Computational Immunobiology Core

摘要--计算免疫生物学核心 计算免疫生物学核心(CIC)将提供全面的技术检测支持服务 以及对以下两个项目中提出的以假设为导向的研究提供分析支持 U19提案。核心的最大综合实力来自于它的技术和移植的交集- 专门的专业知识，最先进的多维生物讯问方法，以及明确的熟练程度 在高级计算分析中。在柯克博士的领导下，Core继续利用 此程序以前的迭代，以实现移植程序的全面表征，具有 在基于多染色流式细胞术的免疫图谱平台方面具有特殊的专业知识。化验是 根据高度标准化和验证，在良好的临床实验室合规环境中执行 标准操作程序，由一个支持NHP移植工作超过25年的团队提供。 对于这个已经建立的团队，已经与国际领先的NC州立大学建立了新的合作 在兽医方面，整合了一种新的平台，用于综合、恒河猴特有的单细胞 RNA序列分析。这是第一个全面提供RNA序列分析的实验室 在恒河猴中的TCR和BCR谱系，因此为分析增加了前所未有的粒度 这两个项目中提出的活体研究。鉴于从这些数据中获取的数据呈指数级增长 能力，通过招聘彭博士，增加了高密度数据分析方面的新专业知识 还有成龙。这些人员在集成基于序列和基于流的数据集方面拥有丰富的专业知识 与传统的临床结果指标相一致，特别是在非人类灵长类动物研究中。中投公司的主要服务对象 将向项目1和项目2提供：1)最先进的标本采集、加工和生物库；2) 分析多色流式细胞术表型和细胞内细胞因子染色；3)单细胞RNA 测序；4)定量病毒学检测；5)全面的组织学和免疫组织化学支持； 6)对化验数据进行计算分析。目前的核心设施容纳了所有 对拟议的灵长类研究进行交钥匙评估所需的先进设备，包括 流程和测序平台，以及为整个公爵提供服务的标本处理和生物库服务 在柯克博士的监督下的社区。现有的病毒检测设施监测了三个最严重的 移植中临床相关病毒：恒河猴巨细胞病毒、恒河猴淋巴病毒 (RhLCV)(与EB病毒恒河猴同源)和猿猴病毒40(SV40)。CIC还提供常规组织学和 免疫组织化学分析通过我们的免疫组织化学服务实验室，允许每个项目 检查实验操作对关键供体组织和宿主组织的影响。的并列 人力和NHP的专业知识代表了这个IPC联盟的一个特殊优势，进一步促进了高度 拟议研究的翻译方面。

ABSTRACT – Computational Immunobiology Core The Computational Immunobiology Core (CIC) will provide comprehensive technical assay support services and analytic support for the hypothesis-driven research studies proposed in the two Projects comprising this U19 proposal. The Core derives its greatest overall strength from its intersection of technical and transplant- specific expertise, state-of-the art methods for multidimensional biological interrogation, and explicit proficiency in advanced computational analytics. Led by Dr. Kirk, the Core continues to utilize the longstanding assets of prior iterations of this program to achieve comprehensive characterization of transplant procedures, with particular expertise in polychromic flow cytometry-based platforms for immune profiling. Assay testing is performed in a Good Clinical Laboratory compliant environment according to highly standardized and validated Standard Operating Procedures, by a team that has been supporting NHP transplant work for over 25 years. To this established team, a new collaboration has been forged with NC State University, an international leader in veterinary medicine, to incorporate a novel platform for comprehensive, rhesus macaque-specific, single cell RNA sequence analysis. This is the first lab to comprehensively provide RNA sequence analysis for the entire TCR and BCR repertoire in the rhesus macaque, and as such, adds unprecedented granularity to the analysis of the in vivo studies proposed in the two Projects. Given the exponential growth in data acquired from these capabilities, new expertise in high-density data analytics has been added through the recruitment of Drs. Peng and Chan. These individuals have extensive expertise in the integration of sequence- and flow-based datasets with traditional metrics of clinical outcome, specifically in nonhuman primate studies. The key services the CIC will provide to Projects 1 and 2 include: 1) state-of-the-art specimen capture, processing, and biobanking; 2) analytical polychromatic flow cytometry phenotyping and intracellular cytokine staining; 3) single cell RNA sequencing; 4) quantitative virologic testing; 5) comprehensive histology and immunohistochemistry support; and 6) computational analysis for the data emerging from the assays. The present core facilities house all the advanced equipment required for turn-key assessment of the proposed primate studies, including exceptional flow and sequencing platforms, and a specimen processing and biobanking service that serves the entire Duke community under Dr. Kirk’s supervision. The established viral testing facility monitors three of the most clinically relevant viruses in transplantation: Rhesus Cytomegalovirus (rhCMV), Rhesus Lymphocryptovirus (rhLCV) (rhesus homology of EBV), and Simian Virus 40 (SV40). The CIC also provides routine histology and immunohistochemistry assays through our immunohistochemistry service laboratory, allowing each project to examine the effects of the experimental manipulations on key donor and host tissues. The juxtaposition of human and NHP expertise represents a particular strength of this IPC consortium, further facilitating the highly translational aspects of the proposed studies.