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：
10570277
负责人：
BENJAMIN K CHEN
金额：
$ 62.87万
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/10570277
关键词：
Acute Animal Model Animals Antibodies Bar Codes Behavior Binding Biological Biological Models CD4 Positive T Lymphocytes Cell Communication Cell Count Cell Lineage Cell Survival 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 Proliferating 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 感染的抗逆转录病毒治疗 (ART) 可抑制病毒复制、保留和改善 CD4+ T 细胞计数并可预防疾病进展然而，ART 治疗并不能治愈疾病，而且无法治愈。治疗中断持续释放病毒复发 ART 后病毒库的持续存在。是治疗艾滋病毒的主要障碍，建议采用“休克和杀死”策略来激活和消除艾滋病毒。目前，储存库尚不了解支持潜伏期的 T 细胞状态或谱系。潜伏研究中最大的挑战之一是区分潜伏细胞和非潜伏细胞，这是就目前的方法而言，如果不扰乱细胞的潜伏状态，就很难做到这一点。需要激活才能计数潜伏细胞，这破坏了我们想要研究的状态。克服了潜伏期研究的这一主要障碍，我们开发了一种艾滋病毒诱导的谱系追踪模型（HILT）在人源化小鼠中与单细胞结合时不可逆地对受感染的细胞进行基因标记。 RNA 测序 (scRNAseq) 方法用于感染 HIV 并接受 ART 治疗的动物，其结果是一种新兴的与 HIV 感染和潜伏期相关的转录状态的基因组分辨率视图。这里提出的开始提供前所未有的 HIV 感染 CD4 T 的单细胞基因组分类急性感染期间和早期抗逆转录病毒治疗期间的细胞谱系和状态在本提案中。探索人源化小鼠中持续感染的人类 CD4 T 细胞的单细胞多组学，并研究如何它对寡克隆 TCR 激活和 T 细胞稳态增殖作出反应。用于剖析新型艾滋病毒小动物模型中的潜在储存库，以了解储存库是如何存在的以不同的细胞状态生成和维持的基因组分析可用于识别药物或生物制品。可以推动细胞主动表达 HIV 且独立于细胞激活的干预措施这些可用于制定旨在增强表达和进步的治疗策略。我们发现单细胞多组学方法将阐明潜在储库的衰变。发育上多样化的 T 细胞谱系和转录状态包含 HIV 储存库，并且每个簇可能显示与逆转 HIV 持久性相关的独特基因程序。与HIV持续存在相关的因素可能会重新激活病毒库。单细胞多组学可能会揭示新的病毒库。拟议的研究利用了一个团队，以从不同的 T 细胞状态中清除 HIV。 HIV免疫发病机制、人源化小鼠、单细胞基因组学、深度人类T细胞表型方面的专业知识新型小动物模型中的细胞储存库。