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.

项目概要 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，并已将艾滋病毒感染从 致命的疾病转变为可控制的慢性病。然而，尽管病毒复制受到抑制 研究表明，潜伏病毒库仍然可以检测到，这会加剧病毒反弹 当抗病毒抑制治疗中断时。这些病毒库几乎立即建立 感染后，HIV 不可逆地将其病毒基因组整合到人类 DNA 中。病毒储存库极为 持久，不易受到现有抗逆转录病毒药物治疗效果的影响，并且已被 对最近的实验性治疗方法无效。 HIV感染的另一个特点是高水平 病毒准种的宿主内基因型多样性。除了与碱基取代相关的遗传多样性 突变，从长期感染的患者体内恢复的病毒 DNA 基因组池 抑制疗法通常包含高频率的基因组截短和/或超突变、非复制- 有效的病毒DNA基因组。这些患者中只有一小部分原病毒基因组是完整的 在没有治疗的情况下，可能会导致有效的病毒复制和病毒学反弹。此外， 李博士和其他小组最近的研究表明，有明确的证据表明，HIV 感染细胞的基因组- 完整的和基因组缺陷的原病毒可以克隆扩增。这种携带病毒的受感染细胞的克隆扩增 基因组完整的艾滋病毒原病毒表明艾滋病毒持续存在的重要机制。然而，纵向 克隆扩增的动力学和机制尚未得到彻底研究，并且克隆扩增之间的多样性 患者特征不明确。重要的是，我们目前对艾滋病毒储存库的理解已经得出 几乎完全来自对称为 B 亚型 HIV-1 的毒株的研究，该毒株是影响首先的主要病毒亚型 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 约占全球 HIV-1 负担的 50%。在此 R21 应用程序中，我们建议纵向跟踪和 比较 B 型和 C 型 HIV 储存库的基因型进化。我们建议检查克隆扩增 HIV感染的细胞。具体来说，我们假设 HIV DNA 基因组的纵向检查和 整合位点将揭示病毒物种独特的特征，这些特征在抑制治疗期间持续存在，这些特征 HIV B 亚型与 C 亚型之间的特征会有所不同，并且这些特征将与 个体免疫学特征的变化。这项研究将产生最大的跨HIV亚型储存库 具有链接的临床和免疫学数据的数据库。病毒基因型数据将用于开发亚型 用于研究 HIV 持久性的特定测定和生物信息学流程。