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.

HIV相关的神经认知障碍在联合抗逆转录病毒治疗时代持续存在 (cART)，而人类中枢神经系统中的 HIV 潜伏期和 HIV 转录物的细胞特异性表达仍然存在 不完全理解。 HIV 相关神经系统疾病的患病率很高，并且呈上升趋势 在 cART 稳定抑制的人群中识别中枢神经系统病毒逃逸，通常因 HIV 感染者/艾滋病患者 (PLWHA) 中共同登记的物质使用障碍 (SUD) 流行情况， SUD 对 CNS 功能也有深远的影响。我们实验室正在进行的工作是首先提供 评估细胞类型特异性艾滋病毒“分子特征”，包括基因组整合模式和 奖赏和成瘾回路中转录组和表观基因组水平的改变 人类死后的大脑。然而，就像该领域几乎所有其他基因组方法一样，我们正在进行的 研究面临两个巨大的局限性：（A）完全是横截面设计，仅限于快照 单个时间点（大脑捐献者死亡时间）的基因组组织和功能。非常 同样的限制显然也适用于细胞培养和动物。这是非常不幸的，因为此类类型 感染和未感染脑细胞的终点表观基因组和转录组图谱无法提供信息 关于细胞生命早期阶段的细胞特异性染色质状态 (B) 传统大脑 迄今为止，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 每次读取对或更少。然而，以碱基对分辨率进行分析会提供更多信息， 表观基因组染色质景观跨越更宽的窗口，涵盖全长逆转录病毒插入 位点，比当前读取长度高两个数量级。在这个前卫项目中，我们将， 首次对每个大脑进行回顾性/纵向表观基因组分析，使用 HIV 领域已建立良好的异种移植模型，以及基因工程人类 iPSC- 衍生的造血祖细胞（HPC）。我们将首次踏上纵向 单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 HIV感染的骨髓来源细胞的表观基因组失调（进行性恶化） 在大脑和血液中。