Mechanisms controlling HIV latency and pathogenesis in microglia

小胶质细胞中控制 HIV 潜伏期和发病机制的机制

• 批准号: 10748702
• 负责人: Johannes Carolus Magnus Schlachetzki
• 金额: $ 43.45万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-14 至 2025-08-13
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10748702
• 关键词: ATAC-seq; Address; Archives; Artificial Intelligence; Atlases; Autopsy; Binding; Biological Models; Brain; Cells; ChIP-seq; Chromatin; Chronic; Cognitive; Computing Methodologies; Data; Epigenetic Process; Evaluation; FDA approved; Gene Expression; Gene Expression Profile; Genes; Genetic Transcription; Genome; HIV; HIV Genome; HIV Infections; HIV-associated neurocognitive disorder; Human; Immune response; Inflammatory; Interferons; Investigation; Knowledge; Length; Life Expectancy; Macrophage; Microglia; Myeloid Cells; National Archive; National NeuroAids Tissue Consortium; Neuropathogenesis; Pathogenesis; Patients; Pattern; Persons; Phenotype; Population; Proviruses; RNA; Regulator Genes; Risk; Sampling; Site; Specimen; Technology; Testing; Transcript; Viral; Virus; Virus Integration; antiretroviral therapy; chemokine; comorbidity; deep learning; epigenomics; frontal lobe; genome sequencing; histone modification; improved; induced pluripotent stem cell; insight; integration site; multiple omics; nanopore; next generation sequencing; novel; novel strategies; single cell technology; transcription factor; transcriptome sequencing; transcriptomics; whole genome

PROJECT SUMMARY The life expectancy of people with HIV (PWH) has improved significantly in the past decades with the introduction of antiretroviral therapies (ART). Nevertheless, the risk for developing comorbidities including HIV-associated neurocognitive impairment even in “well-controlled” PWH is significantly increased. One obstacle to the eradication of HIV and treatment of HIV-associated neurocognitive impairment is the lack of knowledge about the epigenetic mechanisms of HIV in microglia. Specifically, little is known about the extent of HIV integration into the host’s genome, specifically that of microglia, in PWH under ART; the viral and epigenetic gene regulatory mechanisms regulating HIV latency and neuropathogenesis; and whether the integrated HIV provirus is intact or defective, potentially inducing a chronic immune response in the brain. To address these knowledge gaps, we will use archived human post-mortem specimens obtained from the National NeuroAIDS Tissue Consortium (NNTC) as well as microglia-like cells generated from human induced pluripotent stem cells (iPSC-MG). We will use single cell multi-omics (RNA/ATAC-Seq) approaches to specifically obtain the transcriptomic and epigenomic landscapes of the viral and host genomes using single cell technologies. To decipher the epigenetic landscape including the potentially altered histone modification landscape of microglia and HIV, we will perform in addition ChIP-seq. Our proposed investigations are strongly supported by compelling preliminary data providing a gene expression and chromatin accessibility atlas of human microglia isolated from three PWH. In addition, we propose a novel approach to identify viral integration sites in microglia from human post-mortem samples and iPSC-MG using state-of-the-art Long-read sequencing and artificial intelligence technologies technology. We will use our established iPSC-MG HIV model system to further test the effect of ART on the epigenetic landscape, including histone modification and transcription factor binding, to understand the mechanisms regulating HIV latency and neuropathogenesis. In Aim 1, we will identify microglia gene expression signatures and their underlying gene regulatory mechanisms in HIV infection. For Aim 2, we will establish Long-read sequencing to decipher HIV-integration sites. In Aim 3, we will use iPSC-MG to identify the viral epigenetic landscape in microglia in the presence and absence of ART.

项目摘要 艾滋病毒感染者的预期寿命在过去几十年中显著提高， 抗逆转录病毒疗法（ART）。然而，发生合并症的风险，包括艾滋病毒相关的 即使在“控制良好”的PWH中，神经认知障碍也显著增加。一个障碍， 根除艾滋病毒和治疗艾滋病毒相关的神经认知障碍是缺乏知识， HIV在小胶质细胞中的表观遗传机制具体而言，人们对艾滋病毒的整合程度知之甚少 病毒和表观遗传基因调控 调节HIV潜伏期和神经发病机制;以及整合的HIV前病毒是否完整或 有缺陷，可能会在大脑中引发慢性免疫反应。 为了解决这些知识差距，我们将使用从以下地点获得的存档人类死后标本： 国家神经艾滋病组织联合会（NNTC）以及从人类产生的小胶质细胞样细胞 诱导多能干细胞（iPSC-MG）。我们将使用单细胞多组学（RNA/ATAC-Seq）方法， 利用单细胞技术， 技术.为了破译表观遗传景观，包括潜在的改变组蛋白修饰， 小胶质细胞和艾滋病毒的景观，我们将执行此外ChIP-seq。我们提议的调查 通过令人信服的初步数据支持，提供了一个基因表达和染色质可及性图谱， 从三个PWH分离的人小胶质细胞。此外，我们提出了一种新的方法来确定病毒整合 使用最先进的长读段测序，从人死后样本和iPSC-MG中的小胶质细胞中的位点 和人工智能技术。我们将使用我们建立的iPSC-MG HIV模型系统， 进一步测试ART对表观遗传景观的影响，包括组蛋白修饰和转录因子 结合，以了解调节HIV潜伏期和神经发病机制。 在目标1中，我们将确定小胶质细胞基因表达特征及其潜在的基因调控， HIV感染的机制。对于目标2，我们将建立长读序测序来破译HIV整合 网站.在目标3中，我们将使用iPSC-MG来鉴定存在和不存在iPSC-MG的小胶质细胞中的病毒表观遗传景观。 没有艺术。