Modeling Host Responses to Understand Severe Human Virus Infections

描述(由申请人提供)：这一全面和高度集成的系统生物学应用程序寻求描述复杂的宿主反应，这些反应决定了感染潜在致命病毒的结果。为了实现这一目标，细胞和老鼠将 这些活动将由两个针对流感和埃博拉病毒或西尼罗河病毒的研究项目进行。技术核心将执行蛋白质组学、磷蛋白质组学、脂类组学和代谢组学分析，而信使核糖核酸和miRNA分析将以收费方式外包 基础。此外，包括病毒学数据和蛋白质-蛋白质数据在内的多种生物数据集 互动，将会产生。所有数据将由计算建模核心进行分析，该核心将 整合不同的数据集，构建预测机制和网络模型，包括虚拟肺和肝脏模型。基于这些分析，这两个研究项目将在体外和体内(即在基因敲除的小鼠中)进行全面的验证研究。来自病毒感染的敲除小鼠和匹配的野生型小鼠的组学研究(如上所述)将用于第二轮分析，从而实现迭代采样、建模和验证的系统生物学范式。数据管理和资源传播核心将协助储存、管理和交换大量多样的数据集，并向社区提供服务，而行政核心将确保处理所有行政任务。综上所述，我们提出了一个全面和交互的系统生物学计划，该计划将增强对传染病的预测建模，并确定可用于开发治疗干预措施的严重人类病毒致病性的关键调节因子。 相关性：埃博拉病毒。西尼罗河病毒和甲型流感病毒分别被国家过敏和传染病研究所(NIAID)列为A、B和C类优先药物。这三种病毒都有能力在人类身上造成严重和/或致命的感染，其原因尚不完全清楚。我们寻求将最先进的系统生物学方法学与高水平的病毒学、技术和计算专业知识相结合，以阐明调节病毒致病性和人类感染这些病毒的致命结果的共同和独特的机制。 项目一：甲型流感病毒和埃博拉病毒的系统生物学分析 项目负责人(PL)：川冈义弘 描述(申请人提供)：感染高致病性禽流感H5N1甲型流感病毒(LAV)或埃博拉病毒(EBOV)可导致严重的呼吸道疾病或出血热，人类死亡率高。对这些病毒如何失调宿主反应的有限了解损害了对病毒引起的疾病的有效治疗。我们假设，比较宿主对H5N1 LAV、EBOV和一系列毒力突变的反应将有助于描述共同的和病毒特异性的免疫颠覆和致病机制。在这里，我们提出了一个高度集成的系统生物学方法来解决这一假设。我们将利用我们现有的来自感染H5N1亚型病毒和突变病毒的细胞和小鼠肺的转录组和蛋白质组数据，在目标1中，将为感染EBOV的细胞和小鼠获得类似的蛋白质组学和转录组数据集。此外，我们还将对这两种病毒进行mirna图谱、磷蛋白质组学、代谢组学和脂类组学分析；量化免疫细胞向受感染的肺或肝组织的运输；收集从lv感染的免疫细胞分离出的免疫细胞群的转录本数据。 并提供LAV和EBOV蛋白与宿主蛋白相互作用的全面数据。 将在几个核心的协助下获取数据集，以进行样本处理、统计和 计算分析，并与本合同第二研究项目下为西尼罗河病毒(WNV)产生的数据进行整合。计算建模核心将产生用于后续分析的优先调控靶标列表，在目标2中，靶标将使用结合宿主因子表达或活性扰动的体外系统进行实验验证。选定的靶点将在体内通过基因敲除(KO)小鼠的生成和KO基因对感染结果的影响的评估来验证。为了完善计算模型和完成系统生物学范式，我们还将从KO小鼠身上获取样本，用于迭代组学研究。总而言之，这一策略有望促进与严重的人类病毒病原体相关的疾病状态的预测性建模，并确定可能成为新干预策略目标的病毒发病机制的重要调节因子。 相关信息：美国国家过敏和传染病研究所(NIAID)将埃博拉病毒(EBOV)和甲型流感病毒(LAV)分别列为“A类”和“C类”优先病原体。这两种病毒都有能力对人类造成严重和/或致命的感染，尽管其机制尚未明确界定。在这里，我们试图使用高度协作的最先进的系统生物学方法来识别这些机制，以促进对人类EBOV和LAV感染的更好理解和治疗。

DESCRIPTION (as provided by applicant): This comprehensive and highly integrated systems biology application seeks to delineate the complex host responses that determine the outcome of infections with potentially lethal viruses. To achieve this goal, cells and mice will be infected with wild-type and mutant influenza A, Ebola, and West Nile viruses to collect a variety of sample sets (these activities will be carried out by two Research Projects for influenza and Ebola or West Nile virus, respectively). A Technical Core will perform proteomics, phosphoproteomics, lipidomics, and metabolomics profiling, whereas mRNA and miRNA profiling will be out-sourced on a fee-for-service basis. In addition, multiple biological datasets, including virological data and data on protein-protein interactions, will be generated. All data will be analyzed by a Computational Modeling Core, which will integrate the diverse datasets and build predictive mechanistic and network models, including virtual lung and liver models. Based on these analyses, the two Research Projects will carry out comprehensive validation studies in vitro and in vivo (i.e., in knock-out mice). OMICs studies (as described above) from virus-infected knock-out and matched wild-type mice will be used for a second round of analysis, thereby achieving the systems biology paradigm of Iterative sampling, modeling, and validation. Storage, management, and exchange of the large and diverse datasets, and outreach to the community, will be facilitated by a Data Management and Resources Dissemination Core, whereas an Administrative Core will ensure that all administrative tasks are addressed. In summary, we propose a comprehensive and interactive systems biology program that will enhance predictive modeling of infectious disease and identify critical regulators of severe human virus pathogenicity that may be exploited for the development of therapeutic interventions. RELEVANCE: Ebola viruses. West Nile virus and Influenza A viruses are classified as Category A, B and C priority agents, respectively, by the National Institute of Allergy and Infectious Diseases (NIAID). All three viruses have the ability to cause severe and/or fatal infections in humans for reasons that are not completely understood. We seek to combine state-of-the-art systems biology methodology with high level virological, technical and computational expertise to elucidate common and unique mechanisms regulating viral pathogenicity and fatal outcomes in humans infected with these viruses. Project 1: Systems Biology Analysis of Influenza A Virus and Ebola Virus Project Leader (PL): Yoshihiro Kawaoka DESCRIPTION (as provided by applicant): Infections with highly pathogenic avian H5N1 influenza A viruses (lAV) or Ebola viruses (EBOV) cause severe respiratory disease or hemorrhagic fever with high mortality rates in humans. The limited understanding of how these viruses dysregulate the host response impairs effective treatments for virus induced disease. We hypothesize that comparing host responses to H5N1 lAV, EBOV and a range of virulence mutants will allow delineation of common and virus-specific mechanisms of immune subversion and pathogenicity. Here, we propose a highly integrated systems biology approach to address this hypothesis. We will leverage our existing transcriptome and proteome data from cells and mouse lungs infected with H5N1 lAV and mutant viruses, and in Aim 1, similar proteomics and transcriptomics datasets will be acquired for EBOV-infected cells and mice. In addition, we will perform miRNA profiling, phosphoproteomics, metabolomics and lipidomics analyses for both viruses; quantify immune cell trafficking into infected lung or liver tissues; collect transcriptomcs data for immune cell populations isolated from lAV-infected lungs; and provide comprehensive data for lAV and EBOV protein interactions with host proteins. Datasets will be acquired with the assistance of several Cores for sample processing, statistical and computational analyses, and integration with data generated for West Nile virus (WNV) under the second Research Project of this contract. The Computational Modeling Core will produce prioritized regulatory target lists for follow-up analysis, and in Aim 2, targets will be experimentally validated using in vitro systems coupled with perturbation of host factor expression or activity. Selected targets then will be validated in vivo by generation of knockout (KO) mice and assessment of the effects of gene KO on the outcome of infection. To allow refinement of computational models and completion of the systems biology paradigm, we will also obtain samples from KO mice for iterative OMICs studies. Collectively, this strategy is expected to facilitate predictive modeling of disease states associated with severe human viral pathogens and identify important regulators of viral pathogenesis that may be targeted for novel intervention strategies. RELEVANCE: Ebola viruses (EBOV) and influenza A viruses (lAV) are classified as 'Category A' and 'Category C' priority agents, respectively, by the National Institute of Allergy and Infectious Diseases (NIAID). Both viruses have the ability to cause severe and/or fatal infections in humans, although the mechanisms are not clearly defined. Here, we seek to identify these mechanisms using a highly collaborative state-of-the-art systems biology methodology, to facilitate better understanding and treatment of EBOV and lAV infections in humans.