Accurately defining the distribution of the genetically intact and potentially replication-competent HIV-1 reservoir during the first 3 years of integrase inhibitor containing antiretroviral therapy

在含有整合酶抑制剂的抗逆转录病毒治疗的前 3 年中，准确定义遗传完整且具有潜在复制能力的 HIV-1 病毒库的分布

• 批准号: 10074604
• 负责人: Anthony Kelleher
• 金额: $ 16.25万
• 依托单位: UNIVERSITY OF NEW SOUTH WALES
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-06-12 至 2022-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10074604
• 关键词: Address; Biological Assay; CD4 Positive T Lymphocytes; Cell Proliferation; Cells; Chronic; Circular DNA; DNA; Evolution; Future; Guidelines; HIV; HIV Genome; HIV-1; Individual; Infection; Integrase; Integrase Inhibitors; Length; Long Terminal Repeats; Maintenance; Measurable; Memory; Participant; Patients; Phase; Population; Proviruses; Regimen; Reporting; Role; T-Lymphocyte Subsets; Techniques; Time; Viral; Virus Replication; antiretroviral therapy; design; effective therapy; in vivo; inhibitor/antagonist; latent HIV reservoir; memory CD4 T lymphocyte; standard of care

PROJECT SUMMARY Accurate identification of the replication-competent HIV-1 latent reservoir provides a basis for the design of any cure strategy; however, this is challenging because of its sparse distribution. Further, HIV-1 DNA exists in different forms and proviruses are genetically variable. The recently developed Full-Length Individual Proviral Sequencing (FLIPS) assay allows for the identification of genetically intact and potentially replication-competent HIV-1. Using FLIPS, 5% of the proviruses were identified as genetically intact and potentially replication competent in participants on effective long-term (3-17 years) antiretroviral therapy (ART). In addition, intact proviruses were enriched in effector memory CD4+ T cells, and multiple intact proviruses were found to be identical, suggesting a role for cellular proliferation in the maintenance of the latent HIV-1 reservoir. We have reported that HIV-1 episomal 2-long terminal repeat circular DNA (2-LTR circles), which are likely dead ends in the viral replication cycle in vivo, persist at relatively high levels for at least 3 years after initiation of ART containing an integrase strand transfer inhibitor (INSTI) during primary or chronic HIV-1 infection. Since INSTIs are now recommended in all guidelines as essential components of initial regimens, most infected individuals initiating contemporary ART may carry persistent levels of 2-LTR circles. It is therefore important to clarify whether genetically intact HIV-1 2-LTR circles are present in individuals who commenced INSTI-containing ART, because their persistence can interfere with the accurate quantification of the genetically intact and most likely replication-competent reservoir. We will therefore answer three important questions in the proposed study: (1) Do persisting HIV-1 2-LTR circles contain genetically intact HIV-1 genomes in CD4+ T cells during the first 3 years of INSTI-containing ART? If yes, at what level compare to genetically intact linear/proviral HIV-1? (2) How do genetically intact, replication-competent proviral forms distribute in CD4+ T cell subsets prior to and following initiation of INSTI-containing ART? Does this distribution change during the first 3 years of therapy? (3) Is HIV-1 replication occurring during the first 3 years of INSTI-containing ART and how do 2-LTR and integrated viral sequences relate to each other and evolve over time? This will be the first characterization of HIV-1 DNA, that accurately accounts for the linear/proviral forms and 2- LTR circles following initiation of treatment with INSTI-containing ART, which is now standard of care in many jurisdictions. Persistence of genetically intact 2-LTR circles will cause an overestimation of the potentially replication-competent latent HIV reservoir even when near full-length sequencing techniques are employed. This will also be the first longitudinal assessment of the landscape of genetically intact provirus and 2-LTR circles and how these evolve within CD4+ T cell subsets during early (0-3 years) therapy. This will inform the potential targeting of cure strategies. Finally, it will clarify whether ongoing viral replication maintains the latent reservoir during the first months of therapy, or whether this is driven by cellular proliferation even at these early time points.

项目概要 准确识别具有复制能力的 HIV-1 潜伏病毒库为设计任何病毒库提供了基础。 治疗策略；然而，由于其分布稀疏，这具有挑战性。此外，HIV-1 DNA 存在于 不同的形式和原病毒在遗传上是可变的。最近开发的全长个体原病毒 测序 (FLIPS) 分析可以鉴定遗传完整且具有潜在复制能力的基因 HIV-1。使用 FLIPS，5% 的原病毒被鉴定为基因完整且具有复制潜力 能够接受有效的长期（3-17年）抗逆转录病毒治疗（ART）的参与者。另外，完好无损 原病毒在效应记忆 CD4+ T 细胞中富集，并且发现多种完整的原病毒 相同，表明细胞增殖在维持潜在的 HIV-1 储存库中发挥着作用。 我们已经报道了 HIV-1 附加型 2 长末端重复环状 DNA（2-LTR 环），这可能是死亡的 体内病毒复制周期结束，在开始 ART 后至少 3 年内保持相对较高的水平 在原发性或慢性 HIV-1 感染期间含有整合酶链转移抑制剂 (INSTI)。自从INSTI以来 现在所有指南都建议将其作为初始治疗方案的重要组成部分，大多数感染者 开始当代 ART 可能会携带持续水平的 2-LTR 环。因此，澄清这一点很重要 开始包含 INSTI 的 ART 的个体中是否存在遗传完整的 HIV-1 2-LTR 环， 因为它们的持续存在会干扰基因完整的准确量化，并且很可能 具有复制能力的储存库。因此，我们将在拟议的研究中回答三个重要问题： (1) 在前 3 个周期中，持续存在的 HIV-1 2-LTR 环是否在 CD4+ T 细胞中包含遗传完整的 HIV-1 基因组？ 包含 INSTI 的 ART 的年数？如果是，与遗传完整的线性/原病毒 HIV-1 相比处于什么水平？ (2) 遗传完整、具有复制能力的原病毒形式在 CD4+ T 细胞亚群中如何分布？ 开始含 INSTI 的 ART 后？在治疗的前 3 年中，这种分布会发生变化吗？ (3) HIV-1 复制是否在包含 INSTI 的 ART 的前 3 年发生，以及 2-LTR 和 整合的病毒序列彼此相关并随着时间的推移而进化？ 这将是 HIV-1 DNA 的首次表征，准确地解释了线性/原病毒形式和 2- 开始使用含 INSTI 的 ART 治疗后出现 LTR 循环，目前该疗法已成为许多国家的标准治疗方法 司法管辖区。遗传完整的 2-LTR 环的持续存在将导致潜在的高估 即使采用接近全长的测序技术，也能形成具有复制能力的潜在HIV病毒库。这 也将是对基因完整的原病毒和 2-LTR 环的首次纵向评估 在早期（0-3 年）治疗期间，这些细胞如何在 CD4+ T 细胞亚群中进化。这将告知潜在的 治疗策略的针对性。最后，它将澄清持续的病毒复制是否维持了潜在的储存库 在治疗的最初几个月，或者这是否是由细胞增殖驱动的，即使在这些早期时间点。