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

基本信息

批准号：
10685384
负责人：
Mark Bender Gerstein
金额：
$ 300万
依托单位：
YALE UNIVERSITY
依托单位国家：
美国
项目类别：
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/10685384
关键词：
ATAC-seq Address Affect Amygdaloid structure Area Astrocytes Atlases Behavior Biological Assay Biological Markers Biology Blood Blood Vessels Brain Brain region Cell Nucleus Cells Central Nervous System 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 Macrophage Methodology Methods Microglia Neuroglia Neurosciences Opioid Pathogenesis Persons Phase Population Prefrontal Cortex Process Production Protocols documentation Research Research Personnel Running Sampling Science Site Specimen T-Lymphocyte Techniques Tissue Sample Tissues Transcript Validation Ventral Striatum Work addiction brain cell cell type cellular targeting computational pipelines data centers data framework data integration data sharing data standards data submission experimental study follow-up improved innovation large scale data neurogenomics neuroimaging neuropsychiatry novel opioid use disorder opioid user receptor response scaffold single nucleus RNA-sequencing syndemic tool transcriptomics

项目摘要

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 感染是独立且独立的综合征性疾病协同导致全球数千万人的中枢神经系统（CNS）功能障碍。然而，OUD 和 HIV 及其组合改变的细胞回路仍然难以捉摸。此外，大脑内可能携带艾滋病毒感染的细胞类型的身份仍然存在争议。为了解决这个问题 HIV 在大脑中的位置以及 HIV 和 OUD 对大脑的影响是一个令人烦恼的关键问题，需要在单细胞水平上进行全面的组织表征来识别新的稀有细胞类型，丰富或耗尽的细胞群以及与发病机制相关的细胞回路。我们建议聘用耶鲁大学中心致力于生成单细胞阿片类药物数据的最先进方法 HIV 发现背景下的应对措施 (SCORCH)，Y-SCORCH。中心组建了一支团队耶鲁大学的研究人员在神经基因组学、艾滋病毒生物学、成瘾神经科学、单细胞分析和联合科学，以及现有合作的记录。我们的纸巾该部分包括计划对来自四个捐赠者组的 20 个大脑进行采样：对照组、HIV（HIV+）、HIV 感染者 OUD (HIV+OUD+) 和不含 HIV 的 OUD (OUD+)。对于每个大脑，我们将研究 4 个区域（前额叶皮质、腹侧纹状体、岛叶皮质和杏仁核），代表 OUD 和疾病相关区域艾滋病病毒。我们的 ASSAY 组件将对 5,000-20,000 个样本进行单核 RNA 测序 (snRNA-seq) 细胞/样本、单核 ATAC-seq (scATAC-seq) 和空间转录组学以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。与此同时，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，促进传播，并将我们的数据与现有的大脑图谱整合。将会发展高通量数据分析管道，包括单核转录组、HIV 检测转录本和 scATAC-seq 数据，并开发创新的分析方法。我们的优先顺序 & 功能验证组件提出了识别大脑区域和供体的过程最好区分疾病状态的类型，并描述验证实验结果的实验转录组和表观遗传学分析。最后，我们的研究管理组件提供了与 SCORCH 数据中心和更广泛的联盟共享数据的框架，并确保及时在实现我们的里程碑方面取得的进展，其中包括通过 640 项检测生成“组学数据”。我们的具体目标是：（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) 对采购的样本运行组合实验和计算工作流程，以及 (3) 遵循通过验证和进一步分析进行大规模数据生产。 Y-SCORCH成立成功创建单核转录组数据所需的所有方法的专业知识，以提供为未来发现的支架提供对 OUD 和 HIV 的中枢神经系统影响的病理生理学理解。