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Sun B, Zhang J, Wang J, Liu Y, Sun H, Lu Z, Chen L, Ding X, Pan J, Hu C, Yang S, Jiang D, Yang K. Comparative Immunoreactivity Analyses of Hantaan Virus Glycoprotein-Derived MHC-I Epitopes in Vaccination. Vaccines (Basel) 2022; 10:564. [PMID: 35455313 PMCID: PMC9030823 DOI: 10.3390/vaccines10040564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 11/25/2022] Open
Abstract
MHC-I antigen processes and presentation trigger host-specific anti-viral cellular responses during infection, in which epitope-recognizing cytotoxic T lymphocytes eliminate infected cells and contribute to viral clearance through a cytolytic killing effect. In this study, Hantaan virus (HTNV) GP-derived 9-mer dominant epitopes were obtained with high affinity to major HLA-I and H-2 superfamilies. Further immunogenicity and conservation analyses selected 11 promising candidates, and molecule docking (MD) was then simulated with the corresponding MHC-I alleles. Two-way hierarchical clustering revealed the interactions between GP peptides and MHC-I haplotypes. Briefly, epitope hotspots sharing good affinity to a wide spectrum of MHC-I molecules highlighted the biomedical practice for vaccination, and haplotype clusters represented the similarities among individuals during T-cell response establishment. Cross-validation proved the patterns observed through both MD simulation and public data integration. Lastly, 148 HTNV variants yielded six types of major amino acid residue replacements involving four in nine hotspots, which minimally influenced the general potential of MHC-I superfamily presentation. Altogether, our work comprehensively evaluates the pan-MHC-I immunoreactivity of HTNV GP through a state-of-the-art workflow in light of comparative immunology, acknowledges present discoveries, and offers guidance for ongoing HTNV vaccine pursuit.
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Affiliation(s)
- Baozeng Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (B.S.); (J.Z.); (J.W.); (Y.L.); (H.S.); (Z.L.); (L.C.); (X.D.); (J.P.); (C.H.); (S.Y.)
| | - Junqi Zhang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (B.S.); (J.Z.); (J.W.); (Y.L.); (H.S.); (Z.L.); (L.C.); (X.D.); (J.P.); (C.H.); (S.Y.)
| | - Jiawei Wang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (B.S.); (J.Z.); (J.W.); (Y.L.); (H.S.); (Z.L.); (L.C.); (X.D.); (J.P.); (C.H.); (S.Y.)
| | - Yang Liu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (B.S.); (J.Z.); (J.W.); (Y.L.); (H.S.); (Z.L.); (L.C.); (X.D.); (J.P.); (C.H.); (S.Y.)
- Shaanxi Provincial Center for Disease Control and Prevention, Xi’an 710054, China
| | - Hao Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (B.S.); (J.Z.); (J.W.); (Y.L.); (H.S.); (Z.L.); (L.C.); (X.D.); (J.P.); (C.H.); (S.Y.)
- Tangshan Sannvhe Airport, Tangshan 063000, China
| | - Zhenhua Lu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (B.S.); (J.Z.); (J.W.); (Y.L.); (H.S.); (Z.L.); (L.C.); (X.D.); (J.P.); (C.H.); (S.Y.)
- Department of Epidemiology, Public Health School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China
| | - Longyu Chen
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (B.S.); (J.Z.); (J.W.); (Y.L.); (H.S.); (Z.L.); (L.C.); (X.D.); (J.P.); (C.H.); (S.Y.)
| | - Xushen Ding
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (B.S.); (J.Z.); (J.W.); (Y.L.); (H.S.); (Z.L.); (L.C.); (X.D.); (J.P.); (C.H.); (S.Y.)
| | - Jingyu Pan
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (B.S.); (J.Z.); (J.W.); (Y.L.); (H.S.); (Z.L.); (L.C.); (X.D.); (J.P.); (C.H.); (S.Y.)
| | - Chenchen Hu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (B.S.); (J.Z.); (J.W.); (Y.L.); (H.S.); (Z.L.); (L.C.); (X.D.); (J.P.); (C.H.); (S.Y.)
| | - Shuya Yang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (B.S.); (J.Z.); (J.W.); (Y.L.); (H.S.); (Z.L.); (L.C.); (X.D.); (J.P.); (C.H.); (S.Y.)
| | - Dongbo Jiang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (B.S.); (J.Z.); (J.W.); (Y.L.); (H.S.); (Z.L.); (L.C.); (X.D.); (J.P.); (C.H.); (S.Y.)
| | - Kun Yang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi’an 710032, China; (B.S.); (J.Z.); (J.W.); (Y.L.); (H.S.); (Z.L.); (L.C.); (X.D.); (J.P.); (C.H.); (S.Y.)
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Evaluation of potential MHC-I allele-specific epitopes in Zika virus proteins and the effects of mutations on peptide-MHC-I interaction studied using in silico approaches. Comput Biol Chem 2021; 92:107459. [PMID: 33636637 DOI: 10.1016/j.compbiolchem.2021.107459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 02/06/2021] [Accepted: 02/12/2021] [Indexed: 11/24/2022]
Abstract
Zika virus (ZIKV) infection is a global health concern due to its association with microcephaly and neurological complications. The development of a T-cell vaccine is important to combat this disease. In this study, we propose ZIKV major histocompatibility complex I (MHC-I) epitopes based on in silico screening consensus followed by molecular docking, PRODIGY, and molecular dynamics (MD) simulation analyses. The effects of the reported mutations on peptide-MHC-I (pMHC-I) complexes were also evaluated. In general, our data indicate an allele-specific peptide-binding human leukocyte antigen (HLA) and potential epitopes. For HLA-B44, we showed that the absence of acidic residue Glu at P2, due to the loss of the electrostatic interaction with Lys45, has a negative impact on the pMHC-I complex stability and explains the low free energy estimated for the immunodominant peptide E-4 (IGVSNRDFV). Our MD data also suggest the deleterious effects of acidic residue Asp at P1 on the pMHC-I stability of HLA-B8 due to destabilization of the α-helix and β-strand. Free energy estimation further indicated that the mutation from Val to Ala at P9 of peptide E-247 (DAHAKRQTV), which was found exclusively in microcephaly samples, did not reduce HLA-B8 affinity. In contrast, the mutation from Thr to Pro at P2 of the peptide NS5-832 (VTKWTDIPY) decreased the interaction energy, number of intermolecular interactions, and adversely affected its binding mode with HLA-A1. Overall, our findings are important with regard to the design of T-cell peptide vaccines and for understanding how ZIKV escapes recognition by CD8 + T-cells.
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Damilano GD, Sued O, Ruiz MJ, Ghiglione Y, Canitano F, Pando M, Turk G, Cahn P, Salomón H, Dilernia D. Computational comparison of availability in CTL/gag epitopes among patients with acute and chronic HIV-1 infection. Vaccine 2018; 36:4142-4151. [PMID: 29802001 DOI: 10.1016/j.vaccine.2018.04.086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/23/2018] [Accepted: 04/29/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND Recent studies indicate that there is selection bias for transmission of viral polymorphisms associated with higher viral fitness. Furthermore, after transmission and before a specific immune response is mounted in the recipient, the virus undergoes a number of reversions which allow an increase in their replicative capacity. These aspects, and others, affect the viral population characteristic of early acute infection. METHODS 160 singlegag-gene amplifications were obtained by limiting-dilution RT-PCR from plasma samples of 8 ARV-naïve patients with early acute infection (<30 days, 22 days average) and 8 ARV-naive patients with approximately a year of infection (10 amplicons per patient). Sanger sequencing and NGS SMRT technology (Pacific Biosciences) were implemented to sequence the amplicons. Phylogenetic analysis was performed by using MEGA 6.06. HLA-I (A and B) typing was performed by SSOP-PCR method. The chromatograms were analyzed with Sequencher 4.10. Epitopes and immune-proteosomal cleavages prediction was performed with CBS prediction server for the 30 HLA-A and -B alleles most prevalent in our population with peptide lengths from 8 to 14 mer. Cytotoxic response prediction was performed by using IEDB Analysis Resource. RESULTS After implementing epitope prediction analysis, we identified a total number of 325 possible viral epitopes present in two or more acute or chronic patients. 60.3% (n = 196) of them were present only in acute infection (prevalent acute epitopes) while 39.7% (n = 129) were present only in chronic infection (prevalent chronic epitopes). Within p24, the difference was equally dramatic with 59.4% (79/133) being acute epitopes (p < 0.05). This is consistent with progressive viral adaptation to immune response in time and further supported by the fact that cytotoxic responses prediction showed that acute epitopes are more likely to generate immune response than chronic epitopes. Interestingly, only 27.5% of acute epitopes match the population-level consensus sequence of the virus. CONCLUSIONS Our results indicate that certain non-consensus viral residues might be transmitted more frequently than consensus-residues when located in immunological relevant positions (epitopes). This observation might be relevant to the rationale behind development of an effective vaccineto reduce viral reservoir and induce functional cure of HIV infection based in prevalent acute epitopes.
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Affiliation(s)
- Gabriel Dario Damilano
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina.
| | - Omar Sued
- Fundación Huésped, Buenos Aires, Argentina.
| | - Maria Julia Ruiz
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina.
| | - Yanina Ghiglione
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina.
| | - Flavia Canitano
- Instituto de Investigaciones Médicas Alfredo Lanari, Buenos Aires, Argentina.
| | - Maria Pando
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina.
| | - Gabriela Turk
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina.
| | - Pedro Cahn
- Fundación Huésped, Buenos Aires, Argentina.
| | - Horacio Salomón
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina.
| | - Dario Dilernia
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA Facultad de Medicina, Universidad de Buenos Aires, Argentina; Emory University, Atlanta, USA.
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Ma RX, Cheng LF, Ying QK, Liu RR, Ma TJ, Zhang XX, Liu ZY, Zhang L, Ye W, Zhang FL, Xu ZK, Wang F, Wu XA. Screening and Identification of an H-2K b-Restricted CTL Epitope within the Glycoprotein of Hantaan Virus. Front Cell Infect Microbiol 2016; 6:151. [PMID: 27933274 PMCID: PMC5122572 DOI: 10.3389/fcimb.2016.00151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 10/31/2016] [Indexed: 12/12/2022] Open
Abstract
The cytotoxic T lymphocyte (CTL) response plays a key role in controlling viral infection, but only a few epitopes within the HTNV glycoprotein (GP) that are recognized by CTLs have been reported. In this study, we identified one murine HTNV GP-derived H2-Kb-restricted CTL epitope in C57BL/6 mice, which could be used to design preclinical studies of vaccines for HTNV infection. First, 15 8-mer peptides were selected from the HTNV GP amino acid sequence based on a percentile rank of <=1% by IEDB which is the most comprehensive collection of epitope prediction and analysis tool. A lower percentile rank indicates higher affinity and higher immune response. In the case of the consensus method, we also evaluated the binding score of peptide-binding affinity by the BIMAS software to confirm that all peptides were able to bind H2-Kb. Second, one novel GP-derived CTL epitope, GP6 aa456-aa463 (ITSLFSLL), was identified in the splenocytes of HTNV-infected mice using the IFN-γ ELISPOT assay. Third, a single peptide vaccine was administered to C57BL/6 mice to evaluate the immunogenic potential of the identified peptides. ELISPOT and cell-mediated cytotoxicity assays showed that this peptide vaccine induced a strong IFN-γ response and potent cytotoxicity in immunized mice. Last, we demonstrated that the peptide-vaccinated mice had partial protection from challenge with HTNV. In conclusion, we identified an H2-Kb-restricted CTL epitope with involvement in the host immune response to HTNV infection.
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Affiliation(s)
- Rui-Xue Ma
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University Xi'an, China
| | - Lin-Feng Cheng
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University Xi'an, China
| | - Qi-Kang Ying
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University Xi'an, China
| | - Rong-Rong Liu
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University Xi'an, China
| | - Tie-Jun Ma
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University Xi'an, China
| | - Xiao-Xiao Zhang
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University Xi'an, China
| | - Zi-Yu Liu
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University Xi'an, China
| | - Liang Zhang
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University Xi'an, China
| | - Wei Ye
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University Xi'an, China
| | - Fang-Lin Zhang
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University Xi'an, China
| | - Zhi-Kai Xu
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University Xi'an, China
| | - Fang Wang
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University Xi'an, China
| | - Xing-An Wu
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University Xi'an, China
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