Project 3: Identifying plasma biomarkers predicting time to HIV rebound after treatment interruption

项目总结/摘要 虽然抗逆转录病毒治疗（ART）的出现显着降低了发病率和死亡率 与HIV感染相关，由于潜伏感染细胞的持续存在， 在治疗期间。因此，抗逆转录病毒疗法必须终生服用。不断积累的数据表明，艾滋病毒- 受感染的个体通常经历持续的免疫失调、慢性炎症和加速的免疫反应。 甚至在ART介导的病毒抑制的情况下也是如此。这些现实造成了一个明显的 对制定根除感染者体内艾滋病毒的战略感兴趣。 艾滋病毒治疗战略的制定、评估和实施将主要取决于我们的 有能力确定何时病毒复发在短期内是不可能在感染的个人，证明 停止抗逆转录病毒治疗（ART）。这个P01项目的目标是确定生物标志物， 我们预测停药后HIV反弹前的滞后期或“缓解”期的持续时间 艾滋病病毒感染者的抗逆转录病毒治疗。在我们的研究中，大量的病毒学和免疫学参数将 在125名接受分析治疗的特征明确的HIV感染者队列中进行测量 中断（ATI），以确定生物标志物，使我们能够可靠地预测ART后病毒反弹的动力学 停止我们的P01提案项目3中描述的实验将专门检查预后 血浆和脑脊液（CSF）中广谱循环因子的价值， 先进的技术和前所未有的多项ATI研究纵向样本收集。 在目标1中，我们将实施下一代测序方法，以确定 循环核酸和病毒反弹，重点是microRNA谱，无细胞DNA，和残留的低水平 HIV病毒血症。在目标2中，我们将评估循环细胞外囊泡的预后意义， 表征它们的丰度、细胞来源以及核酸和病毒蛋白质货物。最后，在目标3中， 可溶性抗病毒免疫因子将作为病毒反弹的预测因子进行评估，重点是高分辨率 分析抗HIV抗体反应、与HIV持续存在相关的细胞因子和趋化因子。 我们将与我们的生物信息学和生物统计学核心密切合作，将我们的高维数据转化为 ART中断后HIV反弹的可靠预测因素，依赖于复杂的集成机器 学习方法。最终，确定一个可靠的基于血浆的病毒反弹预测因子， 将代表该领域的最佳方案，能够快速开发、扩展和部署成本- 有效的，非侵入性的诊断方法，以促进艾滋病毒治疗的研究。

PROJECT SUMMARY/ABSTRACT While the advent of antiretroviral therapy (ART) has dramatically reduced the morbidity and mortality associated with HIV infection, viral eradication is not achievable due to the persistence of latently-infected cells during treatment. ART must therefore be taken on a lifelong basis. Accumulating data suggest that HIV- infected individuals often experience persistent immune dysregulation, chronic inflammation, and accelerated aging even in the setting of ART-mediated viral suppression. These realities have created a pronounced interest in developing strategies to eradicate HIV in infected individuals. The development, evaluation and implementation of HIV curative strategies will depend critically on our capacity to determine when viral recrudescence in the near term is unlikely in an infected individual, justifying cessation of antiretroviral therapy (ART). The goal of this P01 project is to identify biomarkers that will enable us to predict the duration of the lag phase or “remission” period prior to HIV rebound following discontinuation of ART in HIV-infected individuals. In our study, a large number of virologic and immunologic parameters will be measured in a cohort of 125 well-characterized HIV-infected individuals undergoing analytical treatment interruption (ATI), to identify biomarkers that allow us to reliably predict the kinetics of viral rebound post-ART cessation. The experiments described in Project 3 of our P01 proposal will specifically examine the prognostic value of a broad spectrum of circulating factors in plasma and cerebrospinal fluid (CSF), leveraging cutting edge technologies and an unprecedented collection of longitudinal specimens from multiple ATI studies. In Aim 1, we will implement next-generation sequencing approaches to determine the relationship between circulating nucleic acids and viral rebound, focusing on microRNA profile, cell-free DNA, and residual low-level HIV viremia. In Aim 2, we will evaluate the prognostic significance of circulating extracellular vesicles, characterizing their abundance, cellular origin, and nucleic acid and viral protein cargo. Finally, in Aim 3, soluble antiviral immune factors will be evaluated as predictors of viral rebound, focusing on high-resolution analyses of anti-HIV antibody responses, cytokines and chemokines associated with HIV persistence. We will work closely with our Bioinformatics and Biostatistics Core to transform our high-dimensional data into robust predictors of HIV rebound following ART interruption, relying on sophisticated ensemble machine learning approaches. Ultimately, the identification of a reliable blood plasma-based predictor of viral rebound will represent an optimal scenario for the field, enabling rapid development, scaling and deployment of cost- effective, non-invasive diagnostic approaches to facilitate the search for an HIV cure.