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

项目摘要 严重急性呼吸综合征冠状病毒2型(SARS-CoV-2)是引起全球 冠状病毒病2019年(新冠肺炎)大流行。阐明获得性免疫的潜在机制 对SARS-CoV-2的反应对于预测疫苗疗效和评估再次感染的风险至关重要。 针对SARS-CoV-2的中和抗体已经被广泛研究，并明显具有保护性，但可能 是短暂的，并不是所有受感染的人都会被感染。越来越多的证据表明，T细胞发挥着至关重要的作用 在清除SARS-CoV-2病毒和形成对该病毒的长期记忆反应方面发挥作用。广泛性 新冠肺炎恢复期患者(CP)的中和抗体结构信息现已公布 与SARS-CoV-2尖峰三聚体或RBD结合(&gt；330个PDB条目)，从而全面了解 B细胞对这种病毒的反应。相比之下，针对SARS-CoV-2的结构信息很少。 TCR与其多肽-MHC(PMHC)靶标结合(4个PDB条目)，尽管其作用越来越受到重视 T细胞免疫在抗击新冠肺炎中的作用。我们的目标是解决这一未得到满足的主要需求，方法是 新冠肺炎中心MHC I类限制性TCR识别SARS-CoV-2的原子级信息。我们 将专注于CD8T细胞表位，因为细胞毒性CD8T细胞直接参与病毒清除。我们的 具体目标是： 目的1：确定TCR-pMHC络合物的晶体结构。我们的目标是X光 结晶学分析导致新冠肺炎CP中高水平TCR扩张的表位的特异性TCR， 以及与保护相关的TCR。为了证明可行性，我们已经确定了结构 新冠肺炎CPS一个公共和一个私人TCR与人类白细胞抗原-A2和两个SARS-CoV-2尖峰病毒复合体(S) 表位、YLQ和RLQ。我们将把这些研究扩展到另外三个S表位(fvf、fqf、rln)和三个 核衣壳(N)表位(LLL、LQL、SPR)，可引起强烈的T细胞反应，由人类白细胞抗原A2呈递 或人类白细胞抗原-B7单核细胞。我们有针对这些CD8 T细胞表位的不同的TCR面板。 目的2：分析TCR-pMHC的结构。目标1中确定的TCR-pMHC复杂结构将 使用先进的计算结构生物学工具进行分析，以描绘其识别的关键特征， 以及预测的SARS-CoV-2和相关冠状病毒表位变体的靶标。 这些研究将产生关于SARS-CoV-2表位的TCR识别的基础知识，关于 表位特异性TCR谱系中克隆多样性的产生及其突变方式 表位可能使病毒逃脱免疫监视。

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.