Background
HIV evolution is driven by immunogenetic factors, particularly HLA alleles. Our group previously demonstrated that HLA-B*39:02, a prevalent allele in Amerindian populations, has been associated with better HIV outcomes in Mexico and selected polymorphisms within p24-Gag; however, the HIV-specific responses restricted by this allele remain undefined. In this study, we characterized an HLA-B*39:02–restricted p24 epitope that induces strong immune responses. Furthermore, competitive peptide assays revealed that polymorphisms selected by HLA-B39:02 alter peptide binding affinity to the HLA molecule.
Methods
We recruited a cohort of 14 men living with HIV expressing HLA-B39:02. CTL responses were assessed by IFN-γ ELISpot using 9-mer overlapping p24 peptides containing previously described HLA-B39:02–selected polymorphisms (315N and 319E). Binding affinity was evaluated through peptide competition assays with substitutions at positions 315 (R, T, G) and 319 (D) using fluorescein-labeled peptides and flow cytometry. Data was analyzed with DFR test to define positive responses and Mann-Whitney tests to compare IC50 values among peptides.
Results
The p24 VKNWMTETL (VL9) peptide was immunodominant, eliciting strong IFN-γ CTL responses (median of 574 SFU/million PBMCs) and harboring the 315N and 319E polymorphisms associated with HLA-B*39:02. Substitutions at position 315 showed different binding affinities for this molecule: N315T maintained structural stability within the HLA binding pocket, whereas N315R exhibited lower affinity for the HLA-B*39:02 molecule compared with N315T (IC50 406.2 nM vs. 204.0 nM; p = 0.0019). The E319D substitution appeared to have no effect on HLA-B*39:02 binding affinity compared with the wild-type peptide (IC50 237.9 nM vs. 204.0 nM; ns). All affinities were further confirmed through molecular modeling of HLA-B*39:02 with each peptide, showing that the N315G substitution was the least favorable, suggesting this substitution abolished the interaction with this molecule.
Conclusions
HLA-B39:02 molecule, common in Mexico but rare worldwide, is associated with better HIV outcomes in people living with HIV and selects polymorphisms within p24-Gag. We identified the first HIV peptide presented by this allele, the VKNWMTETL (VL9, p24) epitope, which elicited strong CTL responses. Variations within this peptide altered HLA-B39:02 binding affinity. These findings support VKNWMTETL as a potential candidate for vaccine or immunotherapy strategies in Amerindian populations.