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

摘要 阿片类药物使用障碍（OUD）和艾滋病毒感染是独立的， 协同导致全球数千万人中枢神经系统（CNS）功能障碍。 然而，由OUD和HIV以及它们的组合改变的细胞回路仍然难以捉摸。此夕h 大脑中可以携带HIV感染的细胞类型的身份仍然存在争议。为了解决这个 HIV在大脑中的位置以及HIV和OUD对大脑的影响是一个关键的棘手问题， 需要在单细胞水平上进行全面的组织表征以鉴定新的稀有细胞类型， 富集或耗尽的细胞群，以及与发病机制相关的细胞回路。我们建议雇用 耶鲁大学的一个中心致力于生成单细胞阿片类药物的数据， 艾滋病毒发现背景下的反应（SCORCH），Y-SCORCH。中心召集了一个 耶鲁大学的研究人员在神经基因组学、艾滋病毒生物学、成瘾的神经科学、 单细胞分析和联盟科学，以及现有合作的记录。我们的组织 该计划包括从四个捐赠组中抽取20个大脑样本：对照组、HIV（HIV+）组、HIV伴 OUD（HIV+OUD+）和无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的疾病相关区域， 艾滋病。我们的分析组件将进行5，000 - 20，000个单核RNA测序（snRNA-seq） 细胞/样品、单核ATAC-seq（scATAC-seq）和空间转录组学，以产生 每个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阳性人群中的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相结合。经济社会发展呈现 用于高通量数据分析的管道，包括单核转录组，艾滋病毒检测 转录本和scATAC-seq数据，并开发创新的分析方法。我们的优先级& 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，并描述了验证由 转录组学和表观遗传学分析。最后，我们的研究管理组件提供了一个 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了进展，其中包括从640次测定中生成“组学”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组合的实验和计算工作流程，以及（3）遵循 进行大规模数据生产，并进行验证和进一步分析。Y-SCORCH已建立 在成功创建单核转录组数据所需的所有方法方面的专业知识， 为未来的发现提供支架，以了解OUD和HIV对CNS影响的病理生理学理解。

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.