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

暴露于麻醉剂和兴奋剂的 HIV 脑细胞的单染色质纤维测序和纵向表观基因组分析

• 批准号: 10595615
• 负责人: Schahram Akbarian
• 金额: $ 118.3万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-04-01 至 2027-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10595615
• 关键词: Affect; Animals; Autopsy; Base Pairing; Blood; Brain; Cell Culture Techniques; Cells; Cessation of life; Chromatin; Chromatin Fiber; Chromosome Structures; Deterioration; Epidemic; Exposure to; Face; Genetic Engineering; Genome; Genomic approach; HIV; HIV Infections; HIV-associated neurocognitive disorder; HIV/AIDS; Hematopoietic stem cells; High Prevalence; Human; Human Engineering; Laboratories; Length; Life; Maps; Microglia; Molecular Profiling; Monitor; Mus; Myelogenous; Narcotics; Pattern; Persons; Predisposition; Resolution; Rewards; Site; Stimulant; Substance Use Disorder; Time; Transcript; Viral; Work; Xenograft Model; addiction; antiretroviral therapy; brain cell; cell type; design; epigenome; epigenomic profiling; epigenomics; induced pluripotent stem cell; neuroAIDS; neurogenomics; novel; transcriptome; virtual

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.

艾滋病毒相关的神经认知障碍在联合抗逆转录病毒治疗时代仍然存在 虽然HIV潜伏期和HIV转录物在人CNS中的细胞特异性表达仍然存在， 不完全理解。艾滋病毒相关神经系统疾病的患病率很高， 在cART稳定抑制的人群中识别CNS病毒逃逸，通常会因 艾滋病毒/艾滋病感染者中共同登记的药物使用障碍流行病， 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首先提供了 评估细胞类型特异性HIV“分子特征”，包括基因组整合模式， 在奖赏和成瘾回路的转录组和表观基因组水平上的改变 人类死后大脑然而，与该领域几乎所有其他基因组方法一样，我们正在进行的 研究面临着两个巨大的局限性：（A）完全的横截面设计，仅限于 基因组的组织和功能在一个单一的时间点-大脑捐赠者的死亡时间。一 同样的限制显然适用于细胞培养和动物。这是非常不幸的，因为这样的类型 感染和未感染脑细胞中的终点表观基因组和转录组图谱不能提供信息， 关于细胞生命早期的细胞特异性染色质状态（B） 因此，神经基因组学仅限于染色质的短读段测序，通常延伸150个碱基 对或更少。然而，在碱基对分辨率下进行分析会提供更多信息， 涵盖全长逆转录病毒插入的更宽窗口的表观基因组染色质景观 位点，其比当前读取长度高两个数量级。在这个前卫的项目中，我们将， 第一次，对于每个大脑，开始回顾性/纵向表观基因组分析，使用 在HIV领域建立良好的异种移植模型，以及基因工程改造的人iPSC- 衍生的造血祖细胞（HPC）。我们将首次踏上 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 进行性恶化）的HIV感染的骨髓衍生细胞中的表观基因组失调， 在大脑和血液中。