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

基本信息

批准号：
10220577
负责人：
Ya-Chi Ho
金额：
$ 194.41万
依托单位：
YALE UNIVERSITY
依托单位国家：
美国
项目类别：
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/10220577
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 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 Ganglia 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 Molecular Molecular Profiling Multiomic Data Neuraxis Neurobiology Neurocognition Neurosciences Nuclear Nuclear RNA Opioid Organoids Outcome Pathway interactions Patients Population Prefrontal Cortex Process Protocols documentation Public Health RNA Recording of previous events Regulator Genes Research Research Personnel Resolution Resources Risk Route Sampling Science Small Nuclear RNA Specific qualifier value Symptoms Techniques Time Tissues Transcript Transposase Validation Ventral Striatum XCL1 gene 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 global health high risk population immune function in vivo induced pluripotent stem cell insight methamphetamine use methamphetamine user nervous system disorder neurogenomics novel response tool transcriptome transcriptome sequencing transmission process viral RNA

项目摘要

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.

项目概要艾滋病毒和甲基苯丙胺 (MA) 的使用是全球性的健康问题，对人类和社会造成毁灭性的影响结果。艾滋病毒和甲基苯丙胺的使用也会对身体产生独立和累加的损害神经认知，以及当前的临床和基础科学研究表明，其复杂且目前还不够充分了解 HIV 和 MA 病理生理学之间的相互作用。因此我们建议进行在单细胞/核水平上对人脑组织和特定区域进行全面表征源自人类诱导多能干细胞的类器官。对于这些单核 (sn)RNA-seq 和 snATAC-seq 分析，我们将采样 3 个大脑区域（前额皮质、腹侧纹状体和基底外侧杏仁核）对于两个供体组各 20 个大脑对 MA 使用的神经生物学反应至关重要， HIV+MA+ 和 HIV-MA+。这些数据生成工作将补充这些同一大脑中正在进行的工作来自 HIV-MA- 和 HIV+MA- 供体的区域，使我们能够阐明基因表达和关键的差异因使用 MA、HIV 或两者的组合而发生的生物途径。此外，我们将分析脑细胞类型中的 HIV 转录本，使我们能够识别供体大脑中 HIV 的细胞储存库。这些努力将通过使用人类皮质类器官和内侧神经节隆起类器官来帮助培养物，提供复杂的、区域匹配的模型系统，重现体内细胞多样性和没有潜在混杂因素的微环境，包括患者病史、不同的合并症、尸检时间间隔延长或组织退化。然后我们将应用尖端和新颖的数据分析整合 snRNA-seq 和 snATAC-seq 数据并识别细胞群和基因表达的管道不同条件下细胞簇（即假定的细胞类型）之间的差异。这些数据也将与 SCORCH 联盟的外部数据集和其他多组学数据（包括基因型）集成，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，神经系统疾病或药物滥用史。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验证细胞类型特异性表达和共表达与 HIV 或 MA 病因学相关的候选基因、生物过程和基因调控网络病理生理学。所有数据生成协议和数据分析工具将免费提供给研究社区，生成的所有数据都将作为原始资源和经过处理的资源提供。采取总之，拟议的实验将产生宝贵的资源，并提供新的生物学见解人类大脑及其疾病。