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: 10432132
• 负责人: HOWARD S FOX
• 金额: $ 19.19万
• 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/10432132
• 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; Persons; 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.

项目概要 提出了一种创新方法来确定骨髓细胞在持久性和根除中的作用 来自大脑的 HIV-1 储存库，回应 RFA-MH-20-702。我们将使用黄金标准执行 非人灵长类系统，在感染 SIV 的动物中使用组合进行慢性病毒抑制 抗逆转录病毒治疗。中枢神经系统内抗 CD8 治疗将发现大脑中受感染的细胞，然后 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 转座酶可及染色质测序 (scATAC-seq) 测定，然后进行生物信息学分析和 验证。这将对骨髓细胞的性质产生无与伦比的洞察力，其中 SIV 作为一种 HIV模型持续存在于大脑中，将个体细胞转录组与表观遗传信息相结合 整个基因组。这些将以新的配对格式完成，获取两种模式的链接信息 来自同一个细胞。结合大脑中病毒的敏感检测。这将发生在 两个具体目标下的两年 R21。在目标 1 中，我们将在存在的情况下发现大脑中受 SIV 感染的细胞 抑制性 cART，允许对其进行识别，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细胞的已知数据，表型 SIV/HIV 可以持续存在的脑髓细胞。在目标 2 中，对这些细胞进行深入的分子表征 将进行，产生有关其表型以及上游控制机制的附加信息， 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域的关系， 及其他条件。我们将确保我们的数据遵循可查找、可访问、可互操作和可重用的原则 （公平）标准，以便我们和其他人可以在未来的策略中利用这些信息来压制或清除 来自大脑的病毒。这些研究的设计考虑了严谨性和可重复性，因此结果 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 来自大脑的水库。