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Kim GJ, Elnaggar JH, Varnado M, Feehan AK, Tauzier D, Rose R, Lamers SL, Sevalia M, Nicholas N, Gravois E, Fort D, Crabtree JS, Miele L. A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population. Front Immunol 2024; 15:1357731. [PMID: 38784379 PMCID: PMC11112498 DOI: 10.3389/fimmu.2024.1357731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024] Open
Abstract
Long-term immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the identification of T-cell epitopes affecting host immunogenicity. In this computational study, we explored the CD8+ epitope diversity estimated in 27 of the most common HLA-A and HLA-B alleles, representing most of the United States population. Analysis of 16 SARS-CoV-2 variants [B.1, Alpha (B.1.1.7), five Delta (AY.100, AY.25, AY.3, AY.3.1, AY.44), and nine Omicron (BA.1, BA.1.1, BA.2, BA.4, BA.5, BQ.1, BQ.1.1, XBB.1, XBB.1.5)] in analyzed MHC class I alleles revealed that SARS-CoV-2 CD8+ epitope conservation was estimated at 87.6%-96.5% in spike (S), 92.5%-99.6% in membrane (M), and 94.6%-99% in nucleocapsid (N). As the virus mutated, an increasing proportion of S epitopes experienced reduced predicted binding affinity: 70% of Omicron BQ.1-XBB.1.5 S epitopes experienced decreased predicted binding, as compared with ~3% and ~15% in the earlier strains Delta AY.100-AY.44 and Omicron BA.1-BA.5, respectively. Additionally, we identified several novel candidate HLA alleles that may be more susceptible to severe disease, notably HLA-A*32:01, HLA-A*26:01, and HLA-B*53:01, and relatively protected from disease, such as HLA-A*31:01, HLA-B*40:01, HLA-B*44:03, and HLA-B*57:01. Our findings support the hypothesis that viral genetic variation affecting CD8 T-cell epitope immunogenicity contributes to determining the clinical severity of acute COVID-19. Achieving long-term COVID-19 immunity will require an understanding of the relationship between T cells, SARS-CoV-2 variants, and host MHC class I genetics. This project is one of the first to explore the SARS-CoV-2 CD8+ epitope diversity that putatively impacts much of the United States population.
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Affiliation(s)
- Grace J. Kim
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Jacob H. Elnaggar
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
- Department of Microbiology, Immunology, and Parasitology, Lousiana State University Health Sciences Center (LSUHSC), New Orleans, LA, United States
| | - Mallory Varnado
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Amy K. Feehan
- Research and Development, Oschner Medical Center, New Orleans, LA, United States
| | - Darlene Tauzier
- Department of Pathology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Rebecca Rose
- Research and Development, BioInfoExperts, LLC, Thibodaux, LA, United States
| | - Susanna L. Lamers
- Research and Development, BioInfoExperts, LLC, Thibodaux, LA, United States
| | - Maya Sevalia
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Najah Nicholas
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Elizabeth Gravois
- Department of Pathology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Daniel Fort
- Research and Development, Oschner Medical Center, New Orleans, LA, United States
| | - Judy S. Crabtree
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Lucio Miele
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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2
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Choi S, Paek E. pXg: Comprehensive Identification of Noncanonical MHC-I-Associated Peptides From De Novo Peptide Sequencing Using RNA-Seq Reads. Mol Cell Proteomics 2024; 23:100743. [PMID: 38403075 PMCID: PMC10979277 DOI: 10.1016/j.mcpro.2024.100743] [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: 07/12/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024] Open
Abstract
Discovering noncanonical peptides has been a common application of proteogenomics. Recent studies suggest that certain noncanonical peptides, known as noncanonical major histocompatibility complex-I (MHC-I)-associated peptides (ncMAPs), that bind to MHC-I may make good immunotherapeutic targets. De novo peptide sequencing is a great way to find ncMAPs since it can detect peptide sequences from their tandem mass spectra without using any sequence databases. However, this strategy has not been widely applied for ncMAP identification because there is not a good way to estimate its false-positive rates. In order to completely and accurately identify immunopeptides using de novo peptide sequencing, we describe a unique pipeline called proteomics X genomics. In contrast to current pipelines, it makes use of genomic data, RNA-Seq abundance and sequencing quality, in addition to proteomic features to increase the sensitivity and specificity of peptide identification. We show that the peptide-spectrum match quality and genetic traits have a clear relationship, showing that they can be utilized to evaluate peptide-spectrum matches. From 10 samples, we found 24,449 canonical MHC-I-associated peptides and 956 ncMAPs by using a target-decoy competition. Three hundred eighty-seven ncMAPs and 1611 canonical MHC-I-associated peptides were new identifications that had not yet been published. We discovered 11 ncMAPs produced from a squirrel monkey retrovirus in human cell lines in addition to the two ncMAPs originating from a complementarity determining region 3 in an antibody thanks to the unrestricted search space assumed by de novo sequencing. These entirely new identifications show that proteomics X genomics can make the most of de novo peptide sequencing's advantages and its potential use in the search for new immunotherapeutic targets.
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Affiliation(s)
- Seunghyuk Choi
- Department of Computer Science, Hanyang University, Seoul, Republic of Korea
| | - Eunok Paek
- Department of Computer Science, Hanyang University, Seoul, Republic of Korea; Institute for Artificial Intelligence Research, Hanyang University, Seoul, Republic of Korea.
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3
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Caobi A, Saeed M. Upping the ante: enhanced expression of interferon-antagonizing ORF6 and ORF9b proteins by SARS-CoV-2 variants of concern. Curr Opin Microbiol 2024; 79:102454. [PMID: 38518551 DOI: 10.1016/j.mib.2024.102454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/24/2024]
Abstract
SARS-CoV-2 exhibits a remarkable capability to subvert the host antiviral innate immune system. This adeptness is orchestrated by viral proteins, which initially attempt to obstruct the activation of the antiviral immune program and then act as a fail-safe mechanism to mitigate the downstream effects of the activated immune response. This dual strategy leads to delayed expression and enfeebled action of type-I and -III interferons at the infection site, enabling the virus to replicate extensively in the lungs and subsequently disseminate to other organs. Throughout the course of the COVID-19 pandemic, SARS-CoV-2 has undergone evolution, giving rise to several variants of concern, some with exceedingly higher transmission and virulence. These improved features have been linked, at least in part, to the heightened expression or activity of specific viral proteins involved in circumventing host defense mechanisms. In this review, we aim to provide a concise summary of two SARS-CoV-2 proteins, ORF6 and ORF9b, which provided selective advantage to certain variants, affecting their biology and pathogenesis.
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Affiliation(s)
- Allen Caobi
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Mohsan Saeed
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA.
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4
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Gomez-Zepeda D, Arnold-Schild D, Beyrle J, Declercq A, Gabriels R, Kumm E, Preikschat A, Łącki MK, Hirschler A, Rijal JB, Carapito C, Martens L, Distler U, Schild H, Tenzer S. Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS 2Rescore with MS 2PIP timsTOF fragmentation prediction model. Nat Commun 2024; 15:2288. [PMID: 38480730 PMCID: PMC10937930 DOI: 10.1038/s41467-024-46380-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we develop a highly sensitive method for identifying HLAIps using liquid chromatography-ion mobility-tandem mass spectrometry (LC-IMS-MS/MS). In addition, we train a timsTOF-specific peak intensity MS2PIP model for tryptic and non-tryptic peptides and implement it in MS2Rescore (v3) together with the CCS predictor from ionmob. The optimized method, Thunder-DDA-PASEF, semi-selectively fragments singly and multiply charged HLAIps based on their IMS and m/z. Moreover, the method employs the high sensitivity mode and extended IMS resolution with fewer MS/MS frames (300 ms TIMS ramp, 3 MS/MS frames), doubling the coverage of immunopeptidomics analyses, compared to the proteomics-tailored DDA-PASEF (100 ms TIMS ramp, 10 MS/MS frames). Additionally, rescoring boosts the HLAIps identification by 41.7% to 33%, resulting in 5738 HLAIps from as little as one million JY cell equivalents, and 14,516 HLAIps from 20 million. This enables in-depth profiling of HLAIps from diverse human cell lines and human plasma. Finally, profiling JY and Raji cells transfected to express the SARS-CoV-2 spike protein results in 16 spike HLAIps, thirteen of which have been reported to elicit immune responses in human patients.
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Affiliation(s)
- David Gomez-Zepeda
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany.
- Helmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, Division 191, Heidelberg, Germany.
| | - Danielle Arnold-Schild
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Julian Beyrle
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
- Helmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Division 191, Heidelberg, Germany
| | - Arthur Declercq
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Elena Kumm
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Annica Preikschat
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Mateusz Krzysztof Łącki
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Aurélie Hirschler
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS, ProFI - FR2048, Strasbourg, France
| | - Jeewan Babu Rijal
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS, ProFI - FR2048, Strasbourg, France
| | - Christine Carapito
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, University of Strasbourg, CNRS, ProFI - FR2048, Strasbourg, France
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Ute Distler
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Hansjörg Schild
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University, Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes-Gutenberg University, Mainz, Germany.
- Helmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, Division 191, Heidelberg, Germany.
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University, Mainz, Germany.
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5
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Omenn GS, Lane L, Overall CM, Lindskog C, Pineau C, Packer NH, Cristea IM, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Guo T, Van Eyk JE, Liu S, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. The 2023 Report on the Proteome from the HUPO Human Proteome Project. J Proteome Res 2024; 23:532-549. [PMID: 38232391 PMCID: PMC11026053 DOI: 10.1021/acs.jproteome.3c00591] [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] [Indexed: 01/19/2024]
Abstract
Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1-4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.
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Affiliation(s)
- Gilbert S. Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and University of Geneva, 1015 Lausanne, Switzerland
| | - Christopher M. Overall
- University of British Columbia, Vancouver, BC V6T 1Z4, Canada, Yonsei University Republic of Korea
| | | | - Charles Pineau
- University Rennes, Inserm U1085, Irset, 35042 Rennes, France
| | | | | | - Susan T. Weintraub
- University of Texas Health Science Center-San Antonio, San Antonio, Texas 78229-3900, United States
| | | | - Michael H. A. Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, United States
| | | | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory, Westlake University, Hangzhou 310024, Zhejiang Province, China
| | - Jennifer E. Van Eyk
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, 127 South San Vicente Boulevard, Pavilion, 9th Floor, Los Angeles, CA, 90048, United States
| | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, CA, 92093, United States
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology in ETH Zurich, 8092 Zurich, Switzerland
- University of Zurich, 8092 Zurich, Switzerland
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W. Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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6
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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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7
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Schrader M. Origins, Technological Advancement, and Applications of Peptidomics. Methods Mol Biol 2024; 2758:3-47. [PMID: 38549006 DOI: 10.1007/978-1-0716-3646-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Peptidomics is the comprehensive characterization of peptides from biological sources instead of heading for a few single peptides in former peptide research. Mass spectrometry allows to detect a multitude of peptides in complex mixtures and thus enables new strategies leading to peptidomics. The term was established in the year 2001, and up to now, this new field has grown to over 3000 publications. Analytical techniques originally developed for fast and comprehensive analysis of peptides in proteomics were specifically adjusted for peptidomics. Although it is thus closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. Fundamental technological advancements of peptidomics since have occurred in mass spectrometry and data processing, including quantification, and more slightly in separation technology. Different strategies and diverse sources of peptidomes are mentioned by numerous applications, such as discovery of neuropeptides and other bioactive peptides, including the use of biochemical assays. Furthermore, food and plant peptidomics are introduced similarly. Additionally, applications with a clinical focus are included, comprising biomarker discovery as well as immunopeptidomics. This overview extensively reviews recent methods, strategies, and applications including links to all other chapters of this book.
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Affiliation(s)
- Michael Schrader
- Department of Bioengineering Sciences, Weihenstephan-Tr. University of Applied Sciences, Freising, Germany.
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8
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Weissert R. Nervous system-related tropism of SARS-CoV-2 and autoimmunity in COVID-19 infection. Eur J Immunol 2024; 54:e2250230. [PMID: 37733584 DOI: 10.1002/eji.202250230] [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: 01/22/2023] [Revised: 08/05/2023] [Accepted: 09/20/2023] [Indexed: 09/23/2023]
Abstract
The effects of SARS-CoV-2 in COVID-19 on the nervous system are incompletely understood. SARS-CoV-2 can infect endothelial cells, neurons, astrocytes, and oligodendrocytes with consequences for the host. There are indications that infection of these CNS-resident cells may result in long-term effects, including emergence of neurodegenerative diseases. Indirect effects of infection with SARS-CoV-2 relate to the induction of autoimmune disease involving molecular mimicry or/and bystander activation of T- and B cells and emergence of autoantibodies against various self-antigens. Data obtained in preclinical models of coronavirus-induced disease gives important clues for the understanding of nervous system-related assault of SARS-CoV-2. The pathophysiology of long-COVID syndrome and post-COVID syndrome in which autoimmunity and immune dysregulation might be the driving forces are still incompletely understood. A better understanding of nervous-system-related immunity in COVID-19 might support the development of therapeutic approaches. In this review, the current understanding of SARS-CoV-2 tropism for the nervous system, the associated immune responses, and diseases are summarized. The data indicates that there is viral tropism of SARS-CoV-2 in the nervous system resulting in various disease conditions. Prevention of SARS-CoV-2 infection by means of vaccination is currently the best strategy for the prevention of subsequent tissue damage involving the nervous system.
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Affiliation(s)
- Robert Weissert
- Department of Neurology, University of Regensburg Hospital, Regensburg, Germany
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9
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Wahle M, Thielert M, Zwiebel M, Skowronek P, Zeng WF, Mann M. IMBAS-MS Discovers Organ-Specific HLA Peptide Patterns in Plasma. Mol Cell Proteomics 2024; 23:100689. [PMID: 38043703 PMCID: PMC10765297 DOI: 10.1016/j.mcpro.2023.100689] [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: 08/22/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023] Open
Abstract
Distinction of non-self from self is the major task of the immune system. Immunopeptidomics studies the peptide repertoire presented by the human leukocyte antigen (HLA) protein, usually on tissues. However, HLA peptides are also bound to plasma soluble HLA (sHLA), but little is known about their origin and potential for biomarker discovery in this readily available biofluid. Currently, immunopeptidomics is hampered by complex workflows and limited sensitivity, typically requiring several mL of plasma. Here, we take advantage of recent improvements in the throughput and sensitivity of mass spectrometry (MS)-based proteomics to develop a highly sensitive, automated, and economical workflow for HLA peptide analysis, termed Immunopeptidomics by Biotinylated Antibodies and Streptavidin (IMBAS). IMBAS-MS quantifies more than 5000 HLA class I peptides from only 200 μl of plasma, in just 30 min. Our technology revealed that the plasma immunopeptidome of healthy donors is remarkably stable throughout the year and strongly correlated between individuals with overlapping HLA types. Immunopeptides originating from diverse tissues, including the brain, are proportionately represented. We conclude that sHLAs are a promising avenue for immunology and potentially for precision oncology.
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Affiliation(s)
- Maria Wahle
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Marvin Thielert
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maximilian Zwiebel
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Patricia Skowronek
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wen-Feng Zeng
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
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10
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Farias TD, Brugiapaglia S, Croci S, Magistroni P, Curcio C, Zguro K, Fallerini C, Fava F, Pettini F, Kichula KM, Pollock NR, Font-Porterias N, Palmer WH, Marin WM, Baldassarri M, Bruttini M, Hollenbach JA, Hendricks AE, Meloni I, Novelli F, Renieri A, Furini S, Norman PJ, Amoroso A. HLA-DPB1*13:01 associates with enhanced, and KIR2DS4*001 with diminished protection from developing severe COVID-19. HLA 2024; 103:e15251. [PMID: 37850268 PMCID: PMC10873037 DOI: 10.1111/tan.15251] [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: 01/04/2023] [Revised: 08/22/2023] [Accepted: 09/26/2023] [Indexed: 10/19/2023]
Abstract
Extreme polymorphism of HLA and killer-cell immunoglobulin-like receptors (KIR) differentiates immune responses across individuals. Additional to T cell receptor interactions, subsets of HLA class I act as ligands for inhibitory and activating KIR, allowing natural killer (NK) cells to detect and kill infected cells. We investigated the impact of HLA and KIR polymorphism on the severity of COVID-19. High resolution HLA class I and II and KIR genotypes were determined from 403 non-hospitalized and 1575 hospitalized SARS-CoV-2 infected patients from Italy collected in 2020. We observed that possession of the activating KIR2DS4*001 allotype is associated with severe disease, requiring hospitalization (OR = 1.48, 95% CI 1.20-1.85, pc = 0.017), and this effect is greater in individuals homozygous for KIR2DS4*001 (OR = 3.74, 95% CI 1.75-9.29, pc = 0.003). We also observed the HLA class II allotype, HLA-DPB1*13:01 protects SARS-CoV-2 infected patients from severe disease (OR = 0.49, 95% CI 0.33-0.74, pc = 0.019). These association analyses were replicated using logistic regression with sex and age as covariates. Autoantibodies against IFN-α associated with COVID-19 severity were detected in 26% of 156 hospitalized patients tested. HLA-C*08:02 was more frequent in patients with IFN-α autoantibodies than those without, and KIR3DL1*01502 was only present in patients lacking IFN-α antibodies. These findings suggest that KIR and HLA polymorphism is integral in determining the clinical outcome following SARS-CoV-2 infection, by influencing the course both of innate and adaptive immunity.
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Affiliation(s)
- Ticiana D.J. Farias
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Silvia Brugiapaglia
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
- Laboratory of Tumor Immunology Center for Experimental Research and Medical Studies, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
| | - Susanna Croci
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Paola Magistroni
- Immunogenetics and Transplant Biology, Azienda Ospedaliera Universitaria, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
| | - Claudia Curcio
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
- Laboratory of Tumor Immunology Center for Experimental Research and Medical Studies, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
| | - Kristina Zguro
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Chiara Fallerini
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, 53100, Italy
| | - Francesco Pettini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, 53100, Italy
| | - Katherine M. Kichula
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Nicholas R. Pollock
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Neus Font-Porterias
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - William H. Palmer
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Wesley M. Marin
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Mirella Bruttini
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, 53100, Italy
| | - Jill A. Hollenbach
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Audrey E. Hendricks
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Mathematical and Statistical Sciences, and Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Ilaria Meloni
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Francesco Novelli
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
- Laboratory of Tumor Immunology Center for Experimental Research and Medical Studies, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
- Molecular Biotechnology Center, University of Turin, Turin, 10126, Italy
| | | | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, 53100, Italy
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, 53100, Italy
| | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Antonio Amoroso
- Immunogenetics and Transplant Biology, Azienda Ospedaliera Universitaria, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
- Department of Medical Sciences, University of Turin, Turin, 10126, Italy
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11
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Wang Y, Yang L, Tang K, Zhang Y, Zhang C, Zhang Y, Jin B, Zhang Y, Zhuang R, Ma Y. Ad5-nCoV Vaccination Could Induce HLA-E Restricted CD8 + T Cell Responses Specific for Epitopes on Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein. Viruses 2023; 16:52. [PMID: 38257752 PMCID: PMC10820189 DOI: 10.3390/v16010052] [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: 11/08/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
We evaluated cellular immune responses induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines in an immunized population based on HLA-E-restricted CD8+ T cell epitope identification. HLA-E-restricted SARS-CoV-2 CD8+ T cell nonamer peptides were predicted with software. An HLA-E-transfected K562 cell binding assay was used to screen for high-affinity peptides. IFN-γ enzyme-linked immunospot assays were used to identify HLA-E-restricted epitopes. An HLA-E/epitope tetramer was employed to detect the frequencies of epitope-specific CD8+ T cells. Four CD8+ T cell epitopes on the spike protein of SARS-CoV-2 restricted by both HLA-E*0101 and E*0103 were identified. HLA-E-restricted epitope-specific IFN-γ-secreting CD8+ T cell responses could be detected in individuals vaccinated with SARS-CoV-2 vaccines. Importantly, the frequencies of epitope-specific CD8+ T cells in Ad5-nCoV vaccinated individuals were higher than in individuals vaccinated with recombinant protein or inactivated vaccines. Moreover, the frequencies of epitope-specific CD8+ T cells could be maintained for at least 120 days after only one dose of Ad5-nCoV vaccine, while the frequencies of epitope-specific CD8+ T cells decreased in individuals after two doses of Ad5-nCoV vaccine. These findings may contribute to a more comprehensive evaluation of the protective effects of vaccines for SARS-CoV-2; meanwhile, they may provide information to characterize HLA-E-restricted CD8+ T cell immunity against SARS-CoV-2 infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ran Zhuang
- Department of Immunology, Air Force Medical University, Xi’an 710032, China; (Y.W.); (L.Y.); (K.T.); (Y.Z.); (C.Z.); (Y.Z.); (B.J.); (Y.Z.)
| | - Ying Ma
- Department of Immunology, Air Force Medical University, Xi’an 710032, China; (Y.W.); (L.Y.); (K.T.); (Y.Z.); (C.Z.); (Y.Z.); (B.J.); (Y.Z.)
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12
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Mayer RL, Mechtler K. Immunopeptidomics in the Era of Single-Cell Proteomics. BIOLOGY 2023; 12:1514. [PMID: 38132340 PMCID: PMC10740491 DOI: 10.3390/biology12121514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Immunopeptidomics, as the analysis of antigen peptides being presented to the immune system via major histocompatibility complexes (MHC), is being seen as an imperative tool for identifying epitopes for vaccine development to treat cancer and viral and bacterial infections as well as parasites. The field has made tremendous strides over the last 25 years but currently still faces challenges in sensitivity and throughput for widespread applications in personalized medicine and large vaccine development studies. Cutting-edge technological advancements in sample preparation, liquid chromatography as well as mass spectrometry, and data analysis, however, are currently transforming the field. This perspective showcases how the advent of single-cell proteomics has accelerated this transformation of immunopeptidomics in recent years and will pave the way for even more sensitive and higher-throughput immunopeptidomics analyses.
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Affiliation(s)
- Rupert L. Mayer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, 1030 Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
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13
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Wang L, Nicols A, Turtle L, Richter A, Duncan CJA, Dunachie SJ, Klenerman P, Payne RP. T cell immune memory after covid-19 and vaccination. BMJ MEDICINE 2023; 2:e000468. [PMID: 38027416 PMCID: PMC10668147 DOI: 10.1136/bmjmed-2022-000468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The T cell memory response is a crucial component of adaptive immunity responsible for limiting or preventing viral reinfection. T cell memory after infection with the SARS-CoV-2 virus or vaccination is broad, and spans multiple viral proteins and epitopes, about 20 in each individual. So far the T cell memory response is long lasting and provides a high level of cross reactivity and hence resistance to viral escape by variants of the SARS-CoV-2 virus, such as the omicron variant. All current vaccine regimens tested produce robust T cell memory responses, and heterologous regimens will probably enhance protective responses through increased breadth. T cell memory could have a major role in protecting against severe covid-19 disease through rapid viral clearance and early presentation of epitopes, and the presence of cross reactive T cells might enhance this protection. T cell memory is likely to provide ongoing protection against admission to hospital and death, and the development of a pan-coronovirus vaccine might future proof against new pandemic strains.
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Affiliation(s)
- Lulu Wang
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Alex Nicols
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Alex Richter
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
| | - Christopher JA Duncan
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Susanna J Dunachie
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University Faculty of Science, Bangkok, Thailand
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, Oxfordshire, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
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14
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Hvidt AK, Guo H, Andersen R, Lende SSF, Vibholm LK, Søgaard OS, Schleimann MH, Russell V, Cheung AMW, Paramithiotis E, Olesen R, Tolstrup M. Long-term humoral and cellular immunity after primary SARS-CoV-2 infection: a 20-month longitudinal study. BMC Immunol 2023; 24:45. [PMID: 37974069 PMCID: PMC10652616 DOI: 10.1186/s12865-023-00583-y] [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: 08/29/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND SARS-CoV-2 remains a world-wide health issue. SARS-CoV-2-specific immunity is induced upon both infection and vaccination. However, defining the long-term immune trajectory, especially after infection, is limited. In this study, we aimed to further the understanding of long-term SARS-CoV-2-specific immune response after infection. RESULTS We conducted a longitudinal cohort study among 93 SARS-CoV-2 recovered individuals. Immune responses were continuously monitored for up to 20 months after infection. The humoral responses were quantified by Spike- and Nucleocapsid-specific IgG levels. T cell responses to Spike- and non-Spike epitopes were examined using both intercellular cytokine staining (ICS) assay and Activation-Induced marker (AIM) assay with quantification of antigen-specific IFNγ production. During the 20 months follow-up period, Nucleocapsid-specific antibody levels and non-Spike-specific CD4 + and CD8 + T cell frequencies decreased in the blood. However, a majority of participants maintained a durable immune responses 20 months after infection: 59% of the participants were seropositive for Nucleocapsid-specific IgG, and more than 70% had persisting non-Spike-specific T cells. The Spike-specific response initially decreased but as participants were vaccinated against COVID-19, Spike-specific IgG levels and T cell frequencies were boosted reaching similar or higher levels compared to 1 month post-infection. The trajectory of infection-induced SARS-CoV-2-specific immunity decreases, but for the majority of participants it persists beyond 20 months. The T cell response displays a greater durability. Vaccination boosts Spike-specific immune responses to similar or higher levels as seen after primary infection. CONCLUSIONS For most participants, the response persists 20 months after infection, and the cellular response appears to be more long-lived compared to the circulating antibody levels. Vaccination boosts the S-specific response but does not affect the non-S-specific response. Together, these findings support the understanding of immune contraction, and with studies showing the immune levels required for protection, adds to the knowledge of durability of protection against future SARS-CoV-2.
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Affiliation(s)
- Astrid Korning Hvidt
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Rebecca Andersen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Stine Sofie Frank Lende
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Line Khalidan Vibholm
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Ole Schmeltz Søgaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Marianne Hoegsbjerg Schleimann
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Victoria Russell
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Angela Man-Wei Cheung
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Medicine, University Health Network, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | | | - Rikke Olesen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
| | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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15
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Meng W, Schreiber RD, Lichti CF. Recent advances in immunopeptidomic-based tumor neoantigen discovery. Adv Immunol 2023; 160:1-36. [PMID: 38042584 DOI: 10.1016/bs.ai.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2023]
Abstract
The role of aberrantly expressed proteins in tumors in driving immune-mediated control of cancer has been well documented for more than five decades. Today, we know that both aberrantly expressed normal proteins as well as mutant proteins (neoantigens) can function as tumor antigens in both humans and mice. Next-generation sequencing (NGS) and high-resolution mass spectrometry (MS) technologies have made significant advances since the early 2010s, enabling detection of rare but clinically relevant neoantigens recognized by T cells. MS profiling of tumor-specific immunopeptidomes remains the most direct method to identify mutant peptides bound to cellular MHC. However, the need for use of large numbers of cells or significant amounts of tumor tissue to achieve neoantigen detection has historically limited the application of MS. Newer, more sensitive MS technologies have recently demonstrated the capacities to detect neoantigens from fewer cells. Here, we highlight recent advancements in immunopeptidomics-based characterization of tumor-specific neoantigens. Various tumor antigen categories and neoantigen identification approaches are also discussed. Furthermore, we summarize recent reports that achieved successful tumor neoantigen detection by MS using a variety of starting materials, MS acquisition modes, and novel ion mobility devices.
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Affiliation(s)
- Wei Meng
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States
| | - Robert D Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States.
| | - Cheryl F Lichti
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States.
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16
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Yin S, Klaeger S, Chea VA, Carulli IP, Rachimi S, Black KE, Filbin M, Hariri LP, Knipe RS, Padera RF, Stevens JD, Lane WJ, Carr SA, Wu CJ, Kim EY, Keskin DB. Integrated Immunopeptidomic and Proteomic Analysis of COVID-19 lung biopsies. Front Immunol 2023; 14:1269335. [PMID: 37942334 PMCID: PMC10628763 DOI: 10.3389/fimmu.2023.1269335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
Introduction Severe respiratory illness is the most prominent manifestation of patients infected with SARS-CoV-2, and yet the molecular mechanisms underlying severe lung disease in COVID-19 affected patients still require elucidation. Human leukocyte antigen class I (HLA-I) expression is crucial for antigen presentation and the host's response to SARS-CoV-2. Methods To gain insights into the immune response and molecular pathways involved in severe lung disease, we performed immunopeptidomic and proteomic analyses of lung tissues recovered at four COVID-19 autopsy and six non-COVID-19 transplants. Results We found signals of tissue injury and regeneration in lung fibroblast and alveolar type I/II cells, resulting in the production of highly immunogenic self-antigens within the lungs of COVID-19 patients. We also identified immune activation of the M2c macrophage as the primary source of HLA-I presentation and immunogenicity in this context. Additionally, we identified 28 lung signatures that can serve as early plasma markers for predicting infection and severe COVID-19 disease. These protein signatures were predominantly expressed in macrophages and epithelial cells and were associated with complement and coagulation cascades. Discussion Our findings emphasize the significant role of macrophage-mediated immunity in the development of severe lung disease in COVID-19 patients.
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Affiliation(s)
- Shanye Yin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Vipheaviny A. Chea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Isabel P. Carulli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Suzanna Rachimi
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Katharine E. Black
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Michael Filbin
- Harvard Medical School, Boston, MA, United States
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Lida P. Hariri
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
- Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
| | - Rachel S. Knipe
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Robert F. Padera
- Harvard Medical School, Boston, MA, United States
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Jonathan D. Stevens
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - William J. Lane
- Harvard Medical School, Boston, MA, United States
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Steven A. Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Edy Yong Kim
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Derin B. Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, United States
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, United States
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17
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Khadri L, Ziraksaz MH, Barekzai AB, Ghauri B. T cell responses to SARS-CoV-2. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 202:183-217. [PMID: 38237986 DOI: 10.1016/bs.pmbts.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This chapter provides a comprehensive analysis of T cell responses in COVID-19, focusing on T cell differentiation, specificity, and functional characteristics during SARS-CoV-2 infection. The differentiation of T cells in COVID-19 is explored, highlighting the key factors that influence T cell fate and effector functions. The immunology of the spike protein, a critical component of SARS-CoV-2, is discussed in detail, emphasizing its role in driving T-cell responses. The cellular immune responses against SARS-CoV-2 during acute infection are examined, including the specificity, phenotype, and functional attributes of SARS-CoV-2-specific T-cell responses. Furthermore, the chapter explores T-cell cross-recognition against other human coronaviruses (HCoVs) and the mechanisms of immune regulation mediated by spike proteins. This includes the induction of regulation through the innate immune system, the activation of self-spike protein-cross-reactive regulatory T cells, and the impact of self-tolerance on the regulation of spike proteins. The chapter investigates T cell responses to self-spike proteins and their implications in disease. The role of spike proteins as immunological targets in the context of COVID-19 is examined, shedding light on potential therapeutic interventions and clinical trials in autoimmune diseases. In conclusion, this chapter provides a comprehensive understanding of T cell responses in COVID-19, highlighting their differentiation, immune regulation, and clinical implications. This knowledge contributes to the development of targeted immunotherapies, vaccine strategies, and diagnostic approaches for COVID-19 and other related diseases.
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Affiliation(s)
- Laiqha Khadri
- Department of Biotechnology, Immune Inspired, Bangalore.
| | | | | | - Baber Ghauri
- Department of Biotechnology, Immune Inspired, Bangalore
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18
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Chen R, Fulton KM, Tran A, Duque D, Kovalchik K, Caron E, Twine SM, Li J. Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2-Infected Calu-3 Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen Presentation. Mol Cell Proteomics 2023; 22:100645. [PMID: 37709257 PMCID: PMC10580047 DOI: 10.1016/j.mcpro.2023.100645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023] Open
Abstract
We present an integrated immunopeptidomics and proteomics study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection to comprehensively decipher the changes in host cells in response to viral infection. Immunopeptidomics analysis identified viral antigens presented by host cells through both class I and class II MHC system for recognition by the adaptive immune system. The host proteome changes were characterized by quantitative proteomics and glycoproteomics and from these data, the activation of toll-like receptor 3-interferon pathway was identified. Glycosylation analysis of human leukocyte antigen (HLA) proteins from the elution and flow-through of immunoprecipitation revealed that SARS-CoV-2 infection changed the glycosylation pattern of certain HLA alleles with different HLA alleles, showing distinct dynamic changes in relative abundance. The difference in the glycosylation and abundance of HLA alleles changed the number of strong binding antigens each allele presented, suggesting the impact of SARS-CoV-2 infection on antigen presentation is allele-specific. These results could be further exploited to explain the imbalanced response from innate and adaptive immune system in coronavirus disease 2019 cases, which would be helpful for the development of therapeutics and vaccine for coronavirus disease 2019 and preparation for future pandemic.
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Affiliation(s)
- Rui Chen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada.
| | - Kelly M Fulton
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Anh Tran
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Diana Duque
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Kevin Kovalchik
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Quebec, Canada
| | - Susan M Twine
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Jianjun Li
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada.
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19
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Zhang B, Bassani-Sternberg M. Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery. J Immunother Cancer 2023; 11:e007073. [PMID: 37899131 PMCID: PMC10619091 DOI: 10.1136/jitc-2023-007073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2023] [Indexed: 10/31/2023] Open
Abstract
Identification of tumor antigens presented by the human leucocyte antigen (HLA) molecules is essential for the design of effective and safe cancer immunotherapies that rely on T cell recognition and killing of tumor cells. Mass spectrometry (MS)-based immunopeptidomics enables high-throughput, direct identification of HLA-bound peptides from a variety of cell lines, tumor tissues, and healthy tissues. It involves immunoaffinity purification of HLA complexes followed by MS profiling of the extracted peptides using data-dependent acquisition, data-independent acquisition, or targeted approaches. By incorporating DNA, RNA, and ribosome sequencing data into immunopeptidomics data analysis, the proteogenomic approach provides a powerful means for identifying tumor antigens encoded within the canonical open reading frames of annotated coding genes and non-canonical tumor antigens derived from presumably non-coding regions of our genome. We discuss emerging computational challenges in immunopeptidomics data analysis and tumor antigen identification, highlighting key considerations in the proteogenomics-based approach, including accurate DNA, RNA and ribosomal sequencing data analysis, careful incorporation of predicted novel protein sequences into reference protein database, special quality control in MS data analysis due to the expanded and heterogeneous search space, cancer-specificity determination, and immunogenicity prediction. The advancements in technology and computation is continually enabling us to identify tumor antigens with higher sensitivity and accuracy, paving the way toward the development of more effective cancer immunotherapies.
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Affiliation(s)
- Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
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20
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Shkurnikov MY, Tonevitskaya SA, Stepanova EV, Slobodov SA. Immunocompetent Mice As a Model for Preclinical Studies of mRNA Vaccine Immunogenicity. DOKL BIOCHEM BIOPHYS 2023; 512:266-269. [PMID: 38093128 PMCID: PMC10719129 DOI: 10.1134/s160767292370045x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 12/17/2023]
Abstract
Conducting preclinical studies of mRNA vaccines is complicated by the lack of relevant animal models of the human immune system. Immunocompetent mice are widely used in biomedical research. However, critical differences in the genetics and immune system of mice and humans prevent the study of unique human immune responses in mice. Within the framework of this work, the possibility of modeling the cytotoxic T-cell response to mRNA vaccines encoding the S-protein of the SARS-CoV-2 virus was investigated. High-affinity peptides from S-protein were analyzed for the most frequent allelic variants of human MHC-I, two immunocompetent mouse lines (C57BL/6, BALB/c) and an outbred mouse model of IRC. The results of computer modeling have shown that mouse models can be used in preclinical studies of mRNA vaccines against SARS-CoV-2. Mouse MHC-I is able to present virus peptides that are highly affine for human MHC-I. Moreover, the immunogenicity of some of them has already been confirmed by examining blood samples from patients who have had COVID-19.
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Affiliation(s)
- M Yu Shkurnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - S A Tonevitskaya
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - E V Stepanova
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - S A Slobodov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
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21
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Weingarten-Gabbay S, Bauer MR, Stanton AC, Klaeger S, Verzani EK, López D, Clauser KR, Carr SA, Abelin JG, Rice CM, Sabeti PC. Pan-viral ORFs discovery using Massively Parallel Ribosome Profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559641. [PMID: 37808651 PMCID: PMC10557741 DOI: 10.1101/2023.09.26.559641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Unveiling the complete proteome of viruses is crucial to our understanding of the viral life cycle and interaction with the host. We developed Massively Parallel Ribosome Profiling (MPRP) to experimentally determine open reading frames (ORFs) in 20,170 designed oligonucleotides across 679 human-associated viral genomes. We identified 5,381 ORFs, including 4,208 non-canonical ORFs, and show successful detection of both annotated coding sequences (CDSs) and reported non-canonical ORFs. By examining immunopeptidome datasets of infected cells, we found class I human leukocyte antigen (HLA-I) peptides originating from non-canonical ORFs identified through MPRP. By inspecting ribosome occupancies on the 5'UTR and CDS regions of annotated viral genes, we identified hundreds of upstream ORFs (uORFs) that negatively regulate the synthesis of canonical viral proteins. The unprecedented source of viral ORFs across a wide range of viral families, including highly pathogenic viruses, expands the repertoire of vaccine targets and exposes new cis-regulatory sequences in viral genomes.
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22
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Staheli JP, Neal ML, Navare A, Mast FD, Aitchison JD. Predicting host-based, synthetic lethal antiviral targets from omics data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553430. [PMID: 37645861 PMCID: PMC10462099 DOI: 10.1101/2023.08.15.553430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Traditional antiviral therapies often have limited effectiveness due to toxicity and development of drug resistance. Host-based antivirals, while an alternative, may lead to non-specific effects. Recent evidence shows that virus-infected cells can be selectively eliminated by targeting synthetic lethal (SL) partners of proteins disrupted by viral infection. Thus, we hypothesized that genes depleted in CRISPR KO screens of virus-infected cells may be enriched in SL partners of proteins altered by infection. To investigate this, we established a computational pipeline predicting SL drug targets of viral infections. First, we identified SARS-CoV-2-induced changes in gene products via a large compendium of omics data. Second, we identified SL partners for each altered gene product. Last, we screened CRISPR KO data for SL partners required for cell viability in infected cells. Despite differences in virus-induced alterations detected by various omics data, they share many predicted SL targets, with significant enrichment in CRISPR KO-depleted datasets. Comparing data from SARS-CoV-2 and influenza infections, we found possible broad-spectrum, host-based antiviral SL targets. This suggests that CRISPR KO data are replete with common antiviral targets due to their SL relationship with virus-altered states and that such targets can be revealed from analysis of omics datasets and SL predictions.
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Affiliation(s)
- Jeannette P. Staheli
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
| | - Maxwell L. Neal
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
| | - Arti Navare
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
| | - Fred D. Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
| | - John D. Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, 98101, USA
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23
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Holly J, Yewdell JW. Game of Omes: ribosome profiling expands the MHC-I immunopeptidome. Curr Opin Immunol 2023; 83:102342. [PMID: 37247567 PMCID: PMC10524008 DOI: 10.1016/j.coi.2023.102342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Peptide ligands presented by cell-surface MHC class-I molecules enable T cells to eradicate intracellular pathogens and cancers. The presented peptide repertoire, the class-I immunopeptidome, is generated from each cell's translatome in a highly biased manner to avoid overrepresenting highly abundant translation products. The immunopeptidome can only be defined by mass spectrometry (MS). Here, we review recent advances in immunopeptidomics, focusing on using ribosome profiling as the optimal MS database to optimize the false- and failed-discovery rates and relate these findings to the contribution of defective ribosomal products and cellular quality control mechanisms to MHC class-I antigen processing and presentation.
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Affiliation(s)
- Jaroslav Holly
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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24
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Lerner A, Benzvi C, Vojdani A. SARS-CoV-2 Gut-Targeted Epitopes: Sequence Similarity and Cross-Reactivity Join Together for Molecular Mimicry. Biomedicines 2023; 11:1937. [PMID: 37509576 PMCID: PMC10376948 DOI: 10.3390/biomedicines11071937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/02/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The gastrointestinal tract can be heavily infected by SARS-CoV-2. Being an auto-immunogenic virus, SARS-CoV-2 represents an environmental factor that might play a role in gut-associated autoimmune diseases. However, molecular mimicry between the virus and the intestinal epitopes is under-investigated. The present study aims to elucidate sequence similarity between viral antigens and human enteric sequences, based on known cross-reactivity. SARS-CoV-2 epitopes that cross-react with human gut antigens were explored, and sequence alignment was performed against self-antigens implicated in enteric autoimmune conditions. Experimental SARS-CoV-2 epitopes were aggregated from the Immune Epitope Database (IEDB), while enteric antigens were obtained from the UniProt Knowledgebase. A Pairwise Local Alignment tool, EMBOSS Matcher, was employed for the similarity search. Sequence similarity and targeted cross-reactivity were depicted between 10 pairs of immunoreactive epitopes. Similar pairs were found in four viral proteins and seven enteric antigens related to ulcerative colitis, primary biliary cholangitis, celiac disease, and autoimmune hepatitis. Antibodies made against the viral proteins that were cross-reactive with human gut antigens are involved in several essential cellular functions. The relationship and contribution of those intestinal cross-reactive epitopes to SARS-CoV-2 or its potential contribution to gut auto-immuno-genesis are discussed.
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Affiliation(s)
- Aaron Lerner
- Chaim Sheba Medical Center, The Zabludowicz Research Center for Autoimmune Diseases, Ramat Gan 52621, Israel
- Research Department, Ariel University, Ariel 40700, Israel
| | - Carina Benzvi
- Chaim Sheba Medical Center, The Zabludowicz Research Center for Autoimmune Diseases, Ramat Gan 52621, Israel
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25
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Becerra-Artiles A, Nanaware PP, Muneeruddin K, Weaver GC, Shaffer SA, Calvo-Calle JM, Stern LJ. Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T-cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2. PLoS Pathog 2023; 19:e1011032. [PMID: 37498934 PMCID: PMC10409285 DOI: 10.1371/journal.ppat.1011032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/08/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023] Open
Abstract
Seasonal "common-cold" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but the T-cell response to seasonal coronaviruses remains largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal coronavirus OC43. We identified MHC-bound peptides derived from each of the viral structural proteins (spike, nucleoprotein, hemagglutinin-esterase, membrane, and envelope) as well as non-structural proteins nsp3, nsp5, nsp6, and nsp12. Eighty MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. Fewer and less abundant MHC-I bound OC43-derived peptides were observed, possibly due to MHC-I downregulation induced by OC43 infection. The MHC-II peptides elicited low-abundance recall T-cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T-cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T-cell lines. Among the validated epitopes, spike protein S903-917 presented by DPA1*01:03/DPB1*04:01 and S1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. Nucleoprotein N54-68 and hemagglutinin-esterase HE128-142 presented by DRB1*15:01 and HE259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow CD4 T-cell cross-reactivity after infection or vaccination, and to guide selection of epitopes for inclusion in pan-coronavirus vaccines.
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Affiliation(s)
- Aniuska Becerra-Artiles
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Padma P. Nanaware
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Khaja Muneeruddin
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury Massachusetts, United States of America
| | - Grant C. Weaver
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Scott A. Shaffer
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - J. Mauricio Calvo-Calle
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Lawrence J. Stern
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
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26
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Bruno PM, Timms RT, Abdelfattah NS, Leng Y, Lelis FJN, Wesemann DR, Yu XG, Elledge SJ. High-throughput, targeted MHC class I immunopeptidomics using a functional genetics screening platform. Nat Biotechnol 2023; 41:980-992. [PMID: 36593401 PMCID: PMC10314971 DOI: 10.1038/s41587-022-01566-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 10/13/2022] [Indexed: 01/03/2023]
Abstract
Identification of CD8+ T cell epitopes is critical for the development of immunotherapeutics. Existing methods for major histocompatibility complex class I (MHC class I) ligand discovery are time intensive, specialized and unable to interrogate specific proteins on a large scale. Here, we present EpiScan, which uses surface MHC class I levels as a readout for whether a genetically encoded peptide is an MHC class I ligand. Predetermined starting pools composed of >100,000 peptides can be designed using oligonucleotide synthesis, permitting large-scale MHC class I screening. We exploit this programmability of EpiScan to uncover an unappreciated role for cysteine that increases the number of predicted ligands by 9-21%, reveal affinity hierarchies by analysis of biased anchor peptide libraries and screen viral proteomes for MHC class I ligands. Using these data, we generate and iteratively refine peptide binding predictions to create EpiScan Predictor. EpiScan Predictor performs comparably to other state-of-the-art MHC class I peptide binding prediction algorithms without suffering from underrepresentation of cysteine-containing peptides. Thus, targeted immunopeptidomics using EpiScan will accelerate CD8+ T cell epitope discovery toward the goal of individual-specific immunotherapeutics.
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Affiliation(s)
- Peter M Bruno
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Richard T Timms
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Nouran S Abdelfattah
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Yumei Leng
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Felipe J N Lelis
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Duane R Wesemann
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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27
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Ternette N, Adamopoulou E, Purcell AW. How mass spectrometric interrogation of MHC class I ligandomes has advanced our understanding of immune responses to viruses. Semin Immunol 2023; 68:101780. [PMID: 37276649 DOI: 10.1016/j.smim.2023.101780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Affiliation(s)
- Nicola Ternette
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX37BN, UK.
| | - Eleni Adamopoulou
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX37BN, UK
| | - Anthony W Purcell
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
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28
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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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29
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Arieta CM, Xie YJ, Rothenberg DA, Diao H, Harjanto D, Meda S, Marquart K, Koenitzer B, Sciuto TE, Lobo A, Zuiani A, Krumm SA, Cadima Couto CI, Hein S, Heinen AP, Ziegenhals T, Liu-Lupo Y, Vogel AB, Srouji JR, Fesser S, Thanki K, Walzer K, Addona TA, Türeci Ö, Şahin U, Gaynor RB, Poran A. The T-cell-directed vaccine BNT162b4 encoding conserved non-spike antigens protects animals from severe SARS-CoV-2 infection. Cell 2023; 186:2392-2409.e21. [PMID: 37164012 PMCID: PMC10099181 DOI: 10.1016/j.cell.2023.04.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/12/2023] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
Abstract
T cell responses play an important role in protection against beta-coronavirus infections, including SARS-CoV-2, where they associate with decreased COVID-19 disease severity and duration. To enhance T cell immunity across epitopes infrequently altered in SARS-CoV-2 variants, we designed BNT162b4, an mRNA vaccine component that is intended to be combined with BNT162b2, the spike-protein-encoding vaccine. BNT162b4 encodes variant-conserved, immunogenic segments of the SARS-CoV-2 nucleocapsid, membrane, and ORF1ab proteins, targeting diverse HLA alleles. BNT162b4 elicits polyfunctional CD4+ and CD8+ T cell responses to diverse epitopes in animal models, alone or when co-administered with BNT162b2 while preserving spike-specific immunity. Importantly, we demonstrate that BNT162b4 protects hamsters from severe disease and reduces viral titers following challenge with viral variants. These data suggest that a combination of BNT162b2 and BNT162b4 could reduce COVID-19 disease severity and duration caused by circulating or future variants. BNT162b4 is currently being clinically evaluated in combination with the BA.4/BA.5 Omicron-updated bivalent BNT162b2 (NCT05541861).
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Affiliation(s)
| | - Yushu Joy Xie
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | | | - Huitian Diao
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | - Dewi Harjanto
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | - Shirisha Meda
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | | | | | | | | | - Adam Zuiani
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | | | | | | | | | | | | | | | - John R Srouji
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA
| | | | | | | | | | - Özlem Türeci
- BioNTech SE, An der Goldgrube 12, 55131 Mainz, Germany; HI-TRON - Helmholtz Institute for Translational Oncology Mainz by DKFZ, Obere Zahlbacherstr. 63, 55131 Mainz, Germany
| | - Uğur Şahin
- BioNTech SE, An der Goldgrube 12, 55131 Mainz, Germany; TRON gGmbH - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Freiligrathstraße 12, 55131 Mainz, Germany
| | | | - Asaf Poran
- BioNTech US, 40 Erie Street, Cambridge, MA 02139, USA.
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30
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Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
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Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
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31
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Abelin JG, Bergstrom EJ, Rivera KD, Taylor HB, Klaeger S, Xu C, Verzani EK, Jackson White C, Woldemichael HB, Virshup M, Olive ME, Maynard M, Vartany SA, Allen JD, Phulphagar K, Harry Kane M, Rachimi S, Mani DR, Gillette MA, Satpathy S, Clauser KR, Udeshi ND, Carr SA. Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues. Nat Commun 2023; 14:1851. [PMID: 37012232 PMCID: PMC10070353 DOI: 10.1038/s41467-023-37547-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Serial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights into changes in protein expression, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and treatment. However, ubiquitylome and HLA peptidome data collection used to understand protein degradation and antigen presentation have not together been serialized, and instead require separate samples for parallel processing using distinct protocols. Here we present MONTE, a highly sensitive multi-omic native tissue enrichment workflow, that enables serial, deep-scale analysis of HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome, and acetylome from the same tissue sample. We demonstrate that the depth of coverage and quantitative precision of each 'ome is not compromised by serialization, and the addition of HLA immunopeptidomics enables the identification of peptides derived from cancer/testis antigens and patient specific neoantigens. We evaluate the technical feasibility of the MONTE workflow using a small cohort of patient lung adenocarcinoma tumors.
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Affiliation(s)
- Jennifer G Abelin
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
| | - Erik J Bergstrom
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Keith D Rivera
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Hannah B Taylor
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Susan Klaeger
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Charles Xu
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Eva K Verzani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - C Jackson White
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Hilina B Woldemichael
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Maya Virshup
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Meagan E Olive
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Myranda Maynard
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Stephanie A Vartany
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Joseph D Allen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Kshiti Phulphagar
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - M Harry Kane
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Suzanna Rachimi
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
- Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Namrata D Udeshi
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
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Yang G, Wang J, Sun P, Qin J, Yang X, Chen D, Zhang Y, Zhong N, Wang Z. SARS-CoV-2 epitope-specific T cells: Immunity response feature, TCR repertoire characteristics and cross-reactivity. Front Immunol 2023; 14:1146196. [PMID: 36969254 PMCID: PMC10036809 DOI: 10.3389/fimmu.2023.1146196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
The devastating COVID-19 pandemic caused by SARS-CoV-2 and multiple variants or subvariants remains an ongoing global challenge. SARS-CoV-2-specific T cell responses play a critical role in early virus clearance, disease severity control, limiting the viral transmission and underpinning COVID-19 vaccine efficacy. Studies estimated broad and robust T cell responses in each individual recognized at least 30 to 40 SARS-CoV-2 antigen epitopes and associated with COVID-19 clinical outcome. Several key immunodominant viral proteome epitopes, including S protein- and non-S protein-derived epitopes, may primarily induce potent and long-lasting antiviral protective effects. In this review, we summarized the immune response features of immunodominant epitope-specific T cells targeting different SRAS-CoV-2 proteome structures after infection and vaccination, including abundance, magnitude, frequency, phenotypic features and response kinetics. Further, we analyzed the epitopes immunodominance hierarchy in combination with multiple epitope-specific T cell attributes and TCR repertoires characteristics, and discussed the significant implications of cross-reactive T cells toward HCoVs, SRAS-CoV-2 and variants of concern, especially Omicron. This review may be essential for mapping the landscape of T cell responses toward SARS-CoV-2 and optimizing the current vaccine strategy.
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Affiliation(s)
- Gang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Junxiang Wang
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Ping Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jian Qin
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Xiaoyun Yang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Daxiang Chen
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Nanshan Zhong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Zhongfang Wang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
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Shapiro IE, Bassani-Sternberg M. The impact of immunopeptidomics: From basic research to clinical implementation. Semin Immunol 2023; 66:101727. [PMID: 36764021 DOI: 10.1016/j.smim.2023.101727] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/10/2023]
Abstract
The immunopeptidome is the set of peptides presented by the major histocompatibility complex (MHC) molecules, in humans also known as the human leukocyte antigen (HLA), on the surface of cells that mediate T-cell immunosurveillance. The immunopeptidome is a sampling of the cellular proteome and hence it contains information about the health state of cells. The peptide repertoire is influenced by intra- and extra-cellular perturbations - such as in the case of drug exposure, infection, or oncogenic transformation. Immunopeptidomics is the bioanalytical method by which the presented peptides are extracted from biological samples and analyzed by high-performance liquid chromatography coupled to tandem mass spectrometry (MS), resulting in a deep qualitative and quantitative snapshot of the immunopeptidome. In this review, we discuss published immunopeptidomics studies from recent years, grouped into three main domains: i) basic, ii) pre-clinical and iii) clinical research and applications. We review selected fundamental immunopeptidomics studies on the antigen processing and presentation machinery, on HLA restriction and studies that advanced our understanding of various diseases, and how exploration of the antigenic landscape allowed immune targeting at the pre-clinical stage, paving the way to pioneering exploratory clinical trials where immunopeptidomics is directly implemented in the conception of innovative treatments for cancer patients.
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Affiliation(s)
- Ilja E Shapiro
- Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland; Agora Cancer Research Centre, 1011 Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland; Agora Cancer Research Centre, 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland.
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34
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Schroeder SM, Nelde A, Walz JS. Viral T-cell epitopes - Identification, characterization and clinical application. Semin Immunol 2023; 66:101725. [PMID: 36706520 DOI: 10.1016/j.smim.2023.101725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023]
Abstract
T-cell immunity, mediated by CD4+ and CD8+ T cells, represents a cornerstone in the control of viral infections. Virus-derived T-cell epitopes are represented by human leukocyte antigen (HLA)-presented viral peptides on the surface of virus-infected cells. They are the prerequisite for the recognition of infected cells by T cells. Knowledge of viral T-cell epitopes provides on the one hand a diagnostic tool to decipher protective T-cell immune responses in the human population and on the other hand various prophylactic and therapeutic options including vaccination approaches and the transfer of virus-specific T cells. Such approaches have already been proven to be effective against various viral infections, particularly in immunocompromised patients lacking sufficient humoral, antibody-based immune response. This review provides an overview on the state of the art as well as current studies regarding the identification and characterization of viral T-cell epitopes and approaches of clinical application. In the first chapter in silico prediction tools and direct, mass spectrometry-based identification of viral T-cell epitopes is compared. The second chapter provides an overview of commonly used assays for further characterization of T-cell responses and phenotypes. The final chapter presents an overview of clinical application of viral T-cell epitopes with a focus on human immunodeficiency virus (HIV), human cytomegalovirus (HCMV) and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), being representatives of relevant viruses.
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Affiliation(s)
- Sarah M Schroeder
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany; Department for Otorhinolaryngology, Head, and Neck Surgery, University Hospital Tübingen, Tübingen, Germany; Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany; Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany; Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany; Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.
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Abd El-Baky N, Amara AA, Redwan EM. HLA-I and HLA-II Peptidomes of SARS-CoV-2: A Review. Vaccines (Basel) 2023; 11:548. [PMID: 36992131 PMCID: PMC10058130 DOI: 10.3390/vaccines11030548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/18/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
The adaptive (T-cell-mediated) immune response is a key player in determining the clinical outcome, in addition to neutralizing antibodies, after SARS-CoV-2 infection, as well as supporting the efficacy of vaccines. T cells recognize viral-derived peptides bound to major histocompatibility complexes (MHCs) so that they initiate cell-mediated immunity against SARS-CoV-2 infection or can support developing a high-affinity antibody response. SARS-CoV-2-derived peptides bound to MHCs are characterized via bioinformatics or mass spectrometry on the whole proteome scale, named immunopeptidomics. They can identify potential vaccine targets or therapeutic approaches for SARS-CoV-2 or else may reveal the heterogeneity of clinical outcomes. SARS-CoV-2 epitopes that are naturally processed and presented on the human leukocyte antigen class I (HLA-I) and class II (HLA-II) were identified for immunopeptidomics. Most of the identified SARS-CoV-2 epitopes were canonical and out-of-frame peptides derived from spike and nucleocapsid proteins, followed by membrane proteins, whereby many of which are not caught by existing vaccines and could elicit effective responses of T cells in vivo. This review addresses the detection of SARS-CoV-2 viral epitopes on HLA-I and HLA-II using bioinformatics prediction and mass spectrometry (HLA peptidomics). Profiling the HLA-I and HLA-II peptidomes of SARS-CoV-2 is also detailed.
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Affiliation(s)
- Nawal Abd El-Baky
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
| | - Amro A. Amara
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
| | - Elrashdy M. Redwan
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah P.O. Box 80203, Saudi Arabia
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He T, Zhang F, Zhang J, Wei S, Ning J, Yuan H, Li B. UreB immunodominant epitope-specific CD8 + T-cell responses were beneficial in reducing gastric symptoms in Helicobacter pylori-infected individuals. Helicobacter 2023; 28:e12959. [PMID: 36828665 DOI: 10.1111/hel.12959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/26/2023]
Abstract
BACKGROUND AND AIMS Although Helicobacter pylori is recognized as an extracellular infection bacterium, it can lead to an increase in the number of CD8+ T cells after infection. At present, the characteristics of H. pylori antigen-specific CD8+ T cells and the epitope response have not been elucidated. This study was focused on putative protective antigen UreB to detect specific CD8+ T-cell responses in vitro and screen for predominant response epitopes. METHODS The PBMCs collected from H. pylori-infected individuals were stimulated by UreB peptide pools in vitro to identify the immunodominant CD8+ T-cell epitopes. Furthermore, their HLA restriction characteristics were detected accordingly by NGS. Finally, the relationship between immunodominant responses and appearance of gastric symptoms after H. pylori infection was conducted. RESULTS UreB-specific CD8+ T-cell responses were detected in H. pylori-infected individuals. Three of UreB dominant epitopes (A-2 (UreB443-451 : GVKPNMIIK), B-4 (UreB420-428 : SEYVGSVEV), and C-1 (UreB5-13 : SRKEYVSMY)) were firstly identified and mainly presented by HLA-A*1101, HLA-B*4001 and HLA-C*0702 alleles, respectively. C-1 responses were mostly occurred in H. pylori-infected subjects without gastric symptoms and may alleviate the degree of gastric inflammation. CONCLUSIONS The UreB dominant epitope-specific CD8+ T-cell response was closely related to the gastric symptoms after H. pylori infection, and the C-1 (UreB5-13 ) dominant peptides may be protective epitopes.
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Affiliation(s)
- Taojun He
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Fang Zhang
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Jin Zhang
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Shanshan Wei
- Department of Digestive Endoscopy Center, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Jie Ning
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Hanmei Yuan
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Bin Li
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
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Lin F, Lin X, Fu B, Xiong Y, Zaky MY, Wu H. Functional studies of HLA and its role in SARS-CoV-2: Stimulating T cell response and vaccine development. Life Sci 2023; 315:121374. [PMID: 36621539 PMCID: PMC9815883 DOI: 10.1016/j.lfs.2023.121374] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
In the biological immune process, the major histocompatibility complex (MHC) plays an indispensable role in the expression of HLA molecules in the human body when viral infection activates the T-cell response to remove the virus. Since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in 2019, how to address and prevent SARS-CoV-2 has become a common problem facing all mankind. The T-cell immune response activated by MHC peptides is a way to construct a defense line and reduce the transmission and harm of the virus. Presentation of SARS-CoV-2 antigen is associated with different types of HLA phenotypes, and different HLA phenotypes induce different immune responses. The prediction of SARS-CoV-2 mutation information and the design of vaccines based on HLAs can effectively activate autoimmunity and cope with virus mutations, which can provide some references for the prevention and treatment of SARS-CoV-2.
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Affiliation(s)
- Feng Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Xiaoyuan Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Mohamed Y Zaky
- Molecular Physiology Division, Zoology Department, Faculty of Science, Beni-Suef University, P.O. Box 62521, Beni-Suef, Egypt; Department of Oncology and Department of Biomedical and Clinical Science, Faculty of Medicine, Linköping University, Sweden
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
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Frasca L, Ocone G, Palazzo R. Safety of COVID-19 Vaccines in Patients with Autoimmune Diseases, in Patients with Cardiac Issues, and in the Healthy Population. Pathogens 2023; 12:pathogens12020233. [PMID: 36839505 PMCID: PMC9964607 DOI: 10.3390/pathogens12020233] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) has been a challenge for the whole world since the beginning of 2020, and COVID-19 vaccines were considered crucial for disease eradication. Instead of producing classic vaccines, some companies pointed to develop products that mainly function by inducing, into the host, the production of the antigenic protein of SARS-CoV-2 called Spike, injecting an instruction based on RNA or a DNA sequence. Here, we aim to give an overview of the safety profile and the actual known adverse effects of these products in relationship with their mechanism of action. We discuss the use and safety of these products in at-risk people, especially those with autoimmune diseases or with previously reported myocarditis, but also in the general population. We debate the real necessity of administering these products with unclear long-term effects to at-risk people with autoimmune conditions, as well as to healthy people, at the time of omicron variants. This, considering the existence of therapeutic interventions, much more clearly assessed at present compared to the past, and the relatively lower aggressive nature of the new viral variants.
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Meyer S, Blaas I, Bollineni RC, Delic-Sarac M, Tran TT, Knetter C, Dai KZ, Madssen TS, Vaage JT, Gustavsen A, Yang W, Nissen-Meyer LSH, Douvlataniotis K, Laos M, Nielsen MM, Thiede B, Søraas A, Lund-Johansen F, Rustad EH, Olweus J. Prevalent and immunodominant CD8 T cell epitopes are conserved in SARS-CoV-2 variants. Cell Rep 2023; 42:111995. [PMID: 36656713 PMCID: PMC9826989 DOI: 10.1016/j.celrep.2023.111995] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
The emergence of SARS-CoV-2 variants of concern (VOC) is driven by mutations that mediate escape from neutralizing antibodies. There is also evidence that mutations can cause loss of T cell epitopes. However, studies on viral escape from T cell immunity have been hampered by uncertain estimates of epitope prevalence. Here, we map and quantify CD8 T cell responses to SARS-CoV-2-specific minimal epitopes in blood drawn from April to June 2020 from 83 COVID-19 convalescents. Among 37 HLA ligands eluted from five prevalent alleles and an additional 86 predicted binders, we identify 29 epitopes with an immunoprevalence ranging from 3% to 100% among individuals expressing the relevant HLA allele. Mutations in VOC are reported in 10.3% of the epitopes, while 20.6% of the non-immunogenic peptides are mutated in VOC. The nine most prevalent epitopes are conserved in VOC. Thus, comprehensive mapping of epitope prevalence does not provide evidence that mutations in VOC are driven by escape of T cell immunity.
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Affiliation(s)
- Saskia Meyer
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Isaac Blaas
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Ravi Chand Bollineni
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Marina Delic-Sarac
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Trung T. Tran
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - Cathrine Knetter
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Ke-Zheng Dai
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | | | - John T. Vaage
- Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - Alice Gustavsen
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - Weiwen Yang
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | | | - Karolos Douvlataniotis
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Maarja Laos
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Morten Milek Nielsen
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Bernd Thiede
- Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | - Arne Søraas
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Fridtjof Lund-Johansen
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway,ImmunoLingo Convergence Center, University of Oslo, 0372 Oslo, Norway
| | - Even H. Rustad
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Corresponding author
| | - Johanna Olweus
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Corresponding author
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40
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Jin X, Liu X, Shen C. A systemic review of T-cell epitopes defined from the proteome of SARS-CoV-2. Virus Res 2023; 324:199024. [PMID: 36526016 PMCID: PMC9757803 DOI: 10.1016/j.virusres.2022.199024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection remains in a global pandemic, and no eradicative therapy is currently available. Host T cells have been shown to play a crucial role in the antiviral immune protection and pathology in Coronavirus disease 2019 (COVID-19) patients; thus, identifying sufficient T-cell epitopes from the SARS-CoV-2 proteome can contribute greatly to the development of T-cell epitope vaccines and the precise evaluation of host SARS-CoV-2-specific cellular immunity. This review presents a comprehensive map of T-cell epitopes functionally validated from SARS-CoV-2 antigens, the human leukocyte antigen (HLA) supertypes to present these epitopes, and the strategies to screen and identify T-cell epitopes. To the best of our knowledge, a total of 1349 CD8+ T-cell epitopes and 790 CD4+ T-cell epitopes have been defined by functional experiments thus far, but most are presented by approximately twenty common HLA supertypes, such as HLA-A0201, A2402, B0702, DR15, DR7 and DR11 molecules, and 74-80% of the T-cell epitopes are derived from S protein and nonstructural protein. These data provide useful insight into the development of vaccines and specific T-cell detection systems. However, the currently defined T-cell epitope repertoire cannot cover the HLA polymorphism of major populations in an indicated geographic region. More research is needed to depict an overall landscape of T-cell epitopes, which covers the overall SARS-CoV-2 proteome and global patients.
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Affiliation(s)
- Xiaoxiao Jin
- Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, China 225002; Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009
| | - Xiaotao Liu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009
| | - Chuanlai Shen
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009.
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41
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Yiang GT, Wu CC, Lu CL, Hu WC, Tsai YJ, Huang YM, Su WL, Lu KC. Endoplasmic Reticulum Stress in Elderly Patients with COVID-19: Potential of Melatonin Treatment. Viruses 2023; 15:156. [PMID: 36680196 PMCID: PMC9863214 DOI: 10.3390/v15010156] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
Aging processes, including immunosenescence, inflammation, inflammasome formation, genomic instability, telomeric attrition, and altered autophagy, are involved in viral infections and they may contribute to increased pathophysiological responses to the SARS-CoV-2 infection in the elderly; this poses additional risks of accelerated aging, which could be found even after recovery. Aging is associated with oxidative damage. Moreover, SARS-CoV-2 infections may increase the production of reactive oxygen species and such infections will disturb the Ca++ balance via an endoplasmic reticulum (ER) stress-mediated unfolded protein response. Although vaccine development and anti-inflammation therapy lower the severity of COVID-19, the prevalence and mortality rates are still alarming in some countries worldwide. In this review, we describe the involvement of viral proteins in activating ER stress transducers and their downstream signals and in inducing inflammation and inflammasome formation. Furthermore, we propose the potential of melatonin as an ER stress modulator, owing to its antioxidant, anti-inflammatory, and immunoregulatory effects in viral infections. Considering its strong safety profile, we suggest that additive melatonin supplementation in the elderly could be beneficial in treating COVID-19.
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Affiliation(s)
- Giou-Teng Yiang
- Department of Emergency Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan
- School of Medicine, Tzu Chi University, Hualien 970, Taiwan
| | - Chia-Chao Wu
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei 114, Taiwan
| | - Chien-Lin Lu
- Division of Nephrology, Department of Medicine, Fu Jen Catholic University Hospital, School of Medicine, Fu Jen Catholic University, New Taipei 24352, Taiwan
| | - Wan-Chung Hu
- Department of Clinical Pathology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan
| | - Yi-Ju Tsai
- Graduate Institute of Biomedical and Pharmaceutical Science, College of Medicine, Fu Jen Catholic University, New Taipei 243, Taiwan
| | - Yiao-Mien Huang
- Department of Dentistry, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan
| | - Wen-Lin Su
- School of Medicine, Tzu Chi University, Hualien 970, Taiwan
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
- Division of Nephrology, Department of Medicine, Fu Jen Catholic University Hospital, School of Medicine, Fu Jen Catholic University, New Taipei 24352, Taiwan
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei 231, Taiwan
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SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to down-regulate MHC-I surface expression. Proc Natl Acad Sci U S A 2023; 120:e2208525120. [PMID: 36574644 PMCID: PMC9910621 DOI: 10.1073/pnas.2208525120] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Major histocompatibility complex class I (MHC-I) molecules, which are dimers of a glycosylated polymorphic transmembrane heavy chain and the small-protein β2-microglobulin (β2m), bind peptides in the endoplasmic reticulum that are generated by the cytosolic turnover of cellular proteins. In virus-infected cells, these peptides may include those derived from viral proteins. Peptide-MHC-I complexes then traffic through the secretory pathway and are displayed at the cell surface where those containing viral peptides can be detected by CD8+ T lymphocytes that kill infected cells. Many viruses enhance their in vivo survival by encoding genes that down-regulate MHC-I expression to avoid CD8+ T cell recognition. Here, we report that two accessory proteins encoded by SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic, down-regulate MHC-I expression using distinct mechanisms. First, ORF3a, a viroporin, reduces the global trafficking of proteins, including MHC-I, through the secretory pathway. The second, ORF7a, interacts specifically with the MHC-I heavy chain, acting as a molecular mimic of β2m to inhibit its association. This slows the exit of properly assembled MHC-I molecules from the endoplasmic reticulum. We demonstrate that ORF7a reduces antigen presentation by the human MHC-I allele HLA-A*02:01. Thus, both ORF3a and ORF7a act post-translationally in the secretory pathway to lower surface MHC-I expression, with ORF7a exhibiting a specific mechanism that allows immune evasion by SARS-CoV-2.
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43
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Pei M, Dong A, Ma X, Li S, Guo Y, Li M, Wang Z, Wang H, Zhu L, Pan C, Wang Y. Identification of potential antigenic peptides of Brucella through proteome and peptidome. Vet Med Sci 2022; 9:523-534. [PMID: 36583994 PMCID: PMC9856995 DOI: 10.1002/vms3.1048] [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] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Brucellosis, caused by Brucella spp., is a major zoonotic public health threat. Although several Brucella vaccines have been demonstrated for use in animals, Brucella spp. can cause human infection and to date, there are no human-use vaccines licensed by any agency. Recently, methods in vaccine informatics have made major breakthroughs in peptide-based epitopes, opening up a new avenue of vaccine development. OBJECTIVES The purpose of this article was to identify potential antigenic peptides in Brucella by proteome and peptidome analyses. METHODS Mouse infection models were first established by injection with Brucella and spleen protein profiles were then analysed. Subsequently, the major histocompatibility complex class I or II (major histocompatibility complex [MHC]-I/II)-binding peptides in blood samples were collected by immunoprecipitation and peptides derived from Brucella proteins were identified through liquid chromatography-mass spectrometry (LC-MS/MS). These peptides were then evaluated in a variety of ways, such as in terms of conservation in Brucella and synchronicity in predicted peptides (similarity and coverage), which allowed us to more effectively measure their antigenic potential. RESULTS The expression of the inflammatory cytokines IL1B and IFN-γ was significantly altered in the spleen of infected mice and some Brucella proteins, such as Muri, AcpP and GroES, were also detected. Meanwhile, in blood, 35 peptides were identified and most showed high conservation, highlighting their potential as antigen epitopes for vaccine development. In particular, we identified four proteins containing both MHC-I- and MHC-II-binding peptides including AtpA, AtpD, DnaK and BAbS19_II02030. They were also compared with the predicted peptides to estimate their reliability. CONCLUSIONS The peptides we screened could bind to MHC molecules. After being stimulated with antigen T epitopes, Memory T cells can stimulate T cell activation and promote immune responses. Our results indicated that the peptides we identified may be good candidate targets for the design of subunit vaccines and these results pave the way for the study of safer vaccines against Brucella.
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Affiliation(s)
- Meijuan Pei
- Department of Clinical LaboratoryThe Third Medical Centre of Chinese PLA General HospitalThe Training Site for Postgraduate of Jinzhou Medical UniversityBeijingChina,State Key Laboratory of Pathogen and BiosecurityBeijing Institute of BiotechnologyBeijingChina
| | - Ao Dong
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of BiotechnologyBeijingChina
| | - Xueping Ma
- Department of Clinical LaboratoryThe Third Medical Centre of Chinese PLA General HospitalBeijingChina
| | - Shulei Li
- Department of Clinical LaboratoryThe Third Medical Centre of Chinese PLA General HospitalThe Training Site for Postgraduate of Jinzhou Medical UniversityBeijingChina,State Key Laboratory of Pathogen and BiosecurityBeijing Institute of BiotechnologyBeijingChina
| | - Yan Guo
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of BiotechnologyBeijingChina
| | - Menglan Li
- Department of Clinical LaboratoryThe Third Medical Centre of Chinese PLA General HospitalBeijingChina
| | - Zhenghui Wang
- Department of Clinical LaboratoryThe Third Medical Centre of Chinese PLA General HospitalBeijingChina
| | - Hengliang Wang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of BiotechnologyBeijingChina
| | - Li Zhu
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of BiotechnologyBeijingChina
| | - Chao Pan
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of BiotechnologyBeijingChina
| | - Yufei Wang
- Department of Clinical LaboratoryThe Third Medical Centre of Chinese PLA General HospitalThe Training Site for Postgraduate of Jinzhou Medical UniversityBeijingChina,Department of Clinical LaboratoryThe Third Medical Centre of Chinese PLA General HospitalBeijingChina
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Xu J, Liu M, Niu X, Hanson J, Jung K, Ru P, Tu H, Jones DM, Vlasova AN, Saif LJ, Wang Q. The Cold-Adapted, Temperature-Sensitive SARS-CoV-2 Strain TS11 Is Attenuated in Syrian Hamsters and a Candidate Attenuated Vaccine. Viruses 2022; 15:95. [PMID: 36680135 PMCID: PMC9867033 DOI: 10.3390/v15010095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Live attenuated vaccines (LAVs) replicate in the respiratory/oral mucosa, mimic natural infection, and can induce mucosal and systemic immune responses to the full repertoire of SARS-CoV-2 structural/nonstructural proteins. Generally, LAVs produce broader and more durable protection than current COVID-19 vaccines. We generated a temperature-sensitive (TS) SARS-CoV-2 mutant TS11 via cold-adaptation of the WA1 strain in Vero E6 cells. TS11 replicated at >4 Log10-higher titers at 32 °C than at 39 °C. TS11 has multiple mutations, including those in nsp3, a 12-amino acid-deletion spanning the furin cleavage site of the S protein and a 371-nucleotide-deletion spanning the ORF7b-ORF8 genes. We tested the pathogenicity and protective efficacy of TS11 against challenge with a heterologous virulent SARS-CoV-2 D614G strain 14B in Syrian hamsters. Hamsters were randomly assigned to mock immunization-challenge (Mock-C) and TS11 immunization-challenge (TS11-C) groups. Like the mock group, TS11-vaccinated hamsters did not show any clinical signs and continuously gained body weight. TS11 replicated well in the nasal cavity but poorly in the lungs and caused only mild lesions in the lungs. After challenge, hamsters in the Mock-C group lost weight. In contrast, the animals in the TS11-C group continued gaining weight. The virus titers in the nasal turbinates and lungs of the TS11-C group were significantly lower than those in the Mock-C group, confirming the protective effects of TS11 immunization of hamsters. Histopathological examination demonstrated that animals in the Mock-C group had severe pulmonary lesions and large amounts of viral antigens in the lungs post-challenge; however, the TS11-C group had minimal pathological changes and few viral antigen-positive cells. In summary, the TS11 mutant was attenuated and induced protection against disease after a heterologous SARS-CoV-2 challenge in Syrian hamsters.
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Affiliation(s)
- Jiayu Xu
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Mingde Liu
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaoyu Niu
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Juliette Hanson
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA
| | - Kwonil Jung
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA
| | - Peng Ru
- The Ohio State University Comprehensive Cancer Center, The Ohio State University James Cancer Center, Columbus, OH 43210, USA
| | - Huolin Tu
- James Molecular Laboratory at Polaris, The Ohio State University James Cancer Center, Columbus, OH 43240, USA
| | - Daniel M. Jones
- The Ohio State University Comprehensive Cancer Center, The Ohio State University James Cancer Center, Columbus, OH 43210, USA
- James Molecular Laboratory at Polaris, The Ohio State University James Cancer Center, Columbus, OH 43240, USA
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Anastasia N. Vlasova
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Linda J. Saif
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Qiuhong Wang
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
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Brito-Sierra CA, Lannan MB, Siegel RW, Malherbe LP. The HLA class-II immunopeptidomes of AAV capsids proteins. Front Immunol 2022; 13:1067399. [PMID: 36605211 PMCID: PMC9807805 DOI: 10.3389/fimmu.2022.1067399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Gene therapies are using Adeno-associated viruses (AAVs) as vectors, but immune responses against the capsids pose challenges to their efficiency and safety. Helper T cell recognition of capsid-derived peptides bound to human leukocyte antigen (HLA) class II molecules is an essential step in the AAV-specific adaptive immunity. Methods Using MHC-associated peptide proteomics, we identified the HLA-DR and HLA-DQ immunopeptidomes of the capsid proteins of three different AAV serotypes (AAV2, AAV6, and AAV9) from a panel of healthy donors selected to represent a majority of allele usage. Results The identified sequences span the capsids of all serotypes, with AAV2 having the highest peptide count. For all the serotypes, multiple promiscuous peptides were identified and displayed by both HLA-DR and -DQ. However, despite high sequence homology, there were few identical peptides among AAV2, AAV6, and AAV9 immunopeptidomes, and none were promiscuous. Discussion Results from this work represent a comprehensive immunopeptidomics research of potential CD4+ T cell epitopes and provide the basis for immunosurveillance efforts for safer and more efficient AAV-based gene therapies.
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Affiliation(s)
| | | | - Robert W. Siegel
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Laurent P. Malherbe
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
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46
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Weingarten-Gabbay S, Pearlman LR, Chen DY, Klaeger S, Taylor HB, Welch NL, Keskin DB, Carr SA, Abelin JG, Saeed M, Sabeti PC. HLA-I immunopeptidome profiling of human cells infected with high-containment enveloped viruses. STAR Protoc 2022; 3:101910. [PMID: 36595954 PMCID: PMC9731565 DOI: 10.1016/j.xpro.2022.101910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/10/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
Immunopeptidome profiling of infected cells is a powerful technique for detecting viral peptides that are naturally processed and loaded onto class I human leukocyte antigens (HLAs-I). Here, we provide a protocol for preparing samples for immunopeptidome profiling that can inactivate enveloped viruses while still preserving the integrity of the HLA-I complex. We detail steps for lysate preparation of infected cells followed by HLA-I immunoprecipitation and virus inactivation. We further describe peptide purification for mass spectrometry outside a high-containment facility. For complete details on the use and execution of this protocol, please refer to Weingarten-Gabbay et al. (2021).1.
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Affiliation(s)
- Shira Weingarten-Gabbay
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA,Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA,Corresponding author
| | | | - Da-Yuan Chen
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nicole L. Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Derin B. Keskin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA,Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Howard Hughes Medical Institute, Chevy Chase, MD, USA
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47
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Wu K, Wang D, Wang J, Zhou Y. Translation landscape of SARS-CoV-2 noncanonical subgenomic RNAs. Virol Sin 2022; 37:813-822. [PMID: 36075564 PMCID: PMC9444306 DOI: 10.1016/j.virs.2022.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/01/2022] [Indexed: 12/27/2022] Open
Abstract
The ongoing COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with a positive-stranded RNA genome. Current proteomic studies of SARS-CoV-2 mainly focus on the proteins encoded by its genomic RNA (gRNA) or canonical subgenomic RNAs (sgRNAs). Here, we systematically investigated the translation landscape of SARS-CoV-2, especially its noncanonical sgRNAs. We first constructed a strict pipeline, named vipep, for identifying reliable peptides derived from RNA viruses using RNA-seq and mass spectrometry data. We applied vipep to analyze 24 sets of mass spectrometry data related to SARS-CoV-2 infection. In addition to known canonical proteins, we identified many noncanonical sgRNA-derived peptides, which stably increase after viral infection. Furthermore, we explored the potential functions of those proteins encoded by noncanonical sgRNAs and found that they can bind to viral RNAs and may have immunogenic activity. The generalized vipep pipeline is applicable to any RNA viruses and these results have expanded the SARS-CoV-2 translation map, providing new insights for understanding the functions of SARS-CoV-2 sgRNAs.
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Affiliation(s)
- Kai Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Dehe Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Junhao Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China,TaiKang Center for Life and Medical Sciences, RNA Institute, Wuhan University, Wuhan, 430072, China,Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China,Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China,Corresponding author
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48
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Becerra-Artiles A, Nanaware PP, Muneeruddin K, Weaver GC, Shaffer SA, Calvo-Calle JM, Stern LJ. Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.01.518643. [PMID: 36482973 PMCID: PMC9727760 DOI: 10.1101/2022.12.01.518643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Seasonal "common-cold" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but identification and characterization of the T cell response to seasonal human coronaviruses remain largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal human coronavirus OC43. We identified MHC-I and MHC-II bound peptides derived from the viral spike, nucleocapsid, hemagglutinin-esterase, 3C-like proteinase, and envelope proteins. Only three MHC-I bound OC43-derived peptides were observed, possibly due to the potent MHC-I downregulation induced by OC43 infection. By contrast, 80 MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. These peptides elicited low-abundance recall T cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T cell lines. Among the validated epitopes, S 903-917 presented by DPA1*01:03/DPB1*04:01 and S 1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. N 54-68 and HE 128-142 presented by DRB1*15:01 and HE 259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow T cell cross-reactivity after infection or vaccination and could aid in the selection of epitopes for inclusion in pan-coronavirus vaccines. Author Summary There is much current interest in cellular immune responses to seasonal common-cold coronaviruses because of their possible role in mediating protection against SARS-CoV-2 infection or pathology. However, identification of relevant T cell epitopes and systematic studies of the T cell responses responding to these viruses are scarce. We conducted a study to identify naturally processed and presented MHC-I and MHC-II epitopes from human cells infected with the seasonal coronavirus HCoV-OC43, and to characterize the T cell responses associated with these epitopes. We found epitopes specific to the seasonal coronaviruses, as well as epitopes cross-reactive between HCoV-OC43 and SARS-CoV-2. These epitopes should be useful in following immune responses to seasonal coronaviruses and identifying their roles in COVID-19 vaccination, infection, and pathogenesis.
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Affiliation(s)
- Aniuska Becerra-Artiles
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Padma P. Nanaware
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Khaja Muneeruddin
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury MA
| | - Grant C. Weaver
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Scott A. Shaffer
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury MA
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - J. Mauricio Calvo-Calle
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Lawrence J. Stern
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA 01655, USA
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49
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Chavda VP, Redwan EM. SARS-CoV-2: Immunopeptidomics and Other Immunological Studies. Vaccines (Basel) 2022; 10:vaccines10111975. [PMID: 36423070 PMCID: PMC9694091 DOI: 10.3390/vaccines10111975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has produced a significant continuing epidemic worldwide [...]
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad 380008, India
- Correspondence: (V.P.C.); (E.M.R.); Tel.: +91-7030-919-407 (V.P.C.)
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA City), Alexandria 21934, Egypt
- Correspondence: (V.P.C.); (E.M.R.); Tel.: +91-7030-919-407 (V.P.C.)
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Durable CD8 T Cell Memory against SARS-CoV-2 by Prime/Boost and Multi-Dose Vaccination: Considerations on Inter-Dose Time Intervals. Int J Mol Sci 2022; 23:ijms232214367. [PMID: 36430845 PMCID: PMC9698736 DOI: 10.3390/ijms232214367] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022] Open
Abstract
Facing the COVID-19 pandemic, anti-SARS-CoV-2 vaccines were developed at unprecedented pace, productively exploiting contemporary fundamental research and prior art. Large-scale use of anti-SARS-CoV-2 vaccines has greatly limited severe morbidity and mortality. Protection has been correlated with high serum titres of neutralizing antibodies capable of blocking the interaction between the viral surface protein spike and the host SARS-CoV-2 receptor, ACE-2. Yet, vaccine-induced protection subsides over time, and breakthrough infections are commonly observed, mostly reflecting the decay of neutralizing antibodies and the emergence of variant viruses with mutant spike proteins. Memory CD8 T cells are a potent weapon against viruses, as they are against tumour cells. Anti-SARS-CoV-2 memory CD8 T cells are induced by either natural infection or vaccination and can be potentially exploited against spike-mutated viruses. We offer here an overview of current research about the induction of anti-SARS-CoV-2 memory CD8 T cells by vaccination, in the context of prior knowledge on vaccines and on fundamental mechanisms of immunological memory. We focus particularly on how vaccination by two doses (prime/boost) or more (boosters) promotes differentiation of memory CD8 T cells, and on how the time-length of inter-dose intervals may influence the magnitude and persistence of CD8 T cell memory.
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