Single-cell multi-omic analysis of opioid-mediated HIV disease pathogenesis

阿片类药物介导的 HIV 疾病发病机制的单细胞多组学分析

• 批准号: 10813914
• 负责人: Kathleen L. Collins
• 金额: $ 51.16万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-30 至 2025-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10813914
• 关键词: ATAC-seq; Affect; Antiviral Response; Atlases; Basic Science; Bioinformatics; Biology; Bone Marrow; Cell Differentiation process; Cell Line; Cells; Central Nervous System; Chromatin; Clinical Treatment; Complex; Detection; Diagnosis; Disease; Epigenetic Process; Foundations; Future; Gene Expression; Genes; Goals; HIV; HIV Infections; Hematopoietic; Hematopoietic stem cells; Histone Deacetylase Inhibitor; Immune; Immune response; Infection; Inflammatory; Innate Immune Response; Joints; Lipopolysaccharides; Macrophage; Maps; Measures; Mediating; Methods; Modeling; Molecular; Myelogenous; Opioid; Opioid Receptor; Pathogenesis; Pathway interactions; Peripheral; Peripheral Blood Mononuclear Cell; Phase; Prevention; Public Health; Residual state; Risk; Role; Site; Stimulus; Substance Use Disorder; Supporting Cell; T-Lymphocyte; Technology; Testing; Therapeutic; Time; Toll-like receptors; Transcriptional Regulation; Viral; Viral Genes; Virion; Virus Activation; Virus Diseases; Virus Integration; Virus Latency; Work; antiretroviral therapy; cell type; computer framework; cytokine; epigenome; epigenomics; hematopoietic differentiation; histone modification; improved; insight; integration site; latent infection; monocyte; multiple omics; new technology; novel; opioid exposure; pathogen; preference; receptor expression; response; single cell sequencing; single cell technology; single-cell RNA sequencing; substance use; transcriptome; transcriptomics

Abstract Routine HIV treatment with combination antiretroviral therapy (cART) eliminates nearly all actively infected cells. Nevertheless, the small reservoir of residual cells, some of which can remain dormant for long periods of time before becoming active and producing new virus particles, represents a crucial barrier to completely curing the disease. Substance use disorders introduce further challenges—for example, many immune cells express opioid receptors and undergo significant molecular changes after opioid exposure, which can increase their vulnerability to HIV infection. Our recent work suggests that the global transcriptomic and epigenomic changes during hematopoietic differentiation affect viral latency and activation. Additionally, we recently found that global inhibition of histone deacetylase activity in HSPCs increases viral activation, further implicating epigenomic changes in activation. Deciphering the contributions of addictive substances, inflammatory stimuli, and cell state to HIV infection and latency is crucial for ongoing efforts to cure HIV. In particular, the following fundamental questions remain unanswered: How does substance use change the transcriptomic and epigenomic states of immune cells? How do these changes in turn affect HIV infection and latency? How do the effects of substance use on HIV infection and latency vary across different immune cell types and states? Here, we will combine our experimental platform for identifying latently and actively infected cells, single-cell transcriptome, and epigenome sequencing, and our recently developed computational integration methods to investigate these questions. Our interdisciplinary team combines expertise in HIV basic science, HIV clinical treatment, and bioinformatics to develop an experimental and computational framework for integrated gene expression, chromatin accessibility, histone modification, and insertion site profiling into a single picture of how opioids affect viral infection and latency. Specifically, this project will (1) use single-cell RNA-seq, single-cell ATAC-seq, and single-cell Cut&Tag to map diversity of infected cell response to opioid exposure, (2) investigate the relationship between immune cell type and differentiation state and viral activation, and (3) determine viral integration sites through single-cell RNA-seq. Together, these aims will produce a comprehensive, integrated transcriptomic and epigenomic atlas of how HIV-infected immune cells respond to opioid exposure as well as how opioids impact HIV infection. Our work also develops a broadly applicable experimental and computational framework, laying a foundation for the discovery of novel insights into HIV infection and latency in the context of substance use disorders.

摘要 常规HIV治疗与联合抗逆转录病毒疗法（cART）消除了几乎所有的活跃感染细胞。 然而，残留细胞的小水库，其中一些可以保持休眠很长一段时间， 在变得活跃并产生新的病毒颗粒之前， 疾病物质使用障碍带来了进一步的挑战-例如，许多免疫细胞表达阿片样物质 受体，并在阿片类药物暴露后发生显着的分子变化，这可能会增加他们的脆弱性 艾滋病毒感染。我们最近的工作表明，全球转录组和表观基因组的变化， 造血分化影响病毒潜伏和激活。此外，我们最近发现，全球 HSPC中组蛋白脱乙酰酶活性的抑制增加了病毒活化，进一步暗示了表观基因组 激活的变化。解读成瘾物质、炎症刺激和细胞状态的贡献 艾滋病毒感染和潜伏期是至关重要的持续努力治愈艾滋病毒。特别是，以下基本 问题仍然没有答案：物质使用如何改变转录组和表观基因组状态， 免疫细胞？这些变化又如何影响艾滋病毒感染和潜伏期？物质的影响是如何 不同免疫细胞类型和状态对HIV感染和潜伏期的影响不同？在这里，我们将联合收割机 用于鉴定潜伏和活动感染细胞、单细胞转录组和表观基因组的实验平台 测序，以及我们最近开发的计算整合方法来研究这些问题。我们 跨学科团队结合了艾滋病毒基础科学、艾滋病毒临床治疗和生物信息学方面的专业知识， 开发一个实验和计算框架，用于整合基因表达，染色质可及性， 组蛋白修饰和插入位点分析成阿片类药物如何影响病毒感染的单一图片， 延迟。具体而言，该项目将（1）使用单细胞RNA-seq，单细胞ATAC-seq和单细胞Cut&Tag 绘制受感染细胞对阿片类药物暴露反应的多样性，（2）研究免疫与阿片类药物暴露之间的关系。 细胞类型和分化状态以及病毒活化，以及（3）通过单细胞 RNA测序总之，这些目标将产生一个全面的，综合的转录组和表观基因组图谱 艾滋病毒感染的免疫细胞如何对阿片类药物暴露作出反应，以及阿片类药物如何影响艾滋病毒感染。我们 工作还开发了一个广泛适用的实验和计算框架，奠定了基础， 在物质使用障碍的背景下发现对艾滋病毒感染和潜伏期的新见解。