1
|
Karagöz IK, Kaya M, Rückert R, Bozman N, Kaya V, Bayram H, Yıldırım M. A bioinformatic analysis: Previous allergen exposure may support anti- SARS-CoV-2 immune response. Comput Biol Chem 2023; 107:107961. [PMID: 37788543 DOI: 10.1016/j.compbiolchem.2023.107961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023]
Abstract
COVID-19, caused by infection with the SARS-CoV-2 has become a global health problem due to significant mortality rates; the exact pathophysiological mechanism remains uncertain. Articles reporting patient data are quite heterogeneous and have several limitations. Surviving patients develop a CD4 and CD8 T-cell response to the virus SARS-CoV-2 during COVID-19. Interestingly, pre-existing virus-reactive T-cells have been found in patients that were not infected before, suggesting some form of cross-reactivity or immunological mimicry. To better understand this phenomenon, we performed a bioinformatic study, which was aimed to identify antigenic structures that may explain the presence of such "reactive" T-cells, which may support or modulate the immune response to SARS-CoV-2 infections. Seven different common environmental allergen epitopes identical to the SARS-CoV-2 S-protein were identified that share affinity to 8 MHCI-specific epitope regions. Pollen showed the greatest similarity with the S protein epitope. In the epitope similarity analysis between the S protein and MHC-II / T helper epitopes, the highest similarity was determined for mites. When S-protein that stimulates B cells and identical epitope antigens are examined, the most common allergens were hornbeam and wheat. The high epitope similarity observed for the allergens examined and S protein epitopes suggest that these allergens may be a reason for pre-existing SARS-CoV-2 - reactive T-cells in previously non-infected subjects and such a previous exposure may affect the course of the disease in COVID-19 infection. It remains to be determined whether such a previous existence of SARS-CoV-2 reactive cells can support the clearance of the virus or if they, in contrast, may even aggravate the disease course. (Table 4, Ref 54).
Collapse
Affiliation(s)
- Isıl Kutluturk Karagöz
- Umraniye Trn. And Rch. Hospital, Division of Ophthalmology, Istanbul, Turkey; Yıldız Technical University, Bioengineering Department, Istanbul, Turkey.
| | | | | | - Nazli Bozman
- Gaziantep University Arts and Science Faculty Department of Biology, Gaziantep, Turkey
| | - Vildan Kaya
- Medstar Antalya Hospital, Division of Radiation Oncology, Antalya, Turkey
| | - Halim Bayram
- Dr. Ersin Arslan Trn. And Rch Hospital, Division of Infection Diseases, Gaziantep, Turkey
| | - Mustafa Yıldırım
- Sanko University, School of Medicine, Internal Diseases, Division of Oncology, Gaziantep, Turkey
| |
Collapse
|
2
|
Zhang B, Ren Z, Zhao J, Zhu Y, Huang B, Xiao C, Zhang Y, Deng J, Mao L, Tang L, Lan D, Gao L, Zhang H, Chen G, Luo OJ. Global analysis of HLA-A2 restricted MAGE-A3 tumor antigen epitopes and corresponding TCRs in non-small cell lung cancer. Theranostics 2023; 13:4449-4468. [PMID: 37649599 PMCID: PMC10465222 DOI: 10.7150/thno.84710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023] Open
Abstract
Background: Advanced non-small cell lung cancer (NSCLC) is the most common type of lung cancer with poor prognosis. Adoptive cell therapy using engineered T-cell receptors (TCRs) targeting cancer-testis antigens, such as Melanoma-associated antigen 3 (MAGE-A3), is a potential approach for the treatment of NSCLC. However, systematic analysis of T cell immune responses to MAGE-A3 antigen and corresponding antigen-specific TCR is still lacking. Methods: In this study, we comprehensively screened HLA-A2 restricted MAGE-A3 tumor epitopes and characterized the corresponding TCRs using in vitro artificial antigen presentation cells (APC) system, single-cell transcriptome and TCR V(D)J sequencing, and machine-learning. Furthermore, the tumor-reactive TCRs with killing potency was screened and verified. Results: We identified the HLA-A2 restricted T cell epitopes from MAGE-A3 that could effectively induce the activation and cytotoxicity of CD8+ T cells using artificial APC in vitro. A cohort of HLA-A2+ NSCLC donors demonstrated that the number of epitope specific CD8+ T cells increased in NSCLC than healthy controls when measured with tetramer derived from the candidate MAGE-A3 epitopes, especially epitope Mp4 (MAGE-A3: 160-169, LVFGIELMEV). Statistical and machine-learning based analyses demonstrated that the MAGE-A3-Mp4 epitope-specific CD8+ T cell clones were mostly in effector and proliferating state. Importantly, T cells artificially expressing the MAGE-A3-Mp4 specific TCRs exhibited strong MAGE-A3+ tumor cell recognition and killing effect. Cross-reactivity risk analysis of the candidates TCRs showed high binding stability to MAGE-A3-Mp4 epitope and low risk of cross-reaction. Conclusions: This work identified candidate TCRs potentially suitable for TCR-T design targeting HLA-A2 restricted MAGE-A3 tumor antigen.
Collapse
Affiliation(s)
- Bei Zhang
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
| | - Zhiyao Ren
- Guangzhou Geriatric Hospital, Guangzhou, China
- Collaborative Innovation Center for Civil Affairs of Guangzhou, Guangzhou, China
| | - Jianfu Zhao
- Department of Oncology, Research Center of Cancer Diagnosis and Therapy, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Yue Zhu
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
| | - Boya Huang
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
| | - Chanchan Xiao
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
- Department of Microbiology and Immunology; Institute of Geriatric Immunology; School of Medicine, Jinan University, Guangzhou, China
| | - Yan Zhang
- Department of Oncology, Research Center of Cancer Diagnosis and Therapy, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jieping Deng
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
| | - Lipeng Mao
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
| | - Lei Tang
- School of Life Science & Technology, China Pharmaceutical University, Nanjing, China
| | - Dan Lan
- Department of Oncology, Research Center of Cancer Diagnosis and Therapy, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Lijuan Gao
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
- Department of Microbiology and Immunology; Institute of Geriatric Immunology; School of Medicine, Jinan University, Guangzhou, China
| | - Hongyi Zhang
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
- Department of Microbiology and Immunology; Institute of Geriatric Immunology; School of Medicine, Jinan University, Guangzhou, China
| | - Guobing Chen
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
- Department of Microbiology and Immunology; Institute of Geriatric Immunology; School of Medicine, Jinan University, Guangzhou, China
| | - Oscar Junhong Luo
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
| |
Collapse
|
3
|
Becerra-Artiles A, Nanaware PP, Muneeruddin K, Weaver GC, Shaffer SA, Calvo-Calle JM, Stern LJ. Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T-cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2. PLoS Pathog 2023; 19:e1011032. [PMID: 37498934 PMCID: PMC10409285 DOI: 10.1371/journal.ppat.1011032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/08/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023] Open
Abstract
Seasonal "common-cold" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but the T-cell response to seasonal coronaviruses remains largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal coronavirus OC43. We identified MHC-bound peptides derived from each of the viral structural proteins (spike, nucleoprotein, hemagglutinin-esterase, membrane, and envelope) as well as non-structural proteins nsp3, nsp5, nsp6, and nsp12. Eighty MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. Fewer and less abundant MHC-I bound OC43-derived peptides were observed, possibly due to MHC-I downregulation induced by OC43 infection. The MHC-II peptides elicited low-abundance recall T-cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T-cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T-cell lines. Among the validated epitopes, spike protein S903-917 presented by DPA1*01:03/DPB1*04:01 and S1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. Nucleoprotein N54-68 and hemagglutinin-esterase HE128-142 presented by DRB1*15:01 and HE259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow CD4 T-cell cross-reactivity after infection or vaccination, and to guide selection of epitopes for inclusion in pan-coronavirus vaccines.
Collapse
Affiliation(s)
- Aniuska Becerra-Artiles
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Padma P. Nanaware
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Khaja Muneeruddin
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury Massachusetts, United States of America
| | - Grant C. Weaver
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Scott A. Shaffer
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - J. Mauricio Calvo-Calle
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Lawrence J. Stern
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| |
Collapse
|
4
|
Xiao C, Ren Z, Zhang B, Mao L, Zhu G, Gao L, Su J, Ye J, Long Z, Zhu Y, Chen P, Su X, Zhou T, Huang Y, Chen X, Xie C, Yuan J, Hu Y, Zheng J, Wang Z, Lou J, Yang X, Kuang Z, Zhang H, Wang P, Liang X, Luo OJ, Chen G. Insufficient epitope-specific T cell clones are responsible for impaired cellular immunity to inactivated SARS-CoV-2 vaccine in older adults. NATURE AGING 2023; 3:418-435. [PMID: 37117789 PMCID: PMC10154213 DOI: 10.1038/s43587-023-00379-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 02/03/2023] [Indexed: 04/30/2023]
Abstract
Aging is a critical risk factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine efficacy. The immune responses to inactivated vaccine for older adults, and the underlying mechanisms of potential differences to young adults, are still unclear. Here we show that neutralizing antibody production by older adults took a longer time to reach similar levels in young adults after inactivated SARS-CoV-2 vaccination. We screened SARS-CoV-2 variant strains for epitopes that stimulate specific CD8 T cell response, and older adults exhibited weaker CD8 T-cell-mediated responses to these epitopes. Comparison of lymphocyte transcriptomes from pre-vaccinated and post-vaccinated donors suggested that the older adults had impaired antigen processing and presentation capability. Single-cell sequencing revealed that older adults had less T cell clone expansion specific to SARS-CoV-2, likely due to inadequate immune receptor repertoire size and diversity. Our study provides mechanistic insights for weaker response to inactivated vaccine by older adults and suggests the need for further vaccination optimization for the old population.
Collapse
Affiliation(s)
- 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, School of Medicine, Jinan University, Guangzhou, China
- Guangzhou Laboratory, Guangzhou, China
| | - Zhiyao Ren
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
- Guangzhou Geriatric Hospital, Guangzhou, China
- NHC Key Laboratory of Male Reproduction and Genetics, Guangzhou, China
- Department of Central Laboratory, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, China
| | - Bei Zhang
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
| | - Lipeng Mao
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
| | - Guodong Zhu
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
- Guangzhou Geriatric Hospital, 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, School of Medicine, Jinan University, Guangzhou, China
| | - Jun Su
- Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
| | - Jiezhou Ye
- 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, School of Medicine, Jinan University, Guangzhou, China
| | - Ze Long
- 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, School of Medicine, Jinan University, Guangzhou, China
| | - Yue Zhu
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
| | - Pengfei Chen
- 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, School of Medicine, Jinan University, Guangzhou, China
| | - Xiangmeng Su
- 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, School of Medicine, Jinan University, Guangzhou, China
| | - Tong Zhou
- 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, School of Medicine, Jinan University, Guangzhou, China
| | - Yanhao Huang
- 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, School of Medicine, Jinan University, Guangzhou, China
| | - Xiongfei Chen
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Chaojun Xie
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Jun Yuan
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Yutian Hu
- Meng Yi Center Limited, Macau, China
| | - Jingshan Zheng
- Shenzhen Kangtai Biological Products Co. Ltd, Shenzhen, China
| | - Zhigang Wang
- Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
| | | | - Xiang Yang
- Leidebio Bioscience Co., Ltd., Guangzhou, China
| | - Zhiqiang Kuang
- Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
| | - Hongyi Zhang
- 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, School of Medicine, 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, School of Medicine, Jinan University, Guangzhou, China.
| | - Xiaofeng Liang
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China.
| | - Oscar Junhong Luo
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, China.
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China.
| | - Guobing Chen
- 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, School of Medicine, Jinan University, Guangzhou, China.
- Guangzhou Laboratory, Guangzhou, China.
- Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China.
| |
Collapse
|
5
|
Jin X, Liu X, Shen C. A systemic review of T-cell epitopes defined from the proteome of SARS-CoV-2. Virus Res 2023; 324:199024. [PMID: 36526016 PMCID: PMC9757803 DOI: 10.1016/j.virusres.2022.199024] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection remains in a global pandemic, and no eradicative therapy is currently available. Host T cells have been shown to play a crucial role in the antiviral immune protection and pathology in Coronavirus disease 2019 (COVID-19) patients; thus, identifying sufficient T-cell epitopes from the SARS-CoV-2 proteome can contribute greatly to the development of T-cell epitope vaccines and the precise evaluation of host SARS-CoV-2-specific cellular immunity. This review presents a comprehensive map of T-cell epitopes functionally validated from SARS-CoV-2 antigens, the human leukocyte antigen (HLA) supertypes to present these epitopes, and the strategies to screen and identify T-cell epitopes. To the best of our knowledge, a total of 1349 CD8+ T-cell epitopes and 790 CD4+ T-cell epitopes have been defined by functional experiments thus far, but most are presented by approximately twenty common HLA supertypes, such as HLA-A0201, A2402, B0702, DR15, DR7 and DR11 molecules, and 74-80% of the T-cell epitopes are derived from S protein and nonstructural protein. These data provide useful insight into the development of vaccines and specific T-cell detection systems. However, the currently defined T-cell epitope repertoire cannot cover the HLA polymorphism of major populations in an indicated geographic region. More research is needed to depict an overall landscape of T-cell epitopes, which covers the overall SARS-CoV-2 proteome and global patients.
Collapse
Affiliation(s)
- Xiaoxiao Jin
- Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, China 225002; Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009
| | - Xiaotao Liu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009
| | - Chuanlai Shen
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009.
| |
Collapse
|
6
|
Becerra-Artiles A, Nanaware PP, Muneeruddin K, Weaver GC, Shaffer SA, Calvo-Calle JM, Stern LJ. Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.01.518643. [PMID: 36482973 PMCID: PMC9727760 DOI: 10.1101/2022.12.01.518643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Seasonal "common-cold" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but identification and characterization of the T cell response to seasonal human coronaviruses remain largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal human coronavirus OC43. We identified MHC-I and MHC-II bound peptides derived from the viral spike, nucleocapsid, hemagglutinin-esterase, 3C-like proteinase, and envelope proteins. Only three MHC-I bound OC43-derived peptides were observed, possibly due to the potent MHC-I downregulation induced by OC43 infection. By contrast, 80 MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. These peptides elicited low-abundance recall T cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T cell lines. Among the validated epitopes, S 903-917 presented by DPA1*01:03/DPB1*04:01 and S 1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. N 54-68 and HE 128-142 presented by DRB1*15:01 and HE 259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow T cell cross-reactivity after infection or vaccination and could aid in the selection of epitopes for inclusion in pan-coronavirus vaccines. Author Summary There is much current interest in cellular immune responses to seasonal common-cold coronaviruses because of their possible role in mediating protection against SARS-CoV-2 infection or pathology. However, identification of relevant T cell epitopes and systematic studies of the T cell responses responding to these viruses are scarce. We conducted a study to identify naturally processed and presented MHC-I and MHC-II epitopes from human cells infected with the seasonal coronavirus HCoV-OC43, and to characterize the T cell responses associated with these epitopes. We found epitopes specific to the seasonal coronaviruses, as well as epitopes cross-reactive between HCoV-OC43 and SARS-CoV-2. These epitopes should be useful in following immune responses to seasonal coronaviruses and identifying their roles in COVID-19 vaccination, infection, and pathogenesis.
Collapse
Affiliation(s)
- Aniuska Becerra-Artiles
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Padma P. Nanaware
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Khaja Muneeruddin
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury MA
| | - Grant C. Weaver
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Scott A. Shaffer
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury MA
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - J. Mauricio Calvo-Calle
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Lawrence J. Stern
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA 01655, USA
| |
Collapse
|
7
|
Development of a T Cell-Based COVID-19 Vaccine Using a Live Attenuated Influenza Vaccine Viral Vector. Vaccines (Basel) 2022; 10:vaccines10071142. [PMID: 35891306 PMCID: PMC9318028 DOI: 10.3390/vaccines10071142] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic emerged in 2020 and has caused an unprecedented burden to all countries in the world. SARS-CoV-2 continues to circulate and antigenically evolve, enabling multiple reinfections. To address the issue of the virus antigenic variability, T cell-based vaccines are being developed, which are directed to more conserved viral epitopes. We used live attenuated influenza vaccine (LAIV) virus vector to generate recombinant influenza viruses expressing various T-cell epitopes of SARS-CoV-2 from either neuraminidase (NA) or non-structural (NS1) genes, via the P2A self-cleavage site. Intranasal immunization of human leukocyte antigen-A*0201 (HLA-A2.1) transgenic mice with these recombinant viruses did not result in significant SARS-CoV-2-specific T-cell responses, due to the immunodominance of NP366 influenza T-cell epitope. However, side-by-side stimulation of peripheral blood mononuclear cells (PBMCs) of COVID-19 convalescents with recombinant viruses and LAIV vector demonstrated activation of memory T cells in samples stimulated with LAIV/SARS-CoV-2, but not LAIV alone. Hamsters immunized with a selected LAIV/SARS-CoV-2 prototype were protected against challenge with influenza virus and a high dose of SARS-CoV-2 of Wuhan and Delta lineages, which was confirmed by reduced weight loss, milder clinical symptoms and less pronounced histopathological signs of SARS-CoV-2 infection in the lungs, compared to LAIV- and mock-immunized animals. Overall, LAIV is a promising platform for the development of a bivalent vaccine against influenza and SARS-CoV-2.
Collapse
|
8
|
Becerra-Artiles A, Calvo-Calle JM, Co MD, Nanaware PP, Cruz J, Weaver GC, Lu L, Forconi C, Finberg RW, Moormann AM, Stern LJ. Broadly recognized, cross-reactive SARS-CoV-2 CD4 T cell epitopes are highly conserved across human coronaviruses and presented by common HLA alleles. Cell Rep 2022; 39:110952. [PMID: 35675811 PMCID: PMC9135679 DOI: 10.1016/j.celrep.2022.110952] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/03/2022] [Accepted: 05/23/2022] [Indexed: 11/24/2022] Open
Abstract
Sequence homology between SARS-CoV-2 and common-cold human coronaviruses (HCoVs) raises the possibility that memory responses to prior HCoV infection can affect T cell response in COVID-19. We studied T cell responses to SARS-CoV-2 and HCoVs in convalescent COVID-19 donors and identified a highly conserved SARS-CoV-2 sequence, S811-831, with overlapping epitopes presented by common MHC class II proteins HLA-DQ5 and HLA-DP4. These epitopes are recognized by low-abundance CD4 T cells from convalescent COVID-19 donors, mRNA vaccine recipients, and uninfected donors. TCR sequencing revealed a diverse repertoire with public TCRs. T cell cross-reactivity is driven by the high conservation across human and animal coronaviruses of T cell contact residues in both HLA-DQ5 and HLA-DP4 binding frames, with distinct patterns of HCoV cross-reactivity explained by MHC class II binding preferences and substitutions at secondary TCR contact sites. These data highlight S811-831 as a highly conserved CD4 T cell epitope broadly recognized across human populations.
Collapse
Affiliation(s)
| | | | - Mary Dawn Co
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Padma P Nanaware
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - John Cruz
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Grant C Weaver
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Liying Lu
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Catherine Forconi
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Robert W Finberg
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Ann M Moormann
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Lawrence J Stern
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA 01655, USA.
| |
Collapse
|
9
|
Xiao C, Qiu C, Deng J, Ye J, Gao L, Su J, Luo OJ, Wang P, Chen G. Optimization of antigen-specific CD8 + T cell activation conditions for infectious diseases including COVID-19. STAR Protoc 2021; 2:100789. [PMID: 34414379 PMCID: PMC8363473 DOI: 10.1016/j.xpro.2021.100789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Here, we describe the use of the artificial antigen-presenting cell (aAPC) system for the verification of T-cell epitopes. We purify and activate CD8+ T cells from blood samples from HLA-A2 that are negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). CD8+ T cells are combined with peptide-loaded T2-A2 cells, which are then stained with a SARS-CoV-2-specific MHC-1 tetramer to identify specific HLA-A2-restricted T-cell epitopes. The use of aAPC and healthy donors means that only BSL2 lab conditions are needed. For details of the use and implementation of this protocol, please refer to Deng et al. (2021). Protocol for convenience to validate SARS-CoV-2 CD8+ T-cell epitopes Rapid cell model applicable to produce a large number of specific CD8+ T cells A cell model applicable to activation of CD8+ T cells with various infectious diseases
Collapse
Affiliation(s)
- 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, Guangzhou, China
| | - Congling Qiu
- 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, Guangzhou, China.,Affiliated Huaqiao Hospital, 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, Guangzhou, China
| | - Jiezhou Ye
- 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, 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, Guangzhou, China
| | - Jun Su
- Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
| | - Oscar Junhong Luo
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou, China.,Department of Systems Biomedical Sciences, School of Medicine, 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, Guangzhou, China
| | - Guobing Chen
- 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, Guangzhou, China.,Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
| |
Collapse
|