Transcriptomic profiling of human peripheral blood samples collected three days or two weeks after the primary RV144 ALVAC/gp120 vaccine series

We previously showed in NHP studies that a protective gene signature that was enriched in uninfected monkeys after Ad26/gp140 vaccination also associated with higher magnitude of ADCP (Ehrenberg et al., 2019). In the RV144 human trial a number of immunological parameters were previously measured as part of the immune-correlates analysis, but not ADCP. The RV306 immunogenicity trial that employed a similar prime boost RV144 vaccine regimen with additional late boosts provided us with a unique opportunity to test if the gene signature was associated with ADCP (Pitisuttithum et al., 2020). We generated transcriptome-wide gene expression data from peripheral blood two weeks after the RV144 vaccine regimen (prior to the additional boosts) and assessed for enrichment of the gene signature with the magnitude of ADCP measured at the same timepoint in 24 participants. The gene signature with 118 enriched genes was significantly associated with higher magnitude of ADCP (NES=3.0, P<0.001). Using the same geneset, 93 genes were found to be enriched in a subset of overlapping participants (N=21), where samples were collected 3 days after the RV144 immunizations (NES=2.5, P<0.001). The RV306 vaccine trial was conducted in Thailand and all participants received the primary RV144 ALVAC/gp120 vaccine series, with additional late boosts assigned to specific groups (Pitisuttithum et al., 2020). Bulk RNA-seq was performed in 24 participants two weeks after the RV144 vaccine regimen (week 26). Additionally, RNA-seq was also performed 3 days after the same primary endpoint in a subset of the participants (N =21).

我们此前在非人灵长类（Non-human Primate, NHP）研究中证实，Ad26/gp140疫苗接种后未感染猴体内富集的保护性基因特征，同样与更高水平的抗体依赖性细胞吞噬作用（Antibody-dependent cellular phagocytosis, ADCP）强度相关（Ehrenberg等人，2019）。在RV144人体试验中，此前作为免疫相关性分析的一部分已测定了多项免疫学参数，但未涉及ADCP。采用与RV144相似的初免-加强免疫疫苗方案，并额外增设晚期加强免疫的RV306免疫原性试验，为我们验证该基因特征是否与ADCP相关提供了独特契机（Pitisuttithum等人，2020）。我们在RV144疫苗方案接种后2周（即额外加强免疫前）采集了24名受试者的外周血，生成了全转录组基因表达数据，并针对该基因特征的富集情况与同期测定的ADCP强度进行了关联分析。包含118个富集基因的该基因特征，与更高水平的ADCP强度呈显著正相关（标准化富集得分（Normalized Enrichment Score, NES）=3.0，P<0.001）。采用同一基因集，我们在21名重叠受试者亚组中发现有93个基因存在富集，该亚组的样本采集于RV144免疫接种后3天（NES=2.5，P<0.001）。RV306疫苗试验在泰国开展，所有受试者均接种了RV144的核心ALVAC/gp120疫苗系列，其中特定组别还接受了额外的晚期加强免疫（Pitisuttithum等人，2020）。本研究对24名受试者在RV144疫苗方案接种后2周（即试验第26周）开展了批量RNA测序（Bulk RNA-sequencing, Bulk RNA-seq）。此外，我们还在21名受试者亚组的同一主要终点后3天开展了RNA测序。