Identifying vulnerabilities in the long-lived HIV reservoir to accelerate its decay

项目摘要 潜伏感染的携带整合和复制能力的HIV基因组的CD4 + T细胞在ART期间持续存在 是根除艾滋病的主要障碍。在大多数艾滋病毒感染者（PWH）中，储存库非常稳定 半衰期超过3年。所有先前试图显著减小其大小或加速其衰变的尝试都失败了。 使用来自MERLIN进化枝B原发性HIV感染队列（利马，秘鲁）参与者的样本，我们观察到 在感染的前3个月内开始抗逆转录病毒治疗的个体中，艾滋病毒储存库的衰减速度快5至10倍 与那些随机开始ART的人相比，这表明早期治疗的人中的HIV感染细胞 更容易被淘汰储存库半衰期的差异，至少在 抗逆转录病毒疗法的前4年，提供了一个独特的机会，以确定可以利用的机制， 在这个项目中，我们建议解开细胞和病毒的特点，负责 单个HIV储库细胞的快速清除或长期存留。我们将测试假设， 储库细胞持续延长时间的能力由细胞和病毒特征的组合驱动， 其在早期和晚期处理的个体之间不同，并导致不同的储层衰减。我们将采取 独特的MERLIN队列在12名开始ART的参与者中研究HIV储库细胞的优势 艾滋病毒感染后3个月（早期ART：快速衰减），12名参与者推迟治疗6个月， 3个月（晚期ART：缓慢衰减）。我们将研究早期，中期和晚期储层，利用低温保存 白细胞分离术（在ART的1年和2 - 3年收集）和新收集的白细胞分离术， 在目标1中，我们将检验内在细胞特征 HIV储存库细胞的差异是储存库衰变差异的基础。我们将采用单细胞方法来识别 与储层稳定性相关的促存活因子（Bcl-2、TCF-1、FOXO 3A等）或者保护感染者 免疫清除细胞（免疫检查点分子的配体，Serpin B9，TGF-β）。我们还将评估 库的克隆性，假设完整基因组的克隆扩增将更常见 晚期治疗的参与者。在目标2中，我们将检验特定病毒特征也有助于 艾滋病毒感染的细胞的持久性，并将随着时间的推移逐渐丰富的艺术。 我们将使用一种将整合位点测序与 HIV转录评估，以确定转录活跃的储库细胞的比例。我们 将使用一种新的方法从潜伏的水库重建分子病毒克隆，并将测量 这些病毒的适应性和功能评估其HIV蛋白质组。这样我们就能确定水库 逐渐富集编码功能性Nef和Vpu的前病毒，其引起抗原呈递的逃逸 并阻止CTL介导的杀伤以及自体抗体的中和和ADCC。结果 这项研究将确定细胞和病毒的机制，可以针对加速衰变的艾滋病毒水库。

PROJECT SUMMARY Latently infected CD4+ T cells harboring integrated and replication-competent HIV genomes persist during ART and are the main obstacle to HIV eradication. In most people with HIV (PWH), the reservoir is extremely stable with a half-life of over 3 years. All prior attempts to significantly reduce its size or accelerate its decay have failed. Using samples from participants in the MERLIN clade B primary HIV infection cohort (Lima, Peru), we observed 5 to 10-times faster decay of the HIV reservoir in individuals initiating ART during the first 3 months of infection compared to those randomized to start ART later, suggesting that HIV-infected cells in people treated early are more susceptible to elimination. Differences in the half-life of the reservoir, which are maintained during at least the first 4 years of ART, offer a unique opportunity to identify mechanisms that could be harnessed to reduce the reservoir in all PWH on ART. In this project, we propose to unravel the cellular and viral features responsible for the rapid clearance or long-term persistence of individual HIV reservoir cells. We will test the hypothesis that the capacity of reservoir cells to persist for prolonged periods is driven by a combination of cellular and viral features, which differ between early and late treated individuals and result in differential reservoir decay. We will take advantage of the unique MERLIN cohort to study HIV reservoir cells in 12 participants who initiated ART less than 3 months after HIV acquisition (early ART: rapid decay) and 12 participants who deferred treatment for 6 months (late ART: slow decay). We will study the early, intermediate and late reservoirs, using cryopreserved leukaphereses (collected at 1 & 2-3 years of ART) and newly collected leukapheresis from the same continually- suppressed participants at >7 years of ART. In Aim 1, we will test the hypothesis that intrinsic cellular features of HIV reservoir cells underlie differences in reservoir decay. We will employ a single cell approach to identify pro-survival factors associated with reservoir stability (Bcl-2, TCF-1, FOXO3A etc.) or that may protect infected cells from immune clearance (ligands of immune checkpoint molecules, Serpin B9, TGF-β). We will also evaluate the clonality of the reservoir with the hypothesis that clonal expansions of intact genomes will be more common in late treated participants. In Aim 2, we will test the hypothesis that specific viral characteristics also contribute to the persistence of HIV-infected cells and will be gradually enriched over time on ART. To determine if specific viruses are selected against during therapy, we will use an assay that couples integration site sequencing with HIV transcription assessment, to determine the proportion of reservoir cells that are transcriptionally active. We will use a novel approach to reconstruct molecular viral clones from the latent reservoir, and will measure the fitness of these viruses and functionally assess their HIV proteomes. In this way, we will determine if the reservoir is gradually enriched in proviruses encoding functional Nef and Vpu, which cause escape of antigen presentation and impede CTL-mediated killing as well as neutralization and ADCC by autologous antibodies. Results from this study will identify cellular and viral mechanisms that can be targeted to accelerate decay of the HIV reservoir.