Multi-omic immune profiling

摘要 我们提出了单细胞技术来量化多参数免疫标记物， 深入的单细胞数据，用于分析我们研究队列中对疫苗接种的免疫应答。的 此服务核心中的共享平台提供高效且可复制的分析，以支持我们的 研究项目具有极大扩展的灵敏度和细胞类型特异性。定义单元格 表型，我们将采用质谱细胞术或CyTOF（飞行时间细胞计数法）， 多参数单细胞分析，使用重金属离子作为抗体标记， 免疫亚群细胞分析的大量细节。为了进一步分析和关联 为了获得具有免疫表型的靶向单细胞的转录组，我们将采用单细胞细胞 通过测序（CITE-Seq）对循环血细胞的转录组和表位进行索引， 通过确定性条形码（DBiT-seq）在活检组织中进行空间分辨率蛋白质转录组学 组织（皮肤、淋巴结）。这些转录组学包括BCR和TCR的深度测序 研究组织中的克隆扩增与循环中的克隆扩增的比较。为了鉴定分子 在我们的队列中，我们将使用基于质谱（MS）的 基于Mstern印迹的血清蛋白质组学平台，可无偏见地发现数百种 具有免疫功能的蛋白质作为免疫状态的良好反映。 在含量测定和分析水平上的标准化将允许比较和整合 跨项目的数据。核心C的目标是提供一个独特的和必要的资源， 能够全面表征来自血液的循环免疫细胞以及细胞 可从组织活检获得，具有通过CyTOF和RNA测序（RNA-seq）的比较数据， 和匹配的蛋白质组环境图谱

Abstract We propose single-cell technologies to quantify multiparameter immune markers that provide in- depth single-cell data for analysis of immune responses to vaccination in our study cohorts. The shared platforms in this service core provide efficient and reproducible profiling in support of our research projects with greatly expanded sensitivity and cell-type specificity. To define cell phenotypes, we will employ mass cytometry or CyTOF (Cytometry by Time-Of-Flight) for multiparameter single-cell analysis, which uses heavy metal ions as antibody labels and provides tremendous detail for cellular analysis of immune subsets. To further profile and correlate the transcriptomes of targeted single cells with immunophenotype, we will employ single-cell cellular indexing of transcriptomes and epitopes by sequencing (CITE-Seq) for circulating blood cells and spatial-resolution proteo-transcriptomics via deterministic barcoding (DBiT-seq) in biopsies from tissues (skin, lymph node). These transcriptomics include in depth sequencing of BCR and TCR to investigate clonal expansion in the tissue compared to the circulation. To identify molecular signatures of vaccine responses across our cohorts, we will use a mass spectrometry (MS)-based MStern blotting-based serum proteomics platform for unbiased discovery of several hundred proteins with immunological function as an excellent reflection of the immunological state. Standardization, both at the assay and analytical levels, will allow comparisons and integration of data across projects. The goals of Core C are to provide a unique and essential resource to enable the comprehensive characterization of circulating immune cells from blood as well as cells available from tissue biopsies, with comparative data by CyTOF and RNA-sequencing (RNA-seq), and matched profiles of proteomic milieu.