Immunoreactivity Analysis of MHC-I Epitopes Derived from the Nucleocapsid Protein of SARS-CoV-2 via Computation and Vaccination
<b>Background</b>: Since 2019, the SARS-CoV-2 virus has been responsible for the global spread of respiratory illness. As of 1 September 2024, the cumulative number of infections worldwide exceeded 776 million. There are many structural proteins of the virus, among which the SARS-CoV-2 n...
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2024-10-01
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| author | Dongbo Jiang Zilu Ma Junqi Zhang Yubo Sun Tianyuan Bai Ruibo Liu Yongkai Wang Liang Guan Shuaishuai Fu Yuanjie Sun Yuanzhe Li Bingquan Zhou Yulin Yang Shuya Yang Yuanhang Chang Baozeng Sun Kun Yang |
| author_facet | Dongbo Jiang Zilu Ma Junqi Zhang Yubo Sun Tianyuan Bai Ruibo Liu Yongkai Wang Liang Guan Shuaishuai Fu Yuanjie Sun Yuanzhe Li Bingquan Zhou Yulin Yang Shuya Yang Yuanhang Chang Baozeng Sun Kun Yang |
| author_sort | Dongbo Jiang |
| collection | DOAJ |
| description | <b>Background</b>: Since 2019, the SARS-CoV-2 virus has been responsible for the global spread of respiratory illness. As of 1 September 2024, the cumulative number of infections worldwide exceeded 776 million. There are many structural proteins of the virus, among which the SARS-CoV-2 nucleocapsid (N) protein plays a pivotal role in the viral life cycle, participating in a multitude of essential activities following viral invasion. An important antiviral immune response is the major histocompatibility complex (MHC)-restricted differentiation cluster 8 (CD8+) T cell cytotoxicity. Therefore, understanding the immunogenicity of SARS-CoV-2 NP-specific MHC-I-restricted epitopes is highly important. <b>Methods</b>: MHC-I molecules from 11 human leukocyte antigen I (HLA-I) superfamilies with 98% population coverage and 6 mouse H2 alleles were selected. The affinity were screened by IEDB, NetMHCpan, SYFPEITHI, SMMPMBEC and Rankpep. Further immunogenicity and conservative analyses were performed using VaxiJen and BLASTp, respectively. EpiDock was used to simulate molecular docking. Cluster analysis was performed. Selective epitopes were validated by enzyme-linked immunospot (ELISpot) assay and flow cytometry in the mice with pVAX-NP<sub>SARS-CoV-2</sub> immunization. Enzyme-Linked Immunosorbent Assay (ELISA) was used to detect whether the preferred epitope induced humoral immunity. <b>Results</b>: There were 64 dominant epitopes for the H-2 haplotype and 238 dominant epitopes for the HLA-I haplotype. Further analysis of immunogenicity and conservation yielded 8 preferred epitopes, and docking simulations were conducted with corresponding MHC-I alleles. The relationships between the NP peptides and MHC-I haplotypes were then determined via two-way hierarchical clustering. ELISA, ELISpot assay, and flow cytometry revealed that the preferred epitope stimulated both humoral and cellular immunity and enhanced cytokine secretion in mice. <b>Conclusions</b>: our study revealed the general patterns among multiple haplotypes within the humans and mice superfamily, providing a comprehensive assessment of the pan-MHC-I immunoreactivity of SARS-CoV-2 NP. Our findings would render prospects for the development and application of epitope-based immunotherapy in lasting viral epidemics. |
| format | Article |
| id | doaj-art-5bcaeebbf04d46f783091cc538c78448 |
| institution | OA Journals |
| issn | 2076-393X |
| language | English |
| publishDate | 2024-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Vaccines |
| spelling | doaj-art-5bcaeebbf04d46f783091cc538c784482025-08-20T02:04:44ZengMDPI AGVaccines2076-393X2024-10-011211121410.3390/vaccines12111214Immunoreactivity Analysis of MHC-I Epitopes Derived from the Nucleocapsid Protein of SARS-CoV-2 via Computation and VaccinationDongbo Jiang0Zilu Ma1Junqi Zhang2Yubo Sun3Tianyuan Bai4Ruibo Liu5Yongkai Wang6Liang Guan7Shuaishuai Fu8Yuanjie Sun9Yuanzhe Li10Bingquan Zhou11Yulin Yang12Shuya Yang13Yuanhang Chang14Baozeng Sun15Kun Yang16Department of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, ChinaDepartment of Immunology, The Key Laboratory of Bio-Hazard Damage and Prevention Medicine, Basic Medicine School, Air Force Medical University (In Former The Fourth Military Medical University), Xi’an 710032, China<b>Background</b>: Since 2019, the SARS-CoV-2 virus has been responsible for the global spread of respiratory illness. As of 1 September 2024, the cumulative number of infections worldwide exceeded 776 million. There are many structural proteins of the virus, among which the SARS-CoV-2 nucleocapsid (N) protein plays a pivotal role in the viral life cycle, participating in a multitude of essential activities following viral invasion. An important antiviral immune response is the major histocompatibility complex (MHC)-restricted differentiation cluster 8 (CD8+) T cell cytotoxicity. Therefore, understanding the immunogenicity of SARS-CoV-2 NP-specific MHC-I-restricted epitopes is highly important. <b>Methods</b>: MHC-I molecules from 11 human leukocyte antigen I (HLA-I) superfamilies with 98% population coverage and 6 mouse H2 alleles were selected. The affinity were screened by IEDB, NetMHCpan, SYFPEITHI, SMMPMBEC and Rankpep. Further immunogenicity and conservative analyses were performed using VaxiJen and BLASTp, respectively. EpiDock was used to simulate molecular docking. Cluster analysis was performed. Selective epitopes were validated by enzyme-linked immunospot (ELISpot) assay and flow cytometry in the mice with pVAX-NP<sub>SARS-CoV-2</sub> immunization. Enzyme-Linked Immunosorbent Assay (ELISA) was used to detect whether the preferred epitope induced humoral immunity. <b>Results</b>: There were 64 dominant epitopes for the H-2 haplotype and 238 dominant epitopes for the HLA-I haplotype. Further analysis of immunogenicity and conservation yielded 8 preferred epitopes, and docking simulations were conducted with corresponding MHC-I alleles. The relationships between the NP peptides and MHC-I haplotypes were then determined via two-way hierarchical clustering. ELISA, ELISpot assay, and flow cytometry revealed that the preferred epitope stimulated both humoral and cellular immunity and enhanced cytokine secretion in mice. <b>Conclusions</b>: our study revealed the general patterns among multiple haplotypes within the humans and mice superfamily, providing a comprehensive assessment of the pan-MHC-I immunoreactivity of SARS-CoV-2 NP. Our findings would render prospects for the development and application of epitope-based immunotherapy in lasting viral epidemics.https://www.mdpi.com/2076-393X/12/11/1214SARS-CoV-2nucleocapsid protein (NP)MHC-I-restricted epitopesCD8+ T cell responseimmunogenicity |
| spellingShingle | Dongbo Jiang Zilu Ma Junqi Zhang Yubo Sun Tianyuan Bai Ruibo Liu Yongkai Wang Liang Guan Shuaishuai Fu Yuanjie Sun Yuanzhe Li Bingquan Zhou Yulin Yang Shuya Yang Yuanhang Chang Baozeng Sun Kun Yang Immunoreactivity Analysis of MHC-I Epitopes Derived from the Nucleocapsid Protein of SARS-CoV-2 via Computation and Vaccination Vaccines SARS-CoV-2 nucleocapsid protein (NP) MHC-I-restricted epitopes CD8+ T cell response immunogenicity |
| title | Immunoreactivity Analysis of MHC-I Epitopes Derived from the Nucleocapsid Protein of SARS-CoV-2 via Computation and Vaccination |
| title_full | Immunoreactivity Analysis of MHC-I Epitopes Derived from the Nucleocapsid Protein of SARS-CoV-2 via Computation and Vaccination |
| title_fullStr | Immunoreactivity Analysis of MHC-I Epitopes Derived from the Nucleocapsid Protein of SARS-CoV-2 via Computation and Vaccination |
| title_full_unstemmed | Immunoreactivity Analysis of MHC-I Epitopes Derived from the Nucleocapsid Protein of SARS-CoV-2 via Computation and Vaccination |
| title_short | Immunoreactivity Analysis of MHC-I Epitopes Derived from the Nucleocapsid Protein of SARS-CoV-2 via Computation and Vaccination |
| title_sort | immunoreactivity analysis of mhc i epitopes derived from the nucleocapsid protein of sars cov 2 via computation and vaccination |
| topic | SARS-CoV-2 nucleocapsid protein (NP) MHC-I-restricted epitopes CD8+ T cell response immunogenicity |
| url | https://www.mdpi.com/2076-393X/12/11/1214 |
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