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 提出了一种新的方法来确定髓系细胞在慢性粒细胞白血病持续和根除中的作用。 大脑中的HIV-1储存库，对RFA-MH-20-702的反应。我们将使用黄金标准进行表演 SIV感染动物的非人灵长类系统与慢性病毒抑制联合使用 抗逆转录病毒治疗。大脑中被感染的细胞将通过中枢神经系统内抗CD8治疗被发现，如下 随后通过髓系细胞分离纯化、单细胞RNA测序(scRNA-seq)和单细胞 转座酶可及染色质测序分析(scATAC-seq)，随后进行生物信息学分析和 验证。这将带来对髓系细胞性质的无与伦比的洞察，其中SIV作为一种 HIV的模型，在大脑中持续存在，将单个细胞转录与表观遗传学信息结合在一起 整个基因组。这些将以一种新的配对格式进行，获得关于两种医疗模式的关联信息 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 两个具体目标下的两年R21。在目标1中，我们将发现大脑中感染SIV的细胞 压制手推车，允许识别他们的身份，与同伴的信息相比较 未感染的细胞，以及来自单细胞和其他研究的关于脑髓系细胞的已知数据，表型 其中SIV/HIV可以持续存在的脑髓系细胞。在目标2中，深入研究这些细胞的分子特征 将被执行，产生关于它们的表型以及上游控制机制的更多信息， 转录潜力，以及与影响艾滋病毒、中枢神经系统疾病的基因及其控制区的关系， 以及其他条件。我们将确保我们的数据符合可查找、可访问、可互操作和可重复使用的 (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来保持沉默或清除 来自大脑的病毒。这些研究的设计考虑了严谨性和重复性，因此结果来自 这些研究将为髓系细胞在持续和根除HIV-1中的作用提供新的见解 大脑中的蓄水池。