Macrophages and Microglia, Gene Expression and Chromatin: Illuminating the Myeloid Viral Reservoir in the Brain through Single Cell Analyses

巨噬细胞和小胶质细胞、基因表达和染色质：通过单细胞分析阐明大脑中的骨髓病毒库

• 批准号: 10327555
• 负责人: HOWARD S FOX
• 金额: $ 22.95万
• 依托单位: UNIVERSITY OF NEBRASKA MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10327555
• 关键词: ATAC-seq; Address; Adverse effects; Affect; Animals; Antibodies; Autopsy; Bioinformatics; Biological Assay; Brain; CD8-Positive T-Lymphocytes; CD8B1 gene; Cell Separation; Cell physiology; Cells; Cellular Assay; Central Nervous System Diseases; Central Nervous System Infections; Characteristics; Chromatin; Chronic; Companions; Data; Development; Ensure; Epigenetic Process; Exploratory/Developmental Grant; FAIR principles; Future; Gene Expression; Genes; Genetic Transcription; Goals; Gold; HIV; HIV Infections; HIV-1; Individual; Infection; Injections; Knowledge; Link; Macaca; Macaca mulatta; Microglia; Modality; Modeling; Molecular; Myelogenous; Myeloid Cells; Nature; Nervous system structure; Neuraxis; Phenotype; Population; Property; Publishing; Reproducibility; Research; Role; SIV; Standard Model; System; Tissues; Transposase; Validation; Viral; Viral Genes; Viral reservoir; Virus; Work; antiretroviral therapy; brain cell; cell type; cisterna magna; design; detection limit; experimental study; innovation; insight; macrophage; neuroAIDS; new technology; nonhuman primate; pandemic disease; prevent; response; single cell analysis; single cell sequencing; single cell technology; single-cell RNA sequencing; transcriptome; viral rebound; whole genome

Project Summary An innovative approach is proposed to determine the Role of Myeloid Cells in Persistence and Eradication of HIV-1 Reservoirs from the Brain, in response to RFA-MH-20-702. We will perform using the gold-standard nonhuman primate system, in SIV-infected animals with chronic viral suppression using combination antiretroviral therapy. The infected cells in the brain will be uncovered by intra-CNS anti-CD8 treatment, following subsequently by myeloid cell isolation and purification, single-cell RNA sequencing (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq), followed by bioinformatic analysis and validation. This will give result into unparalleled insight into the nature of the myeloid cells in which SIV, as a model for HIV, persists in the brain, combining individual cellular transcriptomes with epigenetic information on the whole genome. These will be done in a new paired format, obtaining linked information on the two modalities from the same cell. combined with sensitive assays for virus in the brain. This will take place in the context of a two-year R21 under two Specific Aims. In Aim 1, we will uncover the SIV-infected cells in the brain in the presence of suppressive cART, allowing their identification and, in comparison with the information on the companion uninfected cells, as well as known data on brain myeloid cells from single cell and other studies, the phenotype of brain myeloid cells in which SIV/HIV can persist. In Aim 2, in-depth molecular characterization of these cells will be performed, yielding additional information on their phenotype, as well as upstream control mechanisms, transcriptional potential, as well as relationships to genes and their control regions that affect HIV, CNS disease, and other conditions. We will ensure our data adhere to the Findable, Accessible, Interoperable, and Reusable (FAIR) standards in order that we and others can utilize this information in future strategies to silence or clear virus from the brain. These studies are designed with rigor and reproducibility factored in, thus the results from these studies will provide new insights into the role of myeloid cells in persistence and eradication of HIV-1 reservoirs from the brain.

项目摘要 提出了一种创新的方法来确定髓样细胞在持续和根除 来自大脑的HIV-1储库，响应RFA-MH-20-702。我们将使用金本位制 非人灵长类动物系统，在SIV感染的动物中使用联合 抗逆转录病毒疗法脑中受感染的细胞将通过CNS内抗CD 8治疗暴露， 随后通过骨髓细胞分离和纯化、单细胞RNA测序（scRNA-seq）和单细胞RNA测序， 用于转座酶可重复染色质测序（scATAC-seq）的测定，随后进行生物信息学分析， 验证。这将导致对骨髓细胞性质的前所未有的深入了解，SIV作为一种免疫缺陷病毒， 艾滋病毒的模型，持续存在于大脑中，结合个别细胞转录组与表观遗传信息， 整个基因组这些将以一种新的配对格式完成，获得关于两种模式的链接信息 来自同一个细胞。再加上对大脑中病毒的敏感检测这将在一个 第21章两个目标在目标1中，我们将在大脑中发现SIV感染的细胞， 抑制性cART，允许他们的识别，并与同伴的信息进行比较， 未感染的细胞，以及来自单细胞和其他研究的脑髓样细胞的已知数据，表型 SIV/HIV可以持续存在的脑骨髓细胞。在目标2中，这些细胞的深入分子表征 将进行，产生额外的信息，他们的表型，以及上游控制机制， 转录潜力，以及与影响HIV，CNS疾病， 和其它条件。我们将确保我们的数据符合“可查找、可验证、可互操作和可重用”原则 （公平）标准，以便我们和其他人可以在未来的战略中利用这些信息， 病毒从大脑。这些研究的设计考虑了严谨性和可重复性，因此， 这些研究将为骨髓细胞在HIV-1持续存在和根除中的作用提供新的见解 大脑的储存库。