Supplement: Human Brain Collection for Study of the Neuropathogenesis of SARS-CoV-2, HIV-1, and Opioid Use Disorder

摘自家长奖UM1DA051410 阿片类药物使用障碍(OUD)和艾滋病毒感染是独立和 协同作用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改变的细胞回路，以及它们的结合，仍然难以捉摸。此外， 大脑中可能藏匿艾滋病毒感染的细胞类型的身份仍然存在争议。要解决这个问题 HIV在大脑中的位置以及HIV和OUD对大脑的影响这一关键令人头疼的问题， 需要在单细胞水平上的全面组织表征来识别新的稀有细胞类型， 丰富或枯竭的细胞群体，以及与发病机制有关的细胞回路。我们建议聘用 耶鲁大学致力于产生单细胞阿片类药物数据的中心的最新方法学 关于艾滋病毒发现的回应(SCOCH)，Y-SCOCH。该中心组建了一支由 耶鲁大学的研究人员在神经基因组学、艾滋病毒生物学、成瘾神经科学方面拥有领先的专业知识， 单细胞分析和联盟科学，以及现有合作的记录。我们的组织 组成部分包括从四个捐赠者群体中抽取20个大脑样本的计划：对照组、艾滋病毒(HIV+)、艾滋病毒和 OUD(HIV+OUD+)和OUD而不是HIV(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)，代表与疾病相关的区域 爱滋病毒。我们的检测组件将进行5,000-20,000个单核RNA测序(SnRNA-seq 细胞/样本、单核ATAC-seq(scatac-seq)和空间转录产物 每个供体类型和每个区域的转录、表观遗传和空间图谱。同时，我们将 检测HIV+组中的HIV转录本。我们的数据存储和分析组件将组装 数据标准，促进传播，并将我们的数据与现有的脑图谱整合。它会发展成 用于高通量数据分析的管道，包括单核转运、艾滋病毒检测 用于SCATAC-SEQ数据和文本，并开发创新的分析方法。我们的优先顺序和 功能验证组件提出了一个识别大脑区域和供体的过程 最能区分疾病状态的类型，并描述了验证由 转录学和表观遗传学分析。最后，我们的Research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次化验中产生“组学数据”。我们的特定 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)对采购的标本运行实验和计算相结合的工作流程，以及(3)如下 关于大规模数据生产的验证和进一步分析。Y-SCOCH已经建立了 成功创建单核转录数据所需的所有方法的专业知识，以提供 为未来的发现奠定基础，以便从病理生理学的角度了解人类免疫缺陷病毒和艾滋病病毒对中枢神经系统的影响。

Abstract from Parent Award UM1DA051410 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.