Single cell and spatial genomic analyses of specimens from patients with autoimmune diseases (Technology Core)

自身免疫性疾病患者标本的单细胞和空间基因组分析（技术核心）

• 批准号: 10451924
• 负责人: Michael B. Brenner
• 金额: $ 62.59万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-03-22 至 2026-12-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10451924
• 关键词: Arthritis; Autoimmune; Autoimmune Diseases; Autoimmunity; Automobile Driving; B-cell receptor repertoire sequencing; Biological; Biopsy; Blood; Blood specimen; Cell Nucleus; Cell Survival; Cells; Cellular Indexing of Transcriptomes and Epitopes by Sequencing; Clinical; Communities; Computer Analysis; Consensus; Custom; Data; Data Set; Disease; Eye; Freezing; Genes; Genomics; Gland; Goals; Human Resources; Image; Industry; Inflammation; Infrastructure; Joints; Kidney; Learning; Leukocytes; Lip structure; Lupus; Methods; Minor salivary gland structure; Modification; Molecular; Morphologic artifacts; Nephritis; Nuclear; Oral cavity; Organ; Pathology; Pathway interactions; Patients; Phase; Pilot Projects; Preparation; Proteomics; Protocols documentation; Psoriasis; Psoriatic Arthritis; Research Personnel; Rheumatoid Arthritis; Running; Salivary; Sampling; Site; Sjogren' s Syndrome; Skin; Small Nuclear RNA; Specimen; Suggestion; Synovial Membrane; Systemic Lupus Erythematosus; Systems Biology; T cell receptor repertoire sequencing; Technical Expertise; Technology; Testing; Time; Tissue Preservation; Tissue Sample; Tissues; Transcript; United States National Institutes of Health; Urine; Vision; Work; Xerostomia; cell preparation; cell type; cohort; computational pipelines; data pipeline; data quality; design; disorder subtype; drug development; experience; eye dryness; flexibility; gene product; high dimensionality; industry partner; lacrimal; multidimensional data; new therapeutic target; novel therapeutic intervention; peripheral blood; preservation; reconstruction; recruit; scale up; single cell analysis; single-cell RNA sequencing; tissue processing; transcriptomics

To better understand the molecular and cellular pathways driving autoimmune diseases, we propose to deeply profile biological samples from patients with rheumatoid arthritis (RA), psoriasis (Ps), psoriatic arthritis (PsA), primary Sjögren’s syndrome (pSS) and systemic lupus erythematosus (SLE). Working closely with the AMP AIM network, we will focus on the cohorts and clinical questions defined by the network of clinicians, biologists and computational biologists together with industry and non-profit partners. For our Technology Core, we selected leading-edge multi-dimensional technologies to deeply profile end organs as well as peripheral blood from patients with autoimmunity. We assembled a team of investigators with expertise in each disease and tissue type, and who have already demonstrated the ability to develop and implement high- throughput pipelines to profile tissue and blood samples. To help us design and interpret the studies, we recruited a team of collaborators and consultants with clinical expertise in each disease, with pathology expertise in each tissue and with technical expertise in spatial profiling methods. In the first year, we will carry out the pilot phase to optimize pipelines for: i) preserving and disaggregating tissues; ii) profiling single cells using scRNA-seq/CITE-seq/TCR-BCR-seq; iii) profiling single nuclei by snRNA-seq/snATAC-seq; iv) preparing tissues for two complementary, leading-edge methods for spatial transcriptomics (Visium) and transcript imaging (MERFISH). We will iterate the protocols to optimize cell viability and yield, technical quality metrics specific to each technology and the representation of all cell types. In year 2, we will run the full set of scaled- up technology pipelines using ~50 samples per tissue type, and will assess data quality, site and batch effects and technical artifacts to inform potential modifications for the single-cell pipeline. In Years 3-5, we will profile the remaining ~1000 biopsies and ~1000 blood samples collected by the disease teams. We will develop a computational pipeline for data pre-processing, primary biological analysis and quality metrics (including technical and biological parameters at the scale of genes, cells and tissues) with customized features for each tissue and disease. Our findings will be rapidly communicated within our Technology Core and across the Network to the Disease Teams, Systems Biology Core, network committees overseeing the project, NIH, FNIH and our industry and non-profit partners. We will also respond in real time to advancing changes in technologies and work with the network to pilot and scale up critical methods. The result of the proposed studies will be a set of multi-dimensional datasets that will be shared with the network and the larger community, and provide a basis for cutting edge disease deconstruction and reconstruction across autoimmune end organ pathologies and thus fulfill the vision of AMP-AIM.

为了更好地了解驱动自身免疫性疾病的分子和细胞途径，我们建议 深入分析类风湿性关节炎 (RA)、银屑病 (Ps)、银屑病关节炎患者的生物样本 (PsA)、原发性干燥综合征 (pSS) 和系统性红斑狼疮 (SLE) 密切合作。 AMP AIM 网络，我们将重点关注精英网络定义的队列和临床问题， 生物学家和计算生物学家与行业和非营利合作伙伴一起支持我们的技术。 核心，我们选择领先的多维技术来深度剖析终末器官以及 我们组建了一个由各自领域具有专业知识的研究人员组成的团队。 疾病和组织类型，以及已经证明有能力开发和实施高 为了帮助我们设计和解释研究，我们使用了分析组织和血液样本的吞吐量管道。 招募了一支由具有每种疾病临床专业知识的合作者和顾问组成的团队，具有病理学 在第一年，我们将拥有每个组织的专业知识以及空间分析方法的技术专业知识。 结束试验阶段以优化以下流程：i) 保存和分解组织；ii) 分析单细胞； 使用 scRNA-seq/CITE-seq/TCR-BCR-seq； iii) 通过 snRNA-seq/snATAC-seq 分析单核； 用于空间转录组学 (Visium) 和转录的两种互补的前沿方法的组织 我们将迭代方案以优化细胞活力和产量、技术质量指标。 针对每种技术和所有细胞类型的代表，我们将在第二年运行全套规模化的- 每种组织类型使用约 50 个样本来建立技术管道，并将评估数据质量、地点和批次效应 以及技术工件，以告知单细胞管道的潜在修改 在第 3-5 年，我们将进行分析。 我们将开发由疾病小组收集的剩余约 1000 个活组织检查和约 1000 个血液样本。 用于数据预处理、初级生物分析和质量指标（包括 基因、细胞和组织规模的技术和生物参数），并为每个参数提供定制功能 我们的研究结果将在我们的技术核心内和整个领域迅速传播。 疾病团队网络、系统生物学核心、监督项目的网络委员会、NIH、FNIH 我们的行业和非营利合作伙伴也将实时响应不断发生的变化。 技术并与网络合作试点和扩大关键方法的结果。 研究将是一组多维数据集，将与网络和更大的数据共享 社区，并为跨领域的前沿疾病解构和重建提供基础 自身免疫性终末器官病理学，从而实现 AMP-AIM 的愿景。