Analysis of HLA A*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial

Abstract

The RV144 HIV-1 vaccine trial demonstrated partial efficacy of 31% against HIV-1 infection. Studies into possible correlates of protection found that antibodies specific to the V1 and V2 (V1/V2) region of envelope correlated inversely with infection risk and that viruses isolated from trial participants contained genetic signatures of vaccine-induced pressure in the V1/V2 region. We explored the hypothesis that the genetic signatures in V1 and V2 could be partly attributed to selection by vaccine-primed T cells. We performed a T-cell-based sieve analysis of breakthrough viruses in the RV144 trial and found evidence of predicted HLA binding escape that was greater in vaccine versus placebo recipients. The predicted escape depended on class I HLA A*02- and A*11-restricted epitopes in the MN strain rgp120 vaccine immunogen. Though we hypothesized that this was indicative of postacquisition selection pressure, we also found that vaccine efficacy (VE) was greater in A*02-positive (A*02(+)) participants than in A*02(-) participants (VE = 54% versus 3%, P = 0.05). Vaccine efficacy against viruses with a lysine residue at site 169, important to antibody binding and implicated in vaccine-induced immune pressure, was also greater in A*02(+) participants (VE = 74% versus 15%, P = 0.02). Additionally, a reanalysis of vaccine-induced immune responses that focused on those that were shown to correlate with infection risk suggested that the humoral responses may have differed in A*02(+) participants. These exploratory and hypothesis-generating analyses indicate there may be an association between a class I HLA allele and vaccine efficacy, highlighting the importance of considering HLA alleles and host immune genetics in HIV vaccine trials.

Importance: The RV144 trial was the first to show efficacy against HIV-1 infection. Subsequently, much effort has been directed toward understanding the mechanisms of protection. Here, we conducted a T-cell-based sieve analysis, which compared the genetic sequences of viruses isolated from infected vaccine and placebo recipients. Though we hypothesized that the observed sieve effect indicated postacquisition T-cell selection, we also found that vaccine efficacy was greater for participants who expressed HLA A*02, an allele implicated in the sieve analysis. Though HLA alleles have been associated with disease progression and viral load in HIV-1 infection, these data are the first to suggest the association of a class I HLA allele and vaccine efficacy. While these statistical analyses do not provide mechanistic evidence of protection in RV144, they generate testable hypotheses for the HIV vaccine community and they highlight the importance of assessing the impact of host immune genetics in vaccine-induced immunity and protection. (This study has been registered at ClinicalTrials.gov under registration no. NCT00223080.).

FIG 1

CD8⁺ T-cell-associated sieve effect. (A) Twelve 9-mer peptides of MN gp120 were identified as potential vaccine epitopes (horizontal bars and boxed residues) based on their predicted binding affinities (IC₅₀) with the HLA alleles of RV144 participants. Their locations in the amino acid sequence of V1/V2 are shown relative to those in the MN strain (subtype B) and the 92TH023 strain (CRF01_AE) gp120 sequences. Three of these 9-mers were identified as peptides in which HLA “binding escapes” were predicted in at least one infected participant (boxed amino acid residues), with the restricting allele appearing below each epitope. (B) The percentage of infected participants with an allele that was predicted to bind each of the 12 potential epitopes is shown, with the epitope identified by its N-terminal starting amino acid. (C) The percentage of each treatment group that had predicted binding escapes in the three 9-mer peptides within which any escape was predicted. These epitopes are indicated at the bottom of the figure with their starting position, designation, and predicted restricting allele. (D) The two bars show the percentage of infected participants in each group whose viral isolate had 0, 1, or 2 predicted binding escapes in the V1/V2 region.

FIG 2

Greater VE in A*02⁺ participants. (A) Estimated VE in the RV144 trial for the entire cohort and also for participants with and without the HLA A*02 allele. Error bars indicate 95% confidence intervals. For each group along the x axis, significant P values are given for the hypothesis test that VE = 0. The P value shown between the A*02^+/− subgroups indicates a significant difference in VE between the two groups. (B) The percentage of infected participants whose isolated virus contained the vaccine-matched lysine at position 169 is reported as a percentage of the treatment group and/or A*02^+/− subgroup indicated along the x axis. The pair of columns on the left refer to the entire cohort, whereas the next two sets divide the cohort into A*02^+/− subgroups. (C) Estimated genotype-specific VE against K169 and X181 viruses. Estimates are reported for the whole cohort and also for A*02^+/− subgroups, as indicated on the x axis. Error bars show the 95% confidence interval for each VE estimate.

FIG 3

HLA A*02 modifies vaccine-induced immune responses and correlates of infection risk. Vaccine-induced immune responses were associated with the expression of HLA A*02. Assays were performed as part of the analysis of case-control immune correlates (15) using serum samples obtained 2 weeks after the fourth and final vaccine injection (week 26). Vaccine recipients were further divided into A*02⁺ (n = 15 infected, 97 uninfected) and A*02⁻ (n = 26 infected, 108 uninfected) subgroups for analysis. (A) Normalized intensity representative of antibody responses to the TSIRDKVQKEYALFY peptide (Env V2 positions 163 to 177 [HXB2 numbering]) in the peptide microarray assay are shown using box plots. The extent of the box indicates the interquartile range, with a line indicating the median and whiskers indicating the full range. Responses from all case-control participants were divided into high, medium, and low tertiles, with the gray box showing the medium responses. Each dot represents a single response, its color indicating whether it is in the high (black), medium (gray), or low (white) tertile. The percentages of responses in each tertile are indicated below the box plot. One outlier response in the A*02⁺-uninfected subgroup (8.07) is not plotted. (B) The IgA-C1 biotin assay was analyzed as a binary variable, with positive responders having a measurement > 0 log(MFI [median fluorescence intensity]). The percentage of positive responders in each subgroup is indicated below the box plot.