Insights into the dynamics of clonal expansion of genome-intact proviruses by examining longitudinal evolution of HIV proviral DNA compositions

通过检查 HIV 原病毒 DNA 组成的纵向进化，深入了解基因组完整的原病毒克隆扩增的动态

• 批准号: 10013710
• 负责人: Kwun Wing Guinevere Lee
• 金额: $ 29.66万
• 依托单位: WEILL MEDICAL COLL OF CORNELL UNIV
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-02-24 至 2022-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10013710
• 关键词: Accounting; Affect; Aftercare; Anti-Retroviral Agents; Antiviral Agents; Archives; Bioinformatics; Biological Assay; Blood specimen; CD4 Lymphocyte Count; CD8B1 gene; Cells; Characteristics; Chronic; Clinical; Clonal Expansion; Computer software; Cytotoxic T-Lymphocytes; DNA; Data; Data Set; Databases; Evolution; Frequencies; Genetic Variation; Genome; Genotype; HIV; HIV Infections; HIV antiretroviral; HIV-1; Immunologics; Individual; Infection; Interferon Type II; Interruption; Knowledge; Lead; Light; Link; Longitudinal Studies; Mutation; Participant; Patients; Peripheral Blood Mononuclear Cell; Prevalence; Proviruses; Publishing; RNA Splicing; Refractory; Research Personnel; Resolution; Sampling; Sequence Homology; Site; T cell response; Therapeutic Effect; Time; Viral; Viral Genome; Viral reservoir; Virus Integration; Virus Latency; Virus Replication; antiretroviral therapy; base; bioinformatics pipeline; deep sequencing; enzyme linked immunospot assay; human DNA; insight; integration site; novel; patient subsets; promoter; response; viral DNA; viral rebound; virology

PROJECT SUMMARY Current HIV antiretroviral treatment successfully controls viral replication and has transformed HIV-infection from a fatal illness to a manageable chronic condition. However, despite suppression of viral replication during treatment, studies have shown that pools of latent viral reservoirs remain detectable, which fuel viral rebound when antiviral suppression treatment is interrupted. These viral reservoirs are established almost immediately upon infection when HIV irreversibly integrates its viral genome into human DNA. Viral reservoirs are extremely durable, not susceptible to therapeutic effects of currently available antiretroviral agents, and have been refractory to recent experimental treatment approaches. HIV infection is also characterized by a high level of intrahost genotypic diversity of viral quasispecies. In addition to genetic diversity associated base substitution mutations, pools of viral DNA genomes recovered from chronically-infected patients under prolonged suppressive therapy often contain high frequencies of genome-truncated and/or hypermutated, non-replication- competent viral DNA genomes. Only a small fraction of proviral genomes in these patients are genome-intact and may lead to productive viral replication and virologic rebound in the absence of treatment. Furthermore, recent studies by Dr. Lee and other groups have shown clear evidence that HIV-infected cells by both genome- intact and genome-defective proviruses can clonally expand. Such clonal-expansion of infected cells carrying genome-intact HIV proviruses suggests an important mechanism of HIV persistence. However, longitudinal dynamics and mechanism of clonal expansion has not been studied thoroughly, and the diversity between patients not well characterized. Importantly, our current understanding of HIV reservoirs has been derived almost exclusively from studies on a strain called subtype B HIV-1, the predominate viral subtype affecting first- world nations. In contrast, subtype C HIV-1 subtypes is the most prevalent HIV-1 strain globally, accounting approximately 50% of the global HIV-1 burden. In this R21 application, we propose to longitudinally track and compare the genotypic evolution of HIV reservoirs in subtype B and C. We propose to examine clonal expansion of HIV-infected cells. Specifically, we hypothesize that longitudinal examination of HIV DNA genomes and integration sites will reveal features unique to viral species that persist during suppressive therapy, that these features will differ between HIV subtype B versus C, and that these features will be associated with the immunological profile changes in an individual. This study will generate the largest cross-HIV-subtype reservoir database with linked clinical and immunological data. Viral genotypic data will be used to develop subtype- specific assays and bioinformatics pipelines for the study of HIV persistence.

项目摘要 当前的HIV抗逆转录病毒治疗成功控制了病毒复制，并从 致命疾病，可控制慢性病。但是，尽管抑制了病毒复制 治疗，研究表明，潜在病毒储存库池仍然可检测 当抗病毒抑制治疗中断时。这些病毒储藏几乎立即建立 感染后，当HIV不可逆地将其病毒基因组整合到人DNA中时。病毒水库极为 耐用，不容易受到当前可用抗逆转录病毒药物的治疗作用，并且已经 对最近的实验治疗方法的难治性。艾滋病毒感染也以高水平的特征 病毒式准植物内基因型多样性。除了遗传多样性相关的基础替代 突变，从延长的慢性感染患者中回收的病毒DNA基因组池 抑制性疗法通常包含高频率的基因组截断和/或过度无重新杀伤的频率 合理的病毒DNA基因组。这些患者中只有一小部分病毒基因组是基因组独立 并可能在没有治疗的情况下导致生产性病毒复制和病毒学反弹。此外， Lee博士和其他群体的最新研究表明，明确的证据表明，HIV感染了两个基因组 - 完整和基因组缺陷的病毒可以在克隆上扩展。这种携带感染细胞的克隆膨胀 基因组实用的HIV病毒提出了艾滋病毒持久性的重要机制。但是，纵向 克隆扩张的动态和机制尚未得到彻底研究，并且之间的多样性 患者表征不佳。重要的是，我们目前对HIV水库的理解已得出 几乎完全来自对称为亚型B HIV-1的菌株的研究，主要影响病毒亚型的主要影响 世界国家。相反，亚型C HIV-1亚型是全球最普遍的HIV-1菌株，会计 大约50％的全球HIV-1负担。在此R21应用程序中，我们建议纵向跟踪和 比较亚型B和C中HIV储存剂的基因型进化。我们建议检查克隆膨胀 感染HIV的细胞。具体而言，我们假设对HIV DNA基因组和 集成站点将揭示病毒物种在抑制性治疗过程中持续存在的特征， HIV亚型B与C相对于C的功能将有所不同，并且这些功能将与 一个人的免疫概况变化。这项研究将产生最大的跨HIV-SUBTYPE水库 具有链接的临床和免疫数据的数据库。病毒基因型数据将用于发展亚型 用于研究HIV持久性的特定测定和生物信息学管道。