Single cell transcriptomics of HIV persistence and latency

HIV持续性和潜伏期的单细胞转录组学

• 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
• 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

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.

总结 HIV-1感染的抗逆转录病毒治疗（ART）可抑制病毒复制， CD 4 + T细胞计数和预防疾病进展。然而，ART治疗不是治愈性的， 中断治疗会持续释放病毒复发。抗逆转录病毒治疗后病毒库的持续存在 是艾滋病治愈的主要障碍提出了“休克和杀死”战略，以激活和消除艾滋病毒 库目前没有通过支持潜伏期的T细胞状态或谱系的知识来通知。一 潜伏期研究中最大的挑战之一是区分潜伏细胞和非潜伏细胞， 这在不干扰细胞的潜伏状态的情况下本质上是难以做到的。通过当前的方法，蜂窝 需要激活来计数潜伏细胞，这破坏了我们想要研究的状态。到 为了克服潜伏期研究的这一主要障碍，我们开发了一个HIV诱导的谱系追踪模型 在人源化小鼠中的HILT，其不可逆地遗传标记受感染的细胞。当与单细胞 RNA测序（scRNAseq）方法在HIV感染，ART治疗的动物中，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。初步研究 开始提供一个前所未有的，单细胞基因组分类的HIV感染的CD 4 T细胞 细胞谱系和状态在急性感染和早期抗逆转录病毒治疗。在本提案中，我们 在人源化小鼠中探索持续感染的人CD 4 T细胞的单细胞多组学， 它响应寡克隆TCR活化而不是稳态增殖。T细胞的系统生物学将 用于解剖新型HIV小动物模型中的潜在储库，以了解储库如何 在不同的细胞状态下产生和维持。基因组分析可用于鉴定药物或生物制品。 干预措施可以推动细胞向活跃的HIV表达方向发展，并且不依赖于细胞活化 状态这些可用于开发旨在增强表达和进行性免疫缺陷的治疗策略。 潜在水库的衰减。我们假设单细胞多组学方法将阐明 发育多样的T细胞谱系和转录状态，窝藏艾滋病毒水库，每一个 簇可能显示与HIV持久性相关的独特基因程序。反转的表达式 与艾滋病毒持续存在有关的因素可能会重新激活储存库。单细胞多组学可能揭示新的 从不同的T细胞状态清除HIV的有针对性的策略。这项拟议的研究利用了一个团队， 在HIV免疫发病机制、人源化小鼠、单细胞基因组学、深入表型人类T细胞方面的专业知识 新型小动物模型中的细胞储库。