Human immunoglobulin gene allelic variation impacts germline-targeting vaccine priming

Vaccine priming immunogens that activate germline precursors for broadly neutralizing antibodies (bnAbs) have promise for development of precision vaccines against major human pathogens. In a clinical trial of the eOD-GT8 60mer germline-targeting immunogen, higher frequencies of vaccine-induced VRC01-class bnAb-precursor B cells were observed in the high dose compared to the low dose group. Through immunoglobulin heavy chain variable (IGHV) genotyping, statistical modeling, quantification of IGHV1-2 allele usage and B cell frequencies in the naive repertoire for each trial participant, and antibody affinity analyses, we found that the difference between dose groups in VRC01-class response frequency was best explained by IGHV1-2 genotype rather than dose and was most likely due to differences in IGHV1-2 B cell frequencies for different genotypes. The results demonstrate the need to define population-level immunoglobulin allelic variations when designing germline-targeting immunogens and evaluating them in clinical trials.


Supplementary Figure 2. Statistical modeling of post-vaccination VRC01-class B cell frequencies. (a)
Model rankings from QAICc (see text and Methods) are shown as best to worst, from top to bottom, for each sample type and timepoint shown left to right.For all MBC timepoints, models were ranked in the same order from best to worst: (i) Allele, (ii) Full, (iii) Dose, and (iv) Null.Each color-coded line connects the ranking of the models across time points.(b) Points and lines show estimates and 95% confidence intervals (CIs) for each model parameter, for different models labelled on the y axis, at each time point labeled at the top of the graph.Model parameters representing the per-allele contributions of *02 and *04, the contributions of dose delta (100μg -20μg) and dose=20μg, and a single estimate for the vaccine dose groups pooled (Null model) are grouped in rows *02, *04, Delta, Low and Vacc., respectively, as indicated on the right side of the panel.Parameter estimates and CIs are colorcoded by model as in panel (a) and are displayed with values on the percent scale as indicated by the x-axis.

Supplementary Figure 3 .
Correlations between pre-vaccination IgM unique HCDR3 frequency (IGHV1-2*02 or *04) and the percent VRC01-class B cell response by visit and treatment group.Points are shape-and color-coded as shown in the legend.Spearman correlation coefficient (r) and P-values are displayed for each time point and dose group.
IGHV genes in each of the 48 IAVI G001 trial participants.The x-axis shows the G001 trial participant cases, and the y-axis shows the IGHV genes in the order they are found in typical IgM repertoires, with the most utilized genes at the top and the least utilized genes at the bottom.Captured (dark blue) and not captured (light blue) genes are indicated for each case.

Table 2 :
Frequency of IGHV1-2 mRNA expression in the naive repertoire.The number of trial participants (n), mean, 95% confidence interval (95% CI), minimum (Min) and maximum (Max) are reported for groups defined by homozygous or heterozygous genotypes including each allele.For participants homozygous for an allele, the per-allele frequency is defined as half the measured frequency of that allele.For * 02/ * 02_S4953 participants, the per-allele usage frequency is defined as half of the sum of the * 02 and * 02_S4953 frequencies and the participant is classified as a * 02 homozygote.
*06 Heterozygote 10 2.43% 1.87% to 2.99% 1.78% 4.18% SupplementaryTable 3: Estimated difference in the mean per-allele frequency of IGHV1-2 mRNA expression between participants homozygotes and heterozygotes for each allele.For participants homozygous for an allele, the per-allele frequency is defined as half the measured frequency of that allele.The 95% confidence interval and P-value are based on a T-test for the null hypothesis that the true difference (mean among homozygous minus mean among heterzygous) is 0%.

Table 4 :
Percent of IgG B cells detected as VRC01-class testing between genotype groups among detectable response participants.Comparisons with at least 2 samples per group are included and P-values displayed for comparisons with at least 3 samples per group.Testing was done using the Wilcoxon rank-sum test.Median, minimum, and maximum values are presented by treatment group and time point.Unadjusted and FDR adjusted P-values displayed.

Table 5 :
Percent of IgG B cells detected as VRC01-class testing between treatment groups among detectable response participants.Comparisons with at least 2 samples per group are included and P-values displayed for comparisons with at least 3 samples per group.Testing was done using the Wilcoxon rank-sum test (two-sided, α = 0.05) and P-values less than 0.05 are highlighted.Median, minimum, and maximum values are presented by treatment group and time point.Unadjusted and FDR adjusted P-values displayed.

Table 6 :
Quasi-likelihood version of Akaike's second-order information criterion (QAICc) results.At each sample time point, the four models (Null, Dose, Allele, and Full) are ranked best-toworst (lower QAICc is better).Each row gives the number of samples analyzed (n), the number of model parameters (K), the log-likelihood (LL) from a Poisson model fit, and the dispersion (Dispersion) from a quasi-Poisson model fit.The QAICc is computed based on these values (see Methods).