Integrative Single Cell isoform and chromatin accessibility Mapping of Chronic Opioid Exposure in Cognitive Brain Areas in HIV

HIV认知脑区慢性阿片类药物暴露的综合单细胞亚型和染色质可及性图谱

• 批准号: 10220523
• 负责人: Teresa A Milner
• 金额: $ 70.35万
• 依托单位: WEILL MEDICAL COLL OF CORNELL UNIV
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-30 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10220523
• 关键词: Affect; Animals; Area; Astrocytes; Autopsy; Behavior assessment; Biological Process; Brain; Brain region; Cells; Characteristics; Chromatin; Chronic; Cognitive; Computer Analysis; Computing Methodologies; Data; Data Set; Detection; Drug Exposure; Event; Exons; Exposure to; Functional disorder; Future; Gene Expression; Generations; Genes; Genetic Transcription; Genomics; Goals; HIV; HIV Infections; Health; Hippocampus (Brain); Human; Infection; Knowledge; Literature; Maps; Methods; Microglia; Modality; Modeling; Molecular; Monitor; Neuroglia; Neurons; Nomenclature; Opioid; Opioid Peptide; Opioid Receptor; Oxycodone; Peptide Receptor; Phenotype; Plant Roots; Poly(A)+ RNA; Prefrontal Cortex; Process; Protein Isoforms; Publishing; Regimen; Reporting; Resolution; Rodent; Signaling Molecule; Site; Slice; Slide; Stress; Tissues; Viral; Work; antiretroviral therapy; behavioral pharmacology; brain cell; brain health; cell type; classical conditioning; epigenome; epigenomics; experimental study; genome-wide; innovation; interest; molecular rearrangement; nonhuman primate; novel; opioid exposure; opioid use disorder; programs; response; sequencing platform; sex; simian human immunodeficiency virus; single cell sequencing; single-cell RNA sequencing; tool; transcriptome; transcriptome sequencing; transcriptomics; Affect; Animals; Area; Astrocytes; Autopsy; Behavior assessment; Biological Process; Brain; Brain region; Cells; Characteristics; Chromatin; Chronic; Cognitive; Computer Analysis; Computing Methodologies; Data; Data Set; Detection; Drug Exposure; Event; Exons; Exposure to; Functional disorder; Future; Gene Expression; Generations; Genes; Genetic Transcription; Genomics; Goals; HIV; HIV Infections; Health; Hippocampus (Brain); Human; Infection; Knowledge; Literature; Maps; Methods; Microglia; Modality; Modeling; Molecular; Monitor; Neuroglia; Neurons; Nomenclature; Opioid; Opioid Peptide; Opioid Receptor; Oxycodone; Peptide Receptor; Phenotype; Plant Roots; Poly(A)+ RNA; Prefrontal Cortex; Process; Protein Isoforms; Publishing; Regimen; Reporting; Resolution; Rodent; Signaling Molecule; Site; Slice; Slide; Stress; Tissues; Viral; Work; antiretroviral therapy; behavioral pharmacology; brain cell; brain health; cell type; classical conditioning; epigenome; epigenomics; experimental study; genome-wide; innovation; interest; molecular rearrangement; nonhuman primate; novel; opioid exposure; opioid use disorder; programs; response; sequencing platform; sex; simian human immunodeficiency virus; single cell sequencing; single-cell RNA sequencing; tool; transcriptome; transcriptome sequencing; transcriptomics

Opioid driven exacerbations of neuropathological events and alterations in HIV transcription contributing to HIV associated CNS dysfunction are well-reported. Despite years of continuous suppressive antiretroviral therapy (ART), latent HIV persists and finds sanctuary in many of the same brain regions involved in opioid use disorder (OUD) suggesting interactions between HIV and opioids in brain cells. However, there is a sizeable gap in our knowledge on how OUD impacts cellular responses and viral persistence in HIV-infected brain on ART in humans or relevant model organsims. This proposal seeks to generate topographical data sets and evidence at single cell resolution across the hippocampus and prefrontal cortex (PFC), two brain regions known for predilection for HIV persistence and OUD in non-human primate (NHP) and in post-mortem human brain. These data will provide an unprecedented cellular landscape of multiple modalities that can be harnessed to develop strategies to limit viral persistence and restore and retain optimal brain health in people living with HIV. In our published and preliminary work we have developed innovative single-cell approaches: (A) Single-cell isoform RNA sequencing (ScISOr-Seq), which enables single-cell long-read RNA sequencing of polyadenylated RNAs across thousands of single cells; (B) Slide-isoform sequencing (Sl-ISO-Seq) to spatially locate isoforms in brain slices and (C) a single-cell platform that identifies HIV sequences at single cell level (ScHIV-Seq). In concert these novel sequencing and computational methods, along with scATAC-Seq for chromatin accessibility, will permit the mapping of cellular gene expression, open chromatin regions, isoforms and the detection of HIV across single- cells of hippocampus and PFC. Recent literature supports the presence of HIV in the brain and more specifically in microglia and astrocytes present within the hippocampus and PFC. Importantly, these brain regions are also involved in associative learning processes for OUD. Moreover, our prior studies in rodent hippocampus have laid the groundwork for the proposed studies by establishing the regional and cell-specific distributions of opioid peptides and receptors as well as related signaling molecules, and how these distributions are impacted by sex, stress and opioid-associated learning. In further preliminary studies, we conduct opioid receptor mapping, brain spatial transcriptomics, NHP cognitive behavioral assessment and pharmacological profiling of current ART regimens in tissues. These approaches will provide a comprehensive regional landscape to support our single cell specific phenotypes. We propose an overarching hypothesis that: (i) our new integrated single-cell methods will map single-cell and cell-type specific human and NHP transcriptome and epigenome signatures in the hippocampus and PFC of S/HIV in NHPs and post-mortem human brain; (ii) chronic opioid exposure adds a distinguishable signature to S/HIV infection with long-term ART and defines cell subtypes in which these signatures are rooted; and (iii) these signatures are different from chronic opioid exposure on uninfected brain. These studies further an understanding of molecular mechanisms in HIV and OUD in brain.

阿片类药物驱动的神经病理事件的加剧和艾滋病毒转录的改变，导致艾滋病毒 相关的中枢神经系统功能障碍已得到很好的报告。尽管多年连续抑制抗逆转录病毒疗法 （艺术），潜在的艾滋病毒持续存在并在许多相同的大脑区域中发现了圣所 （OUD）提示脑细胞中HIV与阿片类药物之间的相互作用。但是，我们的差距很大 了解OUD如何影响艾滋病毒感染大脑对人类艺术的细胞反应和病毒持久性的知识 或相关的模型organsims。该提案旨在单一生成地形数据集和证据 跨海马和前额叶皮层（PFC）的细胞分辨率，这是两个因偏见而闻名的大脑区域 非人类灵长类动物（NHP）和验尸后的人类脑中的HIV持久性和OUD。这些数据将提供 可以利用的多种方式的前所未有的蜂窝景观，以制定限制策略 病毒持续性，恢复并保留艾滋病毒患者的最佳大脑健康。在我们发表的 初步工作我们开发了创新的单细胞方法：（a）单细胞同工型RNA测序 （Scisor-seq），它可以使数千个聚腺苷酸化RNA的单细胞长阅读RNA测序 单细胞； （b）幻灯片 - 相工测序（SL-ISO-SEQ）以空间定位在脑切片中，（c）A 单细胞序列（SCHIV-SEQ）识别HIV序列的单细胞平台。在音乐会上这些小说 测序和计算方法以及用于染色质访问性的SCATAC-SEQ将允许 细胞基因表达，开放染色质区域，同工型和HIV的检测 海马和PFC的细胞。最近的文献支持大脑中的HIV存在，更具体地 在海马和PFC中存在的小胶质细胞和星形胶质细胞中。重要的是，这些大脑区域也是 参与OUD的关联学习过程。此外，我们先前在啮齿动物海马的研究已经 通过建立阿片类药物的区域和细胞特异性分布来为拟议的研究奠定基础 肽和受体以及相关信号分子，以及这些分布如何受到性影响， 压力和阿片类药物相关的学习。在进一步的初步研究中，我们进行阿片类药物受体映射，大脑 空间转录组学，NHP认知行为评估和当前艺术的药理分析 组织中的方案。这些方法将提供全面的区域景观，以支持我们的单一 细胞特异性表型。我们提出了一个总体假设：（i）我们的新型集成单细胞 方法将绘制单细胞和细胞类型的特定人类和NHP转录组和表观基因组特异性的特异性。 NHPS和验尸后人脑的海马和PFC； （ii）慢性阿片类药物暴露增加了 具有长期艺术的S/HIV感染的可区分签名，并定义了这些细胞亚型 签名是扎根的； （iii）这些特征与未感染大脑的慢性阿片类药物暴露不同。 这些研究进一步了解了大脑中HIV和OUD中的分子机制。