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

项目 2：描绘病毒和宿主细胞衍生的生物标志物，预测治疗中断后 HIV 反弹的时间

• 批准号: 10223996
• 负责人: Warner C. Greene
• 金额: $ 76.27万
• 依托单位: J. DAVID GLADSTONE INSTITUTES
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-08 至 2023-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10223996
• 关键词: Aftercare; Antiviral Agents; Apoptosis; Automobile Driving; Bioinformatics; Biological Assay; Biological Markers; Biological Process; Biostatistics Core; Blood; Blood Cells; Blood specimen; CASP1 gene; CD4 Positive T Lymphocytes; Cell Therapy; Cells; Chemicals; Chronic; Cleaved cell; DNA; Data; Data Set; Disease remission; Ensure; Future; Gene Expression Profile; Gene Expression Profiling; Genes; Genetic; Goals; Gold; HIV; Hour; Immune; Individual; Inflammation; Interleukin-1 beta; Interleukin-15; Interleukin-18; Interruption; Length; Leukapheresis; Libraries; Logistics; Maintenance; Measurement; Measures; Mediating; Mediator of activation protein; Messenger RNA; MicroRNAs; Morbidity - disease rate; Patients; Peripheral Blood Mononuclear Cell; Plasma; Population; Positioning Attribute; Process; Production; Proteins; Proviruses; RNA; Research; Rest; Risk; Scientist; Surrogate Endpoint; T memory cell; T-Lymphocyte; Testing; Therapeutic; Therapeutic Intervention; Time; Tissues; United States National Institutes of Health; Viral; Viral Load result; Viremia; Virus; Work; acute infection; antiretroviral therapy; antiviral immunity; base; chronic infection; clinical decision-making; cohort; complex data; cost; curative treatments; cytokine; design; digital; drug development; exhaustion; extracellular vesicles; inflammatory marker; insight; latent HIV reservoir; memory CD4 T lymphocyte; miRNA expression profiling; mortality; novel; patient subsets; potential biomarker; predictive marker; programmed cell death protein 1; research clinical testing; specific biomarkers; transcriptome sequencing; viral DNA; viral RNA; viral rebound; volunteer

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.

项目摘要/摘要 尽管抗逆转录病毒疗法（ART）抑制了HIV复制并下降了发病率和死亡率 无法治愈。通常会从一个小但耐用 潜在感染，长期存在的记忆CD4 T细胞的储层。新的化学，免疫和基因和细胞 现在正在开发基于基于的疗法，该疗法将旨在消除该水库（难以实现）或 降低其大小并提高抗病毒免疫力，以使艺术可以安全地停止而无需 高水平的病毒反弹（功能治疗）。寻找治疗疗法将由 一组可靠的生物标志物可以准确预测特定疗法是否有效 或不。这样的生物标志物可以帮助确保只有最有前途的候选人晋升为分析 治疗中断 - 治疗治疗临床测试的当前黄金标准。 ATI研究需要 最小化，因为它们本质上是昂贵的，逻辑上的挑战并为患者带来潜在的风险 在病毒反弹期间。这些生物标志物也可能提供关键的见解，了解最多的生物过程 有望攻击水库，并实现预期的弹性延迟。我们假设这一点 可以在血液中鉴定出高度健壮的病毒特异性和宿主特异性生物标志物，以准确预测 治疗中断后的病毒缓解持续时间以及即将发生的病毒反弹。 为了鉴定病毒和宿主指导的生物标志物，来自125 HIV的血液样本 在ATI之前和病毒反弹后获得的感染受试者（均经过急性和慢性感染治疗） 将通过三种不同的方法对分析：（1）静止的血液CD4 T细胞将通过新型的数字测试 液滴PCR分析（IPDA），可有选择地检测储层中完整的病毒DNA - 这些完整的病毒 代表储层中的Proviruse的关键小部分具有复制能力，因此能够 推动病毒反弹。在ATI之前的IPDA结果低可能与长时间的病毒反弹有关。这 测定可以在6个小时内进行，只需要等效于20 mL抽血。 （2）两者的RNA CD4 T和非CD4 T细胞将进行RNA-SEQ和miRNA-SEQ分析，以鉴定 与明显延迟或加速时间与病毒反弹相关的基因表达和（3）测量 细胞和血浆中的凋亡炎症标志物作为生物标志物，预测病毒控制的迅速丧失或 ATI期间即将发生病毒反弹。 RNA-seq生成的复杂数据集将在帮助下分析 生物信息学和生物统计学核心。该项目还将与两个项目1和2紧密接口 在搜索血细胞和血浆或血浆或等离子体或 循环细胞外蔬菜。通过仔细执行这种综合病毒和宿主指导的搜索， 我们的项目团队应该坚定地发现一套坚固的新生物标志物，可以真正 激发未来的HIV治疗研究。