Mapping cross-clade HIV-1 vaccine epitopes using a bioinformatics approach.
The genomic variability of HIV viruses circulating in different regions of the world has impeded the development of a globally relevant HIV vaccine. Broadly conserved HIV-1 cytotoxic T cell (CTL) epitopes were identified by screening protein sequences in the Los Alamos National Laboratory (LANL) HIV sequence database with a sequence parsing and matching algorithm (Conservatrix). Putative HIV-1 CTL epitopes were selected from this list using the epitope prediction tool EpiMatrix.


METHODS
One hundred peptides representing putative HLA A*0201, HLA A*1101, HLA A*0301, and HLA B*07 ligands conserved in many isolates of HIV-1 were synthesized. Seventy-five HLA A*0201, HLA A*1101 and HLA B*07 peptides were incubated with transport associated protein (TAP)-deficient T2 cells transfected with the gene for the corresponding human HLA molecule (HLA A*0201, HLA A*1101, and HLA B*07). Binding and stabilization of peptide-HLA complexes on the surface of the T2 cells was measured by FACS. T cell responses to the entire set of 100 peptides (HLA A*0201, HLA A*1101, HLA A*0301, and HLA B*07) were measured in ELIspot assays using PBMC from healthy HIV-1 infected subjects who possessed a matching HLA allele.


RESULTS
Fifty-seven (76%) of the 75 peptides tested in binding studies, including all (three of three) of the control (published) ligands bound to the T2 cells expressing the corresponding MHC molecule. Forty-three of the 100 peptides (43%) including all (four of four) of the control (published) epitopes tested in ELIspot assays stimulated gamma-interferon release. Thirty-one of these 43 epitopes are novel, highly conserved HIV-1 epitopes. EpiMatrix predicted and assays confirmed MHC-restriction by more than one HLA allele for nine of the 43 novel epitopes; of these epitopes five were recognized in the context of MHC "supertypes" and four were promiscuous epitopes.


CONCLUSIONS
Epitopes identified using this approach were conserved in a broad range of HIV-1 sequences derived from isolates obtained in Latin America, Africa, Asia, the Pacific Islands, Europe and the US. The successful identification of cross-clade epitopes by this bioinformatics approach may accelerate the development of a globally relevant HIV-1 vaccine.
D016915:AIDS Vaccines / Q000737:chemistry / Q000276:immunology*; D000483:Alleles; D019295:Computational Biology; D004797:Enzyme-Linked Immunosorbent Assay; D018604:Epitope Mapping; D000939:Epitopes / Q000737:chemistry / Q000276:immunology*; D005805:Genes, MHC Class I / Q000235:genetics / Q000276:immunology; D015497:HIV-1 / Q000737:chemistry / Q000276:immunology*; D015234:HLA-A Antigens / Q000276:immunology; D015235:HLA-B Antigens / Q000276:immunology; D015236:HLA-C Antigens / Q000276:immunology; D006650:Histocompatibility Testing; D006801:Humans; D011485:Protein Binding; D013601:T-Lymphocytes / Q000276:immunology; D022223:Vaccines, Subunit / Q000138:chemical synthesis / Q000276:immunology
D016915:AIDS Vaccines; D000939:Epitopes; D015234:HLA-A Antigens; D015235:HLA-B Antigens; D015236:HLA-C Antigens; D022223:Vaccines, Subunit