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

项目总结 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，并将艾滋病毒感染从 一种致命的疾病到一种可控制的慢性病。然而，尽管病毒复制在 在治疗方面，研究表明，潜伏的病毒库仍然可被检测到，这助长了病毒的反弹 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 一旦感染，当艾滋病毒不可逆转地将其病毒基因组整合到人类DNA中时。病毒库是极其重要的 耐用，对目前可用的抗逆转录病毒药物的治疗效果不敏感，并已 对最近的实验性治疗方法难以奏效。艾滋病毒感染的特征也是高水平的 病毒准种的寄主内基因多样性。除了与遗传多样性相关的碱基替换 从长期感染的慢性感染患者中恢复的突变和病毒DNA基因组池 抑制疗法通常包含基因组截断和/或超突变、非复制的高频率- 有能力的病毒DNA基因组。这些患者中只有一小部分前病毒基因组是基因组完整的 在没有治疗的情况下，可能会导致病毒的高效复制和病毒学反弹。此外， 李博士和其他研究小组最近的研究表明，明确的证据表明，艾滋病毒感染细胞通过基因组- 完整和基因组缺陷的前病毒可以克隆性扩张。这种携带感染细胞的克隆扩增 基因组完整的HIV前病毒提示了HIV持续存在的一个重要机制。然而，纵向的 克隆扩张的动力学和机制还没有得到深入的研究，克隆扩张之间的多样性 病人没有很好的特征。重要的是，我们目前对艾滋病毒携带者的理解是 几乎完全来自对一种名为B亚型HIV-1的毒株的研究，这种主要的病毒亚型影响第一- 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 全球艾滋病毒-1负担的大约50%。在此R21应用程序中，我们建议纵向跟踪和 比较B亚型和C亚型HIV储备库的基因进化。我们建议检查克隆扩张 感染艾滋病毒的细胞。具体地说，我们假设对艾滋病毒DNA基因组和 整合站点将揭示在抑制治疗期间持续存在的病毒物种的独特特征，即这些 艾滋病毒B亚型和C亚型之间的特征将不同，并且这些特征将与 个体的免疫学特征会发生变化。这项研究将产生最大的交叉HIV亚型水库 与临床和免疫学数据相关联的数据库。病毒基因分型数据将被用来开发亚型- 用于艾滋病毒持久性研究的具体分析和生物信息学管道。

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.