M-SCORCH: Methamphetamine use disorder data generation center for Single Cell Opioid Responses in the Context of HIV

M-SCORCH：艾滋病毒背景下单细胞阿片类药物反应的甲基苯丙胺使用障碍数据生成中心

• 批准号: 10588171
• 负责人: Ya-Chi Ho
• 金额: $ 189.56万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-05-15 至 2026-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10588171
• 关键词: ATAC-seq; Address; Amygdaloid structure; Atlases; Autopsy; Basic Science; Biological; Biological Assay; Biological Models; Biological Process; Biology; Brain; Brain region; Candidate Disease Gene; Cell Nucleus; Cells; Central Nervous System; ChIP-seq; Characteristics; Chromatin; Clinical Sciences; Collaborations; Communities; Complement; Complex; Confounding Factors (Epidemiology); Data; Data Analyses; Data Set; Detection; Disease; Drug abuse; Ensure; Etiology; Fluorescent in Situ Hybridization; Functional disorder; Gene Expression; Gene Expression Regulation; Generations; Genes; Genomics; Genotype; HIV; HIV Infections; HIV-associated neurocognitive disorder; Human; Immune System Diseases; Immunohistochemistry; Impaired cognition; Impairment; Individual; Injections; Lead; Medial; Methamphetamine; Methamphetamine use disorder; Molecular; Molecular Profiling; Multiomic Data; Neurobiology; Neurocognition; Neuroimmune; Neurosciences; Nuclear; Nuclear RNA; Opioid; Organoids; Outcome; Pathway interactions; Patients; Population; Prefrontal Cortex; Process; Productivity; Protocols documentation; Public Health; RNA; Recording of previous events; Research; Research Personnel; Resolution; Resources; Risk; Route; Sampling; Science; Specific qualifier value; Symptoms; Techniques; Tissues; Transcript; Transposase; Validation; Ventral Striatum; addiction; adverse outcome; analysis pipeline; brain cell; brain tissue; cell type; cognitive function; comorbidity; data analysis pipeline; data centers; data quality; data sharing; data standards; epigenetic regulation; experimental study; gene regulatory network; global health; high risk population; immune function; in vivo; induced pluripotent stem cell; insight; methamphetamine use; methamphetamine user; nervous system disorder; neurogenomics; novel; response; single nucleus RNA-sequencing; syndemic; tool; transcriptome; transcriptome sequencing; transmission process; viral RNA

PROJECT SUMMARY HIV and methamphetamine (MA) use are global health problems with devastating human and societal consequences. HIV and methamphetamine use also produce independent and additive impairments in neurocognition, and current clinical and basic science research suggest complex and currently inadequately understood interactions between HIV and MA pathophysiologies. We therefore propose to conduct comprehensive characterization, at the single cell/nuclear level, of human brain tissue and regionally specified organoids derived from human induced pluripotent stem cells. For these single nuclear (sn)RNA-seq and snATAC-seq analyses, we will sample 3 brain regions (prefrontal cortex, ventral striatum, and basolateral amygdala) critical for the neurobiological response to MA use in 20 brains from each of two donor groups, HIV+MA+ and HIV-MA+. These data generation efforts will complement ongoing efforts in these same brain regions from HIV-MA- and HIV+MA- donors and allow us to elucidate differences in gene expression and key biological pathways that occur in response to MA use, HIV, or the combination of the two. In addition, we will assay brain cell types for HIV transcripts, allowing us to identify cellular reservoirs of HIV in donor brains. These efforts will be aided by the use of human cortical organoid and medial ganglionic eminence organoid cultures, which offer complex, region-matched model systems recapitulating in vivo-like cellular diversity and microenvironments without potentially confounding factors including patient history, varying co-morbidities, prolonged postmortem intervals, or tissue degradation. We will then apply cutting edge and novel data analysis pipelines to integrate snRNA-seq and snATAC-seq data and identify cell population and gene expression differences between cell clusters (i.e., putative cell types) in different conditions. These data will also be integrated with external datasets from the SCORCH Consortium and other multi-omic data including genotype, RNA-seq, HiC, ChIP-seq, and ATAC-seq data from both healthy subjects and subjects with HIV infection, neurological disease, or a history of drug abuse. Finally, we will use multiplexed immunohistochemistry and single molecular fluorescent in situ hybridization to validate the cell type specific expression and co-expression of candidate genes, biological processes, and gene regulatory networks implicated in the etiology of HIV or MA pathophysiology. All data generation protocols and data analysis tools will be made freely available to the research community, and all data generated will be provided as both raw and processed resources. Taken together, the proposed experiments will generate invaluable resources and offer new biological insights into the human brain and its disorders.

项目摘要 艾滋病毒和甲基苯丙胺（MA）的使用是毁灭性人和社会的全球健康问题 结果。艾滋病毒和甲基苯丙胺的使用还会在 神经认知以及当前的临床和基础科学研究表明复杂，目前不充分 了解艾滋病毒和MA病理生理学之间的相互作用。因此，我们建议进行 在人脑组织和区域指定的单细胞/核水平上的全面表征 源自人诱导的多能干细胞的器官。对于这些单个核（SN）RNA-seq和 SNATAC-SEQ分析，我们将采样3个大脑区域（前额叶皮层，腹侧和基底外侧 杏仁核）对于在两个捐助者组中每个大脑中对MA使用的神经生物学反应至关重要， HIV+MA+和HIV-MA+。这些数据生成的工作将补充这些大脑中的持续努力 来自HIV-MA-和HIV+Ma-供体的区域，使我们能够阐明基因表达和钥匙的差异 响应MA使用，HIV或两者的组合而发生的生物途径。此外，我们将 测定HIV转录本的脑细胞类型，使我们能够鉴定供体大脑中HIV的细胞储藏。 这些努力将通过使用人皮质器官和内侧神经节巨型器官的帮助来帮助这些努力 培养物提供了复杂的区域匹配模型系统，可在体内样细胞多样性中概括 微环境没有潜在混淆因素，包括患者病史，不同的合并症， 长时间验尸间隔或组织降解。然后，我们将应用最前沿和新型数据分析 集成SNRNA-SEQ和SNATAC-SEQ数据并识别细胞群和基因表达的管道 在不同条件下，细胞簇（即推定的细胞类型）之间的差异。这些数据也将是 与来自烧焦联盟和其他多摩变数据的外部数据集集成在一起，包括基因型， 来自健康受试者和HIV感染受试者的RNA-Seq，HIC，CHIP-SEQ和ATAC-SEQ数据， 神经疾病或药物滥用史。最后，我们将使用多重免疫组织化学和 单分子荧光原位杂交以验证细胞类型特异性表达和共表达 候选基因，生物过程和基因调节网络与HIV或MA的病因有关 病理生理学。所有数据生成协议和数据分析工具都将免费提供给 研究社区以及生成的所有数据将作为原始资源和处理资源提供。拍摄 拟议的实验将共同产生宝贵的资源，并为 人脑及其疾病。