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Designing and Assessing HIV Vaccines for Cross-Clade Immunogenicity Using Bio-Informatics A. S. DE GROOT1‚3, M. GONZALEZ1, J. FROST1, A. BOSMA1, J. R. SCHAFER1, G. SKOWRON3, and W. MARTIN2.
1Brown Univ., 2EpiVax, Inc., and 3Roger Williams Hosp., Providence, RI We used a bioinformatics approach to identify broadly conserved (across clades) HIV-1 peptides that are likely to be processed and presented to T cells. These epitopes may be useful for the design of novel cross-clade vaccines, for improving existing vaccines, or for assessing cross-clade immunogenicity of vaccines that are currently in Phase I-III trials.
Method: The Los Alamos National Laboratory HIV sequence database was scanned for highly conserved, putatively immunogenic HIV-1 peptides (derived from all HIV-1 proteins) using Conservatrix™ and EpiMatrix™. 10-mer peptides representing sequences conserved in more than 50 strains of HIV-1 (average >500) were selected for further study. Binding and stabilization of 72 peptides on the surface of allele-specific TAP deficient cells (T2 cells) was measured by FACS. ELISPOT assays were performed using PBMC from HIV-1 patients recruited in Providence, RI.
Results: 15 of 24 A2 peptides (62%), 18 of 24 A11 peptides (75%), and 18 of 24 B7 (75%) peptides bound to MHC as measured by increased T2 surface fluorescence (p<0.05) in replicate assays. Control peptides (published epitopes for A2, A11, B7) also bound. Measurement of gamma-interferon release (by ELISPOT) in response to target cells pulsed with the peptides was performed using PBMC derived from two HIV-infected patients. Three A2 peptides and several (2-10) of the 24 A11 peptides stimulated gamma IFN release from PBMC from these two patients. These novel HIV-1 T epitopes are conserved in as many as 1238 HIV-1 strains, including strains from Africa, Asia, and the Americas.
Interpretation: Conservatrix and EpiMatrix provide a rapid and accurate means of MHC ligand/epitope selection. Thus far we’ve identified several novel, highly conserved HIV-1 ligands and epitopes from the sequences of HIV-1. Additional CTL assays and CD4 depletion studies are required to confirm the MHC Class I-restriction of these epitopes.
Key Words: clade, CTL, vaccine
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