Systems Immunology profiling of respiratory viral infections in vulnerable populations

易感人群呼吸道病毒感染的系统免疫学分析

• 批准号: 10598123
• 负责人: Peter S Linsley
• 金额: $ 33.56万
• 依托单位: BENAROYA RESEARCH INST AT VIRGINIA MASON
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-03-29 至 2027-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10598123
• 关键词: Acute; Adult; Allergens; Antibodies; Antigens; Autoantigens; B-Cell Antigen Receptor; Blood; Blood Cells; Blood specimen; Cell Separation; Cell surface; Cells; Child; Chromium; Chronic Disease; Clinical; Collection; DNA; Data; Data Analyses; Gene Expression; Genomics; Genotype; Human; Immune; Immunology; Immunophenotyping; Individual; Link; Measurement; Measures; Methylation; Nose; Pathogenesis; Phenotype; Population; Process; Protocols documentation; RNA; Research Project Grants; Rheumatoid Arthritis; Sampling; Specific qualifier value; Sputum; Stains; System; T-Cell Receptor; T-Lymphocyte; Viral; Viral Respiratory Tract Infection; Vulnerable Populations; Work; antigen-specific T cells; data management; genome-wide; next generation sequencing; proteogenomics; reconstruction; reference genome; respiratory infection virus; single-cell RNA sequencing; transcriptome; transcriptome sequencing; transcriptomics

SUMMARY/ABSTRACT The Genomics Core will provide sample processing and next-generation sequencing for the BRI HIPC Center entitled “Systems immunology profiling of respiratory viral infections in vulnerable populations”. This core will serve both Research Projects, receiving samples from the Clinical Core, and sharing high quality ‘omics profiles with the Data Management and Analysis Core. The Genomics Core has two Specific Aims, In Specific Aim 1, the Genomics Core will process nasal, blood and sputum samples and then perform genome scale bulk RNA sequencing. In Specific Aim 2, the Genomics Core will perform single cell proteogenomic sequencing (Total-seq) of both global and antigen-specific populations to elucidate single cell transcriptomes, single cell immunophenotypes, and T cell receptor (TCR)/B cell receptor (BCR) clonotypes. For the global T cell analysis, the Genomics Core will utilize the 10X Chromium platform with 10X Single Cell Immune Profiling and BioLegend TotalSeq protocols for simultaneous single cell measurements of gene expression, cell surface antibody staining and TCR/BCR reconstruction. For rare autoantigen-specific populations where too few cells are available for use on the 10X system, the Genomics Core will utilize cell sorting on a flow cytometer into multi-well plates. In both cases, the Genomics Core will integrate transcriptomic and TCR/BCR clonotype measurements to link cells sharing ancestral relationships. The antigen-specific T cells to be examined is dependent on the project with Research Project 1 focused on allergen-specific T cells and Research Project 2 focused on citrullinated-antigen-specific T cells, implicated in the pathogenesis of rheumatoid arthritis. All transcriptomic data generated by the Genomics Core will be aligned to human and viral reference genomes and processed prior to transfer to the Data Management and Analysis Core for advanced analysis. The Genomics Core will work closely with each of the Project and Core Leads in the HIPC Center.

总结/摘要 Genomics Core将为BRI HIPC中心提供样本处理和下一代测序 题为“脆弱人群呼吸道病毒感染的系统免疫学分析”。核心将 服务于两个研究项目，从临床核心接收样本，并分享高质量的“组学” 数据管理和分析核心。基因组学核心有两个具体目标，具体而言， 目标1，Genomics Core将处理鼻，血液和痰液样本，然后进行基因组规模批量 RNA测序。在特定目标2中，基因组学核心将执行单细胞蛋白质基因组测序 （全序列）的全局和抗原特异性群体，以阐明单细胞转录组、单 免疫表型和T细胞受体（TCR）/B细胞受体（BCR）克隆型。对于整体T细胞分析， 基因组学核心将利用10倍Chromium平台和10倍单细胞免疫分析， BioLegend TotalSeq方案用于同时单细胞测量基因表达、细胞表面 抗体染色和TCR/BCR重建。对于罕见的自身抗原特异性群体， 可用于10 X系统，Genomics Core将利用流式细胞仪上的细胞分选， 多孔板。在这两种情况下，基因组学核心将整合转录组和TCR/BCR克隆型 测量以链接共享祖先关系的细胞。待检查的抗原特异性T细胞是 研究项目1侧重于过敏原特异性T细胞，研究项目2 专注于瓜氨酸抗原特异性T细胞，与类风湿关节炎的发病机制有关。所有 Genomics Core生成的转录组数据将与人类和病毒参考基因组进行比对 并在传输到数据管理和分析核心进行高级分析之前进行处理。的 Genomics Core将与HIPC中心的每个项目和核心领导密切合作。