The Y-SCORCH Data Generation Center at Yale for Single-Cell Opioid Responses in the Context of HIV

耶鲁大学 Y-SCORCH 数据生成中心用于艾滋病毒背景下的单细胞阿片类药物反应

• 批准号: 10461029
• 负责人: Mark Bender Gerstein
• 金额: $ 300万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-01 至 2025-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10461029
• 关键词: ATAC-seq; Address; Affect; Amygdaloid structure; Area; Astrocytes; Atlases; Behavior; Biological Assay; Biological Markers; Biology; Blood; Brain; Brain region; Cell Nucleus; Cells; Cerebrospinal Fluid; Cognition; Collaborations; Complement; Data; Data Analyses; Data Discovery; Data Set; Deposition; Detection; Disease; Ensure; Epigenetic Process; Functional disorder; Future; Generations; Genes; HIV; HIV Infections; Human; Immune; In Situ Hybridization; Infection; Investigation; Knowledge; Lead; Ligands; Location; Methodology; Methods; Microglia; Neuraxis; Neuroglia; Neurosciences; Opioid; Pathogenesis; Persons; Phase; Population; Prefrontal Cortex; Process; Production; Protocols documentation; Research; Research Personnel; Running; Sampling; Science; Site; Small Nuclear RNA; Specimen; T-Lymphocyte; Techniques; Time; Tissue Sample; Tissues; Transcript; Validation; Ventral Striatum; Work; addiction; brain cell; cell type; cellular targeting; computational pipelines; data centers; data framework; data integration; data management; data sharing; data standards; data submission; experimental study; follow-up; improved; innovation; large scale data; macrophage; neurogenomics; neuroimaging; neuropsychiatry; novel; opioid use disorder; opioid user; receptor; response; scaffold; syndemic; tool; transcriptome sequencing; transcriptomics

Abstract Opioid use disorder (OUD) and HIV infection are syndemic conditions that independently and synergistically lead to central nervous system (CNS) dysfunction in tens of millions of people globally. However, the cellular circuits altered by OUD and HIV, and their combination, remain elusive. Further, the identities of cell types within the brain that can harbor HIV infection remain controversial. To address this key vexing question of HIV location within the brain and the effects of HIV and OUD on the brain, comprehensive tissue characterization at the single-cell level is needed to identify novel rare cell types, enriched or depleted cellular populations, and cellular circuits tied to pathogenesis. We propose to employ state-of-the-art methodologies in a center at Yale devoted to generating data on Single Cell Opioid Responses in the Context of HIV Discovery (SCORCH), Y-SCORCH. The center assembles a team of investigators at Yale with leading expertise in neurogenomics, HIV biology, neuroscience of addiction, single-cell analytics and consortium science, and a record of existing collaborations. Our TISSUE Component includes plans to sample 20 brains from four donor groups: controls, HIV (HIV+), HIV with OUD (HIV+OUD+), and OUD without HIV (OUD+). For each brain we will study 4 regions (prefrontal cortex, ventral striatum, insular cortex, and amygdala), representing disease-relevant areas for OUD and HIV. Our ASSAY Component will carry out single nucleus RNA sequencing (snRNA-seq) for 5,000-20,000 cells/sample, single-nucleus ATAC-seq (scATAC-seq), and spatial transcriptomics to generate transcriptomic, epigenetic, and spatial atlases for each donor type and each region. In parallel, we will detect HIV transcripts in the HIV+ groups. Our DATA Deposition & Analysis Component will assemble data standards, facilitate dissemination, and integrate our data with existing brain atlases. It will develop pipelines for high-throughput data analysis, including for single nucleus transciptomes, detection of HIV transcripts and for scATAC-seq data, and develop innovative analysis methods. Our Prioritization & Functional VALIDATION Component proposes a process of identification of brain regions and donor types that best differentiate disease states, and describes experiments to validate the findings generated by transcriptomic and epigenetic analyses. Finally, our Research MANAGEMENT Component provides a framework for data sharing with the SCORCH Data Center and broader Consortium and ensures timely progress in achieving our milestones which include generating `omics data from 640 assays. Our Specific Aims are to: (1) Establish a workflow from tissue samples to single-cell data deposited in the data center, (2) Run the combined experimental and computational workflows on procured specimens, and (3) Follow up on large-scale data production with validation and further analysis. Y-SCORCH has established expertise in all approaches necessary to successfully create single-nucleus transcriptomic data to provide a scaffold for future discovery to inform pathophysiological understanding of CNS effects of OUD and HIV.

抽象的 阿片类药物使用障碍（OUD）和HIV感染是独立和 在全球数千万人中，协同导致中枢神经系统（CNS）功能障碍。 但是，由Oud和HIV改变的细胞回路及其组合仍然难以捉摸。此外， 大脑中可能具有艾滋病毒感染的细胞类型的身份仍然存在争议。解决这个问题 大脑内的艾滋病毒位置的关键问题以及艾滋病毒和奥德对大脑的影响， 需要在单细胞水平上进行全面的组织表征来识别新型稀有细胞类型， 富集或耗尽的细胞群，以及与发病机理有关的细胞回路。我们建议雇用 耶鲁大学中心的最先进方法论专门用于在单细胞阿片类药物上生成数据 在HIV发现（Scorch）的背景下的反应，Y-Scorch。该中心组建了一个团队 耶鲁大学的研究人员在神经基因组学，HIV生物学，成瘾神经科学方面具有领先的专业知识， 单细胞分析和财团科学，以及现有合作的记录。我们的组织 组件包括从四个捐助者组中采样20个大脑的计划：对照组，艾滋病毒（HIV+），艾滋病毒 OUD（HIV+OUD+），并且没有HIV（OUD+）的OUD。对于每个大脑，我们将研究4个区域（前额叶 皮层，腹侧纹状体，岛状皮质和杏仁核），代表与疾病相关的OUD和疾病区域 艾滋病病毒。我们的测定部分将以5,000-20,000进行单核RNA测序（SNRNA-SEQ） 细胞/样品，单核ATAC-SEQ（SCATAC-SEQ）和空间转录组学生成 每种供体类型和每个区域的转录组，表观遗传和空间图谱。同时，我们将 检测HIV+组中的HIV转录本。我们的数据沉积和分析组件将组装 数据标准标准，促进传播并将我们的数据与现有的大脑图书馆相结合。它将发展 用于高通量数据分析的管道，包括单核转载体，HIV检测 成绩单和SCATAC-SEQ数据，并开发创新的分析方法。我们的优先级和 功能验证组件提出了识别大脑区域和供体的过程 最能区分疾病状态的类型，并描述了实验以验证由 转录组和表观遗传分析。最后，我们的研究管理组件提供了 与灼烧数据中心和更广泛的财团共享数据共享的框架，并确保及时 在实现我们的里程碑方面的进展，包括从640种测定中生成“ OMICS数据”。我们的具体 目的是：（1）建立从组织样本到存放在数据中心的单细胞数据的工作流程， （2）在采购的标本上运行合并的实验和计算工作流，（3）遵循 通过验证和进一步分析来进行大规模数据生产。 Y-Scorch已建立 成功创建单核转录组数据所需的所有方法的专业知识，以提供 未来发现的脚手架，以告知对OUD和HIV的中枢神经系统影响的病理生理理解。