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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.
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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
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Study of the Effects of Several SARS-CoV-2 Structural Proteins on Antiviral Immunity. Vaccines (Basel) 2023; 11:vaccines11030524. [PMID: 36992107 DOI: 10.3390/vaccines11030524] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike (S) protein is a critical viral antigenic protein that enables the production of neutralizing antibodies, while other structural proteins, including the membrane (M), nucleocapsid (N) and envelope (E) proteins, have unclear roles in antiviral immunity. In this study, S1, S2, M, N and E proteins were expressed in 16HBE cells to explore the characteristics of the resultant innate immune response. Furthermore, peripheral blood mononuclear cells (PBMCs) from mice immunized with two doses of inactivated SARS-CoV-2 vaccine or two doses of mRNA vaccine were isolated and stimulated by these five proteins to evaluate the corresponding specific T-cell immune response. In addition, the levels of humoral immunity induced by two-dose inactivated vaccine priming followed by mRNA vaccine boosting, two homologous inactivated vaccine doses and two homologous mRNA vaccine doses in immunized mice were compared. Our results suggested that viral structural proteins can activate the innate immune response and elicit a specific T-cell response in mice immunized with the inactivated vaccine. However, the existence of the specific T-cell response against M, N and E is seemingly insufficient to improve the level of humoral immunity.
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Lin F, Lin X, Fu B, Xiong Y, Zaky MY, Wu H. Functional studies of HLA and its role in SARS-CoV-2: Stimulating T cell response and vaccine development. Life Sci 2023; 315:121374. [PMID: 36621539 PMCID: PMC9815883 DOI: 10.1016/j.lfs.2023.121374] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
In the biological immune process, the major histocompatibility complex (MHC) plays an indispensable role in the expression of HLA molecules in the human body when viral infection activates the T-cell response to remove the virus. Since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in 2019, how to address and prevent SARS-CoV-2 has become a common problem facing all mankind. The T-cell immune response activated by MHC peptides is a way to construct a defense line and reduce the transmission and harm of the virus. Presentation of SARS-CoV-2 antigen is associated with different types of HLA phenotypes, and different HLA phenotypes induce different immune responses. The prediction of SARS-CoV-2 mutation information and the design of vaccines based on HLAs can effectively activate autoimmunity and cope with virus mutations, which can provide some references for the prevention and treatment of SARS-CoV-2.
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Affiliation(s)
- Feng Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Xiaoyuan Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Mohamed Y Zaky
- Molecular Physiology Division, Zoology Department, Faculty of Science, Beni-Suef University, P.O. Box 62521, Beni-Suef, Egypt; Department of Oncology and Department of Biomedical and Clinical Science, Faculty of Medicine, Linköping University, Sweden
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
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Early CD4 + T cell responses induced by the BNT162b2 SARS-CoV-2 mRNA vaccine predict immunological memory. Sci Rep 2022; 12:20376. [PMID: 36437407 PMCID: PMC9701808 DOI: 10.1038/s41598-022-24938-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Longitudinal studies have revealed large interindividual differences in antibody responses induced by SARS-CoV-2 mRNA vaccines. Thus, we performed a comprehensive analysis of adaptive immune responses induced by three doses of the BNT162b2 SARS-CoV-2 mRNA vaccines. The responses of spike-specific CD4+ T cells, CD8+ T cells and serum IgG, and the serum neutralization capacities induced by the two vaccines declined 6 months later. The 3rd dose increased serum spike IgG and neutralizing capacities against the wild-type and Omicron spikes to higher levels than the 2nd dose, and this was supported by memory B cell responses, which gradually increased after the 2nd dose and were further enhanced by the 3rd dose. The 3rd dose moderately increased the frequencies of spike-specific CD4+ T cells, but the frequencies of spike-specific CD8+ T cells remained unchanged. T cells reactive against the Omicron spike were 1.3-fold fewer than those against the wild-type spike. The early responsiveness of spike-specific CD4+ T, circulating T follicular helper cells and circulating T peripheral helper cells correlated with memory B cell responses to the booster vaccination, and early spike-specific CD4+ T cell responses were also associated with spike-specific CD8+ T cell responses. These findings highlight the importance of evaluating cellular responses to optimize future vaccine strategies.
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Qiu C, Xiao C, Wang Z, Zhu G, Mao L, Chen X, Gao L, Deng J, Su J, Su H, Fang EF, Zhang ZJ, Zhang J, Xie C, Yuan J, Luo OJ, Huang L, Wang P, Chen G. CD8+ T-Cell Epitope Variations Suggest a Potential Antigen HLA-A2 Binding Deficiency for Spike Protein of SARS-CoV-2. Front Immunol 2022; 12:764949. [PMID: 35116022 PMCID: PMC8804355 DOI: 10.3389/fimmu.2021.764949] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/14/2021] [Indexed: 12/15/2022] Open
Abstract
We identified SARS-CoV-2 specific antigen epitopes by HLA-A2 binding affinity analysis and characterized their ability to activate T cells. As the pandemic continues, variations in SARS-CoV-2 virus strains have been found in many countries. In this study, we directly assess the immune response to SARS-CoV-2 epitope variants. We first predicted potential HLA-A*02:01-restricted CD8+ T-cell epitopes of SARS-CoV-2. Using the T2 cell model, HLA-A*02:01-restricted T-cell epitopes were screened for their binding affinity and ability to activate T cells. Subsequently, we examined the identified epitope variations and analyzed their impact on immune response. Here, we identified specific HLA-A2-restricted T-cell epitopes in the spike protein of SARS-CoV-2. Seven epitope peptides were confirmed to bind with HLA-A*02:01 and potentially be presented by antigen-presenting cells to induce host immune responses. Tetramers containing these peptides could interact with specific CD8+ T cells from convalescent COVID-19 patients, and one dominant epitope (n-Sp1) was defined. These epitopes could activate and generate epitope-specific T cells in vitro, and those activated T cells showed cytolytic activity toward target cells. Meanwhile, n-Sp1 epitope variant 5L>F significantly decreased the proportion of specific T-cell activation; n-Sp1 epitope 8L>V variant showed significantly reduced binding to HLA-A*02:01 and decreased proportion of n-Sp1-specific CD8+ T cell, which potentially contributes to the immune escape of SARS-CoV-2. Our data indicate that the variation of a dominant epitope will cause the deficiency of HLA-A*02:01 binding and T-cell activation, which subsequently requires the formation of a new CD8+ T-cell immune response in COVID-19 patients.
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Affiliation(s)
- Congling Qiu
- Department of Neurology, Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
| | - Chanchan Xiao
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
| | - Zhigang Wang
- Department of Neurology, Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
| | - Guodong Zhu
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- Department of Geriatrics, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Lipeng Mao
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
| | - Xiongfei Chen
- Department of Primary Public Health, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Lijuan Gao
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
| | - Jieping Deng
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
| | - Jun Su
- Department of Neurology, Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
| | - Huanxing Su
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, Macau SAR, China
| | - Evandro Fei Fang
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Zhang-Jin Zhang
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- School of Chinese Medicine, Li Ka Shing (LKS) Faculty of Medicine, the University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jikai Zhang
- Department of Biological Products and Materia Medica, Institute of Biologics and Pharmaceuticals Research, Guangzhou, China
| | - Caojun Xie
- Department of Primary Public Health, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Jun Yuan
- Department of Primary Public Health, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Oscar Junhong Luo
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
| | - Li`an Huang
- Department of Neurology, Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
| | - Pengcheng Wang
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- *Correspondence: Pengcheng Wang, ; Guobing Chen,
| | - Guobing Chen
- Department of Neurology, Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- *Correspondence: Pengcheng Wang, ; Guobing Chen,
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In silico Design and Characterization of Multi-epitopes Vaccine for SARS-CoV2 from Its Spike Protein. Int J Pept Res Ther 2022; 28:37. [PMID: 35002585 PMCID: PMC8722413 DOI: 10.1007/s10989-021-10348-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2021] [Indexed: 11/04/2022]
Abstract
COVID 19 is a disease caused by a novel coronavirus, SARS-CoV2 originated in China most probably of Bat origin. Multiepitopes vaccine would be useful in eliminating SARS-CoV2 infections as asymptomatic patients are in large numbers. In response to this, we utilized bioinformatic tools to develop an efficient vaccine candidate against SARS-CoV2. The designed vaccine has effective BCR and TCR epitopes screened from the sequence of S-protein of SARS-CoV2. Predicted BCR and TCR epitopes found antigenic, non-toxic and probably non-allergen. Modeled and the refined tertiary structure predicted as valid for further use. Protein–Protein interaction prediction of TLR2/4 and designed vaccine indicates promising binding. The designed multiepitope vaccine has induced cell-mediated and humoral immunity along with increased interferon-gamma response. Macrophages and dendritic cells were also found to increase upon the vaccine exposure. In silico codon optimization and cloning in expression vector indicates that the vaccine can be efficiently expressed in E. coli. In conclusion, the predicted vaccine is a good antigen, probable no allergen, and has the potential to induce cellular and humoral immunity.
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Jin X, Ding Y, Sun S, Wang X, Zhou Z, Liu X, Li M, Chen X, Shen A, Wu Y, Liu B, Zhang J, Li J, Yang Y, Qiu H, Shen C, He Y, Zhao G. Screening HLA-A-restricted T cell epitopes of SARS-CoV-2 and the induction of CD8 + T cell responses in HLA-A transgenic mice. Cell Mol Immunol 2021; 18:2588-2608. [PMID: 34728796 PMCID: PMC8561351 DOI: 10.1038/s41423-021-00784-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/23/2021] [Indexed: 11/22/2022] Open
Abstract
Since severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-specific T cells have been found to play essential roles in host immune protection and pathology in patients with coronavirus disease 2019 (COVID-19), this study focused on the functional validation of T cell epitopes and the development of vaccines that induce specific T cell responses. A total of 120 CD8+ T cell epitopes from the E, M, N, S, and RdRp proteins were functionally validated. Among these, 110, 15, 6, 14, and 12 epitopes were highly homologous with SARS-CoV, OC43, NL63, HKU1, and 229E, respectively; in addition, four epitopes from the S protein displayed one amino acid that was distinct from the current SARS-CoV-2 variants. Then, 31 epitopes restricted by the HLA-A2 molecule were used to generate peptide cocktail vaccines in combination with Poly(I:C), R848 or poly (lactic-co-glycolic acid) nanoparticles, and these vaccines elicited robust and specific CD8+ T cell responses in HLA-A2/DR1 transgenic mice as well as wild-type mice. In contrast to previous research, this study established a modified DC-peptide-PBL cell coculture system using healthy donor PBMCs to validate the in silico predicted epitopes, provided an epitope library restricted by nine of the most prevalent HLA-A allotypes covering broad Asian populations, and identified the HLA-A restrictions of these validated epitopes using competitive peptide binding experiments with HMy2.CIR cell lines expressing the indicated HLA-A allotype, which initially confirmed the in vivo feasibility of 9- or 10-mer peptide cocktail vaccines against SARS-CoV-2. These data will facilitate the design and development of vaccines that induce antiviral CD8+ T cell responses in COVID-19 patients.
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Affiliation(s)
- Xiaoxiao Jin
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Yan Ding
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Shihui Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xinyi Wang
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Zining Zhou
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Xiaotao Liu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Miaomiao Li
- Blood Component Preparation Section, Jiangsu Province Blood Center, Nanjing, 210042, Jiangsu, China
| | - Xian Chen
- Blood Component Preparation Section, Jiangsu Province Blood Center, Nanjing, 210042, Jiangsu, China
| | - Anran Shen
- Institute of Nephrology, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Yandan Wu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Bicheng Liu
- Institute of Nephrology, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Jianqiong Zhang
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Jian Li
- Life Science & Technology School of Southeast University, Nanjing, 210096, Jiangsu, China
| | - Yi Yang
- Jiangsu Province Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Haibo Qiu
- Jiangsu Province Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Chuanlai Shen
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China.
- Jiangsu Province Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China.
| | - Yuxian He
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
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8
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Smith CC, Olsen KS, Gentry KM, Sambade M, Beck W, Garness J, Entwistle S, Willis C, Vensko S, Woods A, Fini M, Carpenter B, Routh E, Kodysh J, O'Donnell T, Haber C, Heiss K, Stadler V, Garrison E, Sandor AM, Ting JPY, Weiss J, Krajewski K, Grant OC, Woods RJ, Heise M, Vincent BG, Rubinsteyn A. Landscape and selection of vaccine epitopes in SARS-CoV-2. Genome Med 2021; 13:101. [PMID: 34127050 PMCID: PMC8201469 DOI: 10.1186/s13073-021-00910-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 05/14/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Early in the pandemic, we designed a SARS-CoV-2 peptide vaccine containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation. The rationale for this design was to drive both humoral and cellular immunity with high specificity while avoiding undesired effects such as antibody-dependent enhancement (ADE). METHODS We explored the set of computationally predicted SARS-CoV-2 HLA-I and HLA-II ligands, examining protein source, concurrent human/murine coverage, and population coverage. Beyond MHC affinity, T cell vaccine candidates were further refined by predicted immunogenicity, sequence conservation, source protein abundance, and coverage of high frequency HLA alleles. B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering for surface accessibility, sequence conservation, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. RESULTS From 58 initial candidates, three B cell epitope regions were identified. From 3730 (MHC-I) and 5045 (MHC-II) candidate ligands, 292 CD8+ and 284 CD4+ T cell epitopes were identified. By combining these B cell and T cell analyses, as well as a manufacturability heuristic, we proposed a set of 22 SARS-CoV-2 vaccine peptides for use in subsequent murine studies. We curated a dataset of ~ 1000 observed T cell epitopes from convalescent COVID-19 patients across eight studies, showing 8/15 recurrent epitope regions to overlap with at least one of our candidate peptides. Of the 22 candidate vaccine peptides, 16 (n = 10 T cell epitope optimized; n = 6 B cell epitope optimized) were manually selected to decrease their degree of sequence overlap and then synthesized. The immunogenicity of the synthesized vaccine peptides was validated using ELISpot and ELISA following murine vaccination. Strong T cell responses were observed in 7/10 T cell epitope optimized peptides following vaccination. Humoral responses were deficient, likely due to the unrestricted conformational space inhabited by linear vaccine peptides. CONCLUSIONS Overall, we find our selection process and vaccine formulation to be appropriate for identifying T cell epitopes and eliciting T cell responses against those epitopes. Further studies are needed to optimize prediction and induction of B cell responses, as well as study the protective capacity of predicted T and B cell epitopes.
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Affiliation(s)
- Christof C Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Kelly S Olsen
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Kaylee M Gentry
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Maria Sambade
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Wolfgang Beck
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Jason Garness
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Sarah Entwistle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Caryn Willis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Allison Woods
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Misha Fini
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Brandon Carpenter
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Eric Routh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Julia Kodysh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Timothy O'Donnell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Erik Garrison
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Adam M Sandor
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Jenny P Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA
- Institute for Inflammatory Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for Translational Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jared Weiss
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Division of Medical Oncology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, NC, USA
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Mark Heise
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA.
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA.
- Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA.
| | - Alex Rubinsteyn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA.
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA.
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA.
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9
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Zhang Y, Chen Y, Li Y, Huang F, Luo B, Yuan Y, Xia B, Ma X, Yang T, Yu F, Liu J, Liu B, Song Z, Chen J, Yan S, Wu L, Pan T, Zhang X, Li R, Huang W, He X, Xiao F, Zhang J, Zhang H. The ORF8 protein of SARS-CoV-2 mediates immune evasion through down-regulating MHC-Ι. Proc Natl Acad Sci U S A 2021; 118:e2024202118. [PMID: 34021074 PMCID: PMC8201919 DOI: 10.1073/pnas.2024202118] [Citation(s) in RCA: 255] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global pandemic and has claimed over 2 million lives worldwide. Although the genetic sequences of SARS-CoV and SARS-CoV-2 have high homology, the clinical and pathological characteristics of COVID-19 differ significantly from those of SARS. How and whether SARS-CoV-2 evades (cellular) immune surveillance requires further elucidation. In this study, we show that SARS-CoV-2 infection leads to major histocompability complex class Ι (MHC-Ι) down-regulation both in vitro and in vivo. The viral protein encoded by open reading frame 8 (ORF8) of SARS-CoV-2, which shares the least homology with SARS-CoV among all viral proteins, directly interacts with MHC-Ι molecules and mediates their down-regulation. In ORF8-expressing cells, MHC-Ι molecules are selectively targeted for lysosomal degradation via autophagy. Thus, SARS-CoV-2-infected cells are much less sensitive to lysis by cytotoxic T lymphocytes. Because ORF8 protein impairs the antigen presentation system, inhibition of ORF8 could be a strategy to improve immune surveillance.
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Affiliation(s)
- Yiwen Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Yingshi Chen
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Yuzhuang Li
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Feng Huang
- Department of Respiratory Diseases, Guangzhou Women and Children Hospital, 510010, Guangzhou, Guangdong, China
| | - Baohong Luo
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Yaochang Yuan
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Baijin Xia
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Xiancai Ma
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Tao Yang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Fei Yu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Jun Liu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Bingfeng Liu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Zheng Song
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Jingliang Chen
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Shumei Yan
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Liyang Wu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Ting Pan
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Xu Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Rong Li
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Wenjing Huang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 510000, Guangzhou, Guangdong, China
| | - Xin He
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Fei Xiao
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, 519000, Zhuhai, Guangdong, China
| | - Junsong Zhang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 510000, Guangzhou, Guangdong, China;
| | - Hui Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China;
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10
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Zhang Y, Chen Y, Li Y, Huang F, Luo B, Yuan Y, Xia B, Ma X, Yang T, Yu F, Liu J, Liu B, Song Z, Chen J, Yan S, Wu L, Pan T, Zhang X, Li R, Huang W, He X, Xiao F, Zhang J, Zhang H. The ORF8 protein of SARS-CoV-2 mediates immune evasion through down-regulating MHC-Ι. Proc Natl Acad Sci U S A 2021; 118:2024202118. [PMID: 34021074 DOI: 10.1101/2020.05.24.111823] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global pandemic and has claimed over 2 million lives worldwide. Although the genetic sequences of SARS-CoV and SARS-CoV-2 have high homology, the clinical and pathological characteristics of COVID-19 differ significantly from those of SARS. How and whether SARS-CoV-2 evades (cellular) immune surveillance requires further elucidation. In this study, we show that SARS-CoV-2 infection leads to major histocompability complex class Ι (MHC-Ι) down-regulation both in vitro and in vivo. The viral protein encoded by open reading frame 8 (ORF8) of SARS-CoV-2, which shares the least homology with SARS-CoV among all viral proteins, directly interacts with MHC-Ι molecules and mediates their down-regulation. In ORF8-expressing cells, MHC-Ι molecules are selectively targeted for lysosomal degradation via autophagy. Thus, SARS-CoV-2-infected cells are much less sensitive to lysis by cytotoxic T lymphocytes. Because ORF8 protein impairs the antigen presentation system, inhibition of ORF8 could be a strategy to improve immune surveillance.
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Affiliation(s)
- Yiwen Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Yingshi Chen
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Yuzhuang Li
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Feng Huang
- Department of Respiratory Diseases, Guangzhou Women and Children Hospital, 510010, Guangzhou, Guangdong, China
| | - Baohong Luo
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Yaochang Yuan
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Baijin Xia
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Xiancai Ma
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Tao Yang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Fei Yu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Jun Liu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Bingfeng Liu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Zheng Song
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Jingliang Chen
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Shumei Yan
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Liyang Wu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Ting Pan
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Xu Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Rong Li
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Wenjing Huang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 510000, Guangzhou, Guangdong, China
| | - Xin He
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Fei Xiao
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, 519000, Zhuhai, Guangdong, China
| | - Junsong Zhang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 510000, Guangzhou, Guangdong, China;
| | - Hui Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China;
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11
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Alam A, Khan A, Imam N, Siddiqui MF, Waseem M, Malik MZ, Ishrat R. Design of an epitope-based peptide vaccine against the SARS-CoV-2: a vaccine-informatics approach. Brief Bioinform 2021; 22:1309-1323. [PMID: 33285567 PMCID: PMC7799329 DOI: 10.1093/bib/bbaa340] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022] Open
Abstract
The recurrent and recent global outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has turned into a global concern which has infected more than 42 million people all over the globe, and this number is increasing in hours. Unfortunately, no vaccine or specific treatment is available, which makes it more deadly. A vaccine-informatics approach has shown significant breakthrough in peptide-based epitope mapping and opens the new horizon in vaccine development. In this study, we have identified a total of 15 antigenic peptides [including thymus cells (T-cells) and bone marrow or bursa-derived cells] in the surface glycoprotein (SG) of SARS-CoV-2 which is nontoxic and nonallergenic in nature, nonallergenic, highly antigenic and non-mutated in other SARS-CoV-2 virus strains. The population coverage analysis has found that cluster of differentiation 4 (CD4+) T-cell peptides showed higher cumulative population coverage over cluster of differentiation 8 (CD8+) peptides in the 16 different geographical regions of the world. We identified 12 peptides ((LTDEMIAQY, WTAGAAAYY, WMESEFRVY, IRASANLAA, FGAISSVLN, VKQLSSNFG, FAMQMAYRF, FGAGAALQI, YGFQPTNGVGYQ, LPDPSKPSKR, QTQTNSPRRARS and VITPGTNTSN) that are $80\hbox{--} 90\%$ identical with experimentally determined epitopes of SARS-CoV, and this will likely be beneficial for a quick progression of the vaccine design. Moreover, docking analysis suggested that the identified peptides are tightly bound in the groove of human leukocyte antigen molecules which can induce the T-cell response. Overall, this study allows us to determine potent peptide antigen targets in the SG on intuitive grounds, which opens up a new horizon in the coronavirus disease (COVID-19) research. However, this study needs experimental validation by in vitro and in vivo.
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Affiliation(s)
- Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia University, New Delhi 110025, India
| | - Arbaaz Khan
- Department of computer science, Jamia Millia Islamia University, New Delhi, India
| | - Nikhat Imam
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia University, New Delhi, India
| | | | - Mohd Waseem
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Md Zubbair Malik
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia University, New Delhi, India
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12
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Shah P, Canziani GA, Carter EP, Chaiken I. The Case for S2: The Potential Benefits of the S2 Subunit of the SARS-CoV-2 Spike Protein as an Immunogen in Fighting the COVID-19 Pandemic. Front Immunol 2021; 12:637651. [PMID: 33767706 PMCID: PMC7985173 DOI: 10.3389/fimmu.2021.637651] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/08/2021] [Indexed: 12/19/2022] Open
Abstract
As COVID-19 cases continue to rise, it is imperative to learn more about antibodies and T-cells produced against the causative virus, SARS-CoV-2, in order to guide the rapid development of therapies and vaccines. While much of the current antibody and vaccine research focuses on the receptor-binding domain of S1, a less-recognized opportunity is to harness the potential benefits of the more conserved S2 subunit. Similarities between the spike proteins of both SARS-CoV-2 and HIV-1 warrant exploring S2. Possible benefits of employing S2 in therapies and vaccines include the structural conservation of S2, extant cross-reactive neutralizing antibodies in populations (due to prior exposure to common cold coronaviruses), the steric neutralization potential of antibodies against S2, and the stronger memory B-cell and T-cell responses. More research is necessary on the effect of glycans on the accessibility and stability of S2, SARS-CoV-2 mutants that may affect infectivity, the neutralization potential of antibodies produced by memory B-cells, cross-reactive T-cell responses, antibody-dependent enhancement, and antigen competition. This perspective aims to highlight the evidence for the potential advantages of using S2 as a target of therapy or vaccine design.
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Affiliation(s)
- Priyanka Shah
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
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13
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Abdullahi IN, Emeribe AU, Adekola HA, Abubakar SD, Dangana A, Shuwa HA, Nwoba ST, Mustapha JO, Haruna MT, Olowookere KA, Animasaun OS, Ugwu CE, Onoja SO, Gadama AS, Mohammed M, Daneji IM, Amadu DO, Ghamba PE, Onukegbe NB, Shehu MS, Isomah C, Babayo A, Ahmad AEF. Leveraging on the genomics and immunopathology of SARS-CoV-2 for vaccines development: prospects and challenges. Hum Vaccin Immunother 2021; 17:620-637. [PMID: 32936732 PMCID: PMC7993231 DOI: 10.1080/21645515.2020.1812313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
The incidence and case-fatality rates (CFRs) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, the etiological agent for Coronavirus Disease 2019 (COVID-19), have been rising unabated. Even though the entire world has been implementing infection prevention and control measures, the pandemic continues to spread. It has been widely accepted that preventive vaccination strategies are the public health measures for countering this pandemic. This study critically reviews the latest scientific advancement in genomics, replication pattern, pathogenesis, and immunopathology of SARS-CoV-2 infection and how these concepts could be used in the development of vaccines. We also offer a detailed discussion on the anticipated potency, efficacy, safety, and pharmaco-economic issues that are and will be associated with candidate COVID-19 vaccines.
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Affiliation(s)
- Idris Nasir Abdullahi
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Anthony Uchenna Emeribe
- Department of Medical Laboratory Science, Faculty of Allied Medical Sciences, University of Calabar, Calabar, Nigeria
| | | | - Sharafudeen Dahiru Abubakar
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Amos Dangana
- Department of Medical Laboratory Services, University of Abuja Teaching Hospital, Gwagwalada, Abuja, Nigeria
| | - Halima Ali Shuwa
- Lydia Becker Institute of Immunology, Manchester Collaborative Center for Inflammation Research, Faculty of Biology, Medicine and Health, The University of Manchester, UK
| | | | - Jelili Olaide Mustapha
- Biological Sciences Department, Faculty of Science, University of Alberta, Edmonton, Canada
| | | | - Kafayat Adepeju Olowookere
- Department of Medical Laboratory Services, Ladoke Akintola University of Technology Teaching Hospital, Ogbomoso, Nigeria
| | - Olawale Sunday Animasaun
- Nigeria Field Epidemiology and Laboratory Training Programme, African Field Epidemiology Network, Abuja, Nigeria
| | - Charles Egede Ugwu
- Department of Medical Laboratory Science, Ebonyi State University, Abakaliki, Nigeria
| | | | - Abdullahi Sani Gadama
- Department of Medical Microbiology and Parasitology, Faculty of Clinical Sciences, Bayero University, Kano, Nigeria
| | - Musa Mohammed
- Department of Medicine, Immunology Unit, Ahmadu Bello University, Zaria, Nigeria
| | - Isa Muhammad Daneji
- Department of Medical Microbiology and Parasitology, Faculty of Clinical Sciences, Bayero University, Kano, Nigeria
| | - Dele Ohinoyi Amadu
- Department of Medical Microbiology and Parasitology, University of Ilorin Teaching Hospital, Ilorin, Nigeria
| | - Peter Elisha Ghamba
- WHO National Polio Reference Laboratory, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | | | - Muhammad Sagir Shehu
- Medical Laboratory Department, College of Health Technology, Ningi, Bauchi State, Nigeria
| | - Chiladi Isomah
- Medical Laboratory Science Department, Rivers State University, Port Harcourt, Nigeria
| | - Adamu Babayo
- Department of Medical Microbiology and Parasitology, Faculty of Clinical Sciences, Bayero University, Kano, Nigeria
| | - Abdurrahman El-Fulaty Ahmad
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
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14
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Shomuradova AS, Vagida MS, Sheetikov SA, Zornikova KV, Kiryukhin D, Titov A, Peshkova IO, Khmelevskaya A, Dianov DV, Malasheva M, Shmelev A, Serdyuk Y, Bagaev DV, Pivnyuk A, Shcherbinin DS, Maleeva AV, Shakirova NT, Pilunov A, Malko DB, Khamaganova EG, Biderman B, Ivanov A, Shugay M, Efimov GA. SARS-CoV-2 Epitopes Are Recognized by a Public and Diverse Repertoire of Human T Cell Receptors. Immunity 2020; 53:1245-1257.e5. [PMID: 33326767 PMCID: PMC7664363 DOI: 10.1016/j.immuni.2020.11.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/02/2020] [Accepted: 11/09/2020] [Indexed: 12/28/2022]
Abstract
Understanding the hallmarks of the immune response to SARS-CoV-2 is critical for fighting the COVID-19 pandemic. We assessed antibody and T cell reactivity in convalescent COVID-19 patients and healthy donors sampled both prior to and during the pandemic. Healthy donors examined during the pandemic exhibited increased numbers of SARS-CoV-2-specific T cells, but no humoral response. Their probable exposure to the virus resulted in either asymptomatic infection without antibody secretion or activation of preexisting immunity. In convalescent patients, we observed a public and diverse T cell response to SARS-CoV-2 epitopes, revealing T cell receptor (TCR) motifs with germline-encoded features. Bulk CD4+ and CD8+ T cell responses to the spike protein were mediated by groups of homologous TCRs, some of them shared across multiple donors. Overall, our results demonstrate that the T cell response to SARS-CoV-2, including the identified set of TCRs, can serve as a useful biomarker for surveying antiviral immunity.
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Affiliation(s)
- Alina S Shomuradova
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Savely A Sheetikov
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ksenia V Zornikova
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Aleksei Titov
- National Research Center for Hematology, Moscow, Russia
| | | | - Alexandra Khmelevskaya
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry V Dianov
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Malasheva
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anton Shmelev
- National Research Center for Hematology, Moscow, Russia
| | - Yana Serdyuk
- National Research Center for Hematology, Moscow, Russia
| | - Dmitry V Bagaev
- Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Anastasia Pivnyuk
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Dmitrii S Shcherbinin
- Pirogov Russian Medical State University, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | | | - Artem Pilunov
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | | | - Alexander Ivanov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Pirogov Russian Medical State University, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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15
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Guo E, Guo H. CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. PLoS One 2020; 15:e0239566. [PMID: 33301503 PMCID: PMC7728258 DOI: 10.1371/journal.pone.0239566] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/23/2020] [Indexed: 01/10/2023] Open
Abstract
The ongoing pandemic of SARS-CoV-2 has brought tremendous crisis on global health care systems and industrial operations that dramatically affect the economic and social life of numerous individuals worldwide. Understanding anti-SARS-CoV-2 immune responses in population with different genetic backgrounds and tracking the viral evolution are crucial for successful vaccine design. In this study, we reported the generation of CD8 T cell epitopes by a total of 80 alleles of three major class I HLAs using NetMHC 4.0 algorithm for the SARS-CoV-2 spike protein, which can be targeted by both B cells and T cells. We found diverse capacities of S protein specific epitope presentation by different HLA alleles with very limited number of predicted epitopes for HLA-B*2705, HLA-B*4402 and HLA-B*4403 and as high as 132 epitopes for HLA-A*6601. Our analysis of 1000 S protein sequences from field isolates collected globally over the past few months identified three recurrent point mutations including L5F, D614G and G1124V. Differential effects of these mutations on CD8 T cell epitope generation by corresponding HLA alleles were observed. Finally, our multiple alignment analysis indicated the absence of seasonal CoV induced cross-reactive CD8 T cells to drive these mutations. Our findings suggested that individuals with certain HLA alleles, such as B*44 are more prone to SARS-CoV-2 infection. Studying anti-S protein specific CD8 T cell immunity in diverse genetic background is critical for better control and prevention of the SARS-CoV-2 pandemic.
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Affiliation(s)
- Elisa Guo
- Mounds View High School, Arden Hills, Minnesota, United States of America
| | - Hailong Guo
- Independent Scientist, St Paul, Minnesota, United States of America
- * E-mail:
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16
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Kim DS, Rowland-Jones S, Gea-Mallorquí E. Will SARS-CoV-2 Infection Elicit Long-Lasting Protective or Sterilising Immunity? Implications for Vaccine Strategies (2020). Front Immunol 2020; 11:571481. [PMID: 33362759 PMCID: PMC7756008 DOI: 10.3389/fimmu.2020.571481] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/06/2020] [Indexed: 12/20/2022] Open
Abstract
In December 2019, an outbreak of a novel coronavirus (SARS-CoV-2) in Wuhan, China resulted in the current COVID-19 global pandemic. The human immune system has not previously encountered this virus, raising the important question as to whether or not protective immunity is generated by infection. Growing evidence suggests that protective immunity can indeed be acquired post-infection-although a handful of reinfection cases have been reported. However, it is still unknown whether the immune response to SARS-CoV-2 leads to some degree of long-lasting protection against the disease or the infection. This review draws insights from previous knowledge regarding the nature and longevity of immunity to the related virus, SARS-CoV, to fill the gaps in our understanding of the immune response to SARS-CoV-2. Deciphering the immunological characteristics that give rise to protective immunity against SARS-CoV-2 is critical to guiding vaccine development and also predicting the course of the pandemic. Here we discuss the recent evidence that characterises the adaptive immune response against SARS-CoV-2 and its potential implications for the generation of memory responses and long-term protection.
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Affiliation(s)
- David S. Kim
- Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Sarah Rowland-Jones
- Viral Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ester Gea-Mallorquí
- Viral Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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17
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Older adults lack SARS CoV-2 cross-reactive T lymphocytes directed to human coronaviruses OC43 and NL63. Sci Rep 2020; 10:21447. [PMID: 33293664 PMCID: PMC7722724 DOI: 10.1038/s41598-020-78506-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
Currently, infections with SARS-Coronavirus-2 (SARS-CoV-2), the causative agent of the COVID-19 pandemic, are responsible for substantial morbidity and mortality worldwide. Older adults subjects > 60 years of age account for > 95% of the over one million fatal cases reported to date. It is unclear why in this age group SARS-CoV-2 infection causes more severe disease than in young adults. We hypothesized that differences in SARS-CoV-2 cross-reactive cellular immunity induced after infection with human coronaviruses (HCoVs), like OC43 and NL63, were at the basis of the differential mortality (and morbidity) observed after SARS-CoV-2 infection, because a small proportion of HCoV-specific T cells cross-react with SARS-CoV-2. Our data demonstrate that pre-existing T cell immunity induced by circulating human alpha- and beta-HCoVs is present in young adult individuals, but virtually absent in older adult subjects. Consequently, the frequency of cross-reactive T cells directed to the novel pandemic SARS-CoV-2 was minimal in most older adults. To the best of our knowledge, this is the first time that the presence of cross-reactive T cells to SARS-CoV-2 is compared in young and older adults. Our findings provide at least a partial explanation for the more severe clinical outcome of SARS-CoV-2 infection observed in the elderly. Moreover, this information could help to design efficacious vaccines for this age group, aiming at the induction of cell-mediated immunity.
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18
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Cun Y, Li C, Shi L, Sun M, Dai S, Sun L, Shi L, Yao Y. COVID-19 coronavirus vaccine T cell epitope prediction analysis based on distributions of HLA class I loci (HLA-A, -B, -C) across global populations. Hum Vaccin Immunother 2020; 17:1097-1108. [PMID: 33175614 PMCID: PMC7754929 DOI: 10.1080/21645515.2020.1823777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
T cell immunity, such as CD4 and/or CD8 T cell responses, plays a vital role in controlling the virus infection and pathological damage. Several studies have reported SARS-CoV-2 proteins could serve as ideal vaccine candidates against SARS-CoV-2 infection by activating the T cell responses. In the current study, based on the SARS-CoV-2 sequence and distribution of host human leukocyte antigen (HLA), we predicted the possible epitopes for the vaccine against SARS-CoV-2 infections. Firstly, the current study retrieved the SARS-CoV-2 S and N protein sequences from the NCBI Database. Then, using the Immune Epitope Database Analysis Resource, we predicted the CTL epitopes of the SARS-CoV-2 S and N proteins according to worldwide frequency distributions of HLA-A, -B, and -C alleles (>1%). Our results predicted 90 and 106 epitopes of N and S proteins, respectively. Epitope cluster analysis showed 16 and 34 respective clusters of SARS-CoV-2 N and S proteins, which covered 95.91% and 96.14% of the global population, respectively. After epitope conservancy analysis, 8 N protein epitopes and 6 S protein epitopes showed conservancy within two SARS-CoV-2 types. Of these 14 epitopes, 13 could cover SARS coronavirus and Bat SARS-like coronavirus. The remaining epitope (KWPWYIWLGF1211-1220) could cover MERS coronavirus. Finally, the 14-epitope combination could vaccinate 89.60% of all individuals worldwide. Our results propose single or combined CTL epitopes predicted in the current study as candidates for vaccines to effectively control SARS-CoV-2 infection and development.
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Affiliation(s)
- Yina Cun
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Yunnan Engineering Research Centre of Vaccine Research & Development on Severe Infectious Diseases, Kunming, China
| | - Chuanyin Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Yunnan Engineering Research Centre of Vaccine Research & Development on Severe Infectious Diseases, Kunming, China
| | - Lei Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Yunnan Engineering Research Centre of Vaccine Research & Development on Severe Infectious Diseases, Kunming, China
| | - Ming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Yunnan Engineering Research Centre of Vaccine Research & Development on Severe Infectious Diseases, Kunming, China
| | - Shuying Dai
- School of Basic Medical Science, Kunming Medical University, Kunming, China
| | - Le Sun
- School of Basic Medical Science, Kunming Medical University, Kunming, China
| | - Li Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Yunnan Engineering Research Centre of Vaccine Research & Development on Severe Infectious Diseases, Kunming, China
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Yunnan Engineering Research Centre of Vaccine Research & Development on Severe Infectious Diseases, Kunming, China
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19
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Minakshi R, Jan AT, Rahman S, Kim J. A Testimony of the Surgent SARS-CoV-2 in the Immunological Panorama of the Human Host. Front Cell Infect Microbiol 2020; 10:575404. [PMID: 33262955 PMCID: PMC7687052 DOI: 10.3389/fcimb.2020.575404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/26/2020] [Indexed: 12/19/2022] Open
Abstract
The resurgence of SARS in the late December of 2019 due to a novel coronavirus, SARS-CoV-2, has shadowed the world with a pandemic. The physiopathology of this virus is very much in semblance with the previously known SARS-CoV and MERS-CoV. However, the unprecedented transmissibility of SARS-CoV-2 has been puzzling the scientific efforts. Though the virus harbors much of the genetic and architectural features of SARS-CoV, a few differences acquired during its evolutionary selective pressure is helping the SARS-CoV-2 to establish prodigious infection. Making entry into host the cell through already established ACE-2 receptor concerted with the action of TMPRSS2, is considered important for the virus. During the infection cycle of SARS-CoV-2, the innate immunity witnesses maximum dysregulations in its molecular network causing fatalities in aged, comorbid cases. The overt immunopathology manifested due to robust cytokine storm shows ARDS in severe cases of SARS-CoV-2. A delayed IFN activation gives appropriate time to the replicating virus to evade the host antiviral response and cause disruption of the adaptive response as well. We have compiled various aspects of SARS-CoV-2 in relation to its unique structural features and ability to modulate innate as well adaptive response in host, aiming at understanding the dynamism of infection.
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Affiliation(s)
- Rinki Minakshi
- Department of Microbiology, Swami Shraddhanand College, University of Delhi, New Delhi, India
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Safikur Rahman
- Munshi Singh College, BR Ambedkar Bihar University, Muzaffarpur, India
| | - Jihoe Kim
- Department of Medical Biotechnology, Research Institute of Cell Culture, Yeungnam University, Gyeongsan-si, South Korea
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20
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Wang YT, Landeras-Bueno S, Hsieh LE, Terada Y, Kim K, Ley K, Shresta S, Saphire EO, Regla-Nava JA. Spiking Pandemic Potential: Structural and Immunological Aspects of SARS-CoV-2. Trends Microbiol 2020; 28:605-618. [PMID: 32507543 PMCID: PMC7237910 DOI: 10.1016/j.tim.2020.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 01/08/2023]
Abstract
SARS-Coronavirus-2 (SARS-CoV-2) causes Coronavirus disease 2019 (COVID-19), an infectious respiratory disease causing thousands of deaths and overwhelming public health systems. The international spread of SARS-CoV-2 is associated with the ease of global travel, and societal dynamics, immunologic naiveté of the host population, and muted innate immune responses. Based on these factors and the expanding geographic scale of the disease, the World Health Organization (WHO) declared the COVID-19 outbreak a pandemic-the first caused by a coronavirus. In this review, we summarize the current epidemiological status of COVID-19 and consider the virological and immunological lessons, animal models, and tools developed in response to prior SARS-CoV and MERS-CoV outbreaks that can serve as resources for development of SARS-CoV-2 therapeutics and vaccines. In particular, we discuss structural insights into the SARS-CoV-2 spike protein, a major determinant of transmissibility, and discuss key molecular aspects that will aid in understanding and fighting this new global threat.
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Affiliation(s)
| | | | - Li-En Hsieh
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yutaka Terada
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kenneth Kim
- Kord Animal Health Diagnostic Laboratory, Tennessee Department of Agriculture, Nashville, TN, USA
| | - Klaus Ley
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sujan Shresta
- La Jolla Institute for Immunology, La Jolla, CA, USA
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21
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Braun J, Loyal L, Frentsch M, Wendisch D, Georg P, Kurth F, Hippenstiel S, Dingeldey M, Kruse B, Fauchere F, Baysal E, Mangold M, Henze L, Lauster R, Mall MA, Beyer K, Röhmel J, Voigt S, Schmitz J, Miltenyi S, Demuth I, Müller MA, Hocke A, Witzenrath M, Suttorp N, Kern F, Reimer U, Wenschuh H, Drosten C, Corman VM, Giesecke-Thiel C, Sander LE, Thiel A. SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19. Nature 2020; 587:270-274. [PMID: 32726801 DOI: 10.1038/s41586-020-2598-9] [Citation(s) in RCA: 877] [Impact Index Per Article: 219.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the rapidly unfolding coronavirus disease 2019 (COVID-19) pandemic1,2. Clinical manifestations of COVID-19 vary, ranging from asymptomatic infection to respiratory failure. The mechanisms that determine such variable outcomes remain unresolved. Here we investigated CD4+ T cells that are reactive against the spike glycoprotein of SARS-CoV-2 in the peripheral blood of patients with COVID-19 and SARS-CoV-2-unexposed healthy donors. We detected spike-reactive CD4+ T cells not only in 83% of patients with COVID-19 but also in 35% of healthy donors. Spike-reactive CD4+ T cells in healthy donors were primarily active against C-terminal epitopes in the spike protein, which show a higher homology to spike glycoproteins of human endemic coronaviruses, compared with N-terminal epitopes. Spike-protein-reactive T cell lines generated from SARS-CoV-2-naive healthy donors responded similarly to the C-terminal region of the spike proteins of the human endemic coronaviruses 229E and OC43, as well as that of SARS-CoV-2. This results indicate that spike-protein cross-reactive T cells are present, which were probably generated during previous encounters with endemic coronaviruses. The effect of pre-existing SARS-CoV-2 cross-reactive T cells on clinical outcomes remains to be determined in larger cohorts. However, the presence of spike-protein cross-reactive T cells in a considerable fraction of the general population may affect the dynamics of the current pandemic, and has important implications for the design and analysis of upcoming trials investigating COVID-19 vaccines.
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Affiliation(s)
- Julian Braun
- Si-M/'Der Simulierte Mensch', Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lucie Loyal
- Si-M/'Der Simulierte Mensch', Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marco Frentsch
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Philipp Georg
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Florian Kurth
- Berlin Institute of Health (BIH), Berlin, Germany.,Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Manuela Dingeldey
- Si-M/'Der Simulierte Mensch', Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Beate Kruse
- Si-M/'Der Simulierte Mensch', Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Florent Fauchere
- Si-M/'Der Simulierte Mensch', Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Emre Baysal
- Si-M/'Der Simulierte Mensch', Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Maike Mangold
- Si-M/'Der Simulierte Mensch', Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Larissa Henze
- Si-M/'Der Simulierte Mensch', Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Roland Lauster
- Si-M/'Der Simulierte Mensch', Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany.,I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marcus A Mall
- Medical Biotechnology, Institute for Biotechnology, Technische Universität Berlin, Berlin, Germany.,Department of Pediatric Pulmonology, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Kirsten Beyer
- Medical Biotechnology, Institute for Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Jobst Röhmel
- Medical Biotechnology, Institute for Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Sebastian Voigt
- Department of Infectious Diseases, Robert Koch Institut, Berlin, Germany
| | | | | | - Ilja Demuth
- Interdisciplinary Metabolism Center, Biology of Aging (BoA) group, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marcel A Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | | | | | - Florian Kern
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK.,JPT Peptide Technologies, Berlin, Germany
| | - Ulf Reimer
- JPT Peptide Technologies, Berlin, Germany
| | | | - Christian Drosten
- Department of Pediatric Pulmonology, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | | | - Andreas Thiel
- Si-M/'Der Simulierte Mensch', Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany. .,Regenerative Immunology and Aging, BIH Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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22
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Wang D, Mai J, Zhou W, Yu W, Zhan Y, Wang N, Epstein ND, Yang Y. Immunoinformatic Analysis of T- and B-Cell Epitopes for SARS-CoV-2 Vaccine Design. Vaccines (Basel) 2020; 8:vaccines8030355. [PMID: 32635180 PMCID: PMC7563688 DOI: 10.3390/vaccines8030355] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/23/2020] [Accepted: 06/30/2020] [Indexed: 12/11/2022] Open
Abstract
Currently, there is limited knowledge about the immunological profiles of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). We used computer-based immunoinformatic analysis and the newly resolved 3-dimensional (3D) structures of the SARS-CoV-2 S trimeric protein, together with analyses of the immunogenic profiles of SARS-CoV, to anticipate potential B-cell and T-cell epitopes of the SARS-CoV-2 S protein for vaccine design, particularly for peptide-driven vaccine design and serological diagnosis. Nine conserved linear B-cell epitopes and multiple discontinuous B-cell epitopes composed of 69 residues on the surface of the SARS-CoV-2 trimeric S protein were predicted to be highly antigenic. We found that the SARS-CoV-2 S protein has a different antigenic profile than that of the SARS-CoV S protein due to the variations in their primary and 3D structures. Importantly, SARS-CoV-2 may exploit an immune evasion mechanism through two point mutations in the critical and conserved linear neutralization epitope (overlap with fusion peptide) around a sparsely glycosylated area. These mutations lead to a significant decrease in the antigenicity of this epitope in the SARS-CoV-2 S protein. In addition, 62 T-cell epitopes in the SARS-CoV-2 S protein were predicted in our study. The structure-based immunoinformatic analysis for the SARS-CoV-2 S protein in this study may improve vaccine design, diagnosis, and immunotherapy against the pandemic of COVID-19.
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Affiliation(s)
- Dongliang Wang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Laboratory of Functional Proteomics (LFP), Research Center of Reverse Vaccinology (RCRV), College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (D.W.); (J.M.); (W.Z.); (W.Y.); (Y.Z.); (N.W.)
| | - Jinhui Mai
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Laboratory of Functional Proteomics (LFP), Research Center of Reverse Vaccinology (RCRV), College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (D.W.); (J.M.); (W.Z.); (W.Y.); (Y.Z.); (N.W.)
| | - Wenfeng Zhou
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Laboratory of Functional Proteomics (LFP), Research Center of Reverse Vaccinology (RCRV), College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (D.W.); (J.M.); (W.Z.); (W.Y.); (Y.Z.); (N.W.)
| | - Wanting Yu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Laboratory of Functional Proteomics (LFP), Research Center of Reverse Vaccinology (RCRV), College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (D.W.); (J.M.); (W.Z.); (W.Y.); (Y.Z.); (N.W.)
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yang Zhan
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Laboratory of Functional Proteomics (LFP), Research Center of Reverse Vaccinology (RCRV), College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (D.W.); (J.M.); (W.Z.); (W.Y.); (Y.Z.); (N.W.)
| | - Naidong Wang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Laboratory of Functional Proteomics (LFP), Research Center of Reverse Vaccinology (RCRV), College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (D.W.); (J.M.); (W.Z.); (W.Y.); (Y.Z.); (N.W.)
| | - Neal D. Epstein
- Cell and Developmental Biology Center, NHLBI, NIH, Bethesda, MD 20892, USA
- Correspondence: (N.D.E.); (Y.Y.)
| | - Yi Yang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, Laboratory of Functional Proteomics (LFP), Research Center of Reverse Vaccinology (RCRV), College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (D.W.); (J.M.); (W.Z.); (W.Y.); (Y.Z.); (N.W.)
- Correspondence: (N.D.E.); (Y.Y.)
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23
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Debnath M, Banerjee M, Berk M. Genetic gateways to COVID-19 infection: Implications for risk, severity, and outcomes. FASEB J 2020; 34:8787-8795. [PMID: 32525600 PMCID: PMC7300732 DOI: 10.1096/fj.202001115r] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/10/2020] [Accepted: 05/12/2020] [Indexed: 01/05/2023]
Abstract
The dynamics, such as transmission, spatial epidemiology, and clinical course of Coronavirus Disease-2019 (COVID-19) have emerged as the most intriguing features and remain incompletely understood. The genetic landscape of an individual in particular, and a population in general seems to play a pivotal role in shaping the above COVID-19 dynamics. Considering the implications of host genes in the entry and replication of SARS-CoV-2 and in mounting the host immune response, it appears that multiple genes might be crucially involved in the above processes. Herein, we propose three potentially important genetic gateways to COVID-19 infection; these could explain at least in part the discrepancies of its spread, severity, and mortality. The variations within Angiotensin-converting enzyme 2 (ACE2) gene might constitute the first genetic gateway, influencing the spatial transmission dynamics of COVID-19. The Human Leukocyte Antigen locus, a master regulator of immunity against infection seems to be crucial in influencing susceptibility and severity of COVID-19 and can be the second genetic gateway. The genes regulating Toll-like receptor and complement pathways and subsequently cytokine storm induced exaggerated inflammatory pathways seem to underlie the severity of COVID-19, and such genes might represent the third genetic gateway. Host-pathogen interaction is a complex event and some additional genes might also contribute to the dynamics of COVID-19. Overall, these three genetic gateways proposed here might be the critical host determinants governing the risk, severity, and outcome of COVID-19. Genetic variations within these gateways could be key in influencing geographical discrepancies of COVID-19.
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Affiliation(s)
- Monojit Debnath
- Department of Human GeneticsNational Institute of Mental Health and NeurosciencesBangaloreIndia
| | - Moinak Banerjee
- Human Molecular Genetics LaboratoryRajiv Gandhi Centre for BiotechnologyThiruvanathapuramIndia
| | - Michael Berk
- IMPACT ‐ the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon HealthDeakin UniversityGeelongVICAustralia
- Florey Institute for Neuroscience and Mental Health, Department of Psychiatry and Orygen, The National Centre of Excellence in Youth Mental HealthThe University of MelbourneMelbourneVICAustralia
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24
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Smith CC, Entwistle S, Willis C, Vensko S, Beck W, Garness J, Sambade M, Routh E, Olsen K, Kodysh J, O’Donnell T, Haber C, Heiss K, Stadler V, Garrison E, Grant OC, Woods RJ, Heise M, Vincent BG, Rubinsteyn A. Landscape and Selection of Vaccine Epitopes in SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.04.135004. [PMID: 32577654 PMCID: PMC7302209 DOI: 10.1101/2020.06.04.135004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
There is an urgent need for a vaccine with efficacy against SARS-CoV-2. We hypothesize that peptide vaccines containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation would drive both humoral and cellular immunity with high specificity, potentially avoiding undesired effects such as antibody-dependent enhancement (ADE). Additionally, such vaccines can be rapidly manufactured in a distributed manner. In this study, we combine computational prediction of T cell epitopes, recently published B cell epitope mapping studies, and epitope accessibility to select candidate peptide vaccines for SARS-CoV-2. We begin with an exploration of the space of possible T cell epitopes in SARS-CoV-2 with interrogation of predicted HLA-I and HLA-II ligands, overlap between predicted ligands, protein source, as well as concurrent human/murine coverage. Beyond MHC affinity, T cell vaccine candidates were further refined by predicted immunogenicity, viral source protein abundance, sequence conservation, coverage of high frequency HLA alleles and co-localization of CD4+ and CD8+ T cell epitopes. B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering to select regions with surface accessibility, high sequence conservation, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. From 58 initial candidates, three B cell epitope regions were identified. By combining these B cell and T cell analyses, as well as a manufacturability heuristic, we propose a set of SARS-CoV-2 vaccine peptides for use in subsequent murine studies and clinical trials.
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Affiliation(s)
- Christof C. Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sarah Entwistle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Caryn Willis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Wolfgang Beck
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jason Garness
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Maria Sambade
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Eric Routh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kelly Olsen
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Julia Kodysh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Timothy O’Donnell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | | | - Erik Garrison
- Genomics Institute, University of California, Santa Cruz, California
| | - Oliver C. Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Mark Heise
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina
| | - Benjamin G. Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, North Carolina
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, North Carolina
- Division of Hematology/Oncology, Department of Medicine, UNC School of Medicine, Chapel Hill, North Carolina
| | - Alex Rubinsteyn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, North Carolina
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25
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A modified HLA-A*0201-restricted CTL epitope from human oncoprotein (hPEBP4) induces more efficient antitumor responses. Cell Mol Immunol 2018; 15:768-781. [PMID: 29375131 DOI: 10.1038/cmi.2017.155] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 11/17/2017] [Accepted: 11/17/2017] [Indexed: 12/26/2022] Open
Abstract
We previously identified human phosphatidylethanolamine-binding protein 4 (hPEBP4) as an antiapoptotic protein with increased expression levels in breast, ovarian and prostate cancer cells, but low expression levels in normal tissues, which makes hPEBP4 an attractive target for immunotherapy. Here, we developed hPEBP4-derived immunogenic peptides for inducing antigen-specific cytotoxic T lymphocytes (CTLs) targeting breast cancer. A panel of hPEBP4-derived peptides predicted by peptide-MHC-binding algorithms was evaluated to characterize their HLA-A2.1 affinity and immunogenicity. We identified a novel immunogenic peptide, P40-48 (TLFCQGLEV), that was capable of eliciting specific CTL responses in HLA-A2.1/Kb transgenic mice, as well as in peripheral blood lymphocytes from breast cancer patients. Furthermore, amino-acid substitutions in the P40-48 sequence improved its immunogenicity against hPEBP4, a self-antigen, thus circumventing tolerance. We designed peptide analogs by preferred auxiliary HLA-A*0201 anchor residue replacement, which induced CTLs that were crossreactive to the native peptide. Several analogs were able to stably bind to HLA-A*0201 and elicit specific CTL responses better than the native sequence. Importantly, adoptive transfer of CTLs induced by vaccination with two analogs more effectively inhibited tumor growth than the native peptide. These data indicate that peptide analogs with high immunogenicity represent promising candidates for peptide-mediated therapeutic cancer vaccines.
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26
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Dikhit MR, Amit A, Singh AK, Kumar A, Mansuri R, Sinha S, Topno RK, Mishra R, Das VNR, Pandey K, Sahoo GC, Ali V, Bimal S, Das P. Vaccine potential of HLA-A2 epitopes from Leishmania
Cysteine Protease Type III (CPC). Parasite Immunol 2017; 39. [DOI: 10.1111/pim.12451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/15/2017] [Indexed: 12/13/2022]
Affiliation(s)
- M. R. Dikhit
- Department of Bioinformatics; Rajendra Memorial Research Institute of Medical Sciences; Patna India
| | - A. Amit
- Department of Immunology; Rajendra Memorial Research Institute of Medical Sciences; Patna India
| | - A. K. Singh
- Department of Immunology; Rajendra Memorial Research Institute of Medical Sciences; Patna India
- Department of Pathology; Rajendra Memorial Research Institute of Medical Sciences; Patna India
| | - A. Kumar
- Department of Immunology; Rajendra Memorial Research Institute of Medical Sciences; Patna India
| | - R. Mansuri
- Department of Bioinformatics; Rajendra Memorial Research Institute of Medical Sciences; Patna India
| | - S. Sinha
- Department of Bioinformatics; Rajendra Memorial Research Institute of Medical Sciences; Patna India
| | - R. K. Topno
- Department of Epidemiology; Rajendra Memorial Research Institute of Medical Sciences; Patna India
| | - R. Mishra
- Department of Clinical Medicine; Rajendra Memorial Research Institute of Medical Sciences; Patna India
| | - V. N. R. Das
- Department of Clinical Medicine; Rajendra Memorial Research Institute of Medical Sciences; Patna India
| | - K. Pandey
- Department of Clinical Medicine; Rajendra Memorial Research Institute of Medical Sciences; Patna India
| | - G. C. Sahoo
- Department of Bioinformatics; Rajendra Memorial Research Institute of Medical Sciences; Patna India
| | - V. Ali
- Department of Biochemistry; Rajendra Memorial Research Institute of Medical Sciences; Patna India
| | - S. Bimal
- Department of Immunology; Rajendra Memorial Research Institute of Medical Sciences; Patna India
| | - P. Das
- Department of Molecular Parasitology; Rajendra Memorial Research Institute of Medical Sciences; Patna India
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27
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Immuno-informatics based approaches to identify CD8+ T cell epitopes within the Leishmania donovani 3-ectonucleotidase in cured visceral leishmaniasis subjects. Microbes Infect 2017; 19:358-369. [DOI: 10.1016/j.micinf.2017.03.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 03/10/2017] [Accepted: 03/24/2017] [Indexed: 01/22/2023]
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28
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Liu WJ, Lan J, Liu K, Deng Y, Yao Y, Wu S, Chen H, Bao L, Zhang H, Zhao M, Wang Q, Han L, Chai Y, Qi J, Zhao J, Meng S, Qin C, Gao GF, Tan W. Protective T Cell Responses Featured by Concordant Recognition of Middle East Respiratory Syndrome Coronavirus-Derived CD8+ T Cell Epitopes and Host MHC. THE JOURNAL OF IMMUNOLOGY 2016; 198:873-882. [PMID: 27903740 DOI: 10.4049/jimmunol.1601542] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/06/2016] [Indexed: 12/20/2022]
Abstract
The coordinated recognition of virus-derived T cell epitopes and MHC molecules by T cells plays a pivotal role in cellular immunity-mediated virus clearance. It has been demonstrated that the conformation of MHC class I (MHC I) molecules can be adjusted by the presented peptide, which impacts T cell activation. However, it is still largely unknown whether the conformational shift of MHC I influences the protective effect of virus-specific T cells. In this study, utilizing the Middle East respiratory syndrome coronavirus-infected mouse model, we observed that through the unusual secondary anchor Ile5, a CD8+ T cell epitope drove the conformational fit of Trp73 on the α1 helix of murine MHC I H-2Kd In vitro renaturation and circular dichroism assays indicated that this shift of the structure did not influence the peptide/MHC I binding affinity. Nevertheless, the T cell recognition and the protective effect of the peptide diminished when we made an Ile to Ala mutation at position 5 of the original peptide. The molecular bases of the concordant recognition of T cell epitopes and host MHC-dependent protection were demonstrated through both crystal structure determination and tetramer staining using the peptide-MHC complex. Our results indicate a coordinated MHC I/peptide interaction mechanism and provide a beneficial reference for T cell-oriented vaccine development against emerging viruses such as Middle East respiratory syndrome coronavirus.
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Affiliation(s)
- William J Liu
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China.,Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jiaming Lan
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang 050017, China
| | - Kefang Liu
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China.,Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yao Deng
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yanfeng Yao
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Key Laboratory of Human Disease Comparative Medicine, Ministry of Health, Beijing 100021, China
| | - Shaolian Wu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Hong Chen
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lingling Bao
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Key Laboratory of Human Disease Comparative Medicine, Ministry of Health, Beijing 100021, China
| | - Haifeng Zhang
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China
| | - Min Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qihui Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lingxia Han
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Yan Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; and
| | - Songdong Meng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chuan Qin
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Key Laboratory of Human Disease Comparative Medicine, Ministry of Health, Beijing 100021, China
| | - George F Gao
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China; .,Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenjie Tan
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China; .,Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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29
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Liu WJ, Zhao M, Liu K, Xu K, Wong G, Tan W, Gao GF. T-cell immunity of SARS-CoV: Implications for vaccine development against MERS-CoV. Antiviral Res 2016; 137:82-92. [PMID: 27840203 PMCID: PMC7113894 DOI: 10.1016/j.antiviral.2016.11.006] [Citation(s) in RCA: 264] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 12/14/2022]
Abstract
Over 12 years have elapsed since severe acute respiratory syndrome (SARS) triggered the first global alert for coronavirus infections. Virus transmission in humans was quickly halted by public health measures and human infections of SARS coronavirus (SARS-CoV) have not been observed since. However, other coronaviruses still pose a continuous threat to human health, as exemplified by the recent emergence of Middle East respiratory syndrome (MERS) in humans. The work on SARS-CoV widens our knowledge on the epidemiology, pathophysiology and immunology of coronaviruses and may shed light on MERS coronavirus (MERS-CoV). It has been confirmed that T-cell immunity plays an important role in recovery from SARS-CoV infection. Herein, we summarize T-cell immunological studies of SARS-CoV and discuss the potential cross-reactivity of the SARS-CoV-specific immunity against MERS-CoV, which may provide useful recommendations for the development of broad-spectrum vaccines against coronavirus infections. T-cell epitopes identified throughout the SARS-CoV proteome may act as candidates for vaccine development. Both SARS-CoV and MERS-CoV-recovered donors have had long-lasting memory T-cell immunity. The structures of HLA/SARS-CoV-epitopes illuminate the molecular bases of cellular immunogenicity. Potential cross-T-cell immune reactivities of SARS-CoV and MERS-CoV benefit vaccine development.
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Affiliation(s)
- William J Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 100052, China; College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518112, China.
| | - Min Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kefang Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 100052, China; College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Kun Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gary Wong
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518112, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Wenjie Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 100052, China; College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - George F Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 100052, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518112, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
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30
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Wang Q, Zhang L, Kuwahara K, Li L, Liu Z, Li T, Zhu H, Liu J, Xu Y, Xie J, Morioka H, Sakaguchi N, Qin C, LIU G. Immunodominant SARS Coronavirus Epitopes in Humans Elicited both Enhancing and Neutralizing Effects on Infection in Non-human Primates. ACS Infect Dis 2016; 2:361-76. [PMID: 27627203 PMCID: PMC7075522 DOI: 10.1021/acsinfecdis.6b00006] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Indexed: 01/21/2023]
Abstract
Severe acute respiratory syndrome (SARS) is caused by a coronavirus (SARS-CoV) and has the potential to threaten global public health and socioeconomic stability. Evidence of antibody-dependent enhancement (ADE) of SARS-CoV infection in vitro and in non-human primates clouds the prospects for a safe vaccine. Using antibodies from SARS patients, we identified and characterized SARS-CoV B-cell peptide epitopes with disparate functions. In rhesus macaques, the spike glycoprotein peptides S471-503, S604-625, and S1164-1191 elicited antibodies that efficiently prevented infection in non-human primates. In contrast, peptide S597-603 induced antibodies that enhanced infection both in vitro and in non-human primates by using an epitope sequence-dependent (ESD) mechanism. This peptide exhibited a high level of serological reactivity (64%), which resulted from the additive responses of two tandem epitopes (S597-603 and S604-625) and a long-term human B-cell memory response with antisera from convalescent SARS patients. Thus, peptide-based vaccines against SARS-CoV could be engineered to avoid ADE via elimination of the S597-603 epitope. We provide herein an alternative strategy to prepare a safe and effective vaccine for ADE of viral infection by identifying and eliminating epitope sequence-dependent enhancement of viral infection.
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Affiliation(s)
- Qidi Wang
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nanwei Rd., Xuanwu Dist, Beijing 100050, P. R. China
| | - Lianfeng Zhang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, P. R. China
| | - Kazuhiko Kuwahara
- Faculty of Life Sciences, Kumamoto University, 1-1-1, Honjo, Kumamoto 860-8556, Japan
| | - Li Li
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nanwei Rd., Xuanwu Dist, Beijing 100050, P. R. China
| | - Zijie Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nanwei Rd., Xuanwu Dist, Beijing 100050, P. R. China
| | - Taisheng Li
- Department of Infectious Disease, Peking Union Medical College Hospital and AIDS Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100071, P. R. China
| | - Hua Zhu
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, P. R. China
| | - Jiangning Liu
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, P. R. China
| | - Yanfeng Xu
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, P. R. China
| | - Jing Xie
- Department of Infectious Disease, Peking Union Medical College Hospital and AIDS Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100071, P. R. China
| | - Hiroshi Morioka
- Faculty of Life Sciences, Kumamoto University, 1-1-1, Honjo, Kumamoto 860-8556, Japan
| | - Nobuo Sakaguchi
- Faculty of Life Sciences, Kumamoto University, 1-1-1, Honjo, Kumamoto 860-8556, Japan
- WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Chuan Qin
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, P. R. China
| | - Gang LIU
- Tsinghua-Peking Center for Life Sciences & School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing 100084, P. R. China
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nanwei Rd., Xuanwu Dist, Beijing 100050, P. R. China
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31
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Sun W, Wei X, Niu A, Ma X, Li JJ, Gao D. Enhanced anti-colon cancer immune responses with modified eEF2-derived peptides. Cancer Lett 2015; 369:112-23. [PMID: 26304717 DOI: 10.1016/j.canlet.2015.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/31/2015] [Accepted: 08/05/2015] [Indexed: 12/22/2022]
Abstract
Eukaryotic elongation factor-2 (eEF2) is overexpressed in many human cancers and is an attractive target for cancer immunotherapy. The eEF2 derived polypeptides have been shown to be able to induce cytotoxic T lymphocytes from healthy donor. Here, we demonstrate the evidence indicating that modification of a segment of peptides from wild type eEF2-derived immunogenic peptides is able to further enhance its capacity of inducing antigen-specific cytotoxic T lymphocytes (CTLs) against colon cancer cells. Using peptide-MHC binding algorithms, potential HLA-A2.1-restricted epitopes capable of inducing specific CD8(+) CTLs were identified. By analyzing HLA-A2.1 affinity and immunogenicity, we further identified one novel immunogenic peptide, P739-747 (RLMEPIYLV), that elicited specific CTL responses in HLA-A2.1/K(b) transgenic mice and culture with peripheral blood lymphocytes from colon cancer patients. Furthermore, replacing certain amino acids (at positions 1, 3, 7) within the P739-747 sequence improved the immunogenicity against eEF2. Several analogs containing the auxiliary HLA-A*0201 anchor residues were able to stably bind to HLA-A*0201 and enhance CTL responses compared with the native sequence; two of them showed increased anti-tumor effects during the adoptive immunotherapy in vivo. Thus, these results support that modified immunogenic analogs are promising candidates for peptide-based cancer vaccination and immunotherapy.
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Affiliation(s)
- Weihong Sun
- Biotherapy Center, The Second Affiliated Hospital, Qingdao University Medical College, Qingdao 266042, China.
| | - Xiaofang Wei
- Biotherapy Center, The Second Affiliated Hospital, Qingdao University Medical College, Qingdao 266042, China
| | - Airong Niu
- Department of Clinical Laboratory, The Second Affiliated Hospital, Qingdao University Medical College, Qingdao 266042, China
| | - Xuezhen Ma
- Department of Oncology, The Second Affiliated Hospital, Qingdao University Medical College, Qingdao 266042, China
| | - Jian Jian Li
- Department of Radiation Oncology, NCI-designated Compressive Cancer Center, University of California Davis, Sacramento, CA 95817, USA.
| | - Daiqing Gao
- Biotherapy Center, The Second Affiliated Hospital, Qingdao University Medical College, Qingdao 266042, China
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32
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Tang B, Zhou W, Du J, He Y, Li Y. Identification of human leukemia antigen A*0201-restricted epitopes derived from epidermal growth factor pathway substrate number 8. Mol Med Rep 2015; 12:1741-52. [PMID: 25936538 PMCID: PMC4463842 DOI: 10.3892/mmr.2015.3673] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 03/12/2015] [Indexed: 12/12/2022] Open
Abstract
T-cell-mediated immunotherapy of hematological malignancies requires selection of targeted tumor-associated antigens and T-cell epitopes contained in these tumor proteins. Epidermal growth factor receptor pathway substrate 8 (EPS8), whose function is pivotal for tumor proliferation, progression and metastasis, has been found to be overexpressed in most human tumor types, while its expression in normal tissue is low. The aim of the present study was to identify human leukemia antigen (HLA)-A*0201-restricted epitopes of EPS8 by using a reverse immunology approach. To achieve this, computer algorithms were used to predict HLA-A*0201 molecular binding, proteasome cleavage patterns as well as translocation of transporters associated with antigen processing. Candidate peptides were experimentally validated by T2 binding affinity assay and brefeldin-A decay assay. The functional avidity of peptide-specific cytotoxic T lymphocytes (CTLs) induced from peripheral blood mononuclear cells of healthy volunteers were evaluated by using an enzyme-linked immunosorbent spot assay and a cytotoxicity assay. Four peptides, designated as P455, P92, P276 and P360, had high affinity and stability of binding towards the HLA-A*0201 molecule, and specific CTLs induced by them significantly responded to the corresponding peptides and secreted IFN-γ. At the same time, the CTLs were able to specifically lyse EPS8-expressing cell lines in an HLA-A*0201-restricted manner. The present study demon-strated that P455, P92, P276 and P360 were CTL epitopes of EPS8, and were able to be used for epitope-defined adoptive T-cell transfer and multi-epitope-based vaccine design.
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Affiliation(s)
- Baishan Tang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Weijun Zhou
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Jingwen Du
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Yanjie He
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Yuhua Li
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
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Yu Y, Jin D, Hu S, Zhang Y, Zheng X, Zheng J, Liao M, Chen X, Graner M, Liu H, Jin Q. A novel tuberculosis antigen identified from human tuberculosis granulomas. Mol Cell Proteomics 2015; 14:1093-103. [PMID: 25605460 DOI: 10.1074/mcp.m114.045237] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Indexed: 12/27/2022] Open
Abstract
Tuberculosis is a global infectious disease caused by Mycobacterium tuberculosis (Mtb). Although novel Mtb biomarkers from both the pathogen and host have been studied, more breakthroughs are still needed to meet different clinic requirements. In an effort to identify Mtb antigens, chaperone-peptide complexes were purified from TB infected lungs using free-solution isoelectric focusing combined with high resolution LTQ Orbitrap Velos mass spectrometry. Antigen specific cellular immune responses in vitro were then examined. Those efforts led to the identification of six Mtb peptides only identified in Tuberculosis lung samples and that were not found in the control samples. Additionally, antigen-specific IFN-γ secretion, T-cell proliferation, cytokine expression, and a cytotoxic assay were also evaluated. Among the peptides isolated, we identified a 34 amino acid peptide named PKAp belonging to a serine/threonine-protein kinase, as being able to generate Mtb-specific cellular immune responses as noted by elevated antigen-specific cytokine secretion levels, increased CD8(+) T-cell proliferation and a strong cytotoxic lymphocyte (CTL) response. Moreover, the immune stimulating abilities of PKAp were further validated in vivo, with target peptide immunized mice showing an increased cellular IFN-γ in both the lungs and spleen without causing immunopathogenesis. In conclusion, we identified novel functional Mtb antigens directly from the granulomatous lesions of Tuberculosis patients, inducing not only significant antigen-specific IFN-γ secretion but also a marked cytotoxic lymphocyte functional response. These findings indicated that PKAp has potential as a novel antigen biomarker for vaccine development.
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Affiliation(s)
- Yang Yu
- From the ‡MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China
| | - Dongdong Jin
- From the ‡MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China
| | - Shizong Hu
- From the ‡MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China
| | - Yan Zhang
- From the ‡MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China
| | - Xiaojing Zheng
- §Beijing Tuberculosis and Thoracic Tumor Research Institute, 101149, China
| | - Jianhua Zheng
- From the ‡MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China
| | - Mingfeng Liao
- ¶Guangdong Key Laboratory for emerging infectious diseases, Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Guangdong Medical College, Shenzhen, 518020, China
| | - Xinchun Chen
- ¶Guangdong Key Laboratory for emerging infectious diseases, Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Guangdong Medical College, Shenzhen, 518020, China
| | - Michael Graner
- ‖Department of Neurosurgery, University of Colorado, Denver, Colorado 80045
| | - Haiying Liu
- From the ‡MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China;
| | - Qi Jin
- From the ‡MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China
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Zhang XW. A combination of epitope prediction and molecular docking allows for good identification of MHC class I restricted T-cell epitopes. Comput Biol Chem 2013; 45:30-5. [PMID: 23666426 PMCID: PMC7106517 DOI: 10.1016/j.compbiolchem.2013.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 03/29/2013] [Accepted: 03/29/2013] [Indexed: 02/04/2023]
Abstract
Combining epitope prediction methods with molecular docking techniques to identify MHC class I restricted T-cell epitopes. Based on available experimental data, the prediction accuracy is up to 90%. Providing a valuable step forward for the design of better vaccines. Better understanding the activation of T-cell epitopes by MHC binding peptides.
In silico identification of T-cell epitopes is emerging as a new methodology for the study of epitope-based vaccines against viruses and cancer. In order to improve accuracy of prediction, we designed a novel approach, using epitope prediction methods in combination with molecular docking techniques, to identify MHC class I restricted T-cell epitopes. Analysis of the HIV-1 p24 protein and influenza virus matrix protein revealed that the present approach is effective, yielding prediction accuracy of over 80% with respect to experimental data. Subsequently, we applied such a method for prediction of T-cell epitopes in SARS coronavirus (SARS-CoV) S, N and M proteins. Based on available experimental data, the prediction accuracy is up to 90% for S protein. We suggest the use of epitope prediction methods in combination with 3D structural modelling of peptide-MHC-TCR complex to identify MHC class I restricted T-cell epitopes for use in epitope based vaccines like HIV and human cancers, which should provide a valuable step forward for the design of better vaccines and may provide in depth understanding about activation of T-cell epitopes by MHC binding peptides.
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Affiliation(s)
- Xue Wu Zhang
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China.
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Huang J, Cao Y, Bu X, Wu C. Residue analysis of a CTL epitope of SARS-CoV spike protein by IFN-gamma production and bioinformatics prediction. BMC Immunol 2012; 13:50. [PMID: 22963340 PMCID: PMC3575293 DOI: 10.1186/1471-2172-13-50] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 08/31/2012] [Indexed: 01/15/2023] Open
Abstract
Background Severe acute respiratory syndrome (SARS) is an emerging infectious disease caused by the novel coronavirus SARS-CoV. The T cell epitopes of the SARS CoV spike protein are well known, but no systematic evaluation of the functional and structural roles of each residue has been reported for these antigenic epitopes. Analysis of the functional importance of side-chains by mutational study may exaggerate the effect by imposing a structural disturbance or an unusual steric, electrostatic or hydrophobic interaction. Results We demonstrated that N50 could induce significant IFN-gamma response from SARS-CoV S DNA immunized mice splenocytes by the means of ELISA, ELISPOT and FACS. Moreover, S366-374 was predicted to be an optimal epitope by bioinformatics tools: ANN, SMM, ARB and BIMAS, and confirmed by IFN-gamma response induced by a series of S358-374-derived peptides. Furthermore, each of S366-374 was replaced by alanine (A), lysine (K) or aspartic acid (D), respectively. ANN was used to estimate the binding affinity of single S366-374 mutants to H-2 Kd. Y367 and L374 were predicated to possess the most important role in peptide binding. Additionally, these one residue mutated peptides were synthesized, and IFN-gamma production induced by G368, V369, A371, T372 and K373 mutated S366-374 were decreased obviously. Conclusions We demonstrated that S366-374 is an optimal H-2 Kd CTL epitope in the SARS CoV S protein. Moreover, Y367, S370, and L374 are anchors in the epitope, while C366, G368, V369, A371, T372, and K373 may directly interact with TCR on the surface of CD8-T cells.
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Affiliation(s)
- Jun Huang
- Institute of Immunology, Zhongshan School of Medicine, Key Laboratory of Tropical Disease Control Research of Ministry of Education, Sun Yat-sen University, Guangzhou, China
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Understanding the T cell immune response in SARS coronavirus infection. Emerg Microbes Infect 2012; 1:e23. [PMID: 26038429 PMCID: PMC3636424 DOI: 10.1038/emi.2012.26] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 07/02/2012] [Accepted: 07/06/2012] [Indexed: 12/17/2022]
Abstract
The severe acute respiratory syndrome (SARS) epidemic started in late 2002 and swiftly spread across 5 continents with a mortality rate of around 10%. Although the epidemic was eventually controlled through the implementation of strict quarantine measures, there continues a need to investigate the SARS coronavirus (SARS-CoV) and develop interventions should it re-emerge. Numerous studies have shown that neutralizing antibodies against the virus can be found in patients infected with SARS-CoV within days upon the onset of illness and lasting up to several months. In contrast, there is little data on the kinetics of T cell responses during SARS-CoV infection and little is known about their role in the recovery process. However, recent studies in mice suggest the importance of T cells in viral clearance during SARS-CoV infection. Moreover, a growing number of studies have investigated the memory T cell responses in recovered SARS patients. This review covers the available literature on the emerging importance of T cell responses in SARS-CoV infection, particularly on the mapping of cytotoxic T lymphocyte (CTL) epitopes, longevity, polyfunctionality and human leukocyte antigen (HLA) association as well as their potential implications on treatment and vaccine development.
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Liu Q, Zheng Y, Yu Y, Tan Q, Huang X. Identification of HLA-A*0201-restricted CD8+ T-cell epitope C₆₄₋₇₂ from hepatitis B virus core protein. Int Immunopharmacol 2012; 13:141-7. [PMID: 22480777 DOI: 10.1016/j.intimp.2012.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 03/20/2012] [Accepted: 03/20/2012] [Indexed: 12/22/2022]
Abstract
The efficacy of a potential therapeutic vaccine against chronic hepatitis B virus (HBV) infection depends on the development of strong and multi-specific T cell responses. The potency of CD8+ cytotoxic T lymphocyte (CTL) responses toward HBV core antigen (HBcAg) has been shown to be critical for the outcomes of HBV chronic infection. In this study we have identified a previously undescribed HLA-A*0201-restricted HBcAg-specific CTL epitope (HBcAg₆₄₋₇₂, C₆₄₋₇₂, ELMTLATWV). T2 binding assay showed that C₆₄₋₇₂ had high affinity to HLA-A*0201 molecule. Functionally, the peptide C₆₄₋₇₂ could induce peptide-specific CTLs both in vivo (HLA-A2.1/K(b) transgenic mice) and in vitro (PBLs of healthy HLA-A2.1+ donors), as demonstrated by interferon-γ (IFN-γ) secretion upon stimulation with C₆₄₋₇₂-pulsed T2 cells or autologous human dendritic cells (DCs) respectively. HLA-A*0201-C₆₄₋₇₂ tetramer staining revealed the presence of a significant population of C₆₄₋₇₂-specific CTLs in C₆₄₋₇₂-stimulated CD8+ T cells. Furthermore, the peptide-specific cytotoxic reactivity and the production of perforin and granzyme B of CTLs also increased after stimulation with C₆₄₋₇₂-pulsed autologous DCs. These results indicate that the newly identified epitope C₆₄₋₇₂ has potential to be used in the development of immunotherapeutic approaches to HBV infection.
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Affiliation(s)
- Qiuyan Liu
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai, China.
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Tian J, Zeng G, Pang X, Liang M, Zhou J, Fang D, Liu Y, Li D, Jiang L. Identification and immunogenicity of two new HLA-A*0201-restricted CD8+ T-cell epitopes on dengue NS1 protein. Int Immunol 2012; 24:207-18. [PMID: 22298881 DOI: 10.1093/intimm/dxr115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Immunopathogenesis of dengue virus (DEN) infection remains poorly studied. Identification and characterization of human CD8(+) T-cell epitopes on DEN are necessary for a better understanding of the immunopathogenesis of dengue infection and would facilitate the development of immunotherapy and vaccines to protect from dengue infection. Here, we identified two new HLA-A*0201-restricted CD8(+) T-cell epitopes, DEN-4 NS1(990)(-998) and DEN-4 NS1(997)(-1005) that are conserved in three or four major DEN serotypes, respectively. Unexpectedly, we found that immunization of HLA-A*0201 transgenic mice with DEN-4 NS1(990)(-998) or DEN-4 NS1(997)(-1005) epitope peptide induced de novo synthesis of tumor necrosis factor (TNF)-α and IFN-γ, two important pro-inflammatory molecules that are hard to be detected directly without in vitro antigenic re-stimulation. Importantly, we demonstrated that CD8(+) T cells specifically activated by DEN-4 NS1(990)(-998) or DEN-4 NS1(997)(-1005) epitope peptide induced de novo synthesis of perforin. Furthermore, we observed that DEN-4 NS1(990)(-998) or DEN-4 NS1(997)(-1005)-specific CD8(+) T cells capable of producing large amounts of perforin, TNF-α and IFN-γ preferentially displayed CD27(+)CD45RA(-), but not CD27(-)CD45RA(+), phenotypes. This study, therefore, suggested the importance of synergistic effects of pro-inflammatory cytokines and cytotoxic molecules which were produced by dengue-specific CD8(+) T cells in immunopathogenesis or anti-dengue immunity during dengue infection.
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Affiliation(s)
- Jiang Tian
- Key Laboratory for Tropic Diseases Control, Ministry of Education of China, Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
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Engineering T cells specific for a dominant severe acute respiratory syndrome coronavirus CD8 T cell epitope. J Virol 2011; 85:10464-71. [PMID: 21813600 DOI: 10.1128/jvi.05039-11] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Severe acute respiratory syndrome (SARS) is a highly contagious and life threatening disease, with a fatality rate of almost 10%. The etiologic agent is a novel coronavirus, severe acute respiratory syndrome coronavirus (SARS-CoV), with animal reservoirs found in bats and other wild animals and thus the possibility of reemergence. In this study, we first investigated at 6 years postinfection whether SARS-specific memory T cells persist in SARS-recovered individuals, demonstrating that these subjects still possess polyfunctional SARS-specific memory CD4+ and CD8+ T cells. A dominant memory CD8+ T cell response against SARS-CoV nucleocaspid protein (NP; amino acids 216 to 225) was then defined in SARS-recovered individuals carrying HLA-B*40:01, a HLA-B molecule present in approximately one-quarter of subjects of Asian ethnicities. To reconstitute such a CD8+ T cell response, we isolated the alpha and beta T cell receptors of the HLA-B*40:01-restricted SARS-specific CD8+ T cells. Using T cell receptor gene transfer, we generated SARS-specific redirected T cells from the lymphocytes of normal individuals. These engineered CD8+ T cells displayed avidity and functionality similar to that of natural SARS-specific memory CD8+ T cells. They were able to degranulate and produce gamma interferon, tumor necrosis factor alpha, and macrophage inflammatory proteins 1α and 1β after antigenic stimulation. Since there is no effective treatment against SARS, these transduced T cells specific for an immunodominant SARS epitope may provide a new avenue for treatment during a SARS outbreak.
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40
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Fu Q, Wu Y, Yan F, Wang N, Wang W, Cao X, Wang Y, Wan T. Efficient induction of a Her2-specific anti-tumor response by dendritic cells pulsed with a Hsp70L1-Her2(341-456) fusion protein. Cell Mol Immunol 2011; 8:424-32. [PMID: 21785448 DOI: 10.1038/cmi.2011.21] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Heat shock proteins (HSPs) have been shown to interact with antigen-presenting cells (APCs), especially dendritic cells (DCs). HSPs act as potent adjuvants, inducing a Th1 response, as well as antigen-specific CD8(+) cytotoxic T lymphocytes (CTL) via cross-presentation. Our previous work has demonstrated that Hsp70-like protein 1 (Hsp70L1), a new member of the Hsp70 subfamily, can act as a powerful Th1 adjuvant in a DC-based vaccine. Here we report the efficient induction of tumor antigen-specific T cell immune response by DCs pulsed with recombinant fusion protein of Hsp70L1 and Her2(341-456), the latter of which is a fragment of Her2/neu (Her2) containing E75 (a HLA-A2 restricted CTL epitope). The fusion protein Hsp70L1-Her2(341-456) promotes the maturation of DCs and activates them to produce cytokines, such as IL-12 and TNF-α, and chemokines, such as MIP-1α, MIP-1β and RANTES. Taken together, these results indicate that the adjuvant activity of Hsp70L1 is maintained in the fusion protein. Her2-specific HLA-A2.1-restricted CD8(+) CTLs can be generated efficiently either from the Peripheral blood lymphocytes (PBL) of healthy donors or from the splenocytes of immunized HLA-A2.1/K(b) transgenic mice by in vitro stimulation or immunization with DCs pulsed with the Hsp70L1-Her2(341-456) fusion protein. This results in more potent target cell killing in an antigen-specific and HLA-A2.1-restricted manner. Adoptive transfer of splenocytes from transgenic mice immunized with Hsp70L1-Her2(341-456)-pulsed DCs can markedly inhibit tumor growth and prolong the survival of nude mice with Her2(+)/HLA-A2.1(+) human carcinomas. These results suggest that Hsp70L1-Her2(341-456)-pulsed DCs could be a new therapeutic vaccine for patients with Her2(+) cancer.
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Affiliation(s)
- Qiang Fu
- Department of Oncology, Changhai Hospital of Shanghai, China
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Zhao K, Wang H, Wu C. The immune responses of HLA-A*0201 restricted SARS-CoV S peptide-specific CD8⁺ T cells are augmented in varying degrees by CpG ODN, PolyI:C and R848. Vaccine 2011; 29:6670-8. [PMID: 21745520 PMCID: PMC7115397 DOI: 10.1016/j.vaccine.2011.06.100] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 06/13/2011] [Accepted: 06/25/2011] [Indexed: 01/13/2023]
Abstract
The induction of antigen specific memory CD8+ T cells in vivo is very important to new vaccines against infectious diseases. In the present study, we aimed to evaluate the immune responses of peptide-specific CD8+ T cells induced by HLA-A*0201 restricted severe acute respiratory syndrome-associated coronavirus (SARS-CoV) S epitopes plus CpG oligodeoxynucleotide (CpG ODN), PolyI:C and R848 as adjuvants. Furthermore, the generation, distribution and phenotype of long-lasting peptide-specific memory CD8+ T cells were assessed by ELISA, ELISPOT and flow cytometry. Our results showed that antigen specific CD8+ T cells were elicited by HLA-A*0201 restricted SARS-CoV S epitopes. Furthermore, the frequency of peptide-specific CD8+ T cells was dramatically increased after both prime and boost immunization with peptides plus CpG ODN, whereas slight enhancements were induced following boost vaccination with peptides plus PolyI:C or R848. SARS-CoV S peptide-specific IFN-γ+CD8+ T cells were distributed throughout the lymphoid and non-lymphoid tissues. Results also demonstrated that the HLA-A*0201 restricted peptide-specific CD8+ T cells induced by peptides plus CpG ODN carried a memory cell phenotype with CD45RB+ and CD62L− and possessed long-term survival ability in vivo. Taken together, our results implied that HLA-A*0201 restricted SARS-CoV S epitopes plus CpG ODN might be the superior candidates for SARS vaccine.
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Affiliation(s)
- Kai Zhao
- Institute of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, Guangdong Province 510080, People' s Republic of China
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Liu H, Cai P, Liu HX, Wang JL, Liu Q, Zhu P. Vaccination with immunoglobulin frame region-derived nonapeptide elicits cellular immune response against lymphoma in human leukocyte antigen-A2.1 transgenic mice. Leuk Lymphoma 2011; 52:1795-802. [DOI: 10.3109/10428194.2011.577257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Satoh R, Kaku A, Satomura M, Kohori M, Noura K, Furukawa T, Kotake M, Takano T, Hohdatsu T. Development of monoclonal antibodies (MAbs) to feline interferon (fIFN)-γ as tools to evaluate cellular immune responses to feline infectious peritonitis virus (FIPV). J Feline Med Surg 2011; 13:427-35. [PMID: 21334239 PMCID: PMC7129491 DOI: 10.1016/j.jfms.2011.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2011] [Indexed: 11/18/2022]
Abstract
Feline infectious peritonitis virus (FIPV) can cause a lethal disease in cats, feline infectious peritonitis (FIP). The antibody-dependent enhancement (ADE) of FIPV infection has been recognised in experimentally infected cats, and cellular immunity is considered to play an important role in preventing the onset of FIP. To evaluate the importance of cellular immunity for FIPV infection, monoclonal antibodies (MAbs) against feline interferon (fIFN)-γ were first created to establish fIFN-γ detection systems using the MAbs. Six anti-fIFN-γ MAbs were created. Then, the difference in epitope which those MAbs recognise was demonstrated by competitive enzyme-linked immunosorbent assay (ELISA) and IFN-γ neutralisation tests. Detection systems for fIFN-γ (sandwich ELISA, ELISpot assay, and two-colour flow cytometry) were established using anti-fIFN-γ MAbs that recognise different epitopes. In all tests, fIFN-γ production from peripheral blood mononuclear cells (PBMCs) obtained from cats experimentally infected with an FIPV isolate that did not develop the disease was significantly increased by heat-inactivated FIPV stimulation in comparison with medium alone. Especially, CD8+fIFN-γ+ cells, but not CD4+fIFN-γ+ cells, were increased. In contrast, fIFN-γ production from PBMCs isolated from cats that had developed FIP and specific pathogen-free (SPF) cats was not increased by heat-inactivated FIPV stimulation. These results suggest that cellular immunity plays an important role in preventing the development of FIP. Measurement of fIFN-γ production with the anti-fIFN-γ MAbs created in this study appeared to be useful in evaluating cellular immunity in cats.
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Affiliation(s)
- Ryoichi Satoh
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan
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Liu J, Zhang S, Tan S, Zheng B, Gao GF. Revival of the identification of cytotoxic T-lymphocyte epitopes for immunological diagnosis, therapy and vaccine development. Exp Biol Med (Maywood) 2011; 236:253-67. [PMID: 21330360 DOI: 10.1258/ebm.2010.010278] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Immunogenic T-cell epitopes have a central role in the cellular immunity against pathogens and tumors. However, in the early stage of cellular immunity studies, it was complicated and time-consuming to identify and characterize T-cell epitopes. Currently, the epitope screening is experiencing renewed enthusiasm due to advances in novel techniques and theories. Moreover, the application of T-cell epitope-based diagnoses for tuberculosis and new data on epitope-based vaccine development have also revived the field. There is a growing knowledge on the emphasis of epitope-stimulated T-cell immune responses in the elimination of pathogens and tumors. In this review, we outline the significance of the identification and characterization of T-cell epitopes. We also summarize the methods and strategies for epitope definition and, more importantly, address the relevance of cytotoxic T-lymphocyte epitopes to clinical diagnoses, therapy and vaccine development.
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Affiliation(s)
- Jun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Satoh R, Kobayashi H, Takano T, Motokawa K, Kusuhara H, Hohdatsu T. Characterization of T helper (Th)1- and Th2-type immune responses caused by baculovirus-expressed protein derived from the S2 domain of feline infectious peritonitis virus, and exploration of the Th1 and Th2 epitopes in a mouse model. Microbiol Immunol 2011; 54:726-33. [PMID: 21091984 PMCID: PMC7168408 DOI: 10.1111/j.1348-0421.2010.00275.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Feline infectious peritonitis virus (FIPV) may cause a lethal infection in cats. Antibody‐dependent enhancement (ADE) of FIPV infection has been recognized, and cellular immunity is considered to play an important role in preventing the onset of feline infectious peritonitis. In the present study, whether or not the T helper (Th)1 epitope was present in the spike (S)2 domain was investigated, the ADE epitope being thought to be absent from this domain. Three kinds of protein derived from the C‐terminal S2 domain of S protein of the FIPV KU‐2 strain were developed using a baculovirus expression system. These expressed proteins were the pre‐coil region which is the N‐terminal side of the putative fusion protein (FP), the region from FP to the heptad repeat (HR)2 (FP‐HR2) region, and the inter‐helical region which is sandwiched between HR1 and HR2. The ability of three baculovirus‐expressed proteins to induce Th1‐ and Th2‐type immune responses was investigated in a mouse model. It was shown that FP‐HR2 protein induced marked Th1‐ and Th2‐type immune responses. Furthermore, 30 peptides derived from the FP‐HR2 region were synthesized. Five and 16 peptides which included the Th1 and Th2 epitopes, respectively, were identified. Of these, four peptides which included both Th1 and Th2 epitopes were identified. These findings suggest that the identification of Th1 epitopes in the S2 domain of FIPV has important implications in the cat.
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Satoh R, Furukawa T, Kotake M, Takano T, Motokawa K, Gemma T, Watanabe R, Arai S, Hohdatsu T. Screening and identification of T helper 1 and linear immunodominant antibody-binding epitopes in the spike 2 domain and the nucleocapsid protein of feline infectious peritonitis virus. Vaccine 2011; 29:1791-800. [PMID: 21216312 PMCID: PMC7115570 DOI: 10.1016/j.vaccine.2010.12.106] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 11/24/2010] [Accepted: 12/22/2010] [Indexed: 01/12/2023]
Abstract
The antibody-dependent enhancement (ADE) of feline infectious peritonitis virus (FIPV) infection has been recognized in experimentally infected cats, and cellular immunity is considered to play an important role in preventing the onset of feline infectious peritonitis (FIP). In the present study, we synthesized eighty-one kinds of peptides derived from the spike (S)2 domain of type I FIPV KU-2 strain, the S2 domain of type II FIPV 79-1146 strain, and the nucleocapcid (N) protein of FIPV KU-2 strain. To detect the T helper (Th)1 epitope, peripheral blood mononuclear cells (PBMCs) obtained from FIPV-infected cats were cultured with each peptide, and Th1-type immune responses were measured using feline interferon (fIFN)-γ production as an index. To detect the linear immunodominant antibody-binding epitope, we investigated the reactivity of plasma collected from FIPV-infected cats against each peptide by ELISA. Four and 2 peptides containing Th1 epitopes were identified in the heptad repeat (HR)1 and inter-helical (IH) regions of the S2 domain of type I FIPV, respectively, and these were located on the N-terminal side of the regions. In the S2 domain of type II FIPV, 2, 3, and 2 peptides containing Th1 epitopes were identified in the HR1, IH, and HR2 regions, respectively, and these were mainly located on the C-terminal side of the regions. In the S2 domain of type I FIPV, 3 and 7 peptides containing linear immunodominant antibody-binding epitopes were identified in the IH and HR2 regions, respectively. In the S2 domain of type II FIPV, 4 peptides containing linear immunodominant antibody-binding epitopes were identified in the HR2 region. The Th1 epitopes in the S2 domain of type I and II FIPV were located in different regions, but the linear immunodominant antibody-binding epitopes were mostly located in the HR2 region. Eight peptides containing Th1 epitopes were identified in N protein, and 3 peptides derived from residues 81 to 100 and 137 to 164 showed strong inductivity of fIFN-γ production in PBMCs isolated from type I FIPV- and type II FIPV-infected non-FIP cats. In N protein, 4 peptides containing linear immunodominant antibody-binding epitopes were identified, and 2 peptides derived from residues 345 to 372 showed strong reactivity with plasma of type I FIPV- and type II FIPV-infected cats. The Th1 and linear immunodominant antibody-binding epitopes were located at different positions in both the S2 domain and N protein. Our results may provide important information for the development of peptide-based vaccine against FIPV infection.
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Affiliation(s)
- Ryoichi Satoh
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan
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Novel immunodominant peptide presentation strategy: a featured HLA-A*2402-restricted cytotoxic T-lymphocyte epitope stabilized by intrachain hydrogen bonds from severe acute respiratory syndrome coronavirus nucleocapsid protein. J Virol 2010; 84:11849-57. [PMID: 20844028 DOI: 10.1128/jvi.01464-10] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Antigenic peptides recognized by virus-specific cytotoxic T lymphocytes (CTLs) are presented by major histocompatibility complex (MHC; or human leukocyte antigen [HLA] in humans) molecules, and the peptide selection and presentation strategy of the host has been studied to guide our understanding of cellular immunity and vaccine development. Here, a severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid (N) protein-derived CTL epitope, N1 (QFKDNVILL), restricted by HLA-A*2402 was identified by a series of in vitro studies, including a computer-assisted algorithm for prediction, stabilization of the peptide by co-refolding with HLA-A*2402 heavy chain and β(2)-microglobulin (β(2)m), and T2-A24 cell binding. Consequently, the antigenicity of the peptide was confirmed by enzyme-linked immunospot (ELISPOT), proliferation assays, and HLA-peptide complex tetramer staining using peripheral blood mononuclear cells (PBMCs) from donors who had recovered from SARS donors. Furthermore, the crystal structure of HLA-A*2402 complexed with peptide N1 was determined, and the featured peptide was characterized with two unexpected intrachain hydrogen bonds which augment the central residues to bulge out of the binding groove. This may contribute to the T-cell receptor (TCR) interaction, showing a host immunodominant peptide presentation strategy. Meanwhile, a rapid and efficient strategy is presented for the determination of naturally presented CTL epitopes in the context of given HLA alleles of interest from long immunogenic overlapping peptides.
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CD8+ T cell response in HLA-A*0201 transgenic mice is elicited by epitopes from SARS-CoV S protein. Vaccine 2010; 28:6666-74. [PMID: 20709007 PMCID: PMC7115361 DOI: 10.1016/j.vaccine.2010.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 07/06/2010] [Accepted: 08/02/2010] [Indexed: 11/20/2022]
Abstract
Cytotoxic CD8(+) T lymphocytes (CTLs) play an important role in antiviral immunity. Several human HLA-A*0201 restricted CTL epitopes of severe acute respiratory syndrome (SARS) spike (S) protein have been identified in HLA-A*0201 transgenic (Tg) mice, but the mechanisms and properties of immune responses are still not well understood. In this study, HLA-A*0201 Tg mice were primed intramuscularly with SARS S DNA and boosted subcutaneously with HLA-A*0201 restricted peptides. The lymphocytes from draining lymph nodes, spleens and lungs were stimulated with the cognate peptides. Three different methods (ELISA, ELISPOT and FACS) were used to evaluate the immune responses during short and long periods of time after immunization. Results showed that peptide-specific CD8(+) T cells secreted IFN-γ, TNF-α and IL-2 and expressed CD107a/b on cell surface. IFN-γ(+)CD8(+) T cells and CD107a/b(+)CD8(+) T cells distributed throughout the lymphoid and non-lymphoid tissues, but the frequency of peptide-specific CD8(+) T cells was higher in lungs than in spleens and lymph nodes. The phenotype of the CD8(+) T cells was characterized based on the expression of IFN-γ. Most of the HLA-A*0201 restricted peptide-specific CD8(+) T cells represented a memory subset with CD45RB(high) and CD62L(low). Taken together, these data demonstrate that immunization with SARS S DNA and HLA-A*0201 restricted peptides can elicit antigen-specific CD8(+) T cell immune responses which may have a significant implication in the long-term protection. We provide novel information in cellular immune responses of SARS S antigen-specific CD8(+) T cells, which are important in the development of vaccine against SARS-CoV infection.
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Chen YZ, Liu G, Senju S, Wang Q, Irie A, Haruta M, Matsui M, Yasui F, Kohara M, Nishimura Y. Identification of SARS-COV spike protein-derived and HLA-A2-restricted human CTL epitopes by using a new muramyl dipeptidederivative adjuvant. Int J Immunopathol Pharmacol 2010; 23:165-77. [PMID: 20378004 DOI: 10.1177/039463201002300115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Severe acute respiratory syndrome (SARS) spread during the winter of 2003, and attempts have been made to develop vaccines against SARS corona virus (SARS-CoV). The present study provides a strategy to rapidly identify SARS-CoV-derived antigenic peptides recognized by HLA-A2-restricted cytotoxic T lymphocytes (CTLs). Forty-three candidate peptides having HLA-A2-binding motifs were selected in silico and HLA-A2/Db chimeric MHC class I-transgenic mice were immunized with these peptides and a new derivative of muramyl dipeptide that can induce upregulation of HLA-DR, CD80, CD86, and CD40 in human CD14+ antigen presenting cells, was administered as an adjuvant. Six HLAA2-restricted mouse CTL epitopes were identified, including two new epitopes which have never been reported before. One of the novel peptides was naturally processed and successfully induced HLAA2-restricted specific CTLs in both HLA transgenic mice and healthy donors. The method was useful, convenient and efficient for rapid identification of CTL epitopes derived from SARS-CoV proteins and will be possibly applicable for other pathogens to develop a peptide-based vaccine.
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Affiliation(s)
- Y-Z Chen
- Department of Immunogenetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
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Mucosally delivered peptides prime strong immunity in HLA-A2.1 transgenic rabbits. Vaccine 2010; 28:3706-13. [PMID: 20332046 DOI: 10.1016/j.vaccine.2010.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 03/05/2010] [Accepted: 03/09/2010] [Indexed: 12/22/2022]
Abstract
DNA vaccines delivered subcutaneously by gene-gun have generated strong protective and therapeutic immunity in rabbits. Recent studies have shown that peptides delivered by the mucosal routes also stimulate local and systemic immune responses. Since mucosal delivery is easier to administer and more cost-effective when compared to gene-gun delivery, we were interested to learn whether mucosally delivered peptides would prime protective immunity comparable to that of gene-gun-delivered DNA in rabbits. Our newly developed HLA-A2.1 transgenic rabbit model was used to test the hypothesis. We chose an HLA-A2.1 restricted cottontail rabbit papillomavirus (CRPV) E1 epitope (E1/303-311, MLQEKPFQL) for the peptide immunization studies because it provided complete protection when used as a DNA vaccine. Adjuvant has been widely used to boost immunity for vaccines. In this study, three adjuvants reported to be effective for rabbits (TT helper motif, PADRE and CpG2007) were tested with the peptide vaccine. Peptide alone or fused to TT helper or PADRE to create chimeric peptides was delivered by two mucosal routes (ocular and intranasal) together. Partial protection was found in HLA-A2.1 transgenic rabbits when peptide was delivered mucosally in the presence of adjuvant. When a subsequent booster of a half-dose of the corresponding DNA vaccine was delivered, complete protections were achieved. We conclude that mucosal peptide immunization can be combined with a single DNA vaccination to provide strong protective immunity in rabbits.
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