Immunoreactivity Analysis of MHC-I Epitopes Derived from the Nucleocapsid Protein of SARS-CoV-2 via Computation and Vaccination
Abstract
:1. Introduction
2. Materials and Methods
2.1. SARS-CoV-2 NP Sequence Retrieval
2.2. SARS-CoV-2 NP Pan-MHC-I Epitope Prediction and Screening
2.3. Conservation Analysis
2.4. Immunogenicity Analysis
2.5. Docking of Pan-MHC-I Molecules
2.6. SARS-CoV-2 NP Peptides and Pan-MHC-I Clustering
2.7. Sequence Alignment of SARS-CoV-2 Variants
2.8. Prediction of Peptide Toxicity and Sensitization
2.9. Application of Pan-MHC-I-Restricted SARS-CoV-2 NP Epitopes via a Literature Review
2.10. Vaccine, Animal, and Immunization
2.11. Peptides and ELISpot Assay
2.12. Enzyme-Linked Immunosorbent Assay (ELISA)
2.13. Flow Cytometry
2.14. Statistical Analysis
3. Results
3.1. Affinity Analysis of SARS-CoV-2 NP Epitopes for Mouse H-2 and Major HLA-I Haplotypes
3.2. Conservation Status of SARS-CoV-2 NP 9-mer Dominant Epitopes
3.3. Immunogenicity of SARS-CoV-2 NP 9-mer Peptides
3.4. Interactions Between Pan-MHC-I Molecules and SARS-CoV-2 NP 9-mer Peptides via Hierarchical Clustering
3.5. Docking of Pan-MHC-I Molecules with Preferred Epitopes
3.6. Multiple Sequence Alignment with 84 SARS-CoV-2 Mutant Strains
3.7. Differences in the Immunoreaction Among SARS-CoV-2 and Its Variants
3.8. Toxicity and Sensitization Analysis of SARS-CoV-2 NP Epitopes
3.9. ELISpot Validation of the SARS-CoV-2 NP Epitopes
3.10. SARS-CoV-2 NP Epitopes Enhanced the Secretion of IFN-γ and IL-2
3.11. The Preferred Epitopes Induced Humoral Immune Responses
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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MHC-IHaplotypes | Prediction Tools | NP Epitopes | NP (Short-Listed) |
---|---|---|---|
HLA-A1 | IEDB | 38 | 25 |
NetMHCpan | 25 | ||
Rankpep | 9 | ||
SMMPMBEC | 11 | ||
SYFPEITHI | 0 | ||
HLA-A2 | IEDB | 25 | 21 |
NetMHCpan | 23 | ||
Rankpep | 27 | ||
SMMPMBEC | 6 | ||
SYFPEITHI | 8 | ||
HLA-A3 | IEDB | 57 | 48 |
NetMHCpan | 49 | ||
Rankpep | 28 | ||
SMMPMBEC | 25 | ||
SYFPEITHI | 16 | ||
HLA-A24 | IEDB | 18 | 16 |
NetMHCpan | 14 | ||
Rankpep | 9 | ||
SMMPMBEC | 7 | ||
SYFPEITHI | 8 | ||
HLA-3201 | IEDB | 14 | 19 |
NetMHCpan | 19 | ||
Rankpep | 0 | ||
SMMPMBEC | 5 | ||
SYFPEITHI | 0 | ||
HLA-B7 | IEDB | 42 | 22 |
NetMHCpan | 33 | ||
Rankpep | 15 | ||
SMMPMBEC | 19 | ||
SYFPEITHI | 32 | ||
HLA-B8 | IEDB | 18 | 10 |
NetMHCpan | 13 | ||
Rankpep | 0 | ||
SMMPMBEC | 5 | ||
SYFPEITHI | 0 | ||
HLA-B15 | IEDB | 23 | 17 |
NetMHCpan | 15 | ||
Rankpep | 0 | ||
SMMPMBEC | 4 | ||
SYFPEITHI | 8 | ||
HLA-B44 | IEDB | 23 | 15 |
NetMHCpan | 15 | ||
Rankpep | 9 | ||
SMMPMBEC | 2 | ||
SYFPEITHI | 16 | ||
HLA-B58 | IEDB | 17 | 11 |
NetMHCpan | 11 | ||
Rankpep | 15 | ||
SMMPMBEC | 6 | ||
SYFPEITHI | 8 | ||
HLA-B46 | IEDB | 21 | 15 |
NetMHCpan | 15 | ||
Rankpep | 0 | ||
SMMPMBEC | 4 | ||
SYFPEITHI | 0 | ||
HLA-B62 | IEDB | 0 | |
NetMHCpan | 23 | ||
Rankpep | 0 | ||
SMMPMBEC | 0 | ||
SYFPEITHI | 0 | ||
HLA-C0401 | IEDB | 22 | 19 |
NetMHCpan | 16 | ||
Rankpep | 0 | ||
SMMPMBEC | 5 | ||
SYFPEITHI | 0 |
MHC-IHaplotypes | Prediction Tools | NP Epitopes | NP (Short-Listed) |
---|---|---|---|
H-2 Db | IEDB | 15 | 9 |
NetMHCpan | 10 | ||
Rankpep | 9 | ||
SMMPMBEC | 5 | ||
SYFPEITHI | 8 | ||
H-2 Dd | IEDB | 31 | 19 |
NetMHCpan | 15 | ||
Rankpep | 9 | ||
SMMPMBEC | 3 | ||
SYFPEITHI | 0 | ||
H-2 Kb | IEDB | 19 | 13 |
NetMHCpan | 11 | ||
Rankpep | 9 | ||
SMMPMBEC | 6 | ||
SYFPEITHI | 0 | ||
H-2 Kd | IEDB | 20 | 7 |
NetMHCpan | 13 | ||
Rankpep | 9 | ||
SMMPMBEC | 4 | ||
SYFPEITHI | 8 | ||
H-2 Kk | IEDB | 11 | 9 |
NetMHCpan | 7 | ||
Rankpep | 9 | ||
SMMPMBEC | 0 | ||
SYFPEITHI | 8 | ||
H-2 Ld | IEDB | 20 | 7 |
NetMHCpan | 16 | ||
Rankpep | 9 | ||
SMMPMBEC | 6 | ||
SYFPEITHI | 8 |
MHC-I Haplotypes | Interspecies− Intraspecies− | Interspecies− Intraspecies+ | Interspecies+ Intraspecies− | Interspecies+ Intraspecies+ |
---|---|---|---|---|
H-2 Db | 9 | 0 | 0 | 0 |
H-2 Dd | 14 | 4 | 0 | 1 |
H-2 Kb | 9 | 2 | 0 | 2 |
H-2 Kd | 7 | 0 | 0 | 0 |
H-2 Kk | 8 | 1 | 0 | 0 |
H-2 Ld | 5 | 1 | 0 | 1 |
HLA-A1 | 21 | 3 | 0 | 1 |
HLA-A2 | 20 | 0 | 0 | 0 |
HLA-A3 | 45 | 2 | 0 | 0 |
HLA-A24 | 13 | 3 | 0 | 0 |
HLA-3201 | 10 | 4 | 0 | 0 |
HLA-B7 | 20 | 1 | 0 | 1 |
HLA-B8 | 4 | 0 | 0 | 0 |
HLA-B15 | 8 | 0 | 0 | 0 |
HLA-B44 | 11 | 4 | 0 | 0 |
HLA-B58 | 7 | 3 | 0 | 1 |
HLA-B4601 | 13 | 1 | 0 | 1 |
HLA-C0401 | 17 | 1 | 0 | 0 |
Amino Acid | NC_045512.2 | Variants | Dominant in | Dominant in | HLA-Ⅰ |
---|---|---|---|---|---|
Number | Variants | NC_045512.2 | Genotype | ||
YES | NO | HLA-A2402 | |||
151–159 | TWLTYTGAI | TWLTYHGAI | YES | NO | HLA-A2301 |
YES | NO | HLA-A2601 | |||
153–161 | LTYTGAIKL | LTYHGAIKL | NO | YES | HLA-B5101 |
Pepitides | MERCI Score | BLAST Score | Prediction | ML Score | Hybrid Score | Prediction |
---|---|---|---|---|---|---|
NTASWFTAL | 0.33 | 0 | Non-Allergen | 0.56 | 0.56 | Non-Toxin |
LSPRWYFYY | 0.29 | 0 | Non-Allergen | 0.55 | 0.55 | Non-Toxin |
SPRWYFYYL | 0.29 | 0 | Non-Allergen | 0.55 | 0.55 | Non-Toxin |
NNAAIVLQL | 0.29 | 0.5 | Allergen | 0.71 | 0.71 | Toxin |
DAALALLLL | 0.41 | 0 | Allergen | 0.73 | 0.73 | Toxin |
LALLLLDRL | 0.36 | 0 | Non-Allergen | 0.76 | 0.76 | Toxin |
KHWPQIAQF | 0.4 | 0 | Non-Allergen | 0.62 | 0.62 | Non-Toxin |
LTYTGAIKL | 0.32 | 0 | Non-Allergen | 0.7 | 0.7 | Non-Toxin |
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Jiang, D.; Ma, Z.; Zhang, J.; Sun, Y.; Bai, T.; Liu, R.; Wang, Y.; Guan, L.; Fu, S.; Sun, Y.; et al. Immunoreactivity Analysis of MHC-I Epitopes Derived from the Nucleocapsid Protein of SARS-CoV-2 via Computation and Vaccination. Vaccines 2024, 12, 1214. https://doi.org/10.3390/vaccines12111214
Jiang D, Ma Z, Zhang J, Sun Y, Bai T, Liu R, Wang Y, Guan L, Fu S, Sun Y, et al. Immunoreactivity Analysis of MHC-I Epitopes Derived from the Nucleocapsid Protein of SARS-CoV-2 via Computation and Vaccination. Vaccines. 2024; 12(11):1214. https://doi.org/10.3390/vaccines12111214
Chicago/Turabian StyleJiang, Dongbo, Zilu Ma, Junqi Zhang, Yubo Sun, Tianyuan Bai, Ruibo Liu, Yongkai Wang, Liang Guan, Shuaishuai Fu, Yuanjie Sun, and et al. 2024. "Immunoreactivity Analysis of MHC-I Epitopes Derived from the Nucleocapsid Protein of SARS-CoV-2 via Computation and Vaccination" Vaccines 12, no. 11: 1214. https://doi.org/10.3390/vaccines12111214