Systems biological assessment of T cell responses to vaccination

摘要-项目2 项目2的目标是在以下拟议研究的背景下评估T细胞应答：（i）COVID-19 利用新平台（mRNA）或佐剂（Novavax疫苗中使用的Matrix M）的疫苗，和（ii） 在狂犬病疫苗接种之前和期间，给予人类广谱抗生素，破坏他们的微生物组。 这一目标与项目1和3的目标高度协同，项目1和3将评估先天和B细胞反应 在相同的临床试验中，我们将使用最先进的技术 这将使我们能够以前所未有的规模和深度探索疫苗反应。三 方法是：（1）用于特异性T细胞的球聚体探针，（2）GLIPH（用于检测淋巴细胞相互作用， TCR特异性组的互补位热点（Paratope Hotspots）分析，和（3）免疫类器官。我们将这些工具应用于 以下目标： 目的1：评估T细胞对COVID-19疫苗接种的应答。 次级目标1a。分析BNT 162 b2 mRNA疫苗在健康与特应性 个体我们将使用上面提到的球形聚合物技术，来创建和使用一组pMHC， 球形体SARS-CoV-2刺突表位覆盖主要的I类和II类HLA等位基因，以分析T细胞 反应，在健康与特应性受试者。此外，我们将使用GLIPH 2进行TCR库分析。 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细胞对初次和二次疫苗接种应答的TCR多样性及免疫应答的变化 健康成人和过敏倾向受试者的引流淋巴结。 子目标1b：评估Novavax Matrix-M佐剂亚单位疫苗诱导的T细胞应答。 我们还将分析从威特沃特斯兰德大学Novavax赞助的试验中收集的样本 球聚体和TCR序列分析，并确定如何响应佐剂亚基 疫苗与mRNA疫苗诱导的疫苗不同 目的2：评估微生物群对抗原特异性T细胞应答的影响。 预防针我们将评估广谱抗生素对狂犬病初级T细胞反应的影响 预防针特别是，我们将分析TCR库和T细胞的表型， 疫苗，因为有明确的迹象表明，微生物组可以影响T细胞表型，我们 假设这也可能对剧目产生影响。

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.