PROJECT 2: Determine clinically relevant host-viral dependency networks for respiratory infections including SARS-CoV-2

项目 2：确定呼吸道感染（包括 SARS-CoV-2）的临床相关宿主病毒依赖性网络

• 批准号: 10550002
• 负责人: Melanie Maria Ott
• 金额: $ 67.25万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-17 至 2028-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10550002
• 关键词: 2019-nCoV; 3-Dimensional; 5 year old; Acute respiratory infection; Affect; Animal Model; Antiviral Agents; Bioinformatics; Biological; COVID-19 pandemic; COVID-19 severity; CRISPR screen; Cell Line; Cell model; Cells; Cessation of life; Child; Clinical; Clinical Data; Cloning; Clustered Regularly Interspaced Short Palindromic Repeats; Computer Models; Data; Data Set; Dependence; Development; Disease; Disease Outbreaks; Economics; Engineering; Epithelial Cells; Event; Evolution; Failure; Future; Gene Expression; Genetic; Genomics; Global Change; Health; Human; In Vitro; Individual; Inequality; Inequity; Infection; Inflammatory; Influenza A virus; Influenza B Virus; Integration Host Factors; Knock-out; Lung; Maps; Mass Spectrum Analysis; Measures; Modeling; Mycobacterium tuberculosis; Open Reading Frames; Organoids; Pathogenesis; Pathogenicity; Pathway Analysis; Pathway interactions; Patients; Phosphorylation; Post-Translational Protein Processing; Protein Secretion; Proteins; Proteomics; Public Health; RNA Viruses; Recombinants; Recording of previous events; Resistance; Resistance development; Respiration; Respiratory Disease; Respiratory Tract Infections; Respiratory syncytial virus; Role; SARS-CoV-2 B.1.1.529; SARS-CoV-2 genome; SARS-CoV-2 infection; SARS-CoV-2 variant; Sampling; Serum; Signal Transduction; System; Systems Biology; Technology; Terminator Codon; Testing; Therapeutic Intervention; Therapeutic Monoclonal Antibodies; Tuberculosis; Vaccination; Vaccinee; Validation; Viral; Viral Pathogenesis; Viral Proteins; Viral Respiratory Tract Infection; Virus; Virus Diseases; Virus Inhibitors; Virus Replication; bronchial epithelium; burden of illness; candidate identification; cell dimension; clinically relevant; cytokine; data integration; data management; experimental study; flexibility; follow-up; functional genomics; future pandemic; genetic analysis; genetic technology; genome wide association study; genome wide screen; genome-wide; genomic data; health care availability; in vivo; influenzavirus; innovation; insight; knock-down; mortality; mouse model; novel; novel therapeutic intervention; overexpression; parainfluenza virus; pathogen; prevent; protein protein interaction; receptor; respiratory; respiratory infection virus; respiratory pathogen; respiratory virus; reverse genetics; social; targeted treatment; therapeutically effective; transcriptome; transcriptome sequencing; transcriptomics; underserved area; vaccine access; variants of concern; virus host interaction

PROJECT 2: DETERMINE CLINICALLY RELEVANT HOST-VIRAL DEPENDENCY NETWORKS FOR RESPIRATORY INFECTIONS INCLUDING SARS-COV-2 SUMMARY Respiratory viral infections caused by SARS-CoV-2, influenza A and B viruses, respiratory syncytial virus, and human parainfluenza virus are a significant public health burden globally. Although vaccines are available for some of these viruses, the inequality in access and the constant virus evolution diminish their efficacy. Moreover, effective therapeutics preventing and treating severe respiratory viral diseases are still largely lacking. In Project 2, we will exploit viral dependencies on host factor networks to gain insight into disease mechanisms and develop new therapeutic approaches. We focus on relevant primary cell models, panviral mechanisms and innovative reverse genetics technologies. In Aim 1, proteomics and transcriptomics analyses will be performed with the Technology Core to determine global changes in protein abundance, post-translational modifications, and gene expression profiles in infected primary human lung cells and three-dimensional human airway organoids. Results will be integrated by the Data Management and Bioinformatics and Modeling Cores using existing -omics and human GWAS datasets to search for signatures that correlate with clinical pathogenesis. In Aim 2, virus and host genetics will be used to uncover host dependency factors critical for respiratory infection, using rapid SARS- CoV-2 cloning as well as genome-wide CRISPR-screens. In Aim 3, using supernatants of infected cells and patient serum samples, we will characterize the pro-inflammatory effects of SARS-CoV-2 ORF8 and other secreted viral proteins in correlation with clinical data. With Project 1, we will test their effect on other respiratory viruses and Mycobacterium tuberculosis infection. We anticipate that these studies will have a significant impact on public health measures against respiratory virus infections in the future.

项目 2：确定临床相关的宿主病毒依赖性网络 呼吸道感染，包括 SARS-COV-2 概括 由 SARS-CoV-2、甲型和乙型流感病毒、呼吸道合胞病毒和 人类副流感病毒是全球重大的公共卫生负担。虽然疫苗可以用于 其中一些病毒的获取不平等和病毒的不断进化削弱了它们的功效。而且， 仍然很大程度上缺乏预防和治疗严重呼吸道病毒性疾病的有效疗法。项目中 2，我们将利用病毒对宿主因子网络的依赖性来深入了解疾病机制并开发 新的治疗方法。我们专注于相关的原代细胞模型、泛病毒机制和创新 反向遗传学技术。在目标 1 中，将使用以下方法进行蛋白质组学和转录组学分析： 确定蛋白质丰度、翻译后修饰和基因的全局变化的技术核心 受感染的原代人肺细胞和三维人气道类器官中的表达谱。结果 将由数据管理、生物信息学和建模核心使用现有的组学进行集成 和人类 GWAS 数据集来搜索与临床发病机制相关的特征。在目标 2 中，病毒和 宿主遗传学将用于揭示对呼吸道感染至关重要的宿主依赖性因素，使用快速的 SARS- CoV-2 克隆以及全基因组 CRISPR 筛选。在目标 3 中，使用受感染细胞的上清液和 患者血清样本，我们将表征 SARS-CoV-2 ORF8 和其他病毒的促炎作用 分泌的病毒蛋白与临床数据相关。在项目 1 中，我们将测试它们对其他呼吸系统的影响 病毒和结核分枝杆菌感染。我们预计这些研究将产生重大影响 关于未来针对呼吸道病毒感染的公共卫生措施。