Project 2: Delineating virus and host cell-derived biomarkers predicting time to HIV rebound after treatment interruption

项目总结/摘要 虽然抗逆转录病毒疗法（ART）抑制艾滋病毒复制，降低发病率和死亡率， 不能治愈。ART中断后通常会出现病毒反弹，从一个小但持久的 潜伏感染的、长寿命的、记忆性CD 4 T细胞的储存库。新的化学、免疫、基因和细胞 目前正在开发的基础疗法旨在根除这一储库（难以实现）， 减少它的大小，并充分增强抗病毒免疫力，使ART可以安全地停止， 高水平病毒反弹（功能性治愈）。研究治疗方法将大大促进 一组强大的生物标志物的可用性，可以准确预测特定治疗是否有效 或不.这些生物标志物可以帮助确保只有最有希望的候选人才能进行分析。 治疗中断--目前临床试验治愈疗法的金标准。ATI研究需要 因为它们本身成本高昂，后勤上具有挑战性，并为患者带来潜在风险， 在病毒反弹期间。这些生物标志物也可能提供关键的洞察力，什么生物过程是最重要的 有希望攻击储层并实现期望的回弹时间延迟。我们假设 可以在血液中鉴定高度稳健的病毒特异性和宿主特异性生物标志物， 治疗中断后病毒缓解的持续时间以及即将发生的病毒反弹。 为了进一步鉴定病毒和宿主导向的生物标志物，从125名艾滋病毒感染者的血液样本中， 在ATI之前和病毒反弹之后获得的感染受试者（在急性和慢性感染期间均接受治疗） 将通过三种不同的方法进行分析：（1）静息血液CD 4 T细胞将用一种新的数字 液滴PCR检测（IPDA），选择性地检测水库中完整的前病毒DNA-这些完整的病毒 代表了储库中有复制能力的前病毒的关键小部分， 来推动病毒反弹ATI之前的低IPDA结果可能与病毒反弹的时间较长相关;这 测定可以在6小时内进行，并且仅需要相当于20 ml的血液抽取;（2）来自两者的RNA CD 4 T细胞和非CD 4 T细胞将进行RNA-Seq和miRNA-Seq分析，以鉴定CD 4 T细胞和非CD 4 T细胞的模式。 与病毒反弹时间显著延迟或加速相关的基因表达和（3）测量 细胞和血浆中的炎性标志物作为预测病毒控制迅速丧失的生物标志物，或 即将出现的病毒反弹RNA-Seq生成的复杂数据集将在帮助下进行分析。 生物信息学和生物统计学的核心。该项目还将与项目1和项目2密切配合 其中将采用互补的方法来寻找血细胞和血浆中的生物标志物， 循环细胞外囊泡。通过仔细执行这种全面的病毒和主机定向搜索， 我们的项目团队应该能够发现一套强大的新生物标志物， 激励未来的艾滋病治疗研究。

Project Summary/Abstract Although antiretroviral therapy (ART) inhibits HIV replication and decreases morbidity and mortality, it does not cure. Interruption of ART is routinely followed by viral rebound springing from a small but durable reservoir of latently infected, long lived, memory CD4 T cells. New chemical-, immune- and gene-and cell- based therapies are now being developed that will be aimed at eradicating this reservoir (difficult to achieve) or reducing its size and boosting boosting antiviral immunity sufficiently that ART can be safely stopped without high level viral rebound (functional cure). The search for curative therapies would be greatly facilitated by the availability of a set of robust biomarkers that can accurately predict whether a specific therapeutic is effective or not. Such biomarkers could help ensure that only the most promising candidates advance to analytic treatment interruption––the current gold standard for clinical testing of cure therapeutics. ATI studies need to be minimized because they are inherently costly, logistically challenging and create potential risks for patients during viral rebound. These biomarkers might also provide key insight into what biological processes are most promising for attacking the reservoir and achieving the desired delay in time to rebound. We hypothesize that highly robust virus-specific and host–specific biomarkers can be identified in blood that accurately predict the duration of viral remission after treatment interruption as well as impending viral rebound. To pursue identification of both virus- and host-directed biomarkers, blood samples from 125 HIV infected subjects (both treated during acute and chronic infection) obtained before ATI and after viral rebound will be analyzed by three different approaches: (1) Resting blood CD4 T cells will be tested with a novel digital droplet PCR assay (IPDA) that selectively detects intact proviral DNA in the reservoir––these intact viruses represent the key small fraction of the proviruses in the reservoir that are replication competent and thus able to drive viral rebound. Low IPDA results prior to ATI could be associated with long times to viral rebound; this assay can be performed in 6 hours and only requires the equivalent of a 20 ml blood draw; (2) RNA from both CD4 T and non-CD4 T cells will be subjected to RNA-Seq and miRNA-Seq analyses to identify patterns of gene expression associated with markedly delayed or accelerated times to viral rebound and (3) Measurement of pyroptotic inflammatory markers in cells and plasma as biomarkers predicting rapid loss of viral control or impending viral rebound during ATI. The complex data sets generated by RNA-Seq will analyzed with the help of the Bioinformatics and Biostatistics core. This project will also closely interface with both Projects 1 and 2 where complementary approaches will be pursued searching for biomarkers in blood cells and in plasma or circulating extracellular vesicles. By careful execution of this comprehensive virus- and host-directed search, our project team should be strongly positioned to discover a robust set of new biomarkers that could truly galvanize future HIV cure research.