Single Chromatin Fiber Sequencing and Longitudinal Epigenomic Profiling in HIV+ Brain Cells Exposed to Narcotic and Stimulant

HIV相关神经认知障碍坚持联合抗逆转录病毒治疗时代 (CART)而HIV潜伏期，以及HIV转录本在人中枢神经系统中的细胞特异性表达 不完全理解。艾滋病毒相关神经系统疾病的发病率很高，而且还在不断增加。 使用CART稳定抑制的人对CNS病毒逃逸的识别，通常会因 共同登记的艾滋病毒/艾滋病患者中的物质使用障碍流行(PLWHA)，如 SUD对中枢神经系统功能也有深远的影响。我们实验室正在进行的工作是提供第一个 评估特定细胞类型的艾滋病毒“分子特征”，包括基因组整合模式和 大鼠奖赏成瘾环路转录组和表观基因组水平的变化 人类的死后大脑。然而，就像该领域的几乎所有其他基因组方法一样，我们正在进行的 研究面临两个巨大的限制：(A)完全横断面设计，仅限于 基因组在一个时间点上的组织和功能--大脑捐赠者的死亡时间。最重要的 同样的限制显然也适用于细胞培养和动物。对于这样的人来说，这是非常不幸的 感染和未感染脑细胞的终点表观基因组和转录组映射不能提供信息 关于细胞生命早期的细胞特异性染色质状态(B)常规大脑 到目前为止，神经基因组学仅限于染色质的短读测序，通常延伸150个碱基 每次读取的对或更少。然而，在碱基对分辨率下，它将提供更多信息， 包含全长逆转录病毒插入的更宽窗口中的表观基因组染色质景观 站点，这比当前读取长度高出两个数量级。在这个前卫的项目中，我们将， 第一次，对于每个大脑，开始追溯/纵向表观基因组图谱，使用 在HIV领域建立了良好的异种移植模型，以及基因工程人IPSC- 来源的造血祖细胞(HPC)。我们将第一次踏上纵向的 单个染色质纤维的表观基因组标记，并探索动态变化甚至可逆性(或 居住在HIV感染的髓系来源细胞中的表观基因组失调 在大脑和血液中。

HIV-associated neurocognitive disorders persist in the era of combination antiretroviral therapy (cART) while HIV latency, and cell-specific expression of HIV transcript in human CNS remains incompletely understood. There is high prevalence of HIV-associated neurologic disease and increasing recognition of CNS viral escape in people stably suppressed with cART, often further complicated by the co-registered epidemic of substance use disorders (SUD) in people living with HIV/AIDS (PLWHA), as SUD also have profound impact on CNS function. Ongoing work in our laboratory is providing first assessments of cell-type specific HIV 'molecular signatures', including genome integration patterns and alterations on the level of the transcriptome and epigenome in reward- and addiction circuitry of the human postmortem brain. However, like virtually all other genomic approaches in the field, our ongoing studies face two massive limitations: (A) Exclusively cross-sectional design, limited to a snapshot of genome organization and function at a single time point – the time of death of the brain donor. The very same limitation obviously applies to cell culture and animals. This is extremely unfortunate as such types of endpoint epigenome and transcriptome mappings in infected and non-infected brain cells cannot inform about cell-specific chromatin status during earlier periods in the life of the cell (B) Conventional brain neurogenomics is thus far limited to short read sequencing of chromatin, typically extending 150 base pairs or less per read. However, it would be much more informative to profile, at base pair resolution, epigenomic chromatin landscapes across a wider window encompassing full length retroviral insertion sites, which are two orders of magnitude above current read length. In this Avant-Garde project, we will, for the first time, for each brain, embark on retrospective/longitudinal epigenomic profiling, using a xenograft model well established in the HIV field, together with genetically engineered human iPSC- derived hematopoietic progenitor cells (HPC). We will, for the first time, embark on the longitudinal epigenomic tagging of single chromatin fibers, and explore dynamic changes and even reversibility (or progressive deterioration) of the epigenomic dysregulation in HIV infected myeloid derived cells residing in brain and blood.