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: 10595635
• 负责人: Michael B. Brenner
• 金额: $ 68.64万
• 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/10595635
• 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; Collaborations; Communication; Communities; Computer Analysis; Consensus; Data; Data Set; Dimensions; Disease; Dissociation; 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; Specimen; Suggestion; Synovial Membrane; Systemic Lupus Erythematosus; Systems Biology; 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 nucleus RNA-sequencing; single-cell RNA sequencing; tissue preparation; 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 来自类风湿关节炎（RA），牛皮癣（PS），牛皮癣关节炎的患者的深度特征生物样品 （PSA），原发性Sjögren综合征（PSS）和全身性红斑狼疮（SLE）。与 AMP AIM网络，我们将重点介绍临床医生网络定义的同类和临床问题， 生物学家和计算生物学家以及行业和非营利合作伙伴。为我们的技术 核心，我们选择了深度概况的端端器官的迈向多维技术以及 自身免疫患者的外周血。我们组建了一个研究人员团队，每个调查人员都有专业知识 疾病和组织类型，并且已经证明了发展和实施高的能力 吞吐管道介绍组织和血液样本。为了帮助我们设计和解释研究，我们 在每种疾病中招募了一个具有临床专业知识的合作者和顾问团队 在每个组织方面的专业知识，并具有空间分析方法方面的技术专业知识。在第一年，我们将携带 消除试点阶段，以优化：i）保存和解开组织； 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； iv）准备 组织两种完整性，领先的空间转录物（森林）和转录的方法 成像（Merfish）。我们将迭代协议以优化细胞活力和产量，技术质量指标 特定于每种技术和所有细胞类型的表示。在第二年，我们将运行完整的缩放范围 - 使用每组类型约50个样品来提高技术管道，并将评估数据质量，现场和批处理效果 和技术工件，以告知单细胞管道的潜在修改。在3 - 5年中，我们将介绍 疾病小组收集的剩下的〜1000活检和〜1000个血样。我们将发展一个 用于数据预处理，主要生物学分析和质量指标的计算管道（包括 具有定制特征的基因，细胞和组织尺度上的技术和生物学参数 组织和疾病。我们的发现将在我们的技术核心和整个技术核心中迅速传达 网络与疾病团队，系统生物学核心，监督该项目的网络委员会，NIH，FNIH 以及我们的行业和非营利合作伙伴。我们还将实时回应，以推动变更 技术并与网络合作，以试行和扩展关键方法。提议的结果 研究将是一组多维数据集，这些数据集将与网络共享，并且更大 社区，并为跨界疾病解构和重建提供了基础 自身免疫性末端器官病理学，从而实现AMP-AIM的愿景。