Systems biological assessment of T cell responses to vaccination

摘要-项目2 项目2的目标是在拟议的以下研究的背景下评估T细胞反应：(I)新冠肺炎 使用新平台(信使核糖核酸)或佐剂(Novavax疫苗中使用的基质M)的疫苗和(Ii) 在接种狂犬病疫苗之前和接种期间，人类服用了广谱抗生素，扰乱了他们的微生物群。 这个目标与项目1和项目3的目标高度协同，项目1和项目3将评估先天和B细胞的反应 分别在相同的临床试验的背景下。我们将使用新开发的最先进的技术 这将使我们能够在这里以前所未有的规模和深度探索疫苗反应。三位一体 方法是：(1)针对特定T细胞的球形探针，(2)Gliph(通过以下方式对淋巴细胞相互作用进行分组 副表位热点)分析TCR特异性组，以及(3)免疫器官类。我们将把这些工具应用于 目标如下： 目的1：评估接种新冠肺炎疫苗后的T细胞反应。 次级目标1a。分析BNT162b2基因疫苗在健康人群和特应性人群中诱导的T细胞应答 个人。我们将使用上面提到的球体技术来创建和使用pMHC面板 免疫球蛋白SARS-CoV-2尖峰表位覆盖主要的I、II类等位基因分析T细胞 反应，在健康受试者和特应性受试者中。此外，我们还将使用GLIPH2执行TCR曲目分析 分析大量和单细胞TCR序列，以确定频率、表型、功能和 血液中抗原特异性T细胞对初免和复种免疫应答的TCR多样性 健康成人和易过敏受试者的淋巴引流。 分目标1b：评估Novavax Matrix-M佐剂亚单位疫苗诱导的T细胞反应。 我们还将分析从威特沃特斯兰德大学进行的Novavax赞助的试验中收集的样本 用球体和TCR序列分析并确定对佐剂亚基的反应 疫苗不同于基因疫苗 目的2：评估微生物区系对抗原特异性T细胞应答的影响 接种疫苗。我们将评估广谱抗生素对狂犬病初级T细胞反应的影响 接种疫苗。特别是，我们将分析对此做出反应的T细胞的TCR谱系和表型 疫苗，因为有明确的迹象表明微生物群可以影响T细胞表型，而且我们 假设这可能也会对曲目产生影响。

ABSTRACT – Project 2 The goal of Project 2 is to assess T cell responses in the context of proposed studies of: (i) COVID-19 vaccines that utilize novel platforms (mRNA) or adjuvants (Matrix M used in the Novavax vaccine) and (ii) Humans given broad spectrum antibiotics that disrupt their microbiome, prior to and during rabies vaccination. This goal is highly synergistic with those of Projects 1 and 3, which will evaluate innate and B cell responses respectively, in the context of the same clinical trials. We will use new developed state-of-the-art techniques that will allow us to probe the vaccine responses here with an unprecedented scale and depth. The three methods are: (1) spheromer probes for specific T cells, (2) GLIPH (for Grouping of Lymphocyte Interactions by Paratope Hotspots) analysis of TCR specificity groups, and (3) immune organoids. We will apply these tools in the following aims: Aim 1: Assessment of T cell responses to vaccination against COVID-19. Sub-aim 1a. Analyze T cell responses induced by the BNT162b2 mRNA vaccine in healthy versus atopic individuals. We will use the spheromer technology mentioned above, to create and use a panel of pMHC Spheromers SARS-CoV-2 spike epitopes covering the major class I and II HLA alleles, to analyze the T cell response, in healthy versus atopic subjects. In addition, we will perform TCR repertoire analysis using GLIPH2 to analyze both bulk and single cell TCR sequences in order to define the frequency, phenotype, function and TCR diversity of antigen specific T cell responses to primary and secondary vaccination in blood and the draining lymph nodes of both healthy adults and allergy prone subjects. Sub-aim 1b: Assessment of T cell responses induced by the Novavax Matrix-M adjuvanted subunit vaccine. We will also analyze samples collected from a Novavax sponsored trial done at the University of Witwatersrand with spheromers and TCR sequence analysis and determine how the response to an adjuvanted subunit vaccine differs from that induced by mRNA vaccination Aim 2: Assessment of the impact of the microbiota on the antigen-specific T cell response to vaccination. We will assess the impact of broad-spectrum antibiotics on the primary T cell response to rabies vaccination. In particular, we will analyze the TCR repertoire and phenotype of T cells responding to this vaccine, since there are clear indications that the microbiome can influence T cell phenotype, and we hypothesize that there might be an influence on the repertoire as well.