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 目前的艾滋病毒抗逆转录病毒治疗成功地控制了病毒复制， 从致命的疾病到可控的慢性病然而，尽管抑制病毒复制期间， 研究表明，潜伏的病毒库仍然是可检测的，这助长了病毒反弹。 当抗病毒抑制治疗中断时。这些病毒库几乎是立即建立起来的 当HIV不可逆地将其病毒基因组整合到人类DNA中时，病毒宿主非常 持久，不易受目前可用的抗逆转录病毒药物的治疗效果的影响， 最近的实验治疗方法难以治疗。艾滋病毒感染的另一个特点是， 病毒准种的宿主内基因型多样性。除了与碱基替换相关的遗传多样性之外， 突变，从慢性感染患者中回收的病毒DNA基因组池， 抑制性治疗通常含有高频率基因组截短和/或高度突变的、非复制的 病毒DNA基因组。在这些患者中只有一小部分前病毒基因组是基因组完整的 并且在没有治疗的情况下可能导致生产性病毒复制和病毒学反弹。此外，委员会认为， 李博士和其他研究小组最近的研究表明，艾滋病毒感染细胞的基因组， 完整和基因组缺陷的前病毒可以克隆扩增。这种携带病毒的感染细胞的克隆扩增 基因组完整的HIV前病毒提示HIV持续存在的重要机制。然而，纵向 克隆扩展的动态和机制尚未得到深入研究， 患者没有很好地描述。重要的是，我们目前对艾滋病病毒宿主的理解来自于 几乎完全来自对一种称为B亚型HIV-1的毒株的研究，这种病毒亚型主要影响第一- 世界各国。相比之下，C亚型HIV-1亚型是全球最流行的HIV-1毒株， 占全球HIV-1负担的50%。在这个R21应用中，我们建议纵向跟踪和 比较B和C亚型HIV宿主的基因型演变。我们建议检查克隆扩张 感染艾滋病病毒的细胞具体地说，我们假设对HIV DNA基因组的纵向检查和 整合位点将揭示在抑制性治疗期间持续存在的病毒物种所特有的特征， HIV亚型B与C之间的特征将有所不同，并且这些特征将与 个体的免疫学特征改变。这项研究将产生最大的交叉艾滋病毒亚型水库 与临床和免疫学数据相关的数据库。病毒基因型数据将用于开发亚型- 用于研究艾滋病毒持久性的特定测定和生物信息学管道。