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Michelo CM, Fiore-Gartland A, Dalel JA, Hayes P, Tang J, McGowan E, Kilembe W, Fernandez N, Gilmour J, Hunter E. Cohort-Specific Peptide Reagents Broaden Depth and Breadth Estimates of the CD8 T Cell Response to HIV-1 Gag Potential T Cell Epitopes. Vaccines (Basel) 2023; 11:472. [PMID: 36851349 PMCID: PMC9961105 DOI: 10.3390/vaccines11020472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
An effective HIV vaccine will need to stimulate immune responses against the sequence diversity presented in circulating virus strains. In this study, we evaluate breadth and depth estimates of potential T-cell epitopes (PTEs) in transmitted founder virus sequence-derived cohort-specific peptide reagents against reagents representative of consensus and global sequences. CD8 T-cells from twenty-six HIV-1+ PBMC donor samples, obtained at 1-year post estimated date of infection, were evaluated. ELISpot assays compared responses to 15mer consensus (n = 121), multivalent-global (n = 320), and 10mer multivalent cohort-specific (n = 300) PTE peptides, all mapping to the Gag antigen. Responses to 38 consensus, 71 global, and 62 cohort-specific PTEs were confirmed, with sixty percent of common global and cohort-specific PTEs corresponding to consensus sequences. Both global and cohort-specific peptides exhibited broader epitope coverage compared to commonly used consensus reagents, with mean breadth estimates of 3.2 (global), 3.4 (cohort) and 2.2 (consensus) epitopes. Global or cohort peptides each identified unique epitope responses that would not be detected if these peptide pools were used alone. A peptide set designed around specific virologic and immunogenetic characteristics of a target cohort can expand the detection of CD8 T-cell responses to epitopes in circulating viruses, providing a novel way to better define the host response to HIV-1 with implications for vaccine development.
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Affiliation(s)
- Clive M. Michelo
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jama A. Dalel
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Peter Hayes
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Edward McGowan
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - William Kilembe
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
| | - Natalia Fernandez
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Eric Hunter
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
- Emory Vaccine Center, Emory University, 954 Gatewood Road NE, Atlanta, GA 30329, USA
- Emory National Primate Research Center, Emory University, 954 Gatewood Road NE, Atlanta, GA 30329, USA
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Bugembe DL, Ekii AO, Ndembi N, Serwanga J, Kaleebu P, Pala P. Computational MHC-I epitope predictor identifies 95% of experimentally mapped HIV-1 clade A and D epitopes in a Ugandan cohort. BMC Infect Dis 2020; 20:172. [PMID: 32087680 PMCID: PMC7036183 DOI: 10.1186/s12879-020-4876-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/12/2020] [Indexed: 12/21/2022] Open
Abstract
Background Identifying immunogens that induce HIV-1-specific immune responses is a lengthy process that can benefit from computational methods, which predict T-cell epitopes for various HLA types. Methods We tested the performance of the NetMHCpan4.0 computational neural network in re-identifying 93 T-cell epitopes that had been previously independently mapped using the whole proteome IFN-γ ELISPOT assays in 6 HLA class I typed Ugandan individuals infected with HIV-1 subtypes A1 and D. To provide a benchmark we compared the predictions for NetMHCpan4.0 to MHCflurry1.2.0 and NetCTL1.2. Results NetMHCpan4.0 performed best correctly predicting 88 of the 93 experimentally mapped epitopes for a set length of 9-mer and matched HLA class I alleles. Receiver Operator Characteristic (ROC) analysis gave an area under the curve (AUC) of 0.928. Setting NetMHCpan4.0 to predict 11-14mer length did not improve the prediction (37–79 of 93 peptides) with an inverse correlation between the number of predictions and length set. Late time point peptides were significantly stronger binders than early peptides (Wilcoxon signed rank test: p = 0.0000005). MHCflurry1.2.0 similarly predicted all but 2 of the peptides that NetMHCpan4.0 predicted and NetCTL1.2 predicted only 14 of the 93 experimental peptides. Conclusion NetMHCpan4.0 class I epitope predictions covered 95% of the epitope responses identified in six HIV-1 infected individuals, and would have reduced the number of experimental confirmatory tests by > 80%. Algorithmic epitope prediction in conjunction with HLA allele frequency information can cost-effectively assist immunogen design through minimizing the experimental effort.
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Affiliation(s)
- Daniel Lule Bugembe
- MRC/UVRI and LSHTM Uganda Research Unit, P. O. Box 49, Plot 51-59 Nakiwogo Road, Entebbe, Uganda.
| | - Andrew Obuku Ekii
- MRC/UVRI and LSHTM Uganda Research Unit, P. O. Box 49, Plot 51-59 Nakiwogo Road, Entebbe, Uganda
| | | | - Jennifer Serwanga
- MRC/UVRI and LSHTM Uganda Research Unit, P. O. Box 49, Plot 51-59 Nakiwogo Road, Entebbe, Uganda.,Uganda Virus Research Institute, Entebbe, Uganda
| | - Pontiano Kaleebu
- MRC/UVRI and LSHTM Uganda Research Unit, P. O. Box 49, Plot 51-59 Nakiwogo Road, Entebbe, Uganda.,Uganda Virus Research Institute, Entebbe, Uganda
| | - Pietro Pala
- MRC/UVRI and LSHTM Uganda Research Unit, P. O. Box 49, Plot 51-59 Nakiwogo Road, Entebbe, Uganda
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Hinkula J, Petkov S, Ljungberg K, Hallengärd D, Bråve A, Isaguliants M, Falkeborn T, Sharma S, Liakina V, Robb M, Eller M, Moss B, Biberfeld G, Sandström E, Nilsson C, Markland K, Blomberg P, Wahren B. HIVIS-DNA or HIVISopt-DNA priming followed by CMDR vaccinia-based boosts induce both humoral and cellular murine immune responses to HIV. Heliyon 2017; 3:e00339. [PMID: 28721397 PMCID: PMC5496381 DOI: 10.1016/j.heliyon.2017.e00339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/19/2017] [Indexed: 02/08/2023] Open
Abstract
Background In order to develop a more effective prophylactic HIV-1 vaccine it is important optimize the components, improve Envelope glycoprotein immunogenicity as well as to explore prime-boost immunization schedules. It is also valuable to include several HIV-1 subtype antigens representing the world-wide epidemic. Methods HIVIS-DNA plasmids which include Env genes of subtypes A, B and C together with Gag subtypes A and B and RTmut/Rev of subtype B were modified as follows: the Envelope sequences were shortened, codon optimized, provided with an FT4 sequence and an immunodominant region mutated. The reverse transcriptase (RT) gene was shortened to contain the most immunogenic N-terminal fragment and fused with an inactivated viral protease vPR gene. HIVISopt-DNA thus contains fewer plasmids but additional PR epitopes compared to the native HIVIS-DNA. DNA components were delivered intradermally to young Balb/c mice once, using a needle-free Biojector® immediately followed by dermal electroporation. Vaccinia-based MVA-CMDR boosts including Env gene E and Gag-RT genes A were delivered intramuscularly by needle, once or twice. Results Both HIVIS-DNA and HIVISopt-DNA primed humoral and cell mediated responses well. When boosted with heterologous MVA-CMDR (subtypes A and E) virus inhibitory neutralizing antibodies were obtained to HIV-1 subtypes A, B, C and AE. Both plasmid compositions boosted with MVA-CMDR generated HIV-1 specific cellular responses directed against HIV-1 Env, Gag and Pol, as measured by IFNγ ELISpot. It was shown that DNA priming augmented the vector MVA immunological boosting effects, the HIVISopt-DNA with a trend to improved (Env) neutralization, the HIVIS-DNA with a trend to better (Gag) cell mediated immune reponses. Conclusions HIVIS-DNA was modified to obtain HIVISopt-DNA that had fewer plasmids, and additional epitopes. Even with one DNA prime followed by two MVA-CMDR boosts, humoral and cell-mediated immune responses were readily induced by priming with either DNA construct composition. Priming by HIV-DNA augmented neutralizing antibody responses revealed by boosting with the vaccinia-based heterologous sequences. Cellular and antibody responses covered selected strains representing HIV-1 subtypes A, B, C and CRF01_AE. We assume this is related to the inclusion of heterologous full genes in the vaccine schedule.
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Affiliation(s)
- J Hinkula
- Department of Clinical and Experimental Medicine, Linköping University, 58183 Linköping, Sweden.,Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - S Petkov
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - K Ljungberg
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - D Hallengärd
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - A Bråve
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - M Isaguliants
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - T Falkeborn
- Department of Clinical and Experimental Medicine, Linköping University, 58183 Linköping, Sweden
| | - S Sharma
- Department of Clinical and Experimental Medicine, Linköping University, 58183 Linköping, Sweden
| | - V Liakina
- Faculty of Medicine, Vilnius University 2, 08661 Vilnius, Lithuania
| | - M Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, 20892 MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, 20892 MD, USA
| | - M Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, 20892 MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, 20892 MD, USA
| | - B Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892 MD, USA
| | - G Biberfeld
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - E Sandström
- Department of South Hospital, Karolinska Institutet, 11883 Stockholm, Sweden
| | - C Nilsson
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - K Markland
- Clinical Research Center and Vecura, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - P Blomberg
- Clinical Research Center and Vecura, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - B Wahren
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
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Park MS, Park SY, Miller KR, Collins EJ, Lee HY. Accurate structure prediction of peptide-MHC complexes for identifying highly immunogenic antigens. Mol Immunol 2013; 56:81-90. [PMID: 23688437 DOI: 10.1016/j.molimm.2013.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/09/2013] [Accepted: 04/15/2013] [Indexed: 12/26/2022]
Abstract
Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide-MHC complex. Here, we present an in silico protocol for predicting peptide-MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformational changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide-MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.
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Affiliation(s)
- Min-Sun Park
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, NY 14642, USA
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