1
|
Yang Y, Miller H, Byazrova MG, Cndotti F, Benlagha K, Camara NOS, Shi J, Forsman H, Lee P, Yang L, Filatov A, Zhai Z, Liu C. The characterization of CD8 + T-cell responses in COVID-19. Emerg Microbes Infect 2024; 13:2287118. [PMID: 37990907 PMCID: PMC10786432 DOI: 10.1080/22221751.2023.2287118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/19/2023] [Indexed: 11/23/2023]
Abstract
This review gives an overview of the protective role of CD8+ T cells in SARS-CoV-2 infection. The cross-reactive responses intermediated by CD8+ T cells in unexposed cohorts are described. Additionally, the relevance of resident CD8+ T cells in the upper and lower airway during infection and CD8+ T-cell responses following vaccination are discussed, including recent worrisome breakthrough infections and variants of concerns (VOCs). Lastly, we explain the correlation between CD8+ T cells and COVID-19 severity. This review aids in a deeper comprehension of the association between CD8+ T cells and SARS-CoV-2 and broadens a vision for future exploration.
Collapse
Affiliation(s)
- Yuanting Yang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, Hubei, People’s Republic of China
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Heather Miller
- Cytek Biosciences, R&D Clinical Reagents, Fremont, CA, USA
| | - Maria G. Byazrova
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, Russia
| | - Fabio Cndotti
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Kamel Benlagha
- Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Niels Olsen Saraiva Camara
- Laboratory of Human Immunology, Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Junming Shi
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, Hubei, People’s Republic of China
| | - Huamei Forsman
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Pamela Lee
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Lu Yang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, Hubei, People’s Republic of China
| | - Alexander Filatov
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, Russia
| | - Zhimin Zhai
- Department of Hematology, The Second Hospital of Anhui Medical University, Hefei, People’s Republic of China
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, Hubei, People’s Republic of China
| |
Collapse
|
2
|
Bean DJ, Monroe J, Liang YM, Borberg E, Senussi Y, Swank Z, Chalise S, Walt D, Weinberg J, Sagar M. Heterotypic immunity from prior SARS-CoV-2 infection but not COVID-19 vaccination associates with lower endemic coronavirus incidence. Sci Transl Med 2024; 16:eado7588. [PMID: 38865483 DOI: 10.1126/scitranslmed.ado7588] [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: 02/19/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Immune responses from prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and COVID-19 vaccination mitigate disease severity, but they do not fully prevent subsequent infections, especially from genetically divergent strains. We examined the incidence of and immune differences against human endemic coronaviruses (eCoVs) as a proxy for response against future genetically heterologous coronaviruses (CoVs). We assessed differences in symptomatic eCoV and non-CoV respiratory disease incidence among those with known prior SARS-CoV-2 infection or previous COVID-19 vaccination but no documented SARS-CoV-2 infection or neither exposure. Retrospective cohort analyses suggest that prior SARS-CoV-2 infection, but not previous COVID-19 vaccination alone, associates with a lower incidence of subsequent symptomatic eCoV infection. There was no difference in non-CoV incidence, implying that the observed difference was eCoV specific. In a second cohort where both cellular and humoral immunity were measured, those with prior SARS-CoV-2 spike protein exposure had lower eCoV-directed neutralizing antibodies, suggesting that neutralization is not responsible for the observed decreased eCoV disease. The three groups had similar cellular responses against the eCoV spike protein and nucleocapsid antigens. However, CD8+ T cell responses to the nonstructural eCoV proteins nsp12 and nsp13 were higher in individuals with previous SARS-CoV-2 infection as compared with the other groups. This association between prior SARS-CoV-2 infection and decreased incidence of eCoV disease may therefore be due to a boost in CD8+ T cell responses against eCoV nsp12 and nsp13, suggesting that incorporation of nonstructural viral antigens in a future pan-CoV vaccine may improve vaccine efficacy.
Collapse
Affiliation(s)
- David J Bean
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Janet Monroe
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Yan Mei Liang
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Ella Borberg
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Yasmeen Senussi
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Zoe Swank
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Sujata Chalise
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - David Walt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Janice Weinberg
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Manish Sagar
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| |
Collapse
|
3
|
Cai C, Keoshkerian E, Wing K, Samir J, Effenberger M, Schober K, Bull RA, Lloyd AR, Busch DH, Luciani F. Discovery of a monoclonal, high-affinity CD8 + T-cell clone following natural hepatitis C virus infection. Immunol Cell Biol 2024. [PMID: 38855806 DOI: 10.1111/imcb.12791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/11/2024]
Abstract
CD8+ T cells recognizing their cognate antigen are typically recruited as a polyclonal population consisting of multiple clonotypes with varying T-cell receptor (TCR) affinity to the target peptide-major histocompatibility complex (pMHC) complex. Advances in single-cell sequencing have increased accessibility toward identifying TCRs with matched antigens. Here we present the discovery of a monoclonal CD8+ T-cell population with specificity for a hepatitis C virus (HCV)-derived human leukocyte antigen (HLA) class I epitope (HLA-B*07:02 GPRLGVRAT) which was isolated directly ex vivo from an individual with an episode of acutely resolved HCV infection. This population was absent before infection and underwent expansion and stable maintenance for at least 2 years after infection as measured by HLA-multimer staining. Furthermore, the monoclonal clonotype was characterized by an unusually long dissociation time (half-life = 794 s and koff = 5.73 × 10-4) for its target antigen when compared with previously published results. A comparison with related populations of HCV-specific populations derived from the same individual and a second individual suggested that high-affinity TCR-pMHC interactions may be inherent to epitope identity and shape the phenotype of responses which has implications for rational TCR selection and design in the age of personalized immunotherapies.
Collapse
Affiliation(s)
- Curtis Cai
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Elizabeth Keoshkerian
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Kristof Wing
- School of Medicine and Health, Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Jerome Samir
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Manuel Effenberger
- School of Medicine and Health, Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Kilian Schober
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rowena A Bull
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Andrew R Lloyd
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Dirk H Busch
- School of Medicine and Health, Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
- German Center for Infection Research (Deutsches Zentrum für Infektionsforschung), Partner Site Munich, Munich, Germany
| | - Fabio Luciani
- School of Biomedical Sciences, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- The Kirby Institute, Faculty of Health and Medicine, UNSW Sydney, Sydney, NSW, Australia
- Cellular Genomics Future Institute, UNSW Sydney, Sydney, NSW, Australia
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY, USA
| |
Collapse
|
4
|
Delmonte OM, Oguz C, Dobbs K, Myint-Hpu K, Palterer B, Abers MS, Draper D, Truong M, Kaplan IM, Gittelman RM, Zhang Y, Rosen LB, Snow AL, Dalgard CL, Burbelo PD, Imberti L, Sottini A, Quiros-Roldan E, Castelli F, Rossi C, Brugnoni D, Biondi A, Bettini LR, D'Angio M, Bonfanti P, Anderson MV, Saracino A, Chironna M, Di Stefano M, Fiore JR, Santantonio T, Castagnoli R, Marseglia GL, Magliocco M, Bosticardo M, Pala F, Shaw E, Matthews H, Weber SE, Xirasagar S, Barnett J, Oler AJ, Dimitrova D, Bergerson JRE, McDermott DH, Rao VK, Murphy PM, Holland SM, Lisco A, Su HC, Lionakis MS, Cohen JI, Freeman AF, Snyder TM, Lack J, Notarangelo LD. Perturbations of the T-cell receptor repertoire in response to SARS-CoV-2 in immunocompetent and immunocompromised individuals. J Allergy Clin Immunol 2024; 153:1655-1667. [PMID: 38154666 PMCID: PMC11162338 DOI: 10.1016/j.jaci.2023.12.011] [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: 05/29/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND Functional T-cell responses are essential for virus clearance and long-term protection after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, whereas certain clinical factors, such as older age and immunocompromise, are associated with worse outcome. OBJECTIVE We sought to study the breadth and magnitude of T-cell responses in patients with coronavirus disease 2019 (COVID-19) and in individuals with inborn errors of immunity (IEIs) who had received COVID-19 mRNA vaccine. METHODS Using high-throughput sequencing and bioinformatics tools to characterize the T-cell receptor β repertoire signatures in 540 individuals after SARS-CoV-2 infection, 31 IEI recipients of COVID-19 mRNA vaccine, and healthy controls, we quantified HLA class I- and class II-restricted SARS-CoV-2-specific responses and also identified several HLA allele-clonotype motif associations in patients with COVID-19, including a subcohort of anti-type 1 interferon (IFN-1)-positive patients. RESULTS Our analysis revealed that elderly patients with COVID-19 with critical disease manifested lower SARS-CoV-2 T-cell clonotype diversity as well as T-cell responses with reduced magnitude, whereas the SARS-CoV-2-specific clonotypes targeted a broad range of HLA class I- and class II-restricted epitopes across the viral proteome. The presence of anti-IFN-I antibodies was associated with certain HLA alleles. Finally, COVID-19 mRNA immunization induced an increase in the breadth of SARS-CoV-2-specific clonotypes in patients with IEIs, including those who had failed to seroconvert. CONCLUSIONS Elderly individuals have impaired capacity to develop broad and sustained T-cell responses after SARS-CoV-2 infection. Genetic factors may play a role in the production of anti-IFN-1 antibodies. COVID-19 mRNA vaccines are effective in inducing T-cell responses in patients with IEIs.
Collapse
Affiliation(s)
- Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
| | - Cihan Oguz
- Integrated Data Sciences Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Katherine Myint-Hpu
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Boaz Palterer
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michael S Abers
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Deborah Draper
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Meng Truong
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | | | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Lindsey B Rosen
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrew L Snow
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md; Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, Md; The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Peter D Burbelo
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Md
| | - Luisa Imberti
- Section of Microbiology, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Alessandra Sottini
- Section of Microbiology, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Francesco Castelli
- Department of Infectious and Tropical Diseases, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Camillo Rossi
- Direzione Sanitaria, ASST Spedali Civili, Brescia, Italy
| | - Duilio Brugnoni
- Laboratorio Analisi Chimico-Cliniche, ASST Spedali Civili, Brescia, Italy
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Laura Rachele Bettini
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Mariella D'Angio
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Megan V Anderson
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Annalisa Saracino
- Clinic of Infectious Diseases, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, University of Bari, Bari, Italy
| | - Maria Chironna
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Mariantonietta Di Stefano
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Jose Ramon Fiore
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Teresa Santantonio
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Riccardo Castagnoli
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Gian Luigi Marseglia
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Mary Magliocco
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Elana Shaw
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Helen Matthews
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sarah E Weber
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sandhya Xirasagar
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Jason Barnett
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Dimana Dimitrova
- Center for Immuno-Oncology, National Cancer Institute, National Institutes of Health, Bethesda, Md
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - David H McDermott
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - V Koneti Rao
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Philip M Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrea Lisco
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | | | - Justin Lack
- Integrated Data Sciences Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
| |
Collapse
|
5
|
Hasan MZ, Claus M, Krüger N, Reusing S, Gall E, Bade-Döding C, Braun A, Watzl C, Uhrberg M, Walter L. SARS-CoV-2 infection induces adaptive NK cell responses by spike protein-mediated induction of HLA-E expression. Emerg Microbes Infect 2024:2361019. [PMID: 38804979 DOI: 10.1080/22221751.2024.2361019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
ABSTRACTHLA-E expression plays a central role for modulation of NK cell function by interaction with inhibitory NKG2A and stimulatory NKG2C receptors on canonical and adaptive NK cells, respectively. Here, we demonstrate that infection of human primary lung tissue with SARS-CoV-2 leads to increased HLA-E expression and show that processing of the peptide YLQPRTFLL from the spike protein is primarily responsible for the strong, dose-dependent increase of HLA-E. Targeting the peptide site within the spike protein revealed that a single point mutation was sufficient to abrogate the increase in HLA-E expression. Spike-mediated induction of HLA-E differentially affected NK cell function: whereas degranulation, IFN-γ production, and target cell cytotoxicity were enhanced in NKG2C+ adaptive NK cells, effector functions were inhibited in NKG2A+ canonical NK cells. Analysis of a cohort of COVID-19 patients in the acute phase of infection revealed that adaptive NK cells were induced irrespective of the HCMV status, challenging the paradigm that adaptive NK cells are only generated during HCMV infection. During the first week of hospitalization, patients exhibited a selective increase of early NKG2C+CD57- adaptive NK cells whereas mature NKG2C+CD57+ cells remained unchanged. Further analysis of recovered patients suggested that the adaptive NK cell response is primarily driven by a wave of early adaptive NK cells during acute infection that wanes once the infection is cleared. Together, this study suggests that NK cell responses to SARS-CoV-2 infection are majorly influenced by the balance between canonical and adaptive NK cells via the HLA-E/NKG2A/C axis.
Collapse
Affiliation(s)
- Mohammad Zahidul Hasan
- Primate Genetics Laboratory, German Primate Center, Leibniz-Institute for Primate Research, Göttingen, Germany
- PhD program Molecular Biology of Cells, GGNB, Georg August University, Göttingen, Germany
| | - Maren Claus
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
| | - Nadine Krüger
- Platform Infection Models, German Primate Center, Leibniz-Institute for Primate Research, Göttingen, Germany
| | - Sarah Reusing
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Eline Gall
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | | | - Armin Braun
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Hannover, Germany, and Institute of Immunology, Medical School Hannover, Hannover, Germany
| | - Carsten Watzl
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
| | - Markus Uhrberg
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Leibniz-Institute for Primate Research, Göttingen, Germany
| |
Collapse
|
6
|
Weisbrod L, Capriotti L, Hofmann M, Spieler V, Dersch H, Voedisch B, Schmidt P, Knake S. FASTMAP-a flexible and scalable immunopeptidomics pipeline for HLA- and antigen-specific T-cell epitope mapping based on artificial antigen-presenting cells. Front Immunol 2024; 15:1386160. [PMID: 38779658 PMCID: PMC11109385 DOI: 10.3389/fimmu.2024.1386160] [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: 02/14/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
The study of peptide repertoires presented by major histocompatibility complex (MHC) molecules and the identification of potential T-cell epitopes contribute to a multitude of immunopeptidome-based treatment approaches. Epitope mapping is essential for the development of promising epitope-based approaches in vaccination as well as for innovative therapeutics for autoimmune diseases, infectious diseases, and cancer. It also plays a critical role in the immunogenicity assessment of protein therapeutics with regard to safety and efficacy concerns. The main challenge emerges from the highly polymorphic nature of the human leukocyte antigen (HLA) molecules leading to the requirement of a peptide mapping strategy for a single HLA allele. As many autoimmune diseases are linked to at least one specific antigen, we established FASTMAP, an innovative strategy to transiently co-transfect a single HLA allele combined with a disease-specific antigen into a human cell line. This approach allows the specific identification of HLA-bound peptides using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Using FASTMAP, we found a comparable spectrum of endogenous peptides presented by the most frequently expressed HLA alleles in the world's population compared to what has been described in literature. To ensure a reliable peptide mapping workflow, we combined the HLA alleles with well-known human model antigens like coagulation factor VIII, acetylcholine receptor subunit alpha, protein structures of the SARS-CoV-2 virus, and myelin basic protein. Using these model antigens, we have been able to identify a broad range of peptides that are in line with already published and in silico predicted T-cell epitopes of the specific HLA/model antigen combination. The transient co-expression of a single affinity-tagged MHC molecule combined with a disease-specific antigen in a human cell line in our FASTMAP pipeline provides the opportunity to identify potential T-cell epitopes/endogenously processed MHC-bound peptides in a very cost-effective, fast, and customizable system with high-throughput potential.
Collapse
Affiliation(s)
- Luisa Weisbrod
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Luigi Capriotti
- Analytical Biochemistry, Research and Development, CSL Behring AG, Bern, Switzerland
| | - Marco Hofmann
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Valerie Spieler
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Herbert Dersch
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Bernd Voedisch
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Peter Schmidt
- Protein Biochemistry, Bio21 Institute, CSL Limited, Parkville, VIC, Australia
| | - Susanne Knake
- Department of Neurology, Epilepsy Center Hessen, Philipps University Marburg, Marburg, Germany
| |
Collapse
|
7
|
Sheetikov SA, Khmelevskaya AA, Zornikova KV, Zvyagin IV, Shomuradova AS, Serdyuk YV, Shakirova NT, Peshkova IO, Titov A, Romaniuk DS, Shagina IA, Chudakov DM, Kiryukhin DO, Shcherbakova OV, Khamaganova EG, Dzutseva V, Afanasiev A, Bogolyubova AV, Efimov GA. Clonal structure and the specificity of vaccine-induced T cell response to SARS-CoV-2 Spike protein. Front Immunol 2024; 15:1369436. [PMID: 38629062 PMCID: PMC11018901 DOI: 10.3389/fimmu.2024.1369436] [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: 01/12/2024] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Adenovirus vaccines, particularly the COVID-19 Ad5-nCoV adenovirus vaccine, have emerged as promising tools in the fight against infectious diseases. In this study, we investigated the structure of the T cell response to the Spike protein of the SARS-CoV-2 virus used in the COVID-19 Ad5-nCoV adenoviral vaccine in a phase 3 clinical trial (NCT04540419). In 69 participants, we collected peripheral blood samples at four time points after vaccination or placebo injection. Sequencing of T cell receptor repertoires from Spike-stimulated T cell cultures at day 14 from 17 vaccinated revealed a more diverse CD4+ T cell repertoire compared to CD8+. Nevertheless, CD8+ clonotypes accounted for more than half of the Spike-specific repertoire. Our longitudinal analysis showed a peak T cell response at day 14, followed by a decline until month 6. Remarkably, multiple T cell clonotypes persisted for at least 6 months after vaccination, as demonstrated by ex vivo stimulation. Examination of CDR3 regions revealed homologous sequences in both CD4+ and CD8+ clonotypes, with major CD8+ clonotypes sharing high similarity with annotated sequences specific for the NYNYLYRLF peptide, suggesting potential immunodominance. In conclusion, our study demonstrates the immunogenicity of the Ad5-nCoV adenoviral vaccine and highlights its ability to induce robust and durable T cell responses. These findings provide valuable insight into the efficacy of the vaccine against COVID-19 and provide critical information for ongoing efforts to control infectious diseases.
Collapse
Affiliation(s)
- Saveliy A. Sheetikov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexandra A. Khmelevskaya
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Ksenia V. Zornikova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ivan V. Zvyagin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alina S. Shomuradova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yana V. Serdyuk
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Naina T. Shakirova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Iuliia O. Peshkova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Aleksei Titov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Dmitrii S. Romaniuk
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Irina A. Shagina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Dmitry M. Chudakov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Dmitry O. Kiryukhin
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Olga V. Shcherbakova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Ekaterina G. Khamaganova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Vitalina Dzutseva
- Novosibirsk State University, Medical School, Novosibirsk, Russia
- NPO Petrovax Pharm LLC, Moscow, Russia
| | | | | | - Grigory A. Efimov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| |
Collapse
|
8
|
Lv J, Ma W. Delay induced stability switch in a mathematical model of CD8 T-cell response to SARS-CoV-2 mediated by receptor ACE2. CHAOS (WOODBURY, N.Y.) 2024; 34:043135. [PMID: 38608314 DOI: 10.1063/5.0187872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/18/2024] [Indexed: 04/14/2024]
Abstract
The pathogen SARS-CoV-2 binds to the receptor angiotensin-converting enzyme 2 (ACE2) of the target cells and then replicates itself through the host, eventually releasing free virus particles. After infection, the CD8 T-cell response is triggered and appears to play a critical role in the defense against virus infections. Infected cells and their activated CD8 T-cells can cause tissue damage. Here, we established a mathematical model of within-host SARS-CoV-2 infection that incorporates the receptor ACE2, the CD8 T-cell response, and the damaged tissues. According to this model, we can get the basic reproduction number R0 and the immune reproduction number R1. We provide the theoretical proof for the stability of the disease-free equilibrium, immune-inactivated equilibrium, and immune-activated equilibrium. Finally, our numerical simulations show that the time delay in CD8 T-cell production can induce complex dynamics such as stability switching. These results provide insights into the mechanisms of SARS-CoV-2 infection and may help in the development of effective drugs against COVID-19.
Collapse
Affiliation(s)
- Jinlong Lv
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, People's Republic of China
| | - Wanbiao Ma
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, People's Republic of China
| |
Collapse
|
9
|
van den Dijssel J, Duurland MC, Konijn VA, Kummer LY, Hagen RR, Kuijper LH, Wieske L, van Dam KP, Stalman EW, Steenhuis M, Geerdes DM, Mok JY, Kragten AH, Menage C, Koets L, Veldhuisen B, Verstegen NJ, van der Schoot CE, van Esch WJ, D'Haens GR, Löwenberg M, Volkers AG, Rispens T, Kuijpers TW, Eftimov F, van Gisbergen KP, van Ham SM, Ten Brinke A, van de Sandt CE. mRNA-1273 vaccinated inflammatory bowel disease patients receiving TNF inhibitors develop broad and robust SARS-CoV-2-specific CD8 + T cell responses. J Autoimmun 2024; 144:103175. [PMID: 38387105 DOI: 10.1016/j.jaut.2024.103175] [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: 11/10/2023] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
SARS-CoV-2-specific CD8+ T cells recognize conserved viral peptides and in the absence of cross-reactive antibodies form an important line of protection against emerging viral variants as they ameliorate disease severity. SARS-CoV-2 mRNA vaccines induce robust spike-specific antibody and T cell responses in healthy individuals, but their effectiveness in patients with chronic immune-mediated inflammatory disorders (IMIDs) is less well defined. These patients are often treated with systemic immunosuppressants, which may negatively affect vaccine-induced immunity. Indeed, TNF inhibitor (TNFi)-treated inflammatory bowel disease (IBD) patients display reduced ability to maintain SARS-CoV-2 antibody responses post-vaccination, yet the effects on CD8+ T cells remain unclear. Here, we analyzed the impact of IBD and TNFi treatment on mRNA-1273 vaccine-induced CD8+ T cell responses compared to healthy controls in SARS-CoV-2 experienced and inexperienced patients. CD8+ T cells were analyzed for their ability to recognize 32 SARS-CoV-2-specific epitopes, restricted by 10 common HLA class I allotypes using heterotetramer combinatorial coding. This strategy allowed in-depth ex vivo profiling of the vaccine-induced CD8+ T cell responses using phenotypic and activation markers. mRNA vaccination of TNFi-treated and untreated IBD patients induced robust spike-specific CD8+ T cell responses with a predominant central memory and activated phenotype, comparable to those in healthy controls. Prominent non-spike-specific CD8+ T cell responses were observed in SARS-CoV-2 experienced donors prior to vaccination. Non-spike-specific CD8+ T cells persisted and spike-specific CD8+ T cells notably expanded after vaccination in these patient cohorts. Our data demonstrate that regardless of TNFi treatment or prior SARS-CoV-2 infection, IBD patients benefit from vaccination by inducing a robust spike-specific CD8+ T cell response.
Collapse
Affiliation(s)
- Jet van den Dijssel
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Mariël C Duurland
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Veronique Al Konijn
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Laura Yl Kummer
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ruth R Hagen
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Lisan H Kuijper
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Luuk Wieske
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands; Department of Clinical Neurophysiology, St Antonius Hospital, Nieuwegein, Netherlands
| | - Koos Pj van Dam
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Eileen W Stalman
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Maurice Steenhuis
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | | | - Juk Yee Mok
- Sanquin Reagents B.V., Amsterdam, Netherlands
| | | | - Charlotte Menage
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Lianne Koets
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; National Screening Laboratory of Sanquin, Research and Laboratory Services, Amsterdam, Netherlands
| | - Barbera Veldhuisen
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Department of Immunohematology Diagnostics, Sanquin Diagnostic Services, Amsterdam, Netherlands
| | - Niels Jm Verstegen
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - C Ellen van der Schoot
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | | | - Geert Ram D'Haens
- Department of Gastroenterology and Hepatology, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Mark Löwenberg
- Department of Gastroenterology and Hepatology, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Adriaan G Volkers
- Department of Gastroenterology and Hepatology, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Theo Rispens
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Disease, University of Amsterdam, Amsterdam, Netherlands
| | - Filip Eftimov
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Klaas Pjm van Gisbergen
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - S Marieke van Ham
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Swammerdam Institute for Life Sciences, University of Amsterdam, Netherlands
| | - Anja Ten Brinke
- Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Carolien E van de Sandt
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands; Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| |
Collapse
|
10
|
Underwood AP, Sølund C, Jacobsen K, Binderup A, Fernandez-Antunez C, Mikkelsen LS, Inekci D, Villadsen SL, Castruita JAS, Pinholt M, Fahnøe U, Ramirez S, Brix L, Weis N, Bukh J. Neutralizing antibody and CD8 + T cell responses following BA.4/5 bivalent COVID-19 booster vaccination in adults with and without prior exposure to SARS-CoV-2. Front Immunol 2024; 15:1353353. [PMID: 38571939 PMCID: PMC10987722 DOI: 10.3389/fimmu.2024.1353353] [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: 12/10/2023] [Accepted: 02/08/2024] [Indexed: 04/05/2024] Open
Abstract
As severe acute respiratory coronavirus 2 (SARS-CoV-2) variants continue to emerge, it is important to characterize immune responses against variants which can inform on protection efficacies following booster vaccination. In this study, neutralizing breadth and antigen-specific CD8+ T cell responses were analyzed in both infection-naïve and infection-experienced individuals following administration of a booster bivalent Wuhan-Hu-1+BA.4/5 Comirnaty® mRNA vaccine. Significantly higher neutralizing titers were found after this vaccination compared to the pre-third booster vaccination time point. Further, neutralizing breadth to omicron variants, including BA.1, BA.2, BA.5, BQ.1 and XBB.1, was found to be boosted following bivalent vaccination. SARS-CoV-2-specific CD8+ T cells were identified, but with no evidence that frequencies were increased following booster vaccinations. Spike protein-specific CD8+ T cells were the only responses detected after vaccination and non-spike-specific CD8+ T cells were only detected after infection. Both spike-specific and non-spike-specific CD8+ T cells were found at much lower frequencies than CD8+ T cells specific to cytomegalovirus (CMV), Epstein-Barr virus (EBV) and influenza (Flu). Taken together, these results show that the bivalent Wuhan-Hu-1+BA.4/5 Comirnaty® mRNA vaccine boosted the breadth of neutralization to newer SARS-CoV-2 variants and that vaccination is able to induce spike protein-specific CD8+ T cell responses, which are maintained longitudinally.
Collapse
Affiliation(s)
- Alexander P. Underwood
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Christina Sølund
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | | | - Alekxander Binderup
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Lotte S. Mikkelsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | | | - Signe Lysemose Villadsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Jose A. S. Castruita
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre, Denmark
| | - Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | | | - Nina Weis
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| |
Collapse
|
11
|
Lidenge SJ, Yalcin D, Bennett SJ, Ngalamika O, Kweyamba BB, Mwita CJ, Tso FY, Mwaiselage J, West JT, Wood C. Viral Epitope Scanning Reveals Correlation between Seasonal HCoVs and SARS-CoV-2 Antibody Responses among Cancer and Non-Cancer Patients. Viruses 2024; 16:448. [PMID: 38543814 PMCID: PMC10975915 DOI: 10.3390/v16030448] [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: 01/27/2024] [Revised: 02/23/2024] [Accepted: 03/09/2024] [Indexed: 04/01/2024] Open
Abstract
Seasonal coronaviruses (HCoVs) are known to contribute to cross-reactive antibody (Ab) responses against SARS-CoV-2. While these responses are predictable due to the high homology between SARS-CoV-2 and other CoVs, the impact of these responses on susceptibility to SARS-CoV-2 infection in cancer patients is unclear. To investigate the influence of prior HCoV infection on anti-SARS-CoV-2 Ab responses among COVID-19 asymptomatic individuals with cancer and controls without cancers, we utilized the VirScan technology in which phage immunoprecipitation and sequencing (PhIP-seq) of longitudinal plasma samples was performed to investigate high-resolution (i.e., epitope level) humoral CoV responses. Despite testing positive for anti-SARS-CoV-2 Ab in the plasma, a majority of the participants were asymptomatic for COVID-19 with no prior history of COVID-19 diagnosis. Although the magnitudes of the anti-SARS-CoV-2 Ab responses were lower in individuals with Kaposi sarcoma (KS) compared to non-KS cancer individuals and those without cancer, the HCoV Ab repertoire was similar between individuals with and without cancer independent of age, sex, HIV status, and chemotherapy. The magnitudes of the anti-spike HCoV responses showed a strong positive association with those of the anti-SARS-CoV-2 spike in cancer patients, and only a weak association in non-cancer patients, suggesting that prior infection with HCoVs might play a role in limiting SARS-CoV-2 infection and COVID-19 disease severity.
Collapse
Affiliation(s)
- Salum J. Lidenge
- Department of Clinical Research, Training, and Consultancy, Ocean Road Cancer Institute, Dar es Salaam P.O. Box 3592, Tanzania; (S.J.L.); (B.B.K.); (J.M.)
- Department of Clinical Oncology, Muhimbili University of Health and Allied Sciences, Dar es Salaam P.O. Box 65001, Tanzania
| | - Dicle Yalcin
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
| | - Sydney J. Bennett
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68516, USA
| | - Owen Ngalamika
- Dermatology and Venereology Division, University Teaching Hospital, University of Zambia School of Medicine, Lusaka P.O. Box 50001, Zambia;
| | - Brenda B. Kweyamba
- Department of Clinical Research, Training, and Consultancy, Ocean Road Cancer Institute, Dar es Salaam P.O. Box 3592, Tanzania; (S.J.L.); (B.B.K.); (J.M.)
| | - Chacha J. Mwita
- Department of Clinical Research, Training, and Consultancy, Ocean Road Cancer Institute, Dar es Salaam P.O. Box 3592, Tanzania; (S.J.L.); (B.B.K.); (J.M.)
| | - For Yue Tso
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
| | - Julius Mwaiselage
- Department of Clinical Research, Training, and Consultancy, Ocean Road Cancer Institute, Dar es Salaam P.O. Box 3592, Tanzania; (S.J.L.); (B.B.K.); (J.M.)
- Department of Clinical Oncology, Muhimbili University of Health and Allied Sciences, Dar es Salaam P.O. Box 65001, Tanzania
| | - John T. West
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
| | - Charles Wood
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68516, USA
| |
Collapse
|
12
|
Maino A, Amen A, Plumas J, Bouquet L, Deschamps M, Saas P, Chaperot L, Manches O. Development of a New Off-the-Shelf Plasmacytoid Dendritic Cell-Based Approach for the Expansion and Characterization of SARS-CoV-2-Specific T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:825-833. [PMID: 38214610 DOI: 10.4049/jimmunol.2300704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/20/2023] [Indexed: 01/13/2024]
Abstract
Global vaccination against COVID-19 has been widely successful; however, there is a need for complementary immunotherapies in severe forms of the disease and in immunocompromised patients. Cytotoxic CD8+ T cells have a crucial role in disease control, but their function can be dysregulated in severe forms of the disease. We report here a cell-based approach using a plasmacytoid dendritic cell line (PDC*line) to expand in vitro specific CD8+ responses against COVID-19 Ags. We tested the immunogenicity of eight HLA-A*02:01 restricted peptides derived from diverse SARS-Cov-2 proteins, selected by bioinformatics analyses in unexposed and convalescent donors. Higher ex vivo frequencies of specific T cells against these peptides were found in convalescent donors compared with unexposed donors, suggesting in situ T cell expansion upon viral infection. The peptide-loaded PDC*line induced robust CD8+ responses with total amplification rates that led up to a 198-fold increase in peptide-specific CD8+ T cell frequencies for a single donor. Of note, six of eight selected peptides provided significant amplifications, all of which were conserved between SARS-CoV variants and derived from the membrane, the spike protein, the nucleoprotein, and the ORF1ab. Amplified and cloned antiviral CD8+ T cells secreted IFN-γ upon peptide-specific activation. Furthermore, specific TCR sequences were identified for two highly immunogenic Ags. Hence, PDC*line represents an efficient platform to identify immunogenic viral targets for future immunotherapies.
Collapse
Affiliation(s)
- Anthony Maino
- Etablissement Français du Sang, Recherche et Développement, Grenoble, France
- Université Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble, France
| | - Axelle Amen
- Laboratoire d'Immunologie, Centre Hospitalier Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, UMR 5075, Institut de Biologie Structurale, Grenoble, France
| | - Joël Plumas
- Etablissement Français du Sang, Recherche et Développement, Grenoble, France
- PDC*line Pharma SAS, Grenoble, France
| | - Lucie Bouquet
- Université de Franche-Comté, Etablissement Français du Sang, INSERM, UMR RIGHT, Besançon, France
| | - Marina Deschamps
- Université de Franche-Comté, Etablissement Français du Sang, INSERM, UMR RIGHT, Besançon, France
| | - Philippe Saas
- Etablissement Français du Sang, Recherche et Développement, Grenoble, France
- Université Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble, France
| | - Laurence Chaperot
- Etablissement Français du Sang, Recherche et Développement, Grenoble, France
- Université Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble, France
| | - Olivier Manches
- Etablissement Français du Sang, Recherche et Développement, Grenoble, France
- Université Grenoble Alpes, INSERM U 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble, France
| |
Collapse
|
13
|
Collins CP, Longo DL, Murphy WJ. The immunobiology of SARS-CoV-2 infection and vaccine responses: potential influences of cross-reactive memory responses and aging on efficacy and off-target effects. Front Immunol 2024; 15:1345499. [PMID: 38469293 PMCID: PMC10925677 DOI: 10.3389/fimmu.2024.1345499] [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: 11/27/2023] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
Immune responses to both SARS-CoV-2 infection and its associated vaccines have been highly variable within the general population. The increasing evidence of long-lasting symptoms after resolution of infection, called post-acute sequelae of COVID-19 (PASC) or "Long COVID," suggests that immune-mediated mechanisms are at play. Closely related endemic common human coronaviruses (hCoV) can induce pre-existing and potentially cross-reactive immunity, which can then affect primary SARS-CoV-2 infection, as well as vaccination responses. The influence of pre-existing immunity from these hCoVs, as well as responses generated from original CoV2 strains or vaccines on the development of new high-affinity responses to CoV2 antigenic viral variants, needs to be better understood given the need for continuous vaccine adaptation and application in the population. Due in part to thymic involution, normal aging is associated with reduced naïve T cell compartments and impaired primary antigen responsiveness, resulting in a reliance on the pre-existing cross-reactive memory cell pool which may be of lower affinity, restricted in diversity, or of shorter duration. These effects can also be mediated by the presence of down-regulatory anti-idiotype responses which also increase in aging. Given the tremendous heterogeneity of clinical data, utilization of preclinical models offers the greatest ability to assess immune responses under a controlled setting. These models should now involve prior antigen/viral exposure combined with incorporation of modifying factors such as age on immune responses and effects. This will also allow for mechanistic dissection and understanding of the different immune pathways involved in both SARS-CoV-2 pathogen and potential vaccine responses over time and how pre-existing memory responses, including potential anti-idiotype responses, can affect efficacy as well as potential off-target effects in different tissues as well as modeling PASC.
Collapse
Affiliation(s)
- Craig P. Collins
- Graduate Program in Immunology, University of California (UC) Davis, Davis, CA, United States
| | - Dan L. Longo
- Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, United States
| | - William J. Murphy
- Departments of Dermatology and Internal Medicine (Hematology/Oncology), University of California (UC) Davis School of Medicine, Sacramento, CA, United States
| |
Collapse
|
14
|
Cankat S, Demael MU, Swadling L. In search of a pan-coronavirus vaccine: next-generation vaccine design and immune mechanisms. Cell Mol Immunol 2024; 21:103-118. [PMID: 38148330 PMCID: PMC10805787 DOI: 10.1038/s41423-023-01116-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 12/28/2023] Open
Abstract
Members of the coronaviridae family are endemic to human populations and have caused several epidemics and pandemics in recent history. In this review, we will discuss the feasibility of and progress toward the ultimate goal of creating a pan-coronavirus vaccine that can protect against infection and disease by all members of the coronavirus family. We will detail the unmet clinical need associated with the continued transmission of SARS-CoV-2, MERS-CoV and the four seasonal coronaviruses (HCoV-OC43, NL63, HKU1 and 229E) in humans and the potential for future zoonotic coronaviruses. We will highlight how first-generation SARS-CoV-2 vaccines and natural history studies have greatly increased our understanding of effective antiviral immunity to coronaviruses and have informed next-generation vaccine design. We will then consider the ideal properties of a pan-coronavirus vaccine and propose a blueprint for the type of immunity that may offer cross-protection. Finally, we will describe a subset of the diverse technologies and novel approaches being pursued with the goal of developing broadly or universally protective vaccines for coronaviruses.
Collapse
Affiliation(s)
- S Cankat
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London, NW3 2PP, UK
| | - M U Demael
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London, NW3 2PP, UK
| | - L Swadling
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London, NW3 2PP, UK.
| |
Collapse
|
15
|
Mormile R. De Novo Vitiligo Following Covid-19 Infection and Vaccination: A Door Open to Future Events? Arch Med Res 2024; 55:102961. [PMID: 38295468 DOI: 10.1016/j.arcmed.2024.102961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Affiliation(s)
- Raffaella Mormile
- Division of Pediatrics and Neonatology, Moscati Hospital, Aversa, Italy.
| |
Collapse
|
16
|
Dos Santos Alves RP, Timis J, Miller R, Valentine K, Pinto PBA, Gonzalez A, Regla-Nava JA, Maule E, Nguyen MN, Shafee N, Landeras-Bueno S, Olmedillas E, Laffey B, Dobaczewska K, Mikulski Z, McArdle S, Leist SR, Kim K, Baric RS, Ollmann Saphire E, Elong Ngono A, Shresta S. Human coronavirus OC43-elicited CD4 + T cells protect against SARS-CoV-2 in HLA transgenic mice. Nat Commun 2024; 15:787. [PMID: 38278784 PMCID: PMC10817949 DOI: 10.1038/s41467-024-45043-2] [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: 08/18/2023] [Accepted: 01/10/2024] [Indexed: 01/28/2024] Open
Abstract
SARS-CoV-2-reactive T cells are detected in some healthy unexposed individuals. Human studies indicate these T cells could be elicited by the common cold coronavirus OC43. To directly test this assumption and define the role of OC43-elicited T cells that are cross-reactive with SARS-CoV-2, we develop a model of sequential infections with OC43 followed by SARS-CoV-2 in HLA-B*0702 and HLA-DRB1*0101 Ifnar1-/- transgenic mice. We find that OC43 infection can elicit polyfunctional CD8+ and CD4+ effector T cells that cross-react with SARS-CoV-2 peptides. Furthermore, pre-exposure to OC43 reduces subsequent SARS-CoV-2 infection and disease in the lung for a short-term in HLA-DRB1*0101 Ifnar1-/- transgenic mice, and a longer-term in HLA-B*0702 Ifnar1-/- transgenic mice. Depletion of CD4+ T cells in HLA-DRB1*0101 Ifnar1-/- transgenic mice with prior OC43 exposure results in increased viral burden in the lung but no change in virus-induced lung damage following infection with SARS-CoV-2 (versus CD4+ T cell-sufficient mice), demonstrating that the OC43-elicited SARS-CoV-2 cross-reactive T cell-mediated cross-protection against SARS-CoV-2 is partially dependent on CD4+ T cells. These findings contribute to our understanding of the origin of pre-existing SARS-CoV-2-reactive T cells and their effects on SARS-CoV-2 clinical outcomes, and also carry implications for development of broadly protective betacoronavirus vaccines.
Collapse
Affiliation(s)
| | - Julia Timis
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Robyn Miller
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kristen Valentine
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Andrew Gonzalez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jose Angel Regla-Nava
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Microbiology and Pathology, University Center for Health Science (CUCS), University of Guadalajara, Guadalajara, 44340, Mexico
| | - Erin Maule
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Michael N Nguyen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Norazizah Shafee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sara Landeras-Bueno
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Eduardo Olmedillas
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Brett Laffey
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Katarzyna Dobaczewska
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Zbigniew Mikulski
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sara McArdle
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth Kim
- Histopathology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Annie Elong Ngono
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
| |
Collapse
|
17
|
Vecchio E, Rotundo S, Veneziano C, Abatino A, Aversa I, Gallo R, Giordano C, Serapide F, Fusco P, Viglietto G, Cuda G, Costanzo F, Russo A, Trecarichi EM, Torti C, Palmieri C. The spike-specific TCRβ repertoire shows distinct features in unvaccinated or vaccinated patients with SARS-CoV-2 infection. J Transl Med 2024; 22:33. [PMID: 38185632 PMCID: PMC10771664 DOI: 10.1186/s12967-024-04852-1] [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: 10/22/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND The evolving variants of SARS-CoV-2 may escape immunity from prior infections or vaccinations. It's vital to understand how immunity adapts to these changes. Both infection and mRNA vaccination induce T cells that target the Spike protein. These T cells can recognize multiple variants, such as Delta and Omicron, even if neutralizing antibodies are weakened. However, the degree of recognition can vary among people, affecting vaccine efficacy. Previous studies demonstrated the capability of T-cell receptor (TCR) repertoire analysis to identify conserved and immunodominant peptides with cross-reactive potential among variant of concerns. However, there is a need to extend the analysis of the TCR repertoire to different clinical scenarios. The aim of this study was to examine the Spike-specific TCR repertoire profiles in natural infections and those with combined natural and vaccine immunity. METHODS A T-cell enrichment approach and bioinformatic tools were used to investigate the Spike-specific TCRβ repertoire in peripheral blood mononuclear cells of previously vaccinated (n = 8) or unvaccinated (n = 6) COVID-19 patients. RESULTS Diversity and clonality of the TCRβ repertoire showed no significant differences between vaccinated and unvaccinated groups. When comparing the TCRβ data to public databases, 692 unique TCRβ sequences linked to S epitopes were found in the vaccinated group and 670 in the unvaccinated group. TCRβ clonotypes related to spike regions S135-177, S264-276, S319-350, and S448-472 appear notably more prevalent in the vaccinated group. In contrast, the S673-699 epitope, believed to have super antigenic properties, is observed more frequently in the unvaccinated group. In-silico analyses suggest that mutations in epitopes, relative to the main SARS-CoV-2 variants of concern, don't hinder their cross-reactive recognition by associated TCRβ clonotypes. CONCLUSIONS Our findings reveal distinct TCRβ signatures in vaccinated and unvaccinated individuals with COVID-19. These differences might be associated with disease severity and could influence clinical outcomes. TRIAL REGISTRATION FESR/FSE 2014-2020 DDRC n. 585, Action 10.5.12, noCOVID19@UMG.
Collapse
Affiliation(s)
- Eleonora Vecchio
- Department of Experimental and Clinical Medicine, University "Magna Graecia", Viale Europa, 88100, Catanzaro, Italy
- Interdepartmental Centre of Services, University "Magna Graecia", 88100, Catanzaro, Italy
| | - Salvatore Rotundo
- Department of Medical and Surgical Sciences, Chair of Infectious and Tropical Diseases, University "Magna Graecia", 88100, Catanzaro, Italy
| | - Claudia Veneziano
- Interdepartmental Centre of Services, University "Magna Graecia", 88100, Catanzaro, Italy
| | - Antonio Abatino
- Department of Experimental and Clinical Medicine, University "Magna Graecia", Viale Europa, 88100, Catanzaro, Italy
| | - Ilenia Aversa
- Department of Experimental and Clinical Medicine, University "Magna Graecia", Viale Europa, 88100, Catanzaro, Italy
| | - Raffaella Gallo
- Department of Experimental and Clinical Medicine, University "Magna Graecia", Viale Europa, 88100, Catanzaro, Italy
| | - Caterina Giordano
- Department of Experimental and Clinical Medicine, University "Magna Graecia", Viale Europa, 88100, Catanzaro, Italy
| | - Francesca Serapide
- Department of Medical and Surgical Sciences, Chair of Infectious and Tropical Diseases, University "Magna Graecia", 88100, Catanzaro, Italy
| | - Paolo Fusco
- Department of Medical and Surgical Sciences, Chair of Infectious and Tropical Diseases, University "Magna Graecia", 88100, Catanzaro, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, University "Magna Graecia", Viale Europa, 88100, Catanzaro, Italy
| | - Giovanni Cuda
- Department of Experimental and Clinical Medicine, University "Magna Graecia", Viale Europa, 88100, Catanzaro, Italy
| | - Francesco Costanzo
- Department of Experimental and Clinical Medicine, University "Magna Graecia", Viale Europa, 88100, Catanzaro, Italy
- Interdepartmental Centre of Services, University "Magna Graecia", 88100, Catanzaro, Italy
| | - Alessandro Russo
- Department of Medical and Surgical Sciences, Chair of Infectious and Tropical Diseases, University "Magna Graecia", 88100, Catanzaro, Italy
| | - Enrico Maria Trecarichi
- Department of Medical and Surgical Sciences, Chair of Infectious and Tropical Diseases, University "Magna Graecia", 88100, Catanzaro, Italy
| | - Carlo Torti
- Department of Medical and Surgical Sciences, Chair of Infectious and Tropical Diseases, University "Magna Graecia", 88100, Catanzaro, Italy
| | - Camillo Palmieri
- Department of Experimental and Clinical Medicine, University "Magna Graecia", Viale Europa, 88100, Catanzaro, Italy.
| |
Collapse
|
18
|
Jung K, Ko D, Jang J, Kim YR, Heo JY, Kim Y. Harnessing SARS-CoV-2-specific CD8 + T cells to kill target tumor cells for cancer immunotherapy. Cancer Commun (Lond) 2024; 44:173-177. [PMID: 37856250 PMCID: PMC10794008 DOI: 10.1002/cac2.12497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Affiliation(s)
- Keunok Jung
- Department of Allergy and Clinical ImmunologyAjou University School of MedicineSuwonRepublic of Korea
| | - Deok‐Han Ko
- Department of Molecular Science and TechnologyAjou UniversitySuwonRepublic of Korea
| | - Jeong‐Yun Jang
- Department of Molecular Science and TechnologyAjou UniversitySuwonRepublic of Korea
| | - Young Rong Kim
- Department of Infectious DiseasesAjou University School of MedicineSuwonRepublic of Korea
| | - Jung Yeon Heo
- Department of Infectious DiseasesAjou University School of MedicineSuwonRepublic of Korea
| | - Yong‐Sung Kim
- Department of Allergy and Clinical ImmunologyAjou University School of MedicineSuwonRepublic of Korea
- Department of Molecular Science and TechnologyAjou UniversitySuwonRepublic of Korea
| |
Collapse
|
19
|
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.
Collapse
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.)
| |
Collapse
|
20
|
Olmedillas E, Rajamanickam RR, Avalos RD, Sosa FA, Zandonatti MA, Harkins SS, Shresta S, Hastie KM, Saphire EO. Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571764. [PMID: 38168261 PMCID: PMC10760097 DOI: 10.1101/2023.12.14.571764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The 800 million human infections with SARS-CoV-2 and the likely emergence of new variants and additional coronaviruses necessitate a better understanding of the essential spike glycoprotein and the development of immunogens that foster broader and more durable immunity. The S2 fusion subunit is more conserved in sequence, is essential to function, and would be a desirable immunogen to boost broadly reactive antibodies. It is, however, unstable in structure and in its wild-type form, cannot be expressed alone without irreversible collapse into a six-helix bundle. In addition to the irreversible conformational changes of fusion, biophysical measurements indicate that spike also undergoes a reversible breathing action. However, spike in an open, "breathing" conformation has not yet been visualized at high resolution. Here we describe an S2-only antigen, engineered to remain in its relevant, pre-fusion viral surface conformation in the absence of S1. We also describe a panel of natural human antibodies specific for S2 from vaccinated and convalescent individuals. One of these mAbs, from a convalescent individual, afforded a high-resolution cryo-EM structure of the prefusion S2. The structure reveals a complex captured in an "open" conformation with greater stabilizing intermolecular interactions at the base and a repositioned fusion peptide. Together, this work provides an antigen for advancement of next-generation "booster" immunogens and illuminates the likely breathing adjustments of the coronavirus spike.
Collapse
Affiliation(s)
- Eduardo Olmedillas
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Roshan R. Rajamanickam
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Ruben Diaz Avalos
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Fernanda A. Sosa
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Michelle A. Zandonatti
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Stephanie S. Harkins
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Kathryn M. Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| |
Collapse
|
21
|
Silva BJDA, Krogstad PA, Teles RMB, Andrade PR, Rajfer J, Ferrini MG, Yang OO, Bloom BR, Modlin RL. IFN-γ-mediated control of SARS-CoV-2 infection through nitric oxide. Front Immunol 2023; 14:1284148. [PMID: 38162653 PMCID: PMC10755032 DOI: 10.3389/fimmu.2023.1284148] [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: 08/28/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction The COVID-19 pandemic has highlighted the need to identify mechanisms of antiviral host defense against SARS-CoV-2. One such mediator is interferon-g (IFN-γ), which, when administered to infected patients, is reported to result in viral clearance and resolution of pulmonary symptoms. IFN-γ treatment of a human lung epithelial cell line triggered an antiviral activity against SARS-CoV-2, yet the mechanism for this antiviral response was not identified. Methods Given that IFN-γ has been shown to trigger antiviral activity via the generation of nitric oxide (NO), we investigated whether IFN-γ induction of antiviral activity against SARS-CoV-2 infection is dependent upon the generation of NO in human pulmonary epithelial cells. We treated the simian epithelial cell line Vero E6 and human pulmonary epithelial cell lines, including A549-ACE2, and Calu-3, with IFN-γ and observed the resulting induction of NO and its effects on SARS-CoV-2 replication. Pharmacological inhibition of inducible nitric oxide synthase (iNOS) was employed to assess the dependency on NO production. Additionally, the study examined the effect of interleukin-1b (IL-1β) on the IFN-g-induced NO production and its antiviral efficacy. Results Treatment of Vero E6 cells with IFN-γ resulted in a dose-responsive induction of NO and an inhibitory effect on SARS-CoV-2 replication. This antiviral activity was blocked by pharmacologic inhibition of iNOS. IFN-γ also triggered a NO-mediated antiviral activity in SARS-CoV-2 infected human lung epithelial cell lines A549-ACE2 and Calu-3. IL-1β enhanced IFN-γ induction of NO, but it had little effect on antiviral activity. Discussion Given that IFN-g has been shown to be produced by CD8+ T cells in the early response to SARS-CoV-2, our findings in human lung epithelial cell lines, of an IFN-γ-triggered, NO-dependent, links the adaptive immune response to an innate antiviral pathway in host defense against SARS-CoV-2. These results underscore the importance of IFN-γ and NO in the antiviral response and provide insights into potential therapeutic strategies for COVID-19.
Collapse
Affiliation(s)
- Bruno J. de Andrade Silva
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine at University of California (UCLA), Los Angeles, CA, United States
| | - Paul A. Krogstad
- Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, United States
| | - Rosane M. B. Teles
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine at University of California (UCLA), Los Angeles, CA, United States
| | - Priscila R. Andrade
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine at University of California (UCLA), Los Angeles, CA, United States
| | - Jacob Rajfer
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Monica G. Ferrini
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
- Department of Health and Life Sciences, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
| | - Otto O. Yang
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Barry R. Bloom
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Robert L. Modlin
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine at University of California (UCLA), Los Angeles, CA, United States
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| |
Collapse
|
22
|
Markov NS, Ren Z, Senkow KJ, Grant RA, Gao CA, Malsin ES, Sichizya L, Kihshen H, Helmin KA, Jovisic M, Arnold JM, Pérez-Leonor XG, Abdala-Valencia H, Swaminathan S, Nwaezeapu J, Kang M, Rasmussen L, Ozer EA, Lorenzo-Redondo R, Hultquist JF, Simons LM, Rios-Guzman E, Misharin AV, Wunderink RG, Budinger GS, Singer BD, Morales-Nebreda L. A distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571479. [PMID: 38168346 PMCID: PMC10760069 DOI: 10.1101/2023.12.13.571479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Pathogen clearance and resolution of inflammation in patients with pneumonia require an effective local T cell response. Nevertheless, local T cell activation may drive lung injury, particularly during prolonged episodes of respiratory failure characteristic of severe SARS-CoV-2 pneumonia. While T cell responses in the peripheral blood are well described, the evolution of T cell phenotypes and molecular signatures in the distal lung of patients with severe pneumonia caused by SARS-CoV-2 or other pathogens is understudied. Accordingly, we serially obtained 432 bronchoalveolar lavage fluid samples from 273 patients with severe pneumonia and respiratory failure, including 74 unvaccinated patients with COVID-19, and performed flow cytometry, transcriptional, and T cell receptor profiling on sorted CD8+ and CD4+ T cell subsets. In patients with COVID-19 but not pneumonia secondary to other pathogens, we found that early and persistent enrichment in CD8+ and CD4+ T cell subsets correlated with survival to hospital discharge. Activation of interferon signaling pathways early after intubation for COVID-19 was associated with favorable outcomes, while activation of NF-κB-driven programs late in disease was associated with poor outcomes. Patients with SARS-CoV-2 pneumonia whose alveolar T cells preferentially targeted the Spike and Nucleocapsid proteins tended to experience more favorable outcomes than patients whose T cells predominantly targeted the ORF1ab polyprotein complex. These results suggest that in patients with severe SARS-CoV-2 pneumonia, alveolar T cell interferon responses targeting structural SARS-CoV-2 proteins characterize patients who recover, yet these responses progress to NF-κB activation against non-structural proteins in patients who go on to experience poor clinical outcomes.
Collapse
Affiliation(s)
- Nikolay S. Markov
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Ziyou Ren
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Karolina J. Senkow
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Rogan A. Grant
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Catherine A. Gao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Elizabeth S. Malsin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Lango Sichizya
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Hermon Kihshen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Kathryn A. Helmin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Milica Jovisic
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Jason M. Arnold
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | | | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Suchitra Swaminathan
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Julu Nwaezeapu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Mengjia Kang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Luke Rasmussen
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Egon A. Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Ramon Lorenzo-Redondo
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Lacy M. Simons
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Estefany Rios-Guzman
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Alexander V. Misharin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Richard G. Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - G.R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Benjamin D. Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | | |
Collapse
|
23
|
Shamabadi NS, Bagasra AB, Pawar S, Bagasra O. Potential use of endemic human coronaviruses to stimulate immunity against pathogenic SARS-CoV-2 and its variants. Libyan J Med 2023; 18:2209949. [PMID: 37186902 DOI: 10.1080/19932820.2023.2209949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
While severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes significant morbidity and mortality in humans, there is a wide range of disease outcomes following virus exposures. Some individuals are asymptomatic while others develop complications within a few days after infection that can lead to fatalities in a smaller portion of the population. In the present study, we have analyzed the factors that may influence the outcome of post-SARS-CoV-2 infection. One factor that may influence virus control is pre-existing immunity conferred by an individual's past exposures to endemic coronaviruses (eCOVIDs) which cause the common cold in humans and generally, most children are exposed to one of the four eCOVIDs before 2 years of age. Here, we have carried out protein sequence analyses to show the amino acid homologies between the four eCOVIDs (i.e. OC43, HKU1, 229E, and NL63) as well as examining the cross-reactive immune responses between SARS-CoV-2 and eCOVIDs by epidemiologic analyses. Our results show that the nations where continuous exposures to eCOVIDs are very high due to religious and traditional causes showed significantly lower cases and low mortality rates per 100,000. We hypothesize that in the areas of the globe where Muslims are in majority and due to religious practices are regularly exposed to eCOVIDs they show a significantly lower infection, as well as mortality rate, and that is due to pre-existing cross-immunity against SARS-CoV-2. This is due to cross-reactive antibodies and T-cells that recognize SARS-CoV-2 antigens. We also have reviewed the current literature that has also proposed that human infections with eCOVIDs impart protection against disease caused by subsequent exposure to SARS-CoV-2. We propose that a nasal spray vaccine consisting of selected genes of eCOVIDs would be beneficial against SARS-CoV-2 and other pathogenic coronaviruses.
Collapse
Affiliation(s)
| | - Anisah B Bagasra
- Department of Psychology, Kennesaw State University, Kennesaw, GA, USA
| | - Shrikant Pawar
- Department of Computer Science and Biology, Claflin University, SC, USA
| | - Omar Bagasra
- South Carolina Center for Biotechnology, Claflin University, Orangeburg, SC, USA
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Al Saihati HA, Hussein HAM, Thabet AA, Wardany AA, Mahmoud SY, Farrag ES, Mohamed TIA, Fathy SM, Elnosary ME, Sobhy A, Ahmed AE, El-Adly AM, El-Shenawy FS, Elsadek AA, Rayan A, Zahran ZAM, El-Badawy O, El-Naggar MGM, Afifi MM, Zahran AM. Memory T Cells Discrepancies in COVID-19 Patients. Microorganisms 2023; 11:2737. [PMID: 38004749 PMCID: PMC10673271 DOI: 10.3390/microorganisms11112737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
The immune response implicated in Coronavirus disease 2019 (COVID-19) pathogenesis remains to be fully understood. The present study aimed to clarify the alterations in CD4+ and CD8+ memory T cells' compartments in SARS-CoV-2-infected patients, with an emphasis on various comorbidities affecting COVID-19 patients. Peripheral blood samples were collected from 35 COVID-19 patients, 16 recovered individuals, and 25 healthy controls, and analyzed using flow cytometry. Significant alterations were detected in the percentage of CD8+ T cells and effector memory-expressing CD45RA CD8+ T cells (TEMRA) in COVID-19 patients compared to healthy controls. Interestingly, altered percentages of CD4+ T cells, CD8+ T cells, T effector (TEff), T naïve cells (TNs), T central memory (TCM), T effector memory (TEM), T stem cell memory (TSCM), and TEMRA T cells were significantly associated with the disease severity. Male patients had more CD8+ TSCMs and CD4+ TNs cells, while female patients had a significantly higher percentage of effector CD8+CD45RA+ T cells. Moreover, altered percentages of CD8+ TNs and memory CD8+CD45RO+ T cells were detected in diabetic and non-diabetic COVID-19 patients, respectively. In summary, this study identified alterations in memory T cells among COVID-19 patients, revealing a sex bias in the percentage of memory T cells. Moreover, COVID-19 severity and comorbidities have been linked to specific subsets of T memory cells which could be used as therapeutic, diagnostic, and protective targets for severe COVID-19.
Collapse
Affiliation(s)
- Hajir A. Al Saihati
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, University of Hafr Al Batin, P.O. Box 1803, Hafar Al Batin 31991, Saudi Arabia; (H.A.A.S.); (E.S.F.)
| | - Hosni A. M. Hussein
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Ali A. Thabet
- Department of Zoology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt;
| | - Ahmed A. Wardany
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Sabry Y. Mahmoud
- Biology Department, College of Sciences, University of Hafr Al-Batin, Hafr Al-Batin 31991, Saudi Arabia;
- Department of Microbiology, Sohag University, Sohag 82524, Egypt
| | - Eman S. Farrag
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, University of Hafr Al Batin, P.O. Box 1803, Hafar Al Batin 31991, Saudi Arabia; (H.A.A.S.); (E.S.F.)
- Department of Microbiology, South Valley University, Qena 83523, Egypt
| | - Taha I. A. Mohamed
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Samah M. Fathy
- Department of Zoology, Faculty of Science, Fayoum University, Fayoum 63514, Egypt;
| | - Mohamed E. Elnosary
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Egypt; (M.E.E.); (M.M.A.)
| | - Ali Sobhy
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, Assiut 71524, Egypt; (A.S.); (A.E.A.)
| | - Abdelazeem E. Ahmed
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, Assiut 71524, Egypt; (A.S.); (A.E.A.)
| | - Ahmed M. El-Adly
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | - Fareed S. El-Shenawy
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt; (A.A.W.); (T.I.A.M.); (A.M.E.-A.); (F.S.E.-S.)
| | | | - Amal Rayan
- Department of Clinical Oncology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | | | - Omnia El-Badawy
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Mohamed G. M. El-Naggar
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut 71515, Egypt; (M.G.M.E.-N.); (A.M.Z.)
| | - Magdy M. Afifi
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Egypt; (M.E.E.); (M.M.A.)
| | - Asmaa M. Zahran
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut 71515, Egypt; (M.G.M.E.-N.); (A.M.Z.)
| |
Collapse
|
26
|
Zhang W, Clemens EB, Kedzierski L, Chua BY, Mayo M, Lonzi C, Hinchcliff A, Rigas V, Middleton BF, Binks P, Rowntree LC, Allen LF, Tan HX, Petersen J, Chaurasia P, Krammer F, Wheatley AK, Kent SJ, Rossjohn J, Miller A, Lynar S, Nelson J, Nguyen THO, Davies J, Kedzierska K. Broad spectrum SARS-CoV-2-specific immunity in hospitalized First Nations peoples recovering from COVID-19. Immunol Cell Biol 2023; 101:964-974. [PMID: 37725525 PMCID: PMC10872797 DOI: 10.1111/imcb.12691] [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: 06/22/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
Indigenous peoples globally are at increased risk of COVID-19-associated morbidity and mortality. However, data that describe immune responses to SARS-CoV-2 infection in Indigenous populations are lacking. We evaluated immune responses in Australian First Nations peoples hospitalized with COVID-19. Our work comprehensively mapped out inflammatory, humoral and adaptive immune responses following SARS-CoV-2 infection. Patients were recruited early following the lifting of strict public health measures in the Northern Territory, Australia, between November 2021 and May 2022. Australian First Nations peoples recovering from COVID-19 showed increased levels of MCP-1 and IL-8 cytokines, IgG-antibodies against Delta-RBD and memory SARS-CoV-2-specific T cell responses prior to hospital discharge in comparison with hospital admission, with resolution of hyperactivated HLA-DR+ CD38+ T cells. SARS-CoV-2 infection elicited coordinated ASC, Tfh and CD8+ T cell responses in concert with CD4+ T cell responses. Delta and Omicron RBD-IgG, as well as Ancestral N-IgG antibodies, strongly correlated with Ancestral RBD-IgG antibodies and Spike-specific memory B cells. We provide evidence of broad and robust immune responses following SARS-CoV-2 infection in Indigenous peoples, resembling those of non-Indigenous COVID-19 hospitalized patients.
Collapse
Affiliation(s)
- Wuji Zhang
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Lukasz Kedzierski
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Brendon Y Chua
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Mark Mayo
- Menzies School of Health Research, Darwin, NT 0811, Australia
| | - Claire Lonzi
- Menzies School of Health Research, Darwin, NT 0811, Australia
| | | | - Vanessa Rigas
- Menzies School of Health Research, Darwin, NT 0811, Australia
| | | | - Paula Binks
- Menzies School of Health Research, Darwin, NT 0811, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Lilith F Allen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Jan Petersen
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Priyanka Chaurasia
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, VIC 3010, Australia
- Melbourne Sexual Health Centre, Infectious Diseases Department, Alfred Health, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Adrian Miller
- Indigenous Engagement, CQUniversity, Townsville, QLD 4810, Australia
| | - Sarah Lynar
- Menzies School of Health Research, Darwin, NT 0811, Australia
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, NT, Australia
| | - Jane Nelson
- Menzies School of Health Research, Darwin, NT 0811, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Jane Davies
- Menzies School of Health Research, Darwin, NT 0811, Australia
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, NT, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
- Center for Influenza Disease and Emergence Response (CIDER), Melbourne, VIC 3000, Australia
| |
Collapse
|
27
|
Diniz MO, Maini MK, Swadling L. T cell control of SARS-CoV-2: When, which, and where? Semin Immunol 2023; 70:101828. [PMID: 37651850 DOI: 10.1016/j.smim.2023.101828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/13/2023] [Indexed: 09/02/2023]
Abstract
Efficient immune protection against viruses such as SARS-CoV-2 requires the coordinated activity of innate immunity, B and T cells. Accumulating data point to a critical role for T cells not only in the clearance of established infection, but also for aborting viral replication independently of humoral immunity. Here we review the evidence supporting the contribution of antiviral T cells and consider which of their qualitative features favour efficient control of infection. We highlight how studies of SARS-CoV-2 and other coronaviridae in animals and humans have provided important lessons on the optimal timing (When), functionality and specificity (Which), and location (Where) of antiviral T cells. We discuss the clinical implications, particularly for the development of next-generation vaccines, and emphasise areas requiring further study.
Collapse
Affiliation(s)
- Mariana O Diniz
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK
| | - Mala K Maini
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK.
| | - Leo Swadling
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, Pears Building, London WC1E 6BT, UK.
| |
Collapse
|
28
|
Schmidt F, Fields HF, Purwanti Y, Milojkovic A, Salim S, Wu KX, Simoni Y, Vitiello A, MacLeod DT, Nardin A, Newell EW, Fink K, Wilm A, Fehlings M. In-depth analysis of human virus-specific CD8 + T cells delineates unique phenotypic signatures for T cell specificity prediction. Cell Rep 2023; 42:113250. [PMID: 37837618 DOI: 10.1016/j.celrep.2023.113250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023] Open
Abstract
Following viral infection, the human immune system generates CD8+ T cell responses to virus antigens that differ in specificity, abundance, and phenotype. A characterization of virus-specific T cell responses allows one to assess infection history and to understand its contribution to protective immunity. Here, we perform in-depth profiling of CD8+ T cells binding to CMV-, EBV-, influenza-, and SARS-CoV-2-derived antigens in peripheral blood samples from 114 healthy donors and 55 cancer patients using high-dimensional mass cytometry and single-cell RNA sequencing. We analyze over 500 antigen-specific T cell responses across six different HLA alleles and observed unique phenotypes of T cells specific for antigens from different virus categories. Using machine learning, we extract phenotypic signatures of antigen-specific T cells, predict virus specificity for bulk CD8+ T cells, and validate these predictions, suggesting that machine learning can be used to accurately predict antigen specificity from T cell phenotypes.
Collapse
Affiliation(s)
| | | | | | | | | | - Kan Xing Wu
- ImmunoScape Pte Ltd, Singapore 228208, Singapore
| | | | | | | | | | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Katja Fink
- ImmunoScape Pte Ltd, Singapore 228208, Singapore
| | - Andreas Wilm
- ImmunoScape Pte Ltd, Singapore 228208, Singapore
| | | |
Collapse
|
29
|
Westmeier J, Brochtrup A, Paniskaki K, Karakoese Z, Werner T, Sutter K, Dolff S, Limmer A, Mittermüller D, Liu J, Zheng X, Koval T, Kaidashev I, Berger MM, Herbstreit F, Brenner T, Witzke O, Trilling M, Lu M, Yang D, Babel N, Westhoff T, Dittmer U, Zelinskyy G. Macrophage migration inhibitory factor receptor CD74 expression is associated with expansion and differentiation of effector T cells in COVID-19 patients. Front Immunol 2023; 14:1236374. [PMID: 37946732 PMCID: PMC10631787 DOI: 10.3389/fimmu.2023.1236374] [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: 06/07/2023] [Accepted: 10/02/2023] [Indexed: 11/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused millions of COVID-19 cases and deaths worldwide. Severity of pulmonary pathologies and poor prognosis were reported to be associated with the activation non-virus-specific bystander T cells. In addition, high concentrations of the macrophage migration inhibitory factor (MIF) were found in serum of COVID-19 patients. We hypothesized that these two pathogenic factors might be related and analyzed the expression of receptors for MIF on T cells in COVID-19. T cells from PBMCs of hospitalized patients with mild and severe COVID-19 were characterized. A significantly higher proportion of CD4+ and CD8+ T cells from COVID-19 patients expressed CD74 on the cell surface compared to healthy controls. To induce intracellular signaling upon MIF binding, CD74 forms complexes with CD44, CXCR2, or CXCR4. The vast majority of CD74+ T cells expressed CD44, whereas expression of CXCR2 and CXCR4 was low in controls but increased upon SARS-CoV-2 infection. Hence, T cells in COVID-19 patients express receptors that render them responsive to MIF. A detailed analysis of CD74+ T cell populations revealed that most of them had a central memory phenotype early in infection, while cells with an effector and effector memory phenotype arose later during infection. Furthermore, CD74+ T cells produced more cytotoxic molecules and proliferation markers. Our data provide new insights into the MIF receptor and co-receptor repertoire of bystander T cells in COVID-19 and uncovers a novel and potentially druggable aspect of the immunological footprint of SARS-CoV-2.
Collapse
Affiliation(s)
- Jaana Westmeier
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Annika Brochtrup
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Krystallenia Paniskaki
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Center for Translational Medicine, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Zehra Karakoese
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Tanja Werner
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Sebastian Dolff
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Andreas Limmer
- Department of Anesthesiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Department of Pediatric Heart Surgery, Friedrich-Alexander- Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Daniela Mittermüller
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jia Liu
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology (HUST), Wuhan, China
- Department of Infectious Diseases, Union Hospital of Tonji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Xin Zheng
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology (HUST), Wuhan, China
- Department of Infectious Diseases, Union Hospital of Tonji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Tetiana Koval
- Department of Infectious Diseases with Epidemiology, Poltava State Medical University, Poltava, Ukraine
| | - Igor Kaidashev
- Department of Internal Medicine №3 with Phthisiology, Poltava State Medical University, Poltava, Ukraine
| | - Marc Moritz Berger
- Department of Anesthesiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Frank Herbstreit
- Department of Anesthesiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Thorsten Brenner
- Department of Anesthesiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Mirko Trilling
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Mengji Lu
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Dongliang Yang
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology (HUST), Wuhan, China
- Department of Infectious Diseases, Union Hospital of Tonji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Nina Babel
- Center for Translational Medicine, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, Berlin, Germany
| | - Timm Westhoff
- Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr University of Bochum, Herne, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Gennadiy Zelinskyy
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology (HUST), Wuhan, China
| |
Collapse
|
30
|
Bean DJ, Monroe J, Liang YM, Borberg E, Senussi Y, Swank Z, Chalise S, Walt D, Weinberg J, Sagar M. Heterotypic responses against nsp12/nsp13 from prior SARS-CoV-2 infection associates with lower subsequent endemic coronavirus incidence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563621. [PMID: 37961343 PMCID: PMC10634759 DOI: 10.1101/2023.10.23.563621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Immune responses from prior SARS-CoV-2 infection and COVID-19 vaccination do not prevent re-infections and may not protect against future novel coronaviruses (CoVs). We examined the incidence of and immune differences against human endemic CoVs (eCoV) as a proxy for response against future emerging CoVs. Assessment was among those with known SARS-CoV-2 infection, COVID-19 vaccination but no documented SARS-CoV-2 infection, or neither exposure. Retrospective cohort analyses suggest that prior SARS-CoV-2 infection, but not COVID-19 vaccination alone, protects against subsequent symptomatic eCoV infection. CD8+ T cell responses to the non-structural eCoV proteins, nsp12 and nsp13, were significantly higher in individuals with previous SARS-CoV-2 infection as compared to the other groups. The three groups had similar cellular responses against the eCoV spike and nucleocapsid, and those with prior spike exposure had lower eCoV-directed neutralizing antibodies. Incorporation of non-structural viral antigens in a future pan-CoV vaccine may improve protection against future heterologous CoV infections.
Collapse
Affiliation(s)
- David J. Bean
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Janet Monroe
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Yan Mei Liang
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Ella Borberg
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Yasmeen Senussi
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Zoe Swank
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Sujata Chalise
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - David Walt
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Janice Weinberg
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Manish Sagar
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| |
Collapse
|
31
|
Pospiech M, Tamizharasan M, Wei YC, Kumar AMS, Lou M, Milstein J, Alachkar H. Features of the TCR repertoire associate with patients' clinical and molecular characteristics in acute myeloid leukemia. Front Immunol 2023; 14:1236514. [PMID: 37928542 PMCID: PMC10620936 DOI: 10.3389/fimmu.2023.1236514] [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: 06/07/2023] [Accepted: 09/07/2023] [Indexed: 11/07/2023] Open
Abstract
Background Allogeneic hematopoietic stem cell transplant remains the most effective strategy for patients with high-risk acute myeloid leukemia (AML). Leukemia-specific neoantigens presented by the major histocompatibility complexes (MHCs) are recognized by the T cell receptors (TCR) triggering the graft-versus-leukemia effect. A unique TCR signature is generated by a complex V(D)J rearrangement process to form TCR capable of binding to the peptide-MHC. The generated TCR repertoire undergoes dynamic changes with disease progression and treatment. Method Here we applied two different computational tools (TRUST4 and MIXCR) to extract the TCR sequences from RNA-seq data from The Cancer Genome Atlas (TCGA) and examine the association between features of the TCR repertoire in adult patients with AML and their clinical and molecular characteristics. Results We found that only ~30% of identified TCR CDR3s were shared by the two computational tools. Yet, patterns of TCR associations with patients' clinical and molecular characteristics based on data obtained from either tool were similar. The numbers of unique TCR clones were highly correlated with patients' white blood cell counts, bone marrow blast percentage, and peripheral blood blast percentage. Multivariable regressions of TCRA and TCRB median normalized number of unique clones with mutational status of AML patients using TRUST4 showed significant association of TCRA or TCRB with WT1 mutations, WBC count, %BM blast, and sex (adjusted in TCRB model). We observed a correlation between TCRA/B number of unique clones and the expression of T cells inhibitory signal genes (TIGIT, LAG3, CTLA-4) and foxp3, but not IL2RA, CD69 and TNFRSF9 suggestive of exhausted T cell phenotypes in AML. Conclusion Benchmarking of computational tools is needed to increase the accuracy of the identified clones. The utilization of RNA-seq data enables identification of highly abundant TCRs and correlating these clones with patients' clinical and molecular characteristics. This study further supports the value of high-resolution TCR-Seq analyses to characterize the TCR repertoire in patients.
Collapse
Affiliation(s)
- Mateusz Pospiech
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Mukund Tamizharasan
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Department of Computer Science, University of Southern California, Los Angeles, CA, United States
| | - Yu-Chun Wei
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Advaith Maya Sanjeev Kumar
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Department of Computer Science, University of Southern California, Los Angeles, CA, United States
| | - Mimi Lou
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Joshua Milstein
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Houda Alachkar
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States
| |
Collapse
|
32
|
Witney MJ, Purcell AW, Tscharke DC. Need to know which MHCs protect against COVID? There's an App for that! Immunol Cell Biol 2023; 101:789-792. [PMID: 37638731 DOI: 10.1111/imcb.12680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
In this article, we discuss the recent observation by Augusto et al. made using a novel mobile phone application-based COVID-19 Citizen Science Study that an HLA genetic variant, HLA-B*15:01, is associated with asymptomatic SARS-CoV-2 infection. To explain this association, Augusto et al. describe a cross-reactive memory CD8+ T-cell response in HLA-B*15:01+ SARS-CoV-2 unexposed individuals that retains high avidity for two structurally conserved epitopes found in SARS-CoV-2 and seasonal coronavirus strains. These observations provide an insight into potential molecular determinants that facilitate rapid, early clearance of virus.
Collapse
Affiliation(s)
- Matthew J Witney
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Anthony W Purcell
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Acton, ACT, Australia
| |
Collapse
|
33
|
Wellington D, Yin Z, Yu Z, Heilig R, Davis S, Fischer R, Felce SL, Antoun E, Hublitz P, Beveridge R, Dong D, Liu G, Yao X, Peng Y, Kessler BM, Dong T. SARS-CoV-2 mutations affect antigen processing by the proteasome to alter CD8 + T cell responses. Heliyon 2023; 9:e20076. [PMID: 37842619 PMCID: PMC10570596 DOI: 10.1016/j.heliyon.2023.e20076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 08/22/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Mutations within viral epitopes can result in escape from T cells, but the contribution of mutations in flanking regions of epitopes in SARS-CoV-2 has not been investigated. Focusing on two SARS-CoV-2 nucleoprotein CD8+ epitopes, we investigated the contribution of these flanking mutations to proteasomal processing and T cell activation. We found decreased NP9-17-B*27:05 CD8+ T cell responses to the NP-Q7K mutation, likely due to a lack of efficient epitope production by the proteasome, suggesting immune escape caused by this mutation. In contrast, NP-P6L and NP-D103 N/Y mutations flanking the NP9-17-B*27:05 and NP105-113-B*07:02 epitopes, respectively, increased CD8+ T cell responses associated with enhanced epitope production by the proteasome. Our results provide evidence that SARS-CoV-2 mutations outside the epitope could have a significant impact on proteasomal processing, either contributing to T cell escape or enhancement that may be exploited for future vaccine design.
Collapse
Affiliation(s)
- Dannielle Wellington
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Zixi Yin
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Zhanru Yu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Raphael Heilig
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Simon Davis
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Roman Fischer
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Elie Antoun
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Philip Hublitz
- Genome Engineering Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Ryan Beveridge
- Virus Screening Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Danning Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Guihai Liu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Xuan Yao
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Yanchun Peng
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Benedikt M. Kessler
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Tao Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| |
Collapse
|
34
|
Francis ME, Jansen EB, Yourkowski A, Selim A, Swan CL, MacPhee BK, Thivierge B, Buchanan R, Lavender KJ, Darbellay J, Rogers MB, Lew J, Gerdts V, Falzarano D, Skowronski DM, Sjaarda C, Kelvin AA. Previous infection with seasonal coronaviruses does not protect male Syrian hamsters from challenge with SARS-CoV-2. Nat Commun 2023; 14:5990. [PMID: 37752151 PMCID: PMC10522707 DOI: 10.1038/s41467-023-41761-1] [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: 02/22/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
SARS-CoV-2 variants and seasonal coronaviruses continue to cause disease and coronaviruses in the animal reservoir pose a constant spillover threat. Importantly, understanding of how previous infection may influence future exposures, especially in the context of seasonal coronaviruses and SARS-CoV-2 variants, is still limited. Here we adopted a step-wise experimental approach to examine the primary immune response and subsequent immune recall toward antigenically distinct coronaviruses using male Syrian hamsters. Hamsters were initially inoculated with seasonal coronaviruses (HCoV-NL63, HCoV-229E, or HCoV-OC43), or SARS-CoV-2 pango B lineage virus, then challenged with SARS-CoV-2 pango B lineage virus, or SARS-CoV-2 variants Beta or Omicron. Although infection with seasonal coronaviruses offered little protection against SARS-CoV-2 challenge, HCoV-NL63-infected animals had an increase of the previously elicited HCoV-NL63-specific neutralizing antibodies during challenge with SARS-CoV-2. On the other hand, primary infection with HCoV-OC43 induced distinct T cell gene signatures. Gene expression profiling indicated interferon responses and germinal center reactions to be induced during more similar primary infection-challenge combinations while signatures of increased inflammation as well as suppression of the antiviral response were observed following antigenically distant viral challenges. This work characterizes and analyzes seasonal coronaviruses effect on SARS-CoV-2 secondary infection and the findings are important for pan-coronavirus vaccine design.
Collapse
Affiliation(s)
- Magen E Francis
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ethan B Jansen
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anthony Yourkowski
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Alaa Selim
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Cynthia L Swan
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brian K MacPhee
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brittany Thivierge
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Rachelle Buchanan
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kerry J Lavender
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Joseph Darbellay
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Matthew B Rogers
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jocelyne Lew
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Danuta M Skowronski
- BC Centre for Disease Control, Immunization Programs and Vaccine Preventable Diseases Service, Vancouver, BC, Canada
- University of British Columbia, School of Population and Public Health, Vancouver, BC, Canada
| | - Calvin Sjaarda
- Department of Psychiatry, Queen's University, Kingston, ON, Canada
- Queen's Genomics Lab at Ongwanada (Q-GLO), Ongwanada Resource Centre, Kingston, ON, Canada
| | - Alyson A Kelvin
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.
| |
Collapse
|
35
|
Hu D, Irving AT. Massively-multiplexed epitope mapping techniques for viral antigen discovery. Front Immunol 2023; 14:1192385. [PMID: 37818363 PMCID: PMC10561112 DOI: 10.3389/fimmu.2023.1192385] [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: 03/23/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Following viral infection, viral antigens bind specifically to receptors on the surface of lymphocytes thereby activating adaptive immunity in the host. An epitope, the smallest structural and functional unit of an antigen, binds specifically to an antibody or antigen receptor, to serve as key sites for the activation of adaptive immunity. The complexity and diverse range of epitopes are essential to study and map for the diagnosis of disease, the design of vaccines and for immunotherapy. Mapping the location of these specific epitopes has become a hot topic in immunology and immune therapy. Recently, epitope mapping techniques have evolved to become multiplexed, with the advent of high-throughput sequencing and techniques such as bacteriophage-display libraries and deep mutational scanning. Here, we briefly introduce the principles, advantages, and disadvantages of the latest epitope mapping techniques with examples for viral antigen discovery.
Collapse
Affiliation(s)
- Diya Hu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Aaron T. Irving
- Department of Clinical Laboratory Studies, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Infection, Immunity & Cancer, Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
- Biomedical and Health Translational Research Centre of Zhejiang Province (BIMET), Haining, China
- College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
36
|
Pakotiprapha D, Kuhaudomlarp S, Tinikul R, Chanarat S. Bridging the Gap: Can COVID-19 Research Help Combat African Swine Fever? Viruses 2023; 15:1925. [PMID: 37766331 PMCID: PMC10536364 DOI: 10.3390/v15091925] [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: 08/09/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
African swine fever (ASF) is a highly contagious and economically devastating disease affecting domestic pigs and wild boar, caused by African swine fever virus (ASFV). Despite being harmless to humans, ASF poses significant challenges to the swine industry, due to sudden losses and trade restrictions. The ongoing COVID-19 pandemic has spurred an unparalleled global research effort, yielding remarkable advancements across scientific disciplines. In this review, we explore the potential technological spillover from COVID-19 research into ASF. Specifically, we assess the applicability of the diagnostic tools, vaccine development strategies, and biosecurity measures developed for COVID-19 for combating ASF. Additionally, we discuss the lessons learned from the pandemic in terms of surveillance systems and their implications for managing ASF. By bridging the gap between COVID-19 and ASF research, we highlight the potential for interdisciplinary collaboration and technological spillovers in the battle against ASF.
Collapse
Affiliation(s)
| | | | | | - Sittinan Chanarat
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| |
Collapse
|
37
|
Li B, Jiang AY, Raji I, Atyeo C, Raimondo TM, Gordon AGR, Rhym LH, Samad T, MacIsaac C, Witten J, Mughal H, Chicz TM, Xu Y, McNamara RP, Bhatia S, Alter G, Langer R, Anderson DG. Enhancing the immunogenicity of lipid-nanoparticle mRNA vaccines by adjuvanting the ionizable lipid and the mRNA. Nat Biomed Eng 2023:10.1038/s41551-023-01082-6. [PMID: 37679571 DOI: 10.1038/s41551-023-01082-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/27/2023] [Indexed: 09/09/2023]
Abstract
To elicit optimal immune responses, messenger RNA vaccines require intracellular delivery of the mRNA and the careful use of adjuvants. Here we report a multiply adjuvanted mRNA vaccine consisting of lipid nanoparticles encapsulating an mRNA-encoded antigen, optimized for efficient mRNA delivery and for the enhanced activation of innate and adaptive responses. We optimized the vaccine by screening a library of 480 biodegradable ionizable lipids with headgroups adjuvanted with cyclic amines and by adjuvanting the mRNA-encoded antigen by fusing it with a natural adjuvant derived from the C3 complement protein. In mice, intramuscular or intranasal administration of nanoparticles with the lead ionizable lipid and with mRNA encoding for the fusion protein (either the spike protein or the receptor-binding domain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)) increased the titres of antibodies against SARS-CoV-2 tenfold with respect to the vaccine encoding for the unadjuvanted antigen. Multiply adjuvanted mRNA vaccines may improve the efficacy, safety and ease of administration of mRNA-based immunization.
Collapse
Affiliation(s)
- Bowen Li
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Allen Yujie Jiang
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Idris Raji
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Division of Medical Sciences, Harvard University, Boston, MA, USA
| | - Theresa M Raimondo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akiva G R Gordon
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke H Rhym
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tahoura Samad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Corina MacIsaac
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jacob Witten
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haseeb Mughal
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Taras M Chicz
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Yue Xu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Ryan P McNamara
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Sangeeta Bhatia
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Wyss Institute at Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
38
|
Luxenburger H, Thimme R. SARS-CoV-2 and the liver: clinical and immunological features in chronic liver disease. Gut 2023; 72:1783-1794. [PMID: 37316169 PMCID: PMC10423489 DOI: 10.1136/gutjnl-2023-329623] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/24/2023] [Indexed: 06/16/2023]
Abstract
SARS-CoV-2 infection may affect the liver in healthy individuals but also influences the course of COVID-19 in patients with chronic liver disease (CLD). As described in healthy individuals, a strong SARS-CoV-2-specific adaptive immune response is important for the outcome of COVID-19, however, knowledge on the adaptive immune response in CLD is limited.Here, we review the clinical and immunological features of SARS-CoV-2 infection in individuals with CLD. Acute liver injury occurs in many cases of SARS-CoV-2 infection and may be induced by multiple factors, such as cytokines, direct viral infection or toxic effects of COVID-19 drugs. In individuals with CLD, SARS-CoV-2 infection may have a more severe course and promote decompensation and particularly in patients with cirrhosis. Compared with healthy individuals, the SARS-CoV-2-specific adaptive immune responses is impaired in patients with CLD after both, natural infection and vaccination but improves at least partially after booster vaccination.Following SARS-CoV-2 vaccination, rare cases of acute vaccine-induced liver injury and the development of autoimmune-like hepatitis have been reported. However, the concomitant elevation of liver enzymes is reversible under steroid treatment.
Collapse
Affiliation(s)
- Hendrik Luxenburger
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Robert Thimme
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| |
Collapse
|
39
|
Kanis FM, Meier JP, Guldan H, Niller HH, Dahm M, Dansard A, Zander T, Struck F, Soutschek E, Deml L, Möbus S, Barabas S. Performance of T-Track ® SARS-CoV-2, an Innovative Dual Marker RT-qPCR-Based Whole-Blood Assay for the Detection of SARS-CoV-2-Reactive T Cells. Diagnostics (Basel) 2023; 13:2722. [PMID: 37685260 PMCID: PMC10486492 DOI: 10.3390/diagnostics13172722] [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: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023] Open
Abstract
T-cell immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a central role in the control of the virus. In this study, we evaluated the performance of T-Track® SARS-CoV-2, a novel CE-marked quantitative reverse transcription-polymerase chain reaction (RT-qPCR) assay, which relies on the combined evaluation of IFNG and CXCL10 mRNA levels in response to the S1 and NP SARS-CoV-2 antigens, in 335 participants with or without a history of SARS-CoV-2 infection and vaccination, respectively. Of the 62 convalescent donors, 100% responded to S1 and 88.7% to NP antigens. In comparison, of the 68 naïve donors, 4.4% were reactive to S1 and 19.1% to NP. Convalescent donors <50 and ≥50 years of age demonstrated a 100% S1 reactivity and an 89.1% and 87.5% NP reactivity, respectively. T-cell responses by T-Track® SARS-CoV-2 and IgG serology by recomLine SARS-CoV-2 IgG according to the time from the last immunisation (by vaccination or viral infection) were comparable. Both assays showed a persistent cellular and humoral response for at least 36 weeks post immunisation in vaccinated and convalescent donors. Our results demonstrate the very good performance of the T-Track® SARS-CoV-2 molecular assay and suggest that it might be suitable to monitor the SARS-CoV-2-specific T-cell response in COVID-19 vaccinations trials and cross-reactivity studies.
Collapse
Affiliation(s)
| | | | | | - Hans-Helmut Niller
- Institute for Medical Microbiology and Hygiene, University of Regensburg, 93053 Regensburg, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Dang TTT, Anzurez A, Nakayama-Hosoya K, Miki S, Yamashita K, de Souza M, Matano T, Kawana-Tachikawa A. Breadth and Durability of SARS-CoV-2-Specific T Cell Responses following Long-Term Recovery from COVID-19. Microbiol Spectr 2023; 11:e0214323. [PMID: 37428088 PMCID: PMC10433967 DOI: 10.1128/spectrum.02143-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
T cell immunity is crucial for long-term immunological memory, but the profile of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific memory T cells in individuals who recovered from COVID-19 (COVID-19-convalescent individuals) is not sufficiently assessed. In this study, the breadth and magnitude of SARS-CoV-2-specific T cell responses were determined in COVID-19-convalescent individuals in Japan. Memory T cells against SARS-CoV-2 were detected in all convalescent individuals, and those with more severe disease exhibited a broader T cell response relative to cases with mild symptoms. Comprehensive screening of T cell responses at the peptide level was conducted for spike (S) and nucleocapsid (N) proteins, and regions frequently targeted by T cells were identified. Multiple regions in S and N proteins were targeted by memory T cells, with median numbers of target regions of 13 and 4, respectively. A maximum of 47 regions were recognized by memory T cells for an individual. These data indicate that SARS-CoV-2-convalescent individuals maintain a substantial breadth of memory T cells for at least several months following infection. Broader SARS-CoV-2-specific CD4+ T cell responses, relative to CD8+ T cell responses, were observed for the S but not the N protein, suggesting that antigen presentation is different between viral proteins. The binding affinity of predicted CD8+ T cell epitopes to HLA class I molecules in these regions was preserved for the Delta variant and at 94 to 96% for SARS-CoV-2 Omicron subvariants, suggesting that the amino acid changes in these variants do not have a major impact on antigen presentation to SARS-CoV-2-specific CD8+ T cells. IMPORTANCE RNA viruses, including SARS-CoV-2, evade host immune responses through mutations. As broader T cell responses against multiple viral proteins could minimize the impact of each single amino acid mutation, the breadth of memory T cells would be one essential parameter for effective protection. In this study, breadth of memory T cells to S and N proteins was assessed in COVID-19-convalescent individuals. While broad T cell responses were induced against both proteins, the ratio of N to S proteins for breadth of T cell responses was significantly higher in milder cases. The breadth of CD4+ and CD8+ T cell responses was also significantly different between S and N proteins, suggesting different contributions of N and S protein-specific T cells for COVID-19 control. Most CD8+ T cell epitopes in the immunodominant regions maintained their HLA binding to SARS-CoV-2 Omicron subvariants. Our study provides insights into understanding the protective efficacy of SARS-CoV-2-specific memory T cells against reinfection.
Collapse
Affiliation(s)
- Thi Thu Thao Dang
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Alitzel Anzurez
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | | | - Shoji Miki
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Mark de Souza
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of AIDS Vaccine Development, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of AIDS Vaccine Development, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| |
Collapse
|
41
|
Chen M, Venturi V, Munier CML. Dissecting the Protective Effect of CD8 + T Cells in Response to SARS-CoV-2 mRNA Vaccination and the Potential Link with Lymph Node CD8 + T Cells. BIOLOGY 2023; 12:1035. [PMID: 37508464 PMCID: PMC10376827 DOI: 10.3390/biology12071035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/04/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
SARS-CoV-2 vaccines have played a crucial role in effectively reducing COVID-19 disease severity, with a new generation of vaccines that use messenger RNA (mRNA) technology being administered globally. Neutralizing antibodies have featured as the heroes of vaccine-induced immunity. However, vaccine-elicited CD8+ T cells may have a significant impact on the early protective effects of the mRNA vaccine, which are evident 12 days after initial vaccination. Vaccine-induced CD8+ T cells have been shown to respond to multiple epitopes of SARS-CoV-2 and exhibit polyfunctionality in the periphery at the early stage, even when neutralizing antibodies are scarce. Furthermore, SARS-CoV-2 mRNA vaccines induce diverse subsets of memory CD8+ T cells that persist for more than six months following vaccination. However, the protective role of CD8+ T cells in response to the SARS-CoV-2 mRNA vaccines remains a topic of debate. In addition, our understanding of CD8+ T cells in response to vaccination in the lymph nodes, where they first encounter antigen, is still limited. This review delves into the current knowledge regarding the protective role of polyfunctional CD8+ T cells in controlling the virus, the response to SARS-CoV-2 mRNA vaccines, and the contribution to supporting B cell activity and promoting immune protection in the lymph nodes.
Collapse
Affiliation(s)
- Mengfei Chen
- The Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | | | | |
Collapse
|
42
|
Abdelaziz MO, Raftery MJ, Weihs J, Bielawski O, Edel R, Köppke J, Vladimirova D, Adler JM, Firsching T, Voß A, Gruber AD, Hummel LV, Fernandez Munoz I, Müller-Marquardt F, Willimsky G, Elleboudy NS, Trimpert J, Schönrich G. Early protective effect of a ("pan") coronavirus vaccine (PanCoVac) in Roborovski dwarf hamsters after single-low dose intranasal administration. Front Immunol 2023; 14:1166765. [PMID: 37520530 PMCID: PMC10372429 DOI: 10.3389/fimmu.2023.1166765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/19/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the danger posed by human coronaviruses. Rapid emergence of immunoevasive variants and waning antiviral immunity decrease the effect of the currently available vaccines, which aim at induction of neutralizing antibodies. In contrast, T cells are marginally affected by antigen evolution although they represent the major mediators of virus control and vaccine protection against virus-induced disease. Materials and methods We generated a multi-epitope vaccine (PanCoVac) that encodes the conserved T cell epitopes from all structural proteins of coronaviruses. PanCoVac contains elements that facilitate efficient processing and presentation of PanCoVac-encoded T cell epitopes and can be uploaded to any available vaccine platform. For proof of principle, we cloned PanCoVac into a non-integrating lentivirus vector (NILV-PanCoVac). We chose Roborovski dwarf hamsters for a first step in evaluating PanCoVac in vivo. Unlike mice, they are naturally susceptible to SARS-CoV-2 infection. Moreover, Roborovski dwarf hamsters develop COVID-19-like disease after infection with SARS-CoV-2 enabling us to look at pathology and clinical symptoms. Results Using HLA-A*0201-restricted reporter T cells and U251 cells expressing a tagged version of PanCoVac, we confirmed in vitro that PanCoVac is processed and presented by HLA-A*0201. As mucosal immunity in the respiratory tract is crucial for protection against respiratory viruses such as SARS-CoV-2, we tested the protective effect of single-low dose of NILV-PanCoVac administered via the intranasal (i.n.) route in the Roborovski dwarf hamster model of COVID-19. After infection with ancestral SARS-CoV-2, animals immunized with a single-low dose of NILV-PanCoVac i.n. did not show symptoms and had significantly decreased viral loads in the lung tissue. This protective effect was observed in the early phase (2 days post infection) after challenge and was not dependent on neutralizing antibodies. Conclusion PanCoVac, a multi-epitope vaccine covering conserved T cell epitopes from all structural proteins of coronaviruses, might protect from severe disease caused by SARS-CoV-2 variants and future pathogenic coronaviruses. The use of (HLA-) humanized animal models will allow for further efficacy studies of PanCoVac-based vaccines in vivo.
Collapse
Affiliation(s)
- Mohammed O. Abdelaziz
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Martin J. Raftery
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julian Weihs
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Pediatrics, Division of Gastroenterology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Olivia Bielawski
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard Edel
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julia Köppke
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Julia M. Adler
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Theresa Firsching
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Anne Voß
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Achim D. Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Luca V. Hummel
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ivan Fernandez Munoz
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Francesca Müller-Marquardt
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gerald Willimsky
- Institute of Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Partner Site Berlin, Berlin, Germany
| | - Nooran S. Elleboudy
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Jakob Trimpert
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Günther Schönrich
- Institute of Virology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| |
Collapse
|
43
|
Jiang N, Malone M, Chizari S. Antigen-specific and cross-reactive T cells in protection and disease. Immunol Rev 2023; 316:120-135. [PMID: 37209375 PMCID: PMC10524458 DOI: 10.1111/imr.13217] [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: 04/01/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/22/2023]
Abstract
Human T cells have a diverse T-cell receptor (TCR) repertoire that endows them with the ability to identify and defend against a broad spectrum of antigens. The universe of possible antigens that T cells may encounter, however, is even larger. To effectively surveil such a vast universe, the T-cell repertoire must adopt a high degree of cross-reactivity. Likewise, antigen-specific and cross-reactive T-cell responses play pivotal roles in both protective and pathological immune responses in numerous diseases. In this review, we explore the implications of these antigen-driven T-cell responses, with a particular focus on CD8+ T cells, using infection, neurodegeneration, and cancer as examples. We also summarize recent technological advances that facilitate high-throughput profiling of antigen-specific and cross-reactive T-cell responses experimentally, as well as computational biology approaches that predict these interactions.
Collapse
Affiliation(s)
- Ning Jiang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA, 19104
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA, 19104
- Institute for RNA Innovation, University of Pennsylvania, Philadelphia, PA, 19104
| | - Michael Malone
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
| | - Shahab Chizari
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
| |
Collapse
|
44
|
Tiezzi C, Vecchi A, Rossi M, Cavazzini D, Bolchi A, Laccabue D, Doselli S, Penna A, Sacchelli L, Brillo F, Meschi T, Ticinesi A, Nouvenne A, Donofrio G, Zanelli P, Benecchi M, Giuliodori S, Fisicaro P, Montali I, Ceccatelli Berti C, Reverberi V, Montali A, Urbani S, Pedrazzi G, Missale G, Telenti A, Corti D, Ottonello S, Ferrari C, Boni C. Natural heteroclitic-like peptides are generated by SARS-CoV-2 mutations. iScience 2023; 26:106940. [PMID: 37275517 PMCID: PMC10200277 DOI: 10.1016/j.isci.2023.106940] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/13/2023] [Accepted: 05/18/2023] [Indexed: 06/07/2023] Open
Abstract
Humoral immunity is sensitive to evasion by SARS-CoV-2 mutants, but CD8 T cells seem to be more resistant to mutational inactivation. By a systematic analysis of 30 spike variant peptides containing the most relevant VOC and VOI mutations that have accumulated overtime, we show that in vaccinated and convalescent subjects, mutated epitopes can have not only a neutral or inhibitory effect on CD8 T cell recognition but can also enhance or generate de novo CD8 T cell responses. The emergence of these mutated T cell function enhancing epitopes likely reflects an epiphenomenon of SARS-CoV-2 evolution driven by antibody evasion and increased virus transmissibility. In a subset of individuals with weak and narrowly focused CD8 T cell responses selection of these heteroclitic-like epitopes may bear clinical relevance by improving antiviral protection. The functional enhancing effect of these peptides is also worth of consideration for the future development of new generation, more potent COVID-19 vaccines.
Collapse
Affiliation(s)
- Camilla Tiezzi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Andrea Vecchi
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Marzia Rossi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Davide Cavazzini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Angelo Bolchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Interdepartmental Center Biopharmanet-Tec, University of Parma, Parma, Italy
| | - Diletta Laccabue
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Sara Doselli
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Amalia Penna
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Luca Sacchelli
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Federica Brillo
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Tiziana Meschi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Andrea Ticinesi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Antonio Nouvenne
- Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Gaetano Donofrio
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Paola Zanelli
- Unità di Immunogenetica dei Trapianti, Azienda Ospedaliero Universitaria di Parma, Parma, Italy
| | - Magda Benecchi
- Unità di Immunogenetica dei Trapianti, Azienda Ospedaliero Universitaria di Parma, Parma, Italy
| | - Silvia Giuliodori
- Unità di Immunogenetica dei Trapianti, Azienda Ospedaliero Universitaria di Parma, Parma, Italy
| | - Paola Fisicaro
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Ilaria Montali
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | - Valentina Reverberi
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Anna Montali
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Simona Urbani
- UO Immunoematologia e Medicina Trasfusionale, Dipartimento Diagnostico, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Giuseppe Pedrazzi
- Department of Neuroscience - Biophysics and Medical Physics Unit, University of Parma, Parma, Italy
| | - Gabriele Missale
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Simone Ottonello
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Interdepartmental Center Biopharmanet-Tec, University of Parma, Parma, Italy
| | - Carlo Ferrari
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Carolina Boni
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| |
Collapse
|
45
|
Zhang W, Kedzierski L, Chua BY, Mayo M, Lonzi C, Rigas V, Middleton BF, McQuilten HA, Rowntree LC, Allen LF, Purcell RA, Tan HX, Petersen J, Chaurasia P, Mordant F, Pogorelyy MV, Minervina AA, Crawford JC, Perkins GB, Zhang E, Gras S, Clemens EB, Juno JA, Audsley J, Khoury DS, Holmes NE, Thevarajan I, Subbarao K, Krammer F, Cheng AC, Davenport MP, Grubor-Bauk B, Coates PT, Christensen B, Thomas PG, Wheatley AK, Kent SJ, Rossjohn J, Chung AW, Boffa J, Miller A, Lynar S, Nelson J, Nguyen THO, Davies J, Kedzierska K. Robust and prototypical immune responses toward COVID-19 vaccine in First Nations peoples are impacted by comorbidities. Nat Immunol 2023; 24:966-978. [PMID: 37248417 PMCID: PMC10232372 DOI: 10.1038/s41590-023-01508-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 04/10/2023] [Indexed: 05/31/2023]
Abstract
High-risk groups, including Indigenous people, are at risk of severe COVID-19. Here we found that Australian First Nations peoples elicit effective immune responses to COVID-19 BNT162b2 vaccination, including neutralizing antibodies, receptor-binding domain (RBD) antibodies, SARS-CoV-2 spike-specific B cells, and CD4+ and CD8+ T cells. In First Nations participants, RBD IgG antibody titers were correlated with body mass index and negatively correlated with age. Reduced RBD antibodies, spike-specific B cells and follicular helper T cells were found in vaccinated participants with chronic conditions (diabetes, renal disease) and were strongly associated with altered glycosylation of IgG and increased interleukin-18 levels in the plasma. These immune perturbations were also found in non-Indigenous people with comorbidities, indicating that they were related to comorbidities rather than ethnicity. However, our study is of a great importance to First Nations peoples who have disproportionate rates of chronic comorbidities and provides evidence of robust immune responses after COVID-19 vaccination in Indigenous people.
Collapse
Affiliation(s)
- Wuji Zhang
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Lukasz Kedzierski
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Brendon Y Chua
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Mark Mayo
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Claire Lonzi
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Vanessa Rigas
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Bianca F Middleton
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Hayley A McQuilten
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Lilith F Allen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Ruth A Purcell
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jan Petersen
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Priyanka Chaurasia
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Francesca Mordant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | | | - Griffith B Perkins
- Central and Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Eva Zhang
- Department of Gastroenterology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Macquarie University, Sydney, New South Wales, Australia
| | - Stephanie Gras
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jennifer A Juno
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jennifer Audsley
- Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - David S Khoury
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Natasha E Holmes
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Irani Thevarajan
- Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Services, Royal Melbourne Hospital and Doherty Department, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Allen C Cheng
- Department of Infectious Diseases, Alfred Hospital and Central Clinical School and School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Monash Infectious Diseases, Monash Health and School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Miles P Davenport
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Branka Grubor-Bauk
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - P Toby Coates
- Central and Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Britt Christensen
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Melbourne, Victoria, Australia
- Melbourne Sexual Health Centre, Infectious Diseases Department, Alfred Health, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Amy W Chung
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - John Boffa
- Central Australian Aboriginal Congress, Alice Springs, Northern Territory, Australia
| | - Adrian Miller
- Indigenous Engagement, CQUniversity, Townsville, Queensland, Australia
| | - Sarah Lynar
- Menzies School of Health Research, Darwin, Northern Territory, Australia
- Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, Northern Territory, Australia
| | - Jane Nelson
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia.
| | - Jane Davies
- Menzies School of Health Research, Darwin, Northern Territory, Australia.
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia.
- Center for Influenza Disease and Emergence Response, Melbourne, Victoria, Australia.
| |
Collapse
|
46
|
Postovskaya A, Vujkovic A, de Block T, van Petersen L, van Frankenhuijsen M, Brosius I, Bottieau E, Van Dijck C, Theunissen C, van Ierssel SH, Vlieghe E, Bartholomeus E, Mullan K, Adriaensen W, Vanham G, Ogunjimi B, Laukens K, Vercauteren K, Meysman P. Leveraging T-cell receptor - epitope recognition models to disentangle unique and cross-reactive T-cell response to SARS-CoV-2 during COVID-19 progression/resolution. Front Immunol 2023; 14:1130876. [PMID: 37325653 PMCID: PMC10264683 DOI: 10.3389/fimmu.2023.1130876] [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: 12/23/2022] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Despite the general agreement on the significance of T cells during SARS-CoV-2 infection, the clinical impact of specific and cross-reactive T-cell responses remains uncertain. Understanding this aspect could provide insights for adjusting vaccines and maintaining robust long-term protection against continuously emerging variants. To characterize CD8+ T-cell response to SARS-CoV-2 epitopes unique to the virus (SC2-unique) or shared with other coronaviruses (CoV-common), we trained a large number of T-cell receptor (TCR) - epitope recognition models for MHC-I-presented SARS-CoV-2 epitopes from publicly available data. These models were then applied to longitudinal CD8+ TCR repertoires from critical and non-critical COVID-19 patients. In spite of comparable initial CoV-common TCR repertoire depth and CD8+ T-cell depletion, the temporal dynamics of SC2-unique TCRs differed depending on the disease severity. Specifically, while non-critical patients demonstrated a large and diverse SC2-unique TCR repertoire by the second week of the disease, critical patients did not. Furthermore, only non-critical patients exhibited redundancy in the CD8+ T-cell response to both groups of epitopes, SC2-unique and CoV-common. These findings indicate a valuable contribution of the SC2-unique CD8+ TCR repertoires. Therefore, a combination of specific and cross-reactive CD8+ T-cell responses may offer a stronger clinical advantage. Besides tracking the specific and cross-reactive SARS-CoV-2 CD8+ T cells in any TCR repertoire, our analytical framework can be expanded to more epitopes and assist in the assessment and monitoring of CD8+ T-cell response to other infections.
Collapse
Affiliation(s)
- Anna Postovskaya
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (BIOMINA), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Clinical Virology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Alexandra Vujkovic
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Clinical Virology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tessa de Block
- Clinical Virology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Lida van Petersen
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Isabel Brosius
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Emmanuel Bottieau
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Caroline Theunissen
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sabrina H. van Ierssel
- Department of General Internal Medicine, Infectious Diseases and Tropical Medicine, Antwerp University Hospital, Edegem, Belgium
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Erika Vlieghe
- Department of General Internal Medicine, Infectious Diseases and Tropical Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Esther Bartholomeus
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Kerry Mullan
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (BIOMINA), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | - Wim Adriaensen
- Clinical Immunology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Guido Vanham
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Department of Paediatrics, Antwerp University Hospital, Antwerp, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (BIOMINA), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | - Koen Vercauteren
- Clinical Virology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Meysman
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (BIOMINA), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| |
Collapse
|
47
|
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: 19] [Impact Index Per Article: 19.0] [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).
Collapse
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.
| |
Collapse
|
48
|
Tai W, Feng S, Chai B, Lu S, Zhao G, Chen D, Yu W, Ren L, Shi H, Lu J, Cai Z, Pang M, Tan X, Wang P, Lin J, Sun Q, Peng X, Cheng G. An mRNA-based T-cell-inducing antigen strengthens COVID-19 vaccine against SARS-CoV-2 variants. Nat Commun 2023; 14:2962. [PMID: 37221158 DOI: 10.1038/s41467-023-38751-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/12/2023] [Indexed: 05/25/2023] Open
Abstract
Herd immunity achieved through mass vaccination is an effective approach to prevent contagious diseases. Nonetheless, emerging SARS-CoV-2 variants with frequent mutations largely evaded humoral immunity induced by Spike-based COVID-19 vaccines. Herein, we develop a lipid nanoparticle (LNP)-formulated mRNA-based T-cell-inducing antigen, which targeted three SARS-CoV-2 proteome regions that enriched human HLA-I epitopes (HLA-EPs). Immunization of HLA-EPs induces potent cellular responses to prevent SARS-CoV-2 infection in humanized HLA-A*02:01/DR1 and HLA-A*11:01/DR1 transgenic mice. Of note, the sequences of HLA-EPs are highly conserved among SARS-CoV-2 variants of concern. In humanized HLA-transgenic mice and female rhesus macaques, dual immunization with the LNP-formulated mRNAs encoding HLA-EPs and the receptor-binding domain of the SARS-CoV-2 B.1.351 variant (RBDbeta) is more efficacious in preventing infection of SARS-CoV-2 Beta and Omicron BA.1 variants than single immunization of LNP-RBDbeta. This study demonstrates the necessity to strengthen the vaccine effectiveness by comprehensively stimulating both humoral and cellular responses, thereby offering insight for optimizing the design of COVID-19 vaccines.
Collapse
Affiliation(s)
- Wanbo Tai
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
| | - Shengyong Feng
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Benjie Chai
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Shuaiyao Lu
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Dong Chen
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
- Wenzhou Central Hospital, Wenzhou, 325000, China
| | - Wenhai Yu
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China
| | - Liting Ren
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Huicheng Shi
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Jing Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200438, China
| | - Zhuming Cai
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Mujia Pang
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Xu Tan
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Penghua Wang
- Department of Immunology, School of Medicine, the University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200438, China.
| | - Qiangming Sun
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China.
| | - Xiaozhong Peng
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China.
| | - Gong Cheng
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
49
|
Chour W, Choi J, Xie J, Chaffee ME, Schmitt TM, Finton K, DeLucia DC, Xu AM, Su Y, Chen DG, Zhang R, Yuan D, Hong S, Ng AHC, Butler JZ, Edmark RA, Jones LC, Murray KM, Peng S, Li G, Strong RK, Lee JK, Goldman JD, Greenberg PD, Heath JR. Large libraries of single-chain trimer peptide-MHCs enable antigen-specific CD8+ T cell discovery and analysis. Commun Biol 2023; 6:528. [PMID: 37193826 PMCID: PMC10186326 DOI: 10.1038/s42003-023-04899-8] [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: 11/08/2022] [Accepted: 05/01/2023] [Indexed: 05/18/2023] Open
Abstract
The discovery and characterization of antigen-specific CD8+ T cell clonotypes typically involves the labor-intensive synthesis and construction of peptide-MHC tetramers. We adapt single-chain trimer (SCT) technologies into a high throughput platform for pMHC library generation, showing that hundreds can be rapidly prepared across multiple Class I HLA alleles. We use this platform to explore the impact of peptide and SCT template mutations on protein expression yield, thermal stability, and functionality. SCT libraries were an efficient tool for identifying T cells recognizing commonly reported viral epitopes. We then construct SCT libraries to capture SARS-CoV-2 specific CD8+ T cells from COVID-19 participants and healthy donors. The immunogenicity of these epitopes is validated by functional assays of T cells with cloned TCRs captured using SCT libraries. These technologies should enable the rapid analyses of peptide-based T cell responses across several contexts, including autoimmunity, cancer, or infectious disease.
Collapse
Affiliation(s)
- William Chour
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jongchan Choi
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jingyi Xie
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, USA
| | - Mary E Chaffee
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Thomas M Schmitt
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Kathryn Finton
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Diana C DeLucia
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Alexander M Xu
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Daniel G Chen
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Microbiology and Department of Informatics, University of Washington, Seattle, WA, 98195, USA
| | - Rongyu Zhang
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Dan Yuan
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Sunga Hong
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Alphonsus H C Ng
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jonah Z Butler
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Rick A Edmark
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Kim M Murray
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Guideng Li
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
- Key Laboratory of Synthetic Biology Regulatory Element, Chinese Academy of Medical Sciences, Beijing, China
| | - Roland K Strong
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - John K Lee
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Jason D Goldman
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, 98104, USA
- Division of Infectious Disease, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Philip D Greenberg
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
- Department of Immunology, University of Washington, Seattle, WA, 98195, USA
| | - James R Heath
- Institute for Systems Biology, Seattle, WA, 98109, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
| |
Collapse
|
50
|
Murray SM, Ansari AM, Frater J, Klenerman P, Dunachie S, Barnes E, Ogbe A. The impact of pre-existing cross-reactive immunity on SARS-CoV-2 infection and vaccine responses. Nat Rev Immunol 2023; 23:304-316. [PMID: 36539527 PMCID: PMC9765363 DOI: 10.1038/s41577-022-00809-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2022] [Indexed: 12/24/2022]
Abstract
Pre-existing cross-reactive immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins in infection-naive subjects have been described by several studies. In particular, regions of high homology between SARS-CoV-2 and common cold coronaviruses have been highlighted as a likely source of this cross-reactivity. However, the role of such cross-reactive responses in the outcome of SARS-CoV-2 infection and vaccination is currently unclear. Here, we review evidence regarding the impact of pre-existing humoral and T cell immune responses to outcomes of SARS-CoV-2 infection and vaccination. Furthermore, we discuss the importance of conserved coronavirus epitopes for the rational design of pan-coronavirus vaccines and consider cross-reactivity of immune responses to ancestral SARS-CoV-2 and SARS-CoV-2 variants, as well as their impact on COVID-19 vaccination.
Collapse
Affiliation(s)
- Sam M Murray
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Azim M Ansari
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - John Frater
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Susanna Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
| | - Ane Ogbe
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|