1
|
Baig MMFA, Wong LY, Wu H. Development of mRNA nano-vaccines for COVID-19 prevention and its biochemical interactions with various disease conditions and age groups. J Drug Target 2024; 32:21-32. [PMID: 38010097 DOI: 10.1080/1061186x.2023.2288996] [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: 06/24/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
This review has focused on the development of mRNA nano-vaccine and the biochemical interactions of anti-COVID-19 mRNA vaccines with various disease conditions and age groups. It studied five major groups of individuals with different disease conditions and ages, including allergic background, infarction background, adolescent, and adult (youngsters), pregnant women, and elderly. All five groups had been reported to have background-related adverse effects. Allergic background individuals were observed to have higher chances of experiencing allergic reactions and even anaphylaxis. Individuals with an infarction background had a higher risk of vaccine-induced diseases, e.g. pneumonitis and interstitial lung diseases. Pregnant women were seen to suffer from obstetric and gynecological adverse effects after receiving vaccinations. However, interestingly, the elderly individuals (> 65 years old) had experienced milder and less frequent adverse effects compared to the adolescent (<19 and >9 years old) and young adulthood (19-39 years old), or middle adulthood (40-59 years old) age groups, while middle to late adolescent (14-17 years old) was the riskiest age group to vaccine-induced cardiovascular manifestations.
Collapse
Affiliation(s)
- Mirza Muhammad Faran Ashraf Baig
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Lok Yin Wong
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongkai Wu
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Hong Kong, China
| |
Collapse
|
2
|
Montoya B, Melo-Silva CR, Tang L, Kafle S, Lidskiy P, Bajusz C, Vadovics M, Muramatsu H, Abraham E, Lipinszki Z, Chatterjee D, Scher G, Benitez J, Sung MMH, Tam YK, Catanzaro NJ, Schäfer A, Andino R, Baric RS, Martinez DR, Pardi N, Sigal LJ. mRNA-LNP vaccine-induced CD8 + T cells protect mice from lethal SARS-CoV-2 infection in the absence of specific antibodies. Mol Ther 2024; 32:1790-1804. [PMID: 38605519 PMCID: PMC11184341 DOI: 10.1016/j.ymthe.2024.04.019] [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: 09/12/2023] [Revised: 03/11/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024] Open
Abstract
The role of CD8+ T cells in SARS-CoV-2 pathogenesis or mRNA-LNP vaccine-induced protection from lethal COVID-19 is unclear. Using mouse-adapted SARS-CoV-2 virus (MA30) in C57BL/6 mice, we show that CD8+ T cells are unnecessary for the intrinsic resistance of female or the susceptibility of male mice to lethal SARS-CoV-2 infection. Also, mice immunized with a di-proline prefusion-stabilized full-length SARS-CoV-2 Spike (S-2P) mRNA-LNP vaccine, which induces Spike-specific antibodies and CD8+ T cells specific for the Spike-derived VNFNFNGL peptide, are protected from SARS-CoV-2 infection-induced lethality and weight loss, while mice vaccinated with mRNA-LNPs encoding only VNFNFNGL are protected from lethality but not weight loss. CD8+ T cell depletion ablates protection in VNFNFNGL but not in S-2P mRNA-LNP-vaccinated mice. Therefore, mRNA-LNP vaccine-induced CD8+ T cells are dispensable when protective antibodies are present but essential for survival in their absence. Hence, vaccine-induced CD8+ T cells may be critical to protect against SARS-CoV-2 variants that mutate epitopes targeted by protective antibodies.
Collapse
Affiliation(s)
- Brian Montoya
- Department of Microbiology and Immunology, Bluemle Life Science Building, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Carolina R Melo-Silva
- Department of Microbiology and Immunology, Bluemle Life Science Building, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Lingjuan Tang
- Department of Microbiology and Immunology, Bluemle Life Science Building, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Samita Kafle
- Department of Microbiology and Immunology, Bluemle Life Science Building, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Peter Lidskiy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Csaba Bajusz
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; National Laboratory for Biotechnology, Institute of Genetics, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Máté Vadovics
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Edit Abraham
- National Laboratory for Biotechnology, Institute of Genetics, HUN-REN Biological Research Centre, Szeged, Hungary; MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Zoltan Lipinszki
- National Laboratory for Biotechnology, Institute of Genetics, HUN-REN Biological Research Centre, Szeged, Hungary; MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Debotri Chatterjee
- Department of Neurosciences, Thomas Jefferson University Vickie and Jack Farber Institute for Neuroscience, Philadelphia, PA, USA
| | - Gabrielle Scher
- Department of Microbiology and Immunology, Bluemle Life Science Building, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Juliana Benitez
- Department of Microbiology and Immunology, Bluemle Life Science Building, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | | | - Ying K Tam
- Acuitas Therapeutics, Vancouver, BC V6T 1Z3, Canada
| | - Nicholas J Catanzaro
- Department of Epidemiology, Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexandra Schäfer
- Department of Epidemiology, Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ralph S Baric
- Department of Epidemiology, Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David R Martinez
- Department of Immunobiology, Center for Infection and Immunity, Yale School of Medicine, New Haven, CT 06520, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Luis J Sigal
- Department of Microbiology and Immunology, Bluemle Life Science Building, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| |
Collapse
|
3
|
Binayke A, Zaheer A, Vishwakarma S, Singh S, Sharma P, Chandwaskar R, Gosain M, Raghavan S, Murugesan DR, Kshetrapal P, Thiruvengadam R, Bhatnagar S, Pandey AK, Garg PK, Awasthi A. A quest for universal anti-SARS-CoV-2 T cell assay: systematic review, meta-analysis, and experimental validation. NPJ Vaccines 2024; 9:3. [PMID: 38167915 PMCID: PMC10762233 DOI: 10.1038/s41541-023-00794-9] [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: 07/02/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
Measuring SARS-CoV-2-specific T cell responses is crucial to understanding an individual's immunity to COVID-19. However, high inter- and intra-assay variability make it difficult to define T cells as a correlate of protection against COVID-19. To address this, we performed systematic review and meta-analysis of 495 datasets from 94 original articles evaluating SARS-CoV-2-specific T cell responses using three assays - Activation Induced Marker (AIM), Intracellular Cytokine Staining (ICS), and Enzyme-Linked Immunospot (ELISPOT), and defined each assay's quantitative range. We validated these ranges using samples from 193 SARS-CoV-2-exposed individuals. Although IFNγ ELISPOT was the preferred assay, our experimental validation suggested that it under-represented the SARS-CoV-2-specific T cell repertoire. Our data indicate that a combination of AIM and ICS or FluoroSpot assay would better represent the frequency, polyfunctionality, and compartmentalization of the antigen-specific T cell responses. Taken together, our results contribute to defining the ranges of antigen-specific T cell assays and propose a choice of assay that can be employed to better understand the cellular immune response against viral diseases.
Collapse
Affiliation(s)
- Akshay Binayke
- Immunology Core Laboratory, Translational Health Science and Technology Institute, Faridabad, India
- Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Aymaan Zaheer
- Immunology Core Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Siddhesh Vishwakarma
- Immunology Core Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Savita Singh
- Translational Health Science and Technology Institute, Faridabad, India
| | - Priyanka Sharma
- Immunology Core Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Rucha Chandwaskar
- Department of Microbiology, AMITY University Rajasthan, Jaipur, India
| | - Mudita Gosain
- Translational Health Science and Technology Institute, Faridabad, India
| | | | | | | | - Ramachandran Thiruvengadam
- Translational Health Science and Technology Institute, Faridabad, India
- Pondicherry Institute of Medical Sciences, Puducherry, India
| | | | | | - Pramod Kumar Garg
- Translational Health Science and Technology Institute, Faridabad, India
- All India Institute of Medical Sciences, New Delhi, India
| | - Amit Awasthi
- Immunology Core Laboratory, Translational Health Science and Technology Institute, Faridabad, India.
- Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, Faridabad, India.
| |
Collapse
|
4
|
van Bergen J, Camps MG, Pardieck IN, Veerkamp D, Leung WY, Leijs AA, Myeni SK, Kikkert M, Arens R, Zondag GC, Ossendorp F. Multiantigen pan-sarbecovirus DNA vaccines generate protective T cell immune responses. JCI Insight 2023; 8:e172488. [PMID: 37707962 PMCID: PMC10721273 DOI: 10.1172/jci.insight.172488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023] Open
Abstract
SARS-CoV-2 is the third zoonotic coronavirus to cause a major outbreak in humans in recent years, and many more SARS-like coronaviruses with pandemic potential are circulating in several animal species. Vaccines inducing T cell immunity against broadly conserved viral antigens may protect against hospitalization and death caused by outbreaks of such viruses. We report the design and preclinical testing of 2 T cell-based pan-sarbecovirus vaccines, based on conserved regions within viral proteins of sarbecovirus isolates of human and other carrier animals, like bats and pangolins. One vaccine (CoVAX_ORF1ab) encoded antigens derived from nonstructural proteins, and the other (CoVAX_MNS) encoded antigens from structural proteins. Both multiantigen DNA vaccines contained a large set of antigens shared across sarbecoviruses and were rich in predicted and experimentally validated human T cell epitopes. In mice, the multiantigen vaccines generated both CD8+ and CD4+ T cell responses to shared epitopes. Upon encounter of full-length spike antigen, CoVAX_MNS-induced CD4+ T cells were responsible for accelerated CD8+ T cell and IgG Ab responses specific to the incoming spike, irrespective of its sarbecovirus origin. Finally, both vaccines elicited partial protection against a lethal SARS-CoV-2 challenge in human angiotensin-converting enzyme 2-transgenic mice. These results support clinical testing of these universal sarbecovirus vaccines for pandemic preparedness.
Collapse
Affiliation(s)
| | - Marcel G.M. Camps
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
| | - Iris N. Pardieck
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
| | - Dominique Veerkamp
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
| | - Wing Yan Leung
- Immunetune BV, Leiden, Netherlands
- Synvolux BV, Leiden, Netherlands
| | - Anouk A. Leijs
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, Netherlands
| | - Sebenzile K. Myeni
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, Netherlands
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, Netherlands
| | - Ramon Arens
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
| | - Gerben C. Zondag
- Immunetune BV, Leiden, Netherlands
- Synvolux BV, Leiden, Netherlands
| | - Ferry Ossendorp
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
| |
Collapse
|
5
|
Chen Y, Mason GH, Scourfield DO, Greenshields-Watson A, Haigh TA, Sewell AK, Long HM, Gallimore AM, Rizkallah P, MacLachlan BJ, Godkin A. Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity. Cell Rep 2023; 42:112827. [PMID: 37471227 PMCID: PMC10840515 DOI: 10.1016/j.celrep.2023.112827] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/21/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023] Open
Abstract
CD4+ T cells recognize a broad range of peptide epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which contribute to immune memory and limit COVID-19 disease. We demonstrate that the immunogenicity of SARS-CoV-2 peptides, in the context of the model allotype HLA-DR1, does not correlate with their binding affinity to the HLA heterodimer. Analyzing six epitopes, some with very low binding affinity, we solve X-ray crystallographic structures of each bound to HLA-DR1. Further structural definitions reveal the precise molecular impact of viral variant mutations on epitope presentation. Omicron escaped ancestral SARS-CoV-2 immunity to two epitopes through two distinct mechanisms: (1) mutations to TCR-facing epitope positions and (2) a mechanism whereby a single amino acid substitution caused a register shift within the HLA binding groove, completely altering the peptide-HLA structure. This HLA-II-specific paradigm of immune escape highlights how CD4+ T cell memory is finely poised at the level of peptide-HLA-II presentation.
Collapse
Affiliation(s)
- Yuan Chen
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Georgina H Mason
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - D Oliver Scourfield
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Alexander Greenshields-Watson
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Tracey A Haigh
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Heather M Long
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Awen M Gallimore
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Pierre Rizkallah
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Bruce J MacLachlan
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
| | - Andrew Godkin
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Department of Gastroenterology & Hepatology, University Hospital of Wales, Cardiff CF14 4XW, UK.
| |
Collapse
|
6
|
Strebinger D, Frangieh CJ, Friedrich MJ, Faure G, Macrae RK, Zhang F. Cell type-specific delivery by modular envelope design. Nat Commun 2023; 14:5141. [PMID: 37612276 PMCID: PMC10447438 DOI: 10.1038/s41467-023-40788-8] [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: 02/03/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023] Open
Abstract
The delivery of genetic cargo remains one of the largest obstacles to the successful translation of experimental therapies, in large part due to the absence of targetable delivery vectors. Enveloped delivery modalities use viral envelope proteins, which determine tropism and induce membrane fusion. Here we develop DIRECTED (Delivery to Intended REcipient Cells Through Envelope Design), a modular platform that consists of separate fusion and targeting components. To achieve high modularity and programmable cell type specificity, we develop multiple strategies to recruit or immobilize antibodies on the viral envelope, including a chimeric antibody binding protein and a SNAP-tag enabling the use of antibodies or other proteins as targeting molecules. Moreover, we show that fusogens from multiple viral families are compatible with DIRECTED and that DIRECTED components can target multiple delivery chassis (e.g., lentivirus and MMLV gag) to specific cell types, including primary human T cells in PBMCs and whole blood.
Collapse
Affiliation(s)
- Daniel Strebinger
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chris J Frangieh
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mirco J Friedrich
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Guilhem Faure
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Rhiannon K Macrae
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| |
Collapse
|
7
|
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: 9] [Impact Index Per Article: 9.0] [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
|
8
|
Yang G, Wang J, Sun P, Qin J, Yang X, Chen D, Zhang Y, Zhong N, Wang Z. SARS-CoV-2 epitope-specific T cells: Immunity response feature, TCR repertoire characteristics and cross-reactivity. Front Immunol 2023; 14:1146196. [PMID: 36969254 PMCID: PMC10036809 DOI: 10.3389/fimmu.2023.1146196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
The devastating COVID-19 pandemic caused by SARS-CoV-2 and multiple variants or subvariants remains an ongoing global challenge. SARS-CoV-2-specific T cell responses play a critical role in early virus clearance, disease severity control, limiting the viral transmission and underpinning COVID-19 vaccine efficacy. Studies estimated broad and robust T cell responses in each individual recognized at least 30 to 40 SARS-CoV-2 antigen epitopes and associated with COVID-19 clinical outcome. Several key immunodominant viral proteome epitopes, including S protein- and non-S protein-derived epitopes, may primarily induce potent and long-lasting antiviral protective effects. In this review, we summarized the immune response features of immunodominant epitope-specific T cells targeting different SRAS-CoV-2 proteome structures after infection and vaccination, including abundance, magnitude, frequency, phenotypic features and response kinetics. Further, we analyzed the epitopes immunodominance hierarchy in combination with multiple epitope-specific T cell attributes and TCR repertoires characteristics, and discussed the significant implications of cross-reactive T cells toward HCoVs, SRAS-CoV-2 and variants of concern, especially Omicron. This review may be essential for mapping the landscape of T cell responses toward SARS-CoV-2 and optimizing the current vaccine strategy.
Collapse
Affiliation(s)
- Gang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Junxiang Wang
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Ping Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jian Qin
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Xiaoyun Yang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Daxiang Chen
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Nanshan Zhong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Zhongfang Wang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| |
Collapse
|
9
|
Jin X, Liu X, Shen C. A systemic review of T-cell epitopes defined from the proteome of SARS-CoV-2. Virus Res 2023; 324:199024. [PMID: 36526016 PMCID: PMC9757803 DOI: 10.1016/j.virusres.2022.199024] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection remains in a global pandemic, and no eradicative therapy is currently available. Host T cells have been shown to play a crucial role in the antiviral immune protection and pathology in Coronavirus disease 2019 (COVID-19) patients; thus, identifying sufficient T-cell epitopes from the SARS-CoV-2 proteome can contribute greatly to the development of T-cell epitope vaccines and the precise evaluation of host SARS-CoV-2-specific cellular immunity. This review presents a comprehensive map of T-cell epitopes functionally validated from SARS-CoV-2 antigens, the human leukocyte antigen (HLA) supertypes to present these epitopes, and the strategies to screen and identify T-cell epitopes. To the best of our knowledge, a total of 1349 CD8+ T-cell epitopes and 790 CD4+ T-cell epitopes have been defined by functional experiments thus far, but most are presented by approximately twenty common HLA supertypes, such as HLA-A0201, A2402, B0702, DR15, DR7 and DR11 molecules, and 74-80% of the T-cell epitopes are derived from S protein and nonstructural protein. These data provide useful insight into the development of vaccines and specific T-cell detection systems. However, the currently defined T-cell epitope repertoire cannot cover the HLA polymorphism of major populations in an indicated geographic region. More research is needed to depict an overall landscape of T-cell epitopes, which covers the overall SARS-CoV-2 proteome and global patients.
Collapse
Affiliation(s)
- Xiaoxiao Jin
- Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, China 225002; Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009
| | - Xiaotao Liu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009
| | - Chuanlai Shen
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009.
| |
Collapse
|
10
|
Tye EXC, Jinks E, Haigh TA, Kaul B, Patel P, Parry HM, Newby ML, Crispin M, Kaur N, Moss P, Drennan SJ, Taylor GS, Long HM. Mutations in SARS-CoV-2 spike protein impair epitope-specific CD4 + T cell recognition. Nat Immunol 2022; 23:1726-1734. [PMID: 36456735 DOI: 10.1038/s41590-022-01351-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 10/04/2022] [Indexed: 12/05/2022]
Abstract
CD4+ T cells are essential for protection against viruses, including SARS-CoV-2. The sensitivity of CD4+ T cells to mutations in SARS-CoV-2 variants of concern (VOCs) is poorly understood. Here, we isolated 159 SARS-CoV-2-specific CD4+ T cell clones from healthcare workers previously infected with wild-type SARS-CoV-2 (D614G) and defined 21 epitopes in spike, membrane and nucleoprotein. Lack of CD4+ T cell cross-reactivity between SARS-CoV-2 and endemic beta-coronaviruses suggested these responses arose from naïve rather than pre-existing cross-reactive coronavirus-specific T cells. Of the 17 epitopes located in the spike protein, 10 were mutated in VOCs and CD4+ T cell clone recognition of 7 of them was impaired, including 3 of the 4 epitopes mutated in omicron. Our results indicated that broad targeting of epitopes by CD4+ T cells likely limits evasion by current VOCs. However, continued genomic surveillance is vital to identify new mutations able to evade CD4+ T cell immunity.
Collapse
Affiliation(s)
- Emily X C Tye
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Elizabeth Jinks
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Tracey A Haigh
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Baksho Kaul
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Prashant Patel
- Institute of Cancer and Genomics, University of Birmingham, Birmingham, UK
| | - Helen M Parry
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Nayandeep Kaur
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Paul Moss
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Samantha J Drennan
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Graham S Taylor
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Heather M Long
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK.
| |
Collapse
|
11
|
Gao X, Fang D, Liang Y, Deng X, Chen N, Zeng M, Luo M. Circular RNAs as emerging regulators in COVID-19 pathogenesis and progression. Front Immunol 2022; 13:980231. [PMID: 36439162 PMCID: PMC9681929 DOI: 10.3389/fimmu.2022.980231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), an infectious acute respiratory disease caused by a newly emerging RNA virus, is a still-growing pandemic that has caused more than 6 million deaths globally and has seriously threatened the lives and health of people across the world. Currently, several drugs have been used in the clinical treatment of COVID-19, such as small molecules, neutralizing antibodies, and monoclonal antibodies. In addition, several vaccines have been used to prevent the spread of the pandemic, such as adenovirus vector vaccines, inactivated vaccines, recombinant subunit vaccines, and nucleic acid vaccines. However, the efficacy of vaccines and the onset of adverse reactions vary among individuals. Accumulating evidence has demonstrated that circular RNAs (circRNAs) are crucial regulators of viral infections and antiviral immune responses and are heavily involved in COVID-19 pathologies. During novel coronavirus infection, circRNAs not only directly affect the transcription process and interfere with viral replication but also indirectly regulate biological processes, including virus-host receptor binding and the immune response. Consequently, understanding the expression and function of circRNAs during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will provide novel insights into the development of circRNA-based methods. In this review, we summarize recent progress on the roles and underlying mechanisms of circRNAs that regulate the inflammatory response, viral replication, immune evasion, and cytokines induced by SARS-CoV-2 infection, and thus highlighting the diagnostic and therapeutic challenges in the treatment of COVID-19 and future research directions.
Collapse
Affiliation(s)
- Xiaojun Gao
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Dan Fang
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Yu Liang
- College of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Traditional Chinese Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Xin Deng
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Ni Chen
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Min Zeng
- Department of Pharmacy, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Mao Luo
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- College of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Traditional Chinese Medicine, Southwest Medical University, Luzhou, Sichuan, China
| |
Collapse
|
12
|
Duhen R, Beymer M, Jensen SM, Abbina S, Abraham S, Jain N, Thomas A, Geall AJ, Hu HM, Fox BA, Weinberg AD. OX40 agonist stimulation increases and sustains humoral and cell-mediated responses to SARS-CoV-2 protein and saRNA vaccines. Front Immunol 2022; 13:896310. [PMID: 36238275 PMCID: PMC9551348 DOI: 10.3389/fimmu.2022.896310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/08/2022] [Indexed: 12/01/2022] Open
Abstract
To prevent SARS-CoV-2 infections and generate long-lasting immunity, vaccines need to generate strong viral-specific B and T cell responses. Previous results from our lab and others have shown that immunizations in the presence of an OX40 agonist antibody lead to higher antibody titers and increased numbers of long-lived antigen-specific CD4 and CD8 T cells. Using a similar strategy, we explored the effect of OX40 co-stimulation in a prime and boost vaccination scheme using an adjuvanted SARS-CoV-2 spike protein vaccine in C57BL/6 mice. Our results show that OX40 engagement during vaccination significantly increases long-lived antibody responses to the spike protein. In addition, after immunization spike protein-specific proliferation was greatly increased for both CD4 and CD8 T cells, with enhanced, spike-specific secretion of IFN-γ and IL-2. Booster (3rd injection) immunizations combined with an OX40 agonist (7 months post-prime) further increased vaccine-specific antibody and T cell responses. Initial experiments assessing a self-amplifying mRNA (saRNA) vaccine encoding the spike protein antigen show a robust antigen-specific CD8 T cell response. The saRNA spike-specific CD8 T cells express high levels of GrzmB, IFN-γ and TNF-α which was not observed with protein immunization and this response was further increased by the OX40 agonist. Similar to protein immunizations the OX40 agonist also increased vaccine-specific CD4 T cell responses. In summary, this study compares and contrasts the effects and benefits of both protein and saRNA vaccination and the extent to which an OX40 agonist enhances and sustains the immune response against the SARS-CoV-2 spike protein.
Collapse
Affiliation(s)
- Rebekka Duhen
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
- *Correspondence: Rebekka Duhen,
| | - Michael Beymer
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
| | - Shawn M. Jensen
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
| | | | | | - Nikita Jain
- Precision NanoSystems Inc, Vancouver, BC, Canada
| | | | | | - Hong-Ming Hu
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
| | - Bernard A. Fox
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
| | - Andrew D. Weinberg
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
| |
Collapse
|
13
|
Karsten H, Cords L, Westphal T, Knapp M, Brehm TT, Hermanussen L, Omansen TF, Schmiedel S, Woost R, Ditt V, Peine S, Lütgehetmann M, Huber S, Ackermann C, Wittner M, Addo MM, Sette A, Sidney J, Schulze Zur Wiesch J. High-resolution analysis of individual spike peptide-specific CD4 + T-cell responses in vaccine recipients and COVID-19 patients. Clin Transl Immunology 2022; 11:e1410. [PMID: 35957961 PMCID: PMC9363231 DOI: 10.1002/cti2.1410] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/06/2022] [Accepted: 07/20/2022] [Indexed: 12/03/2022] Open
Abstract
Objectives Potential differences in the breadth, distribution and magnitude of CD4+ T‐cell responses directed against the SARS‐CoV‐2 spike glycoprotein between vaccinees, COVID‐19 patients and subjects who experienced both ways of immunisation have not been comprehensively compared on a peptide level. Methods Following virus‐specific in vitro cultivation, we determined the T‐cell responses directed against 253 individual overlapping 15‐mer peptides covering the entire SARS‐CoV‐2 spike glycoprotein using IFN‐γ ELISpot and intracellular cytokine staining. In vitro HLA binding was determined for selected peptides. Results We mapped 955 single peptide‐specific CD4+ T‐cell responses in a cohort of COVID‐19 patients (n = 8), uninfected vaccinees (n = 16) and individuals who experienced both infection and vaccination (n = 11). Patients and vaccinees (two‐time and three‐time vaccinees alike) had a comparable number of CD4+ T‐cell responses (median 26 vs. 29, P = 0.7289). Most of these specificities were conserved in B.1.1.529 and the BA.4 and BA.5 sublineages. The highest magnitude of these in vitro IFN‐γ CD4+ T‐cell responses was observed in COVID‐19 patients (median 0.35%), and three‐time vaccinees showed a higher magnitude than two‐time vaccinees (median 0.091% vs. 0.175%, P < 0.0001). Twelve peptide specificities were each detected in at least 40% of subjects. In vitro HLA binding showed promiscuous presentation by DRB1 molecules for several peptides. Conclusion Both SARS‐CoV‐2 infection and vaccination prime broadly directed T‐cell responses directed against the SARS‐CoV‐2 spike glycoprotein. This comprehensive high‐resolution analysis of spike peptide specificities will be a useful resource for further investigation of spike‐specific T‐cell responses.
Collapse
Affiliation(s)
- Hendrik Karsten
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Leon Cords
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Tim Westphal
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany.,German Center for Infection Research (DZIF) Partner Site Hamburg-Lübeck-Borstel-Riems Hamburg Germany
| | - Maximilian Knapp
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Thomas Theo Brehm
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany.,German Center for Infection Research (DZIF) Partner Site Hamburg-Lübeck-Borstel-Riems Hamburg Germany
| | - Lennart Hermanussen
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Till Frederik Omansen
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany.,Department of Tropical Medicine Bernhard Nocht Institute for Tropical Medicine Hamburg Germany
| | - Stefan Schmiedel
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Robin Woost
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Vanessa Ditt
- Institute of Transfusion Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Sven Peine
- Institute of Transfusion Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Marc Lütgehetmann
- German Center for Infection Research (DZIF) Partner Site Hamburg-Lübeck-Borstel-Riems Hamburg Germany.,Institute of Medical Microbiology, Virology and Hygiene University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Samuel Huber
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Christin Ackermann
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Melanie Wittner
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany.,German Center for Infection Research (DZIF) Partner Site Hamburg-Lübeck-Borstel-Riems Hamburg Germany
| | - Marylyn Martina Addo
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany.,German Center for Infection Research (DZIF) Partner Site Hamburg-Lübeck-Borstel-Riems Hamburg Germany.,Department of Tropical Medicine Bernhard Nocht Institute for Tropical Medicine Hamburg Germany
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research La Jolla Institute for Immunology (LJI) La Jolla CA USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research La Jolla Institute for Immunology (LJI) La Jolla CA USA
| | - Julian Schulze Zur Wiesch
- Infectious Diseases Unit, 1. Department of Medicine University Medical Center Hamburg-Eppendorf Hamburg Germany.,German Center for Infection Research (DZIF) Partner Site Hamburg-Lübeck-Borstel-Riems Hamburg Germany
| |
Collapse
|
14
|
Egri N, Olivé V, Hernández-Rodríguez J, Castro P, De Guzman C, Heredia L, Segura AC, Fernandez M, de Moner N, Torradeflot M, Ballús J, Martinez R, Vazquez M, Costa MV, Dobaño C, Mazza M, Mazzotti L, Pascal M, Juan M, González-Navarro EA, Calderón H. CoVITEST: A Fast and Reliable Method to Monitor Anti-SARS-CoV-2 Specific T Cells From Whole Blood. Front Immunol 2022; 13:848586. [PMID: 35865538 PMCID: PMC9295597 DOI: 10.3389/fimmu.2022.848586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/30/2022] [Indexed: 01/08/2023] Open
Abstract
Cellular and humoral immune responses are essential for COVID-19 recovery and protection against SARS-CoV-2 reinfection. To date, the evaluation of SARS-CoV-2 immune protection has mainly focused on antibody detection, generally disregarding the cellular response, or placing it in a secondary position. This phenomenon may be explained by the complex nature of the assays needed to analyze cellular immunity compared with the technically simple and automated detection of antibodies. Nevertheless, a large body of evidence supports the relevance of the T cell's role in protection against SARS-CoV-2, especially in vulnerable individuals with a weakened immune system (such as the population over 65 and patients with immunodeficiencies). Here we propose to use CoVITEST (Covid19 anti-Viral Immunity based on T cells for Evaluation in a Simple Test), a fast, affordable and accessible in-house assay that, together with a diagnostic matrix, allows us to determine those patients who might be protected with SARS-CoV-2-reactive T cells. The method was established using healthy SARS-CoV-2-naïve donors pre- and post-vaccination (n=30), and further validated with convalescent COVID-19 donors (n=51) in a side-by-side comparison with the gold standard IFN-γ ELISpot. We demonstrated that our CoVITEST presented reliable and comparable results to those obtained with the ELISpot technique in a considerably shorter time (less than 8 hours). In conclusion, we present a simple but reliable assay to determine cellular immunity against SARS-CoV-2 that can be used routinely during this pandemic to monitor the immune status in vulnerable patients and thereby adjust their therapeutic approaches. This method might indeed help to optimize and improve decision-making protocols for re-vaccination against SARS-CoV-2, at least for some population subsets.
Collapse
Affiliation(s)
- Natalia Egri
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Victoria Olivé
- Occupational Health Department, Hospital Clínic de Barcelona, Barcelona, Spain
| | - José Hernández-Rodríguez
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
- Vasculitis Research Unit and Autoinflammatory Diseases Clinical Unit, Department of Autoimmune Diseases, Hospital Clínic of Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Pedro Castro
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Medical Intensive Care Unit, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Catherine De Guzman
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Libertad Heredia
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Ana Castellet Segura
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - M. Dolores Fernandez
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Noemi de Moner
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
| | - María Torradeflot
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Judit Ballús
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Robert Martinez
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mario Vazquez
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Marta Vidal Costa
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Carlota Dobaño
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- CIBER Infectious Diseases (CIBERINFEC), Barcelona, Spain
| | - Massimiliano Mazza
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, FC, Italy
| | - Lucia Mazzotti
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, FC, Italy
| | - Mariona Pascal
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Allergy Network ARADyAL, Instituto de Salud Carlos III, Madrid, Spain
| | - Manel Juan
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Europa Azucena González-Navarro
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Hugo Calderón
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| |
Collapse
|
15
|
Cords L, Knapp M, Woost R, Schulte S, Kummer S, Ackermann C, Beisel C, Peine S, Johansson AM, Kwok WWH, Günther T, Fischer N, Wittner M, Addo MM, Huber S, Schulze zur Wiesch J. High and Sustained Ex Vivo Frequency but Altered Phenotype of SARS-CoV-2-Specific CD4 + T-Cells in an Anti-CD20-Treated Patient with Prolonged COVID-19. Viruses 2022; 14:v14061265. [PMID: 35746736 PMCID: PMC9228841 DOI: 10.3390/v14061265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
Here, we longitudinally assessed the ex vivo frequency and phenotype of SARS-CoV-2 membrane protein (aa145-164) epitope-specific CD4+ T-cells of an anti-CD20-treated patient with prolonged viral positivity in direct comparison to an immunocompetent patient through an MHC class II DRB1*11:01 Tetramer analysis. We detected a high and stable SARS-CoV-2 membrane-specific CD4+ T-cell response in both patients, with higher frequencies of virus-specific CD4+ T-cells in the B-cell-depleted patient. However, we found an altered virus-specific CD4+ T-cell memory phenotype in the B-cell-depleted patient that was skewed towards late differentiated memory T-cells, as well as reduced frequencies of SARS-CoV-2-specific CD4+ T-cells with CD45RA- CXCR5+ PD-1+ circulating T follicular helper cell (cTFH) phenotype. Furthermore, we observed a delayed contraction of CD127- virus-specific effector cells. The expression of the co-inhibitory receptors TIGIT and LAG-3 fluctuated on the virus-specific CD4+ T-cells of the patient, but were associated with the inflammation markers IL-6 and CRP. Our findings indicate that, despite B-cell depletion and a lack of B-cell-T-cell interaction, a robust virus-specific CD4+ T-cell response can be primed that helps to control the viral replication, but which is not sufficient to fully abrogate the infection.
Collapse
Affiliation(s)
- Leon Cords
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
| | - Maximilian Knapp
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
| | - Robin Woost
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20246 Hamburg, Germany;
| | - Sophia Schulte
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
| | - Silke Kummer
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
| | - Christin Ackermann
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
| | - Claudia Beisel
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20246 Hamburg, Germany;
| | - Sven Peine
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | | | - William Wai-Hung Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA; (A.M.J.); (W.W.-H.K.)
| | - Thomas Günther
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany;
| | - Nicole Fischer
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20246 Hamburg, Germany;
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany;
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Melanie Wittner
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20246 Hamburg, Germany;
| | - Marylyn Martina Addo
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20246 Hamburg, Germany;
| | - Samuel Huber
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
| | - Julian Schulze zur Wiesch
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20246 Hamburg, Germany;
- Correspondence:
| |
Collapse
|
16
|
Identification of cytotoxic T cells and their T cell receptor sequences targeting COVID-19 using MHC class I-binding peptides. J Hum Genet 2022; 67:411-419. [PMID: 35110673 PMCID: PMC8807680 DOI: 10.1038/s10038-022-01013-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 11/29/2022]
Abstract
Since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) was first reported in China in December 2019, various variants have been identified in different areas of the world such as United Kingdom (alpha), South Africa (beta and omicron), Brazil (gamma), and India (delta). Some of SARS-CoV-2 variants, each of which is characterized by a unique mutation(s) in spike protein, are concerned due to their high infectivity and the capability to escape from neutralizing antibodies elicited by vaccinations. To identify peptide epitopes that are derived from SARS-CoV-2 viral proteins and possibly induce CD8+ T cell immunity, we investigated SARS-CoV-2-derived peptides that are likely to bind to major histocompatibility complex (MHC) class I molecules. We identified a total of 15 peptides that bind to human leukocyte antigen (HLA)-A*24:02, HLA-A*02:01, or HLA-A*02:06, and possibly induce cytotoxic T lymphocytes (CTLs); thirteen of them corresponded to ORF1ab polyprotein, one peptide to spike protein and the remaining one to membrane glycoprotein. CD8+ T cells that recognize these peptides were detected in peripheral blood samples in three individuals recovered from COVID-19 as well as non-infected individuals. Since most of these peptides are commonly conserved among other coronaviruses including SARS-CoV and/or MERS-CoV, these might be useful to maintain T cell responses to coronaviruses that are pandemic at present and will become the future threat. We could define pairs of TRA and TRB sequences of nine CTL clones that recognize SARS-CoV-2-derived peptides. We might use these SARS-CoV-2-derived peptide-reactive TCR sequences for investigating the history of SARS-CoV-2 infection.
Collapse
|
17
|
Dijkstra JM, Frenette AP, Dixon B. Most Japanese individuals are genetically predisposed to recognize an immunogenic protein fragment shared between COVID-19 and common cold coronaviruses. F1000Res 2021; 10:196. [PMID: 34026045 PMCID: PMC8108557 DOI: 10.12688/f1000research.51479.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
In the spring of 2020, we and others hypothesized that T cells in COVID-19 patients may recognize identical protein fragments shared between the coronaviruses of the common cold and COVID-19 and thereby confer cross-virus immune memory. Here, we look at this issue by screening studies that, since that time, have experimentally addressed COVID-19 associated T cell specificities. Currently, the identical T cell epitope shared between COVID-19 and common cold coronaviruses most convincingly identified as immunogenic is the CD8 + T cell epitope VYIGDPAQL if presented by the MHC class I allele HLA-A*24:02. The HLA-A*24:02 allele is found in the majority of Japanese individuals and several indigenous populations in Asia, Oceania, and the Americas. In combination with histories of common cold infections, HLA-A*24:02 may affect their protection from COVID-19.
Collapse
Affiliation(s)
- Johannes M. Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health Universit, Toyoake-shi, 470-1192, Japan
| | - Aaron P. Frenette
- Department of Biology, University of Waterlo, Waterloo, ON, N2L 3G1, Canada
| | - Brian Dixon
- Department of Biology, University of Waterlo, Waterloo, ON, N2L 3G1, Canada
| |
Collapse
|