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

项目摘要/摘要 治疗人类免疫缺陷病毒(HIV)和减轻艾滋病毒/艾滋病影响的研究 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 实验感染猴免疫缺陷病毒(SIV)。诱导有效CD8的干预措施 猕猴对SIV和结核分枝杆菌(MTB)的T细胞反应正在积极发展。 门槛。这些研究受到SIV和MTB特异性CD8 T细胞反应受限的限制 由常见的猕猴主要组织相容性复合体(MHC)I类等位基因决定。 我们在之前的资助期间就开始解决这个问题，并确定了数十种新颖的CD8 SIV和MTB中的T细胞反应以及寨卡病毒、埃博拉病毒和流感中的T细胞反应。我们也意识到 传统的T细胞表位发现和表征是笨拙、缓慢和繁琐的。 因此，我们证明了MHC-I类分子与数百万个多肽的结合是可以被测量的。 为定义CD8T细胞表位提供了一种变革性的、极其快速的方法。 这项竞争性修订的目的是使用这项新技术来定义CD8T细胞表位 SIV和MTB受16个常见的猕猴MHC I类等位基因的限制。 具体来说，我们会： 目的1：鉴定16种常见猕猴MHC所限制的SIV和MTB CD8 T细胞应答 I类分子。我们将评估每个8-、9-、10和11-肽在亲 目前在Genbank和MTB Erdman株中的每个SIV和SIV基因组的基因组使用UL-1 高密度多肽阵列。MHC：将为实验中的反应生产多肽四聚体 已验证。 目的2：通过确定16个常见的MHC I类分子的多肽结合基序 CD8T细胞表位每个残基的氨基酸替换对肽的影响 有约束力的。多肽结合基序可用于改进计算机预测的算法。 MHC：多肽结合。 这项研究的研究资源将通过实时提供给研究界 共享多肽阵列数据，在免疫中沉积实验验证的CD8T细胞表位 表位数据库，以及通过NIH四聚体核心设施的MHC：多肽四聚体的分布。 此外，使用超高密度多肽阵列对CD8T细胞表位的定义是可推广的 可以彻底改变包括人类在内的所有物种中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.