Sequence and vector shapes vaccine induced antibody effector functions in HIV vaccine trials

Abstract

Despite the advent of long-acting anti-retroviral therapy able to control and prevent infection, a preventative vaccine remains a global priority for the elimination of HIV. The moderately protective RV144 vaccine trial suggested functional IgG1 and IgG3 antibodies were a potential correlate of protection, but the RV144-inspired HVTN702 validation trial failed to demonstrate efficacy despite inducing targeted levels of IgG1/IgG3. Alterations in inserts, and antigens, adjuvant, and regimen also resulted in vaccine induced target quantitative levels of the immune correlates, but drove qualitative changes to the humoral immune response, pointing to the urgent need to define the influence of vaccine strategies on shaping antibody quality, not just quantity. Thus, defining how distinct prime/boost approaches tune long-lived functional antibodies represents an important goal in vaccine development. Here, we compared vaccine responses in Phase I and II studies in humans utilizing various combinations of DNA/vector, vector/vector and DNA/protein HIV vaccines. We found that adenoviral vector immunization, compared to pox-viral vectors, resulted in the most potent IgG1 and IgG3 responses, linked to highly functional antibody activity, including assisting NK cell related functions. Minimal differences were observed in the durability of the functional humoral immune response across vaccine regimens, except for antibody dependent phagocytic function, which persisted for longer periods in the DNA/rAd5 and rAd35/rAd5 regimen, likely driven by higher IgG1 levels. Collectively, these findings suggest adenoviral vectors drive superior antibody quality and durability that could inform future clinical vaccine studies. Trial registration: ClinicalTrials.gov NCT00801697, NCT00961883, NCT02207920, NCT00125970, NCT02852005).

Conflict of interest statement

I have read the journal’s policy and the authors of this manuscript have the following competing interests: Galit Alter is a founder of Seromyx Systems. All other authors declare no competing interests. Author Yevcy Donastorg was unable to confirm their authorship contributions. On their behalf, the corresponding author has reported their contributions to the best of their knowledge.

Figures

Fig 1. Subclasses/isotypes are tuned differentially across vaccine regimens.

Plasma samples were assayed with a customized Luminex assay against gp140 ConS antigen and IgG1, IgG3, IgA1 and IgA2 relative titers in mean fluorescence intensity (MFI) are depicted here. A: The violin plot shows relative antibody titers for each vaccination arm for 5 HVTN trials at the peak immunogenicity time point, lines are indicating median and quartiles. The dotted line indicates placebo levels (averaged across all trials). IgG1, IgG3, IgA1 and IgA2 were measured against gp140 ConS. B: The radar plot shows combined IgG1, IgG3, IgA1 and IgA2 data, data for each subclass were z-scored. Colors correspond to the different trials as indicated in legend. C-D: Each line plot shows IgG1 (C) and IgG3 (D) levels for each trial over time starting at baseline (B), post prime (PP), post-boost (PB) and durability (D) time point. For trial 078, PP indicates Month 1, after the first but before the second prime administration. Different trial arms are depicted in different colors, placebo is indicated in black for panel A.

Fig 2. Vaccine regimens drive distinct antibody functional profiles.

A: The violin plots depict six functional assays which were performed against a gp140 ConS antigen at peak immunogenicity (Month 6.5/7 post vaccination initiation), lines are indicating median and quartiles. The different trials and trial arms are depicted along the x-axis, each trial arm is shown in a different color, placebo levels are represented by the dotted line. B: Each line graph depicts one effector function over time for each trial arm. Time points include baseline (B), post prime (PP), post-boost (PB) and durability (D). For trial 078, PP indicates Month 1, after the first but before the second prime administration. The lines represent the median of each trial arm, with each trial arm depicted in a different color. The stacked bar graphs show the polyfunctional profile across all trial arms at peak immunogenicity (C) or the durability time point (month 12) (D), calculated as the number of functions within the group above the overall median across the whole cohort for each function. Colors indicate the polyfunctionality from light (0,1,2 functions) to dark (more polyfunctional).

Fig 3. Subclass/isotype functional coordination varies by regimen/vaccine strategy.

The heatmaps show Spearman correlations across antibody functional measurements and subclass/isotype levels for: A: 077 trials, with each heatmap depicting a different trial arm, left to right: T1, T2, T3; B: the DNA and rAd5 trial 204; C: the DNA/AIDSVAX B/E trial 105, trial arms T1 to T4; D: Trial 078 NYVAC/rAd5 (T1 and T2 arms); E: Trial 205 using DNA/MVA (T3 and T4). Red depicts high positive correlation coefficients, whereas blue displays a negative correlation, P values were Bonferroni corrected for multiple comparisons, *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001.

Fig 4. DNA and rAd5 including regimens induce distinct antibody profiles.

Multivariate analysis of antibody profiles using 69 features for each plasma sample was performed. A: An unsupervised principal component analysis (PCA) was first used and demonstrates the separation of the different vaccine trials based on their antibody profiles. Each dot represents one vaccinated individual at peak immunogenicity and the colors indicate the trial arm as depicted in the legend. Next using a supervised PLSDA, differences in antibody profiles was examined in: B: DNA containing regimens (HVTN 077 T2, T3; 105 T1, T2, T3; 204; 205 T3) versus trials which do not incorporate DNA in their vaccine regimen (HVTN 077 T1; 078; 105 T3; 205 T4)- with a model accuracy of 77.3%; C: protein containing regimens (HVTN 105 all arms) compared to non-protein containing immunizations (HVTN 077, 078, 204, 205, all arms), with a model accuracy of 75.8%; and D: DNA/rAd containing regimens (HVTN 077 T2, T3; 204) versus all other regimens (HVTN 078, 105, 205) -with a model accuracy of 90.7%. E and F show the antibody features that were differed most significantly across the vaccine groups, ranked based on their Variable in Projection Score (VIP). Features are color coded based on the vaccine group in which they were enriched. E: variables pointing to the left (dark green) are enriched in vaccines without a protein component whereas features pointing to the right are increased in protein vaccine trials (light green). F: Features that point to the left were enriched in DNA + rAd5/rAd35 trials (blue), while those ordered on the right side are enhanced in other vaccine regimen trials (pink).

Fig 5. IgG1 and Fcγ-receptor binding profiles at peak immunogenicity track with polyfunctionality and durability.

A: A Partial Least Squares Regression analysis (PLSR) shows the regression of all antibody profile features (72 features) on polyfunctionality for all the trials at peak immunogenicity. Trials are indicated by different shapes. The degree of polyfunctionality is depicted by the blue shade. B: The Loadings plot shows variables associated with polyfunctionality, loadings were scaled, and the color indicates the VIP score, VIP scores >0.7 are shown. C: The network shows the features associated with the selected variables from the Loadings plot which are drawn as rectangles, whereas co-correlated features are depicted as circles. Colors indicate the type of measurement as indicated in the legend. A Spearman correlation was performed, and only features with r>0.7 and p<0.01 after Benjamini-Hochberg correction were included. D: The PLSR plot shows the regression of all antibody features (72 features) at peak immunogenicity and ADCP levels at the durability time point (12 months). The shape depicts the trial. The shade of blue indicates the ADCP phagoscore, which was z-scored across all trial responses. E: The Loadings plot shows the only 2 critical features at peak immunogenicity associated with ADCP levels at the durability time point, colors indicate the Z-score and loadings were scaled. F: The network shows the co-correlates of peak immunogenicity predictors of ADCP durability. Squares depict the PLSR selected features and circles depict the co-correlates, while the color indicates the type of measurement. A Spearman correlation was performed to select the co-correlates, only features with r>0.7 and p<0.01 were included.