Epitopes recognized by HIV-SF2 nef-specific CD4+ T-cell clones generated from HIV-1-uninfected donors

Scanning the HIV genome for CD4+ T cell epitopes restricted to HLA-DP4, the most prevalent HLA class II molecule

HLA-DP4 alleles are carried by 75% of individuals and are the most frequent HLA II alleles worldwide. Because we have recently characterized the peptide-binding specificity of HLA-DP4 molecules, we developed a peptide-binding prediction method to identify HLA-DP4-restricted peptides in multiple Ags. CD4(+) T cell response plays a key role in the immune control of HIV infection, but few HIV-specific T cell epitopes with multi-individual specificity have been identified. They are mostly restricted to HLA-DR molecules, which are very polymorphic molecules. We therefore looked for HLA-DP4-restricted CD4(+) T cell epitopes in the whole genome of HIV. Twenty-one peptides were selected from the HXB2 HIV genome based on the prediction of binding to HLA-DP4 molecules. They were submitted to HLA-DP4-binding assays. Seventeen peptides bound to the HLA-DP401 molecule, whereas 15 peptides bound to HLA-DP402. Six peptides bound very tightly to HLA-DP401 and were investigated for their capacity to induce specific CD4(+) T cell lines in vitro using dendritic cells and CD4(+) T cells collected from eight seronegative HLA-DP4(+) donors. Four peptides from env and reverse transcriptase proteins induced in vitro-specific T cell lines restricted to HLA-DP4 molecules. Peptide-induced T cells recognized variants other than the HXB2 sequence and were stimulated by native Ags processed by immature dendritic cells. The reverse transcriptase peptide is present in 65% of the isolated HIV variants. To our knowledge, we describe the first HIV epitopes restricted to HLA-DP4 molecules.

Statistical comparison of established T-cell epitope predictors against a large database of human and murine antigens

Identification of T-cell epitopes within a protein antigen is an important tool in vaccine design. The T-cell epitope prediction schemes often are exploited by workers but have proved unreliable in comparison with experimental techniques. We compared published T-cell epitope predictors against two databases of human and murine T-cell epitopes. Each predictor was assessed against random cyclic permutations of epitopes in order to determine significance. Predictor performance was expressed in terms of two parameters, specificity and sensitivity. Specificity is an expression of the quality of predictions, whereas sensitivity is an expression of the quantity of epitopes predicted. Against the human data set, the strip-of-hydrophobic helix algorithm [Stille et al., Molec. Immun. 24, 1021-1027 (1987)] was the only significant predictor (p < 0.05), whereas against murine data only, the Roth2 pattern [Rothbard and Taylor, EMBO J. 7, 93-100 (1988)] was significant (p < 0.05). Not only were the majority of algorithms no better than random against both data sets, against the murine data two schemes were significant (p < 0.05) anti-predictors. This report indicates which predictors are relevant statistically and is the first to describe anti-predictors which can themselves be useful in the identification of T-cell epitopes.

Characterization of human CD4+, HIV-SF2 Nef-specific T-cell clones for antigen-processing and presentation requirements and for cytotoxic activity

We have described previously the generation of seven HIV-SF2 Nef-specific, CD4+ T-cell clones, identification of epitopes within which are recognized by these clones, and the MHC alleles that restrict their responses. In this study, we have extended this characterization to include evaluation of antigen-processing and presentation requirements and cytotoxic activity. Clones were generated from five HIV-1 uninfected donors by in vitro stimulation of peripheral blood mononuclear cells with purified recombinant Nef1. In experiments with fixed cells, with the exception of two clones, recognition of Nef, but not Nef peptides, required processing. Also, at higher concentrations of antigen, the clones themselves were capable of presenting Nef peptides, but not soluble Nef. All clones had the ability to specifically lyse autologous, Epstein-Barr virus-transformed lines sensitized with Nef synthetic peptides, or, in some cases, soluble Nef. The cytotoxic activity mapped to the same epitopes identified for the proliferative response (a.a. 14-22, 47-53, 68-77, 70-77, 195-203 and 185-192) and was restricted by the same HLA class II molecules (DRw6, DQw7, DRw15(2), DR1 and DP5). Sensitization of the cytolytic clones with specific Nef peptides, but not soluble Nef, resulted in autolysis.