High-throughput identification of common CD8+ T cell responses to SIV and M. tuberculosis in rhesus macaques

项目概要/摘要 研究如何治愈人体免疫机能丧失病毒（艾滋病毒）和减轻艾滋病毒/艾滋病的影响 结核病合并感染是NIH的优先事项。这两个研究领域都依赖于对猕猴的研究 实验性感染猴免疫缺陷病毒（SIV）。干预措施，以获得有效的CD8 + 猕猴对SIV和结核分枝杆菌（MTb）的T细胞反应正在积极发展中， 我是说。这些研究受到缺乏SIV和MTb特异性CD8 + T细胞应答的限制。 主要组织相容性复合体（MHC）I类等位基因。 我们在上一个资助期开始解决这个问题，并确定了数十个新的CD8+细胞。 SIV和MTb以及寨卡病毒、埃博拉病毒和流感中的T细胞应答。我们也意识到 常规T细胞表位发现和表征是笨拙、缓慢和麻烦的。 因此，我们证明，MHC I类分子与数百万肽的结合可以在体外测量， multicompatibility，提供了一个变革性的和非常快速的方式来定义CD8 + T细胞表位。 这项竞争性修订的目的是使用这项新技术来定义CD8 + T细胞表位， SIV和MTb受16种常见猕猴MHC I类等位基因限制。 具体而言，我们将： 目的1：鉴定16种常见猕猴MHC限制的SIV和MTb CD8 + T细胞应答 I类分子。我们将评估前体中每个8-、9-、10和11-聚体肽的肽结合， 使用ul-PCR方法，对目前在Genbank中的每种SIV和SHIV基因组和MTb Erdman株的基因组进行了比较。 tradense肽阵列。MHC：肽四聚体将产生用于实验上 验证. 目的2：通过确定16种常见的MHC I类分子的肽结合基序， CD8 + T细胞表位中每个残基上每个氨基酸取代对肽的影响 约束力肽结合基序可用于改进用于计算机模拟预测的算法。 MHC：肽结合。 本研究的研究资源将通过实时 共享肽阵列数据，在免疫系统中沉积实验验证的CD8 + T细胞表位 表位数据库，和分布的MHC：肽四聚体通过NIH四聚体核心设施。 此外，使用超密肽阵列的CD8 + T细胞表位的定义是可推广的， 可以彻底改变所有物种，包括人类的病原体特异性表位的鉴定。

Project Summary/Abstract Research towards a cure for human immunodeficiency virus (HIV) and mitigation of the impact of HIV/ tuberculosis co-infections are NIH priorities. Both research areas rely on studies of macaque monkeys experimentally infected with simian immunodeficiency virus (SIV). Interventions to elicit effective CD8+ T cell responses to SIV and Mycobacterium tuberculosis (MTb) in macaques are under active develop- ment. These studies are limited by the dearth of SIV- and MTb-specific CD8+ T cell responses restricted by common macaque major histocompatibility complex (MHC) class I alleles. We began addressing this problem in the previous grant period and identified dozens of novel CD8+ T cell responses in SIV and MTb, as well as in Zika virus, ebolavirus, and influenza. We also realized that conventional T cell epitope discovery and characterization is unwieldy, slow, and cumbersome. Consequently, we demonstrated that MHC class I binding to millions of peptides can be measured si- multaneously, providing a transformative and extremely rapid way to define CD8+ T cell epitopes. The purpose of this competitive revision is to use this new technology to define CD8+ T cell epitopes in SIV and MTb restricted by 16 common macaque MHC class I alleles. Specifically, we will: Aim 1: Identify SIV and MTb CD8+ T cell responses restricted by 16 common macaque MHC class I molecules. We will assess peptide binding of each 8-, 9-, 10, and 11-mer peptide in the pro- teomes of every SIV and SHIV genome currently in Genbank and the MTb Erdman strain using an ul- tradense peptide array. MHC:peptide tetramers will be produced for responses that are experimentally validated. Aim 2: Define peptide binding motifs for the 16 common MHC class I molecules by determining the impact of every amino acid substitution at each residue in CD8+ T cell epitopes on peptide binding. The peptide binding motifs can be used to improve algorithms for in silico prediction of MHC:peptide binding. Research resources from this study will be made available to the research community through real-time sharing of peptide array data, deposition of experimentally validated CD8+ T cell epitopes in the Immune Epitope Database, and distribution of MHC:peptide tetramers through the NIH Tetramer Core Facility. Furthermore, the definition of CD8+ T cell epitopes using ultradense peptide arrays is generalizable and could revolutionize the identification of pathogen-specific epitopes in all species, including humans.