Single cell transcriptomics of HIV persistence and latency

HIV持续性和潜伏期的单细胞转录组学

基本信息

批准号：
10258566
负责人：
BENJAMIN K CHEN
金额：
$ 63.02万
依托单位：
ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-03-19 至 2026-02-28
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10258566
关键词：
Acute Animal Model Animals Antibodies Bar Codes Behavior Biological Biological Models CD4 Positive T Lymphocytes Cell Communication Cell Count Cell Lineage Cells Cellular Indexing of Transcriptomes and Epitopes by Sequencing Classification Development Disease Progression Gastrointestinal tract structure Gene Expression Profile Genes Genetic Transcription Genomics HIV HIV Infections HIV-1 Human Image Immune system Immunologic Deficiency Syndromes In Vitro Infection Interruption Intervention Knowledge Maps Measures Memory Methods Modeling Morphology Mucous Membrane Mus Pathway Analysis Pathway interactions Pattern Pharmaceutical Preparations Phenotype Relapse Research Resolution Shock Spleen Stimulus Superantigens System Systems Biology T-Cell Activation T-Lymphocyte TCR Activation Testing Time Tissue-Specific Gene Expression Tissues Viral Viral reservoir Virus Virus Replication acute infection antiretroviral therapy humanized mouse improved in vivo migration mouse model multiple omics novel preservation prevent programs purge response single-cell RNA sequencing transcriptomics

项目摘要

Summary Antiretroviral therapy (ART) in HIV-1 infection suppresses viral replication, preserves and improves the CD4+ T cell count and prevents disease progression. However, treatment with ART is not curative, and interruption of therapy consistently unleashes viral relapse. The persistence of a viral reservoir following ART is the major obstacle to an HIV cure. Proposed “shock and kill” strategies to activate and eliminate the HIV reservoir are currently not informed by a knowledge of the T cell states or lineages that support latency. One of the greatest challenges in latency research is to distinguish latent cells from non-latent cells, which is inherently difficult to do without perturbing the latent state of the cells. With current approaches, cellular activation is required to enumerate latent cells, which disrupts the very state that we would like to study. To overcome this major roadblock to latency studies, we have developed an HIV-induced lineage tracing model (HILT) in humanized mouse that irreversibly genetically marks infected cells. When combined with single cell RNA sequencing (scRNAseq) approaches in HIV-infected, ART-treated animals, the result is an emerging genomic resolution view of transcriptional states associated with HIV infection and latency. Preliminary studies presented here begin to provide an unprecedented, single cell genomic classification of HIV-infected CD4 T cell lineages and states during acute infection and during early antiretroviral treatment. In this proposal, we explore single cell multi-omics of persistently infected human CD4 T cells in humanized mice and examine how it responds to oligoclonal TCR activation versus homeostatic proliferation. The systems biology of T cells will be used to dissect latent reservoirs in novel small animal models for HIV to understand how a reservoir is generated and maintained in distinct cell states. Genomic analysis may be used to identify drugs or biologic interventions that can push cells towards active HIV expression and are independent of cellular activation state. These could be used to develop cure strategies aimed at enhancing expression and the progressive decay of the latent reservoir. We hypothesize that a single cell multi-omics approach will elucidate developmentally diverse T cell lineages and transcriptional states that harbor HIV reservoirs, and that each cluster may display unique gene programs associated with HIV persistence. Reversing the expression of factors associated with HIV persistence may reactivate the reservoir. Single cell multi-omics may unveil new targeted strategies to purge HIV from different T cell states. The proposed study leverages a team with expertise in HIV immunopathogenesis, humanized mice, single cell genomics, to deeply phenotype human T cell reservoirs in novel small animal models.

概括 HIV-1感染中的抗逆转录病毒疗法（ART）抑制病毒复制，保留并改善 CD4+ T细胞计数并防止疾病进展。但是，用艺术治疗无法治愈，并且治疗的中断始终释放出病毒释放。遵循艺术的病毒研究器的持久性是艾滋病毒治愈的主要障碍。提出了激活和消除艾滋病毒的“震惊和杀戮”策略目前，水库尚未了解支持潜伏期的T细胞状态或谱系。一潜伏期研究中最大的挑战是将潜在细胞与非lantent细胞区分开本质上很难在不扰动细胞的潜在状态。使用当前的方法，细胞需要激活以枚举潜在细胞，这破坏了我们想要研究的状态。到克服了这一主要的潜伏期研究障碍，我们开发了一种HIV引起的谱系追踪模型（握在人源化的小鼠中）在不可逆地遗传上标记感染细胞。当与单细胞结合使用时 RNA测序（SCRNASEQ）在受HIV感染的，艺术处理的动物中的方法，结果是出现转录状态与HIV感染和潜伏期相关的转录状态的基因组分辨率视图。初步研究这里提出的开始提供了前所未有的单细胞基因组分类的HIV感染CD4 T 急性感染和抗逆转录病毒治疗期间的细胞谱系和状态。在这个建议中，我们探索人文化小鼠中持续感染的人类CD4 T细胞的单细胞多词，并检查如何它响应寡克隆TCR激活与稳态增殖。 T细胞的系统生物学将用于在新颖的小动物模型中剖析潜在储层，以了解储层的方式在不同的细胞状态下生成和维护。基因组分析可用于鉴定药物或生物学可以将细胞推向活性HIV表达并且与细胞激活无关的干预措施状态。这些可用于制定旨在增强表达和进步性的旨在的治疗策略潜在水库的腐烂。我们假设单个单元格多词方法将阐明发育中的T细胞谱系和具有艾滋病毒水库的转录状态的发展，每个状态群集可能显示与HIV持久性相关的独特基因程序。颠倒表达与HIV持久性相关的因素可能会重新激活储层。单细胞多媒体可能会推出新的从不同T细胞状态清除HIV的有针对性策略。拟议的研究利用了一个团队 HIV免疫病发生，人性化小鼠，单细胞基因组学的专业知识，深层表型新型小动物模型中的细胞库。