Structural Basis for T Cell Recognition of SARS-CoV-2

项目摘要 严重急性呼吸道综合征冠状病毒2（SARS-CoV-2）是导致全球 2019冠状病毒病（COVID-19）大流行。阐明适应性免疫的机制 对SARS-CoV-2的反应对于预测疫苗效力和评估再感染风险至关重要。 针对SARS-CoV-2的中和抗体已被广泛研究，并且显然具有保护作用，但可能 是短暂的，并不是在所有受感染的个体中引起的。越来越多的证据表明，T细胞在免疫系统中起着至关重要的作用。 在清除SARS-CoV-2和形成对这种病毒的长期记忆反应中发挥作用。广泛 现在可以获得COVID-19康复期患者（CP）中和抗体的结构信息 结合到SARS-CoV-2刺突三聚体或RBD（> 330 PDB条目），从而全面了解 B细胞对这种病毒的反应。相比之下，SARS-CoV-2特异性的结构信息非常少。 TCR与其肽-MHC（pMHC）靶标结合（4个PDB条目），尽管TCR的作用越来越受到重视， T细胞介导的免疫力对抗COVID-19。我们的目标是通过以下方式解决这一主要未满足的需求： 来自COVID-19 CP的MHC I类限制性TCR识别SARS-CoV-2的原子级信息。我们 将集中在CD8 + T细胞表位，因为细胞毒性CD8 + T细胞直接参与病毒清除。我们 具体目标是： 目的1：确定TCR-pMHC复合物的晶体结构。我们会用X光 晶体学分析对COVID-19 CP中引起高水平TCR扩增的表位特异的TCR， 以及与保护相关的TCR。为了证明可行性，我们已经确定了 来自与HLA-A2复合的COVID-19 CP的公共和私人TCR和两个SARS-CoV-2峰值（S） 表位，YLQ和RLQ。我们将这些研究扩展到三个额外的S表位（FVF，BVF，RLN）和三个 核衣壳（N）表位（LLL、LQL、SPR），其引起强烈的T细胞应答，并由HLA-A2呈递 或HLA-B7 MHC。我们具有靶向这些CD8 + T细胞表位中的每一个的不同TCR组。 目的2：分析TCR-pMHC的结构。目标1中确定的TCR-pMHC复合物结构将 使用先进的计算结构生物学工具进行分析，以描述其识别的关键特征， 以及来自SARS-CoV-2和相关冠状病毒的表位变体的预测靶向。 这些研究将产生关于TCR识别SARS-CoV-2表位的基础知识， 表位特异性TCR库中克隆多样性的产生，以及这些TCR库中突变的方式， 表位可能使病毒逃避免疫监视。

Project Summary Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the global coronavirus disease 2019 (COVID-19) pandemic. Elucidating the mechanisms underlying the adaptive immune response to SARS-CoV-2 is crucial for predicting vaccine efficacy and assessing the risk of reinfection. Neutralizing antibodies against SARS-CoV-2 have been studied extensively and are clearly protective, but may be short-lived and are not elicited in all infected individuals. Mounting evidence indicates that T cells play a vital role in the clearance of SARS-CoV-2 and in formation of long-term memory responses to this virus. Extensive structural information is now available on neutralizing antibodies from COVID-19 convalescent patients (CPs) bound to the SARS-CoV-2 spike trimer or RBD (>330 PDB entries), resulting in a comprehensive picture of the B cell response to this virus. By contrast, very little structural information is available for SARS-CoV-2-specific TCRs bound to their peptide–MHC (pMHC) targets (4 PDB entries), despite the increasingly appreciated role of T cell-mediated immunity in combatting COVID-19. Our goal is to address this major unmet need by obtaining atomic-level information on SARS-CoV-2 recognition by MHC class I-restricted TCRs from COVID-19 CPs. We will focus on CD8+ T cell epitopes because cytotoxic CD8+ T cells participate directly in viral clearance. Our Specific Aims are: Aim 1: Determine crystal structures of TCR–pMHC complexes. We will target for X-ray crystallographic analysis TCRs specific for epitopes that elicit high levels of TCR expansion in COVID-19 CPs, as well as TCRs associated with protection. To demonstrate feasibility, we have already determined structures of a public and a private TCR from COVID-19 CPs in complex with HLA-A2 and two SARS-CoV-2 spike (S) epitopes, YLQ and RLQ. We will extend these studies to three additional S epitopes (FVF, FQF, RLN) and three nucleocapsid (N) epitopes (LLL, LQL, SPR), which elicit strong T cell responses, and are presented by HLA-A2 or HLA-B7 MHCs. We have diverse panels of TCRs targeting each of these CD8+ T cell epitopes. Aim 2: Analysis of TCR–pMHC structures. TCR–pMHC complex structures determined in Aim 1 will be analyzed using advanced computational structural biology tools to delineate key features of their recognition, as well as the predicted targeting of epitope variants from SARS-CoV-2 and related coronaviruses. These studies will yield foundational knowledge about TCR recognition of SARS-CoV-2 epitopes, about the generation of clonal diversity in epitope-specific TCR repertoires, and about the ways mutations in these epitopes may enable the virus to escape immune surveillance.