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

阿片类药物导致的神经病理学事件恶化和HIV转录的改变导致HIV 相关的CNS功能障碍有很多报道。尽管多年来持续的抑制性抗逆转录病毒治疗 (ART)潜伏的艾滋病毒持续存在，并在许多与阿片类药物使用障碍有关的大脑区域中找到庇护所 (OUD)表明艾滋病病毒和阿片类药物在脑细胞中相互作用。然而，在我们的国家， 了解OUD如何影响人类ART中HIV感染大脑中的细胞反应和病毒持续存在 或相关的模型器官。这一行政补充建议旨在产生新的地形 来自父母奖的数据集和海马体（大脑区域）单细胞分辨率的证据 已知在非人灵长类动物（NHP）中对HIV持久性和OUD有偏好。这些数据将提供一个 前所未有的多种模式的细胞景观，可以利用这些模式来制定限制病毒感染的策略。 持久性和恢复和保持艾滋病毒感染者的最佳大脑健康。在我们发布的初步报告中， 我们开发了创新的单细胞方法，包括单细胞亚型RNA测序 （ScISOr-Seq），其能够对数千个多聚腺苷酸化RNA进行单细胞长读段RNA测序 单个细胞。与这些新的测序和计算方法一致，沿着ScATAC-Seq用于 染色质可及性，将允许绘制细胞基因表达、开放染色质区域、同种型 以及海马单细胞SIV的检测。最近的文献支持艾滋病毒在 大脑，更具体地说是海马体内的小胶质细胞和星形胶质细胞。重要的是这 大脑区域也参与了OUD的联想学习过程。此外，我们之前在啮齿动物中的研究 海马已经通过建立区域和细胞特异性， 阿片肽和受体以及相关信号分子的分布，以及这些分布 受到性压力和阿片类药物相关学习的影响使用最先进的单细胞多组 整合基因组学，我们建议在这个补充申请，以产生多维的单细胞 数据集，并定义了这些观察结果在受控SIV感染的NHP模型中的相关性， 记录慢性吗啡暴露的不同阿片类药物，用于与母研究进行比较， 羟考酮我们还建议验证选择基因的单细胞表达中观察到的任何变化， 原位杂交我们建议在以下具体目标下实现这些目标：目标1。一代 在SIV感染的受控环境中， 接受ART监测并暴露于慢性吗啡的NHP。目标二。建立全基因组单细胞 在AIM 1中检查的组中海马的表观基因组谱。

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 administrative supplement proposal seeks to generate new topographical data sets from the parent award and evidence at single cell resolution across the hippocampus, a brain region known for predilection for HIV persistence and OUD in non-human primate (NHP). 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 including Single-cell isoform RNA sequencing (ScISOr-Seq), which enables single-cell long-read RNA sequencing of polyadenylated RNAs across thousands of single cells. 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 SIV across single-cells of hippocampus. Recent literature supports the presence of HIV in the brain and more specifically in microglia and astrocytes present within the hippocampus. Importantly, this brain region is 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. Using new cutting-edge single-cell mulitomic integrated genomics, we propose in this supplemental application to generate multi-dimensional single-cell data sets and define the relevance of such observations in a controlled SIV infected NHP model with and without a different opioid of documented chronic morphine exposure for comparison with the parent study evaluating oxycodone. We also propose to validate any changes observed in single-cell expression in select genes using in situ hybridization. We propose to achieve these goals under the following specific aims: Aim 1. Generation of genome-wide single-cell transcriptomic profiles in the hippocampus in a controlled setting of SIV infection of NHPs monitored on ART and exposed to chronic morphine. Aim 2. Establish genome-wide single-cell epigenomic profiles of the hippocampus in the groups examined in aim 1.