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旨在描述决定潜在致命病毒感染结果的复杂宿主反应。为了实现这一目标，细胞和小鼠将 感染了野生型和突变型甲型流感病毒、埃博拉病毒和西尼罗河病毒，以收集各种样本集（这些活动将分别由流感和埃博拉病毒或西尼罗河病毒的两个研究项目开展）。技术核心将进行蛋白质组学、磷酸化蛋白质组学、脂质组学和代谢组学分析，而mRNA和miRNA分析将以收费服务的方式外包 基础此外，多个生物数据集，包括病毒学数据和蛋白质-蛋白质数据， 互动，将产生。所有数据将由计算建模核心进行分析， 整合不同的数据集并构建预测机制和网络模型，包括虚拟肺和肝脏模型。根据这些分析，这两个研究项目将进行全面的体外和体内验证研究（即，在敲除小鼠中）。来自病毒感染的敲除小鼠和匹配的野生型小鼠的OMIC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。大型和多样化数据集的存储、管理和交换，以及对社区的宣传，将由数据管理和资源传播核心来促进，而行政核心将确保所有行政任务得到解决。总之，我们提出了一个全面的和互动的系统生物学计划，将加强传染病的预测建模，并确定严重的人类病毒致病性，可用于治疗干预措施的发展的关键监管机构。 相关性：埃博拉病毒。西尼罗河病毒和甲型流感病毒分别被美国国家过敏和传染病研究所（NIAID）列为A、B和C类优先病原体。所有这三种病毒都有能力在人类中引起严重和/或致命的感染，原因尚不完全清楚。我们寻求将联合收割机最先进的系统生物学方法与高水平的病毒学、技术和计算专业知识相结合，以阐明调节病毒致病性和感染这些病毒的人类的致命结果的共同和独特的机制。 项目1：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）：Yoshihiro Kawaoka 描述（如申请人所提供）：高致病性禽H5 N1甲型流感病毒（IAV）或埃博拉病毒（EBOV）感染会导致严重的呼吸道疾病或出血热，在人类中具有高死亡率。对这些病毒如何失调宿主反应的有限理解损害了对病毒诱导的疾病的有效治疗。我们假设比较宿主对H5 N1 IAV、EBOV和一系列毒力突变体的反应将允许描绘免疫颠覆和致病性的共同和病毒特异性机制。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个假设。我们将利用我们现有的来自感染H5 N1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Aim 1中，将获得EBOV感染细胞和小鼠的类似蛋白质组和转录组数据集。此外，我们还将对两种病毒进行miRNA谱分析、磷酸化蛋白质组学、代谢组学和脂质组学分析;量化免疫细胞向感染的肺或肝组织的运输;收集从感染的肺或肝组织中分离的免疫细胞群的转录组学数据。 肺;并提供IAV和EBOV蛋白与宿主蛋白相互作用的综合数据。 数据集将在几个核心的协助下获得，用于样本处理、统计和 计算分析，并根据本合同的第二个研究项目与西尼罗河病毒（WNV）产生的数据集成。计算建模核心将产生优先的监管目标清单，用于后续分析，在目标2中，将使用体外系统结合宿主因子表达或活性的扰动对目标进行实验验证。然后通过产生敲除（KO）小鼠并评估基因KO对感染结果的影响来在体内验证选定的靶标。为了改进计算模型和完成系统生物学范式，我们还将从KO小鼠中获得样品用于迭代OMIC研究。总的来说，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建模，并确定可能成为新型干预策略目标的病毒发病机制的重要调节因子。 相关性：埃博拉病毒（EBOV）和甲型流感病毒（IAV）分别被国家过敏和传染病研究所（NIAID）分类为“A类”和“C类”优先因子。这两种病毒都有能力在人类中引起严重和/或致命的感染，尽管其机制尚不清楚。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，以促进更好地理解和治疗人类中的EBOV和IAV感染。

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.