Core D: Antigen Receptor Identification and Tracking Core

项目摘要 U19的总体目标是通过研究PD-1通路在人类免疫中的作用， 治疗性PD-1阻断对慢性病毒免疫应答的影响（项目1）和预防性PD-1阻断对慢性病毒免疫应答的影响（项目1） 疫苗（项目2）。为了监测患者的适应性免疫反应，我们需要跟踪 T和B细胞的库，因为克隆型可能随着时间的推移和对感染的反应而表现不同， 疗法虽然有几种方法用于追踪抗原特异性淋巴细胞，但大量的血液是不可能的。 由于需要监测多种抗原，活组织检查的标准管道和克隆型材料有限， 与不同的抗原受体没有区别。TCR和BCR的标准批量测序可提供 定量克隆型频率;然而，它的效用是有限的，因为靶抗原是未知的， 不能确定每个TCR/BCR和每个克隆型的激活状态。核心D提供了 追踪患者血液和组织中抗原特异性T和B细胞的创新服务， 和2以定量淋巴细胞的频率、抗原特异性和活化状态。目标1提供了一个 通过对患者T和B细胞中的抗原受体进行测序来使TCR和BCR与抗原匹配的方法 用病毒或疫苗抗原刺激或标记。Aim 2使用更具成本效益的批量TCR-和BCR-seq 量化抗PD-1治疗患者系列样本中克隆型的频率，但需要 Aim 1中结果的优点是将来自库的抗原受体与特异性病毒或疫苗连接 抗原Aim 3使用前沿的基于液滴的RNA-seq对成对的抗原受体链（TCRα）进行测序 & β; IgH & IgK/L）沿着单个淋巴细胞中数千种mRNA，将功能途径与 抗原受体从这三个目标得到的数据集将被整合，以提供频率， T和B细胞的抗原特异性和活化状态，使我们能够测试抗PD-1的假设， 治疗不同地影响每个淋巴细胞亚群的增殖和活化， 抗原特异性和治疗前的分化状态。简而言之，核心D能够监测抗原- 特异性淋巴细胞，并将有助于解剖免疫保护的变化， 慢性感染（包括HBV、HCV、CMV和EBV）和抗PD-1导致的流感疫苗接种 疗法这些方法的建立和完善以及核心D基础设施的建立将 使审讯免疫机制，并提供深入了解发展和持久性， 在检查点阻断或任何其他免疫疗法的背景下，免疫记忆。

Project Summary The overall objective of the U19 is to discover the role of the PD-1 pathway in human immunity by studying the effects of therapeutic PD-1 blockade on immune responses to chronic viruses (Project 1) and preventive vaccines (Project 2). To monitor adaptive immune responses in patients, we need to track the complex repertoire of T and B cells since clonotypes may behave differently over time and in response to infection and therapy. While there are several methods for tracking antigen-specific lymphocytes, large volumes of blood are needed for monitoring multiple antigens, biopsies have limited material for standard pipelines, and clonotypes with distinct antigen receptors are not distinguished. Standard bulk sequencing of TCRs and BCRs can provide quantitative clonotype frequencies; however, its utility is limited because the target antigens are not known for each TCR/BCR and the activation states of each clonotype cannot be determined. Core D provides an innovative service for tracking antigen-specific T and B cells in patient blood and tissues, allowing Projects 1 and 2 to quantify the frequency, antigen specificity and activation states of lymphocytes. Aim 1 provides an approach to match TCRs and BCRs to antigens by sequencing antigen receptors in patient T and B cells stimulated or tagged with viral or vaccine antigens. Aim 2 uses the more cost-effective bulk TCR- and BCR-seq to quantify the frequencies of clonotypes in serial samples of patients treated with anti-PD-1 therapy, but takes advantage of the results in Aim 1 to link antigen receptors from the repertoire with specific viral or vaccine antigens. Aim 3 uses leading-edge droplet-based RNA-seq to sequence paired antigen receptor chains (TCRα & β; IgH & IgK/L) along with thousands of mRNAs in single lymphocytes, linking functional pathways with antigen receptors. The resulting dataset from the three Aims will be integrated to provide the frequencies, antigen specificities and activation states of T and B cells, allowing us to test the hypothesis that anti-PD-1 therapy differentially impacts the proliferation and activation of each lymphocyte subset depending on its antigen specificity and pre-therapy differentiation state. In short, Core D enables the monitoring of antigen- specific lymphocytes at unprecedented resolution, and will help dissect changes in immune protection against chronic infections (including HBV, HCV, CMV, and EBV), and influenza vaccination as result of anti-PD-1 therapy. The establishment and refinement of these approaches and creation of a Core D infrastructure will enable interrogation of immune mechanisms and provide insights into development and durability of immunological memory in the context of checkpoint blockade or any other immunotherapies.