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: 10457112
• 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/10457112
• 关键词: AIDS/HIV problem; 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; Hematopoietic stem cells; High Prevalence; Human; Human Engineering; Laboratories; Length; Life; Microglia; Molecular Profiling; Monitor; Mus; Myelogenous; Narcotics; Pattern; Persons; Resolution; Rewards; Site; Stimulant; Substance Use Disorder; Time; Transcript; Viral; Work; Xenograft Model; addiction; antiretroviral therapy; brain cell; cell type; design; epigenome; 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.

在抗逆转录病毒疗法的时代，与HIV相关的神经认知疾病持续存在 （CART）而HIV潜伏期和HIV转录本在人CNS中的细胞特异性表达仍然存在 不完全理解。与HIV相关的神经系统疾病的患病率很高 认识到CNS病毒逃生的人稳定地被推车抑制，通常会更加复杂 艾滋病毒/艾滋病患者（PLWHA）的物质使用障碍的共同注册流行病（SUD） 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 评估细胞类型的特异性HIV“分子特征”，包括基因组整合模式和 奖励和成瘾电路中转录组和表观基因组水平的改变 人类后大脑。但是，就像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）专门的横截面设计，仅限于 基因组组织和功能在一个时间点 - 大脑供体死亡的时间。那是 相同的限制显然适用于细胞培养和动物。这是非常不幸的 感染和未感染的脑细胞中端点表观基因组和转录组映射无法告知 在细胞生命的早期（b）常规大脑中，大约在细胞特异性的染色质状态（b） 迄今为止，神经基因组学仅限于染色质的简短读取测序，通常扩展150个碱基 对或更少的每读。但是，以基础分辨率为基础，概况将更加信息丰富 横跨更宽窗口的表观基因组染色质景观，包括全长逆转录病毒插入 站点，高于当前读取长度的两个数量级。在这个前卫项目中，我们将 对于每个大脑 异种移植模型在HIV领域已建立了良好的基因工程人IPSC- 衍生的造血祖细胞（HPC）。我们将第一次开始纵向 单个染色质纤维的表观基因组标记，探索动态变化甚至可逆性（或 居住在HIV感染的髓样细胞中表观基因组失调的逐步影响） 在大脑和血液中。