PDF(Pubmed)
Abstract：
UNASSIGNED: The HVTN 105 vaccine clinical trial tested four combinations of two immunogens - the DNA vaccine DNA-HIV-PT123, and the protein vaccine AIDSVAX B/E. All combinations induced substantial antibody and CD4+ T cell responses in many participants. We have now re-examined the intracellular cytokine staining flow cytometry data using the high-resolution SWIFT clustering algorithm, which is very effective for enumerating rare populations such as antigen-responsive T cells, and also determined correlations between the antibody and T cell responses.
UNASSIGNED: Flow cytometry samples across all the analysis batches were registered using the swiftReg registration tool, which reduces batch variation without compromising biological variation. Registered data were clustered using the SWIFT algorithm, and cluster template competition was used to identify clusters of antigen-responsive T cells and to separate these from constitutive cytokine producing cell clusters.
UNASSIGNED: Registration strongly reduced batch variation among batches analyzed across several months. This in-depth clustering analysis identified a greater proportion of responders than the original analysis. A subset of antigen-responsive clusters producing IL-21 was identified. The cytokine patterns in each vaccine group were related to the type of vaccine - protein antigens tended to induce more cells producing IL-2 but not IFN-γ, whereas DNA vaccines tended to induce more IL-2+ IFN-γ+ CD4 T cells. Several significant correlations were identified between specific antibody responses and antigen-responsive T cell clusters. The best correlations were not necessarily observed with the strongest antibody or T cell responses.
UNASSIGNED: In the complex HVTN105 dataset, alternative analysis methods increased sensitivity of the detection of antigen-specific T cells; increased the number of identified vaccine responders; identified a small IL-21-producing T cell population; and demonstrated significant correlations between specific T cell populations and serum antibody responses. Multiple analysis strategies may be valuable for extracting the most information from large, complex studies.
UNASSIGNED: Flow cytometry samples across all the analysis batches were registered using the swiftReg registration tool, which reduces batch variation without compromising biological variation. Registered data were clustered using the SWIFT algorithm, and cluster template competition was used to identify clusters of antigen-responsive T cells and to separate these from constitutive cytokine producing cell clusters.
UNASSIGNED: Registration strongly reduced batch variation among batches analyzed across several months. This in-depth clustering analysis identified a greater proportion of responders than the original analysis. A subset of antigen-responsive clusters producing IL-21 was identified. The cytokine patterns in each vaccine group were related to the type of vaccine - protein antigens tended to induce more cells producing IL-2 but not IFN-γ, whereas DNA vaccines tended to induce more IL-2+ IFN-γ+ CD4 T cells. Several significant correlations were identified between specific antibody responses and antigen-responsive T cell clusters. The best correlations were not necessarily observed with the strongest antibody or T cell responses.
UNASSIGNED: In the complex HVTN105 dataset, alternative analysis methods increased sensitivity of the detection of antigen-specific T cells; increased the number of identified vaccine responders; identified a small IL-21-producing T cell population; and demonstrated significant correlations between specific T cell populations and serum antibody responses. Multiple analysis strategies may be valuable for extracting the most information from large, complex studies.
摘要：
■HVTN105疫苗临床试验测试了两种免疫原的四种组合-DNA疫苗DNA-HIV-PT123和蛋白质疫苗AIDSVAXB/E。所有组合在许多参与者中诱导大量抗体和CD4+T细胞应答。我们现在使用高分辨率SWIFT聚类算法重新检查了细胞内细胞因子染色流式细胞仪数据，这是非常有效的计数罕见的群体，如抗原反应性T细胞，并且还确定了抗体和T细胞应答之间的相关性。
■使用swiftReg注册工具对所有分析批次的流式细胞仪样本进行注册，在不损害生物变异的情况下减少批次变异。使用SWIFT算法对注册数据进行聚类，和簇模板竞争用于鉴定抗原反应性T细胞簇，并将其与组成型细胞因子产生细胞簇分离。
■注册大大减少了在几个月内分析的批次之间的批次差异。这种深入的聚类分析比原始分析确定了更大比例的响应者。鉴定了产生IL-21的抗原应答簇的子集。每个疫苗组中的细胞因子模式与疫苗的类型有关-蛋白质抗原倾向于诱导更多的细胞产生IL-2而不是IFN-γ，而DNA疫苗倾向于诱导更多的IL-2+IFN-γ+CD4T细胞。在特异性抗体应答和抗原应答性T细胞簇之间鉴定了几个显著的相关性。不一定与最强的抗体或T细胞应答观察到最好的相关性。
■在复杂的HVTN105数据集中，替代分析方法提高了抗原特异性T细胞检测的灵敏度;增加了已鉴定的疫苗应答者的数量;鉴定了少量产生IL-21的T细胞群;并证明了特定T细胞群与血清抗体应答之间的显着相关性。多重分析策略对于从大量信息中提取最多信息可能是有价值的，复杂的研究。
■使用swiftReg注册工具对所有分析批次的流式细胞仪样本进行注册，在不损害生物变异的情况下减少批次变异。使用SWIFT算法对注册数据进行聚类，和簇模板竞争用于鉴定抗原反应性T细胞簇，并将其与组成型细胞因子产生细胞簇分离。
■注册大大减少了在几个月内分析的批次之间的批次差异。这种深入的聚类分析比原始分析确定了更大比例的响应者。鉴定了产生IL-21的抗原应答簇的子集。每个疫苗组中的细胞因子模式与疫苗的类型有关-蛋白质抗原倾向于诱导更多的细胞产生IL-2而不是IFN-γ，而DNA疫苗倾向于诱导更多的IL-2+IFN-γ+CD4T细胞。在特异性抗体应答和抗原应答性T细胞簇之间鉴定了几个显著的相关性。不一定与最强的抗体或T细胞应答观察到最好的相关性。
■在复杂的HVTN105数据集中，替代分析方法提高了抗原特异性T细胞检测的灵敏度;增加了已鉴定的疫苗应答者的数量;鉴定了少量产生IL-21的T细胞群;并证明了特定T细胞群与血清抗体应答之间的显着相关性。多重分析策略对于从大量信息中提取最多信息可能是有价值的，复杂的研究。
