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.

项目概要/摘要 尽管抗逆转录病毒疗法 (ART) 可抑制 HIV 复制并降低发病率和死亡率，但它 ART 中断后通常会出现小而持久的病毒反弹。 潜伏感染、长寿、记忆 CD4 T 细胞库。 目前正在开发基于疗法，旨在根除这种储存库（难以实现）或 充分减小其大小并增强抗病毒免疫力，从而可以安全地停止 ART，而无需 高水平的病毒反弹（功能性治愈）将极大地促进治疗方法的探索。 提供一组强大的生物标志物，可以准确预测特定治疗是否有效 此类生物标志物可以帮助确保只有最有前途的候选人才能进入分析阶段。 治疗中断——当前治愈疗法临床测试的黄金标准。 被最小化，因为它们本身成本高昂，在后勤方面具有挑战性，并且给患者带来潜在风险 在病毒反弹期间，这些生物标志物也可能提供对最重要的生物过程的关键见解。 我们承诺攻击水库并实现预期的延迟反弹时间。 可以在血液中识别出高度稳健的病毒特异性和宿主特异性生物标志物，从而准确预测 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。 为了鉴定病毒和宿主导向的生物标志物，来自 125 名 HIV 患者的血液样本 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接受治疗） 将通过三种不同的方法进行分析：(1) 将使用新型数字化方法测试静息血液 CD4 T 细胞 液滴 PCR 检测 (IPDA) 可选择性检测储存库中完整的原病毒 DNA——这些完整的病毒 代表储存库中原病毒的关键小部分，它们具有复制能力，因此能够 ATI 之前的低 IPDA 结果可能与病毒反弹时间较长有关； (2) 来自两者的RNA CD4 T 和非 CD4 T 细胞将接受 RNA-Seq 和 miRNA-Seq 分析，以确定 与病毒反弹时间明显延迟或加速相关的基因表达和（3）测量 细胞和血浆中的焦亡炎症标记物作为预测病毒控制迅速丧失的生物标记物或 ATI 期间即将发生的病毒反弹将借助 RNA-Seq 生成的复杂数据集进行分析。 该项目还将与项目 1 和 2 密切相关。 将采用补充方法寻找血细胞和血浆或 通过仔细执行这种针对病毒和宿主的全面搜索， 我们的项目团队应该有能力发现一组强大的新生物标志物，这些标志物可以真正 激发未来的艾滋病毒治疗研究。