it leverages these diverse training data and our improved machine learning framework, MARIA (area under the curve = 0.89-0.92) outperformed existing methods in validation datasets. Across independent cancer neoantigen studies, peptides with high MARIA scores are more likely to elicit strong CD4+ T cell responses. MARIA allows identification of immunogenic epitopes in diverse cancers and autoimmune disease.
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Affiliation(s)
- Binbin Chen
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Michael S Khodadoust
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Niclas Olsson
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Lisa E Wagar
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Ethan Fast
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Nash, Vaduz, Liechtenstein
| | - Chih Long Liu
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Yagmur Muftuoglu
- Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Brian J Sworder
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Ronald Levy
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, Stanford University, Stanford, CA, USA
| | - Russ B Altman
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Ash A Alizadeh
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Center for Cancer Systems Biology, Stanford University, Stanford, CA, USA.
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7
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Lorente E, Barriga A, Barnea E, Palomo C, García-Arriaza J, Mir C, Esteban M, Admon A, López D. Immunoproteomic analysis of a Chikungunya poxvirus-based vaccine reveals high HLA class II immunoprevalence. PLoS Negl Trop Dis 2019; 13:e0007547. [PMID: 31276466 PMCID: PMC6636782 DOI: 10.1371/journal.pntd.0007547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/17/2019] [Accepted: 06/11/2019] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Efficient adaptive antiviral cellular and humoral immune responses require previous recognition of viral antigenic peptides bound to human leukocyte antigen (HLA) class I and II molecules, which are exposed on the surface of infected and antigen presenting cells, respectively. The HLA-restricted immune response to Chikungunya virus (CHIKV), a mosquito-borne Alphavirus of the Togaviridae family responsible for severe chronic polyarthralgia and polyarthritis, is largely unknown. METHODOLOGY/PRINCIPAL FINDINGS In this study, a high-throughput mass spectrometry analysis of complex HLA-bound peptide pools isolated from large amounts of human cells infected with a vaccinia virus (VACV) recombinant expressing CHIKV structural proteins was carried out. Twelve viral ligands from the CHIKV polyprotein naturally presented by different HLA-A, -B, and -C class I, and HLA-DR and -DP class II molecules were identified. CONCLUSIONS/SIGNIFICANCE The immunoprevalence of the HLA class II but not the HLA class I-restricted cellular immune response against the CHIKV structural polyprotein was greater than that against the VACV vector itself. In addition, most of the CHIKV HLA class I and II ligands detected by mass spectrometry are not conserved compared to its closely related O'nyong-nyong virus. These findings have clear implications for analysis of both cytotoxic and helper immune responses against CHIKV as well as for the future studies focused in the exacerbated T helper response linked to chronic musculoskeletal disorders in CHIKV patients.
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Affiliation(s)
- Elena Lorente
- Unidad de Presentación y Regulación Inmunes, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda (Madrid), Spain
| | - Alejandro Barriga
- Unidad de Presentación y Regulación Inmunes, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda (Madrid), Spain
| | - Eilon Barnea
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Concepción Palomo
- Unidad de Presentación y Regulación Inmunes, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda (Madrid), Spain
| | - Juan García-Arriaza
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Carmen Mir
- Unidad de Presentación y Regulación Inmunes, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda (Madrid), Spain
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Arie Admon
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Daniel López
- Unidad de Presentación y Regulación Inmunes, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda (Madrid), Spain
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