Studies of HCV Infection And HCV-Host interactions

HCV 感染和 HCV-宿主相互作用的研究

• 批准号: 9148842
• 负责人: T. Jake Liang
• 金额: $ 97.4万
• 依托单位: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9148842
• 关键词: Animal Model; Antiviral Agents; Biochemical; Biogenesis; Bioinformatics; Biological Assay; Biological Models; Cell Culture System; Cell Nucleus; Cell physiology; Cells; Choline Kinase; Complex; Cytoplasmic Granules; Cytoplasmic Structures; Data; Databases; Dependency; Deubiquitinating Enzyme; Disease; E-Cadherin; Elements; Eligibility Determination; Family; Family member; Gene Expression; Genes; Genetic; Genomic approach; Hepatitis C; Hepatitis C virus; Hepatocyte; Host resistance; Human; IKK alpha; Image; In Vitro; Individual; Infectious hepatitides; Insulinase; Integration Host Factors; Internal Ribosome Entry Site; Investigation; Life Cycle Stages; Link; Lipids; Mediating; Meta-Analysis; MicroRNAs; Modeling; Molecular; Morbidity - disease rate; NADPH Oxidase; Pathogenesis; Pathway interactions; Play; Predisposition; Process; Production; Proteins; Published Database; Publishing; RNA Interference; RNA replication; Regulation; Replicon; Role; Signal Pathway; Signal Transduction; Site; Staging; Stress; Surface; Technology; Translations; Ubiquitin-Conjugating Enzymes; Validation; Viral; Viral Proteins; Virus; Virus Assembly; Virus Diseases; Virus Replication; base; follow-up; functional genomics; genome-wide; genome-wide analysis; guanine nucleotide binding protein; hepatitis C virus nucleocapsid protein; in vivo; inhibitor/antagonist; insight; mortality; new therapeutic target; novel; particle; programs; resistance factors; rho GTP-Binding Proteins; screening; text searching; therapeutic target; viral RNA; virus host interaction; virus pathogenesis

HCV dependencies on the host machinery are both intricate and extensive. Each of these host dependencies is a potential therapeutic target. Previous efforts have been successful in discovering important steps in HCV replication, yet many fundamental processes in the viral life cycle remain uncharacterized. Using RNAi-based genetics and an infectious HCV cell culture system, we performed an unbiased genome-wide screen to identify host factors required for productive HCV infection. We applied a two-part screening protocol to identify host factors involved in the complete viral lifecycle, from viral entry to production of infectious virus. A validation screen was subsequently performed to minimize potential off-target effects. 512 genes were identified in the initial screen and 262 were confirmed by the validation assay. We identified 238 host susceptibility factors (HSFs) and 24 host resistance factors (HRFs), the majority of which were not previously linked to HCV. Of these 262 validated hits, 45 target late-stage viral infection. Integrative bioinformatics analyses of these host genes and other published database revealed a broad and complex dependency of HCV on cellular processes and molecular functions, and also implicated novel cellular signaling pathways modulating HCV infection. We further applied an unbiased and systematic strategy to functionally interrogate HCV host dependencies uncovered from the GW siRNA screen. By applying functional genomics approaches and various in vitro HCV model systems, including HCV pseudoparticles (HCVpp), single-cycle infectious particles (HCVsc), subgenomic replicons, and HCV cell culture systems (HCVcc), we identified and characterized novel host factors or pathways required for each individual step of the HCV replication cycle. Particularly, we uncovered multiple HCV entry factors, including E-cadherin, choline kinase-alpha, NADPH oxidase CYBA, Rho GTPase RAC1 and SMAD family member 6. We also demonstrated that guanine nucleotide binding protein GNB2L1, E2 ubiquitin-conjugating enzyme UBE2J1, and 39 other host factors are required for HCV RNA replication, while the deubiquitinating enzyme USP11 and multiple other cellular genes are specifically involved in HCV IRES-mediated translation. Families of antiviral factors that target HCV replication or translation were also identified. In addition, various virologic assays validated that 66 host factors are involved in HCV assembly or secretion. These genes included insulin-degrading enzyme (IDE), a proviral factor, and N-Myc down regulated Gene 1 (NDRG1), an antiviral factor. Bioinformatics meta-analyses of our results integrated with literature mining of previously published HCV host factors allows the construction of an extensive roadmap of cellular networks and pathways involved in the complete HCV replication cycle. This comprehensive study of HCV host dependencies yields novel insights into viral infection, pathogenesis and potential therapeutic targets. As a follow-up of GW RNAi screen above, we showed that DDX3X specifically recognizes HCV 3UTR leading to activation of IKK-alpha and a cascade of lipogenic signaling to facilitate lipid droplet biogenesis and viral assembly. Interaction of DDX3X with HCV core protein seems to be dispensable for its proviral role. By applying systematic imaging, biochemical and virologic approaches, we identified a dynamic association between DDX3X and various cellular compartments and viral elements mediating multiple functions of DDX3X in productive HCV infection. Upon HCV infection, HCV 3UTR interacts with DDX3X and IKK-alpha that redistribute to speckle-like cytoplasmic structures shown to be stress granules (SGs). As viral proteins accumulate in infected cells, DDX3X granules together with SG-associated proteins redistribute and co-localize with HCV core protein around lipid droplets (LDs). IKK-alpha, however, does not relocate to the LD but translocates to the nucleus. In HCV-infected cells, various HCV non-structural proteins also interact or co-localize with DDX3X in close proximity to SGs and LDs, consistent with the tight juxtaposition of the replication complex and the assembly site at the surface of LDs. SiRNA-mediated silencing of DDX3X and multiple SG components markedly inhibits HCV infection. Our data suggest that DDX3X initiates a multifaceted cellular program involving dynamic associations with HCV RNA and proteins, IKK-alpha, SG and LD surface for its crucial role in HCV life cycle. Using the same screening technology, we performed an unbiased strategy to identify cellular microRNAs associated with HCV infection and functionally interrogate these miRNAs with our previous HCV small interference RNA (siRNA) screen database to derive an extensive cellular/viral regulatory network in productive HCV infection. We performed a combined genome-wide miRNA (1000 miRNA in miRBase Sequence 13.0) mimic-inhibitor screen by using a two-part immunostaining format. 60 mirRNAs were identified and validated to interact with HCV infection and replication. 20 miRNAs were proviral and 40 antiviral. miR122 was a confirmed proviral miRNA in the screen and one other miRNA, miR196, recently shown to play a role HCV replication, was also a confirmed hit. By using various HCV model systems, the majority of these novel miRNAs can be assigned to different stages of HCV life cycle, such as entry, IRES-mediated translation, viral RNA replication, and assembly/release. In addition, our global miRNA expression analyses in both Huh7.5.1 cells and primary human hepatocytes revealed that many miRNAs are regulated by HCV infection and some of them are also validated hits of the above genome-wide functional screen, suggesting a complicated interaction between miRNA regulation and HCV infection. We further characterized several of the validated miRNAs for their effects on HCV propagation and demonstrated that these miRNAs target certain host factors identified in our siRNA screen, potentially explaining the functional effects of these miRNAs on HCV infection. A comprehensive investigation of cellular miRNAs modulating the complete HCV life cycle will yield critical insights into HCV pathogenesis and provide novel therapeutic targets.

HCV对宿主机制的依赖既复杂又广泛。每一种宿主依赖性都是潜在的治疗靶点。先前的努力已经成功地发现了HCV复制的重要步骤，但病毒生命周期中的许多基本过程仍未被描述。使用基于rnai的遗传学和感染性HCV细胞培养系统，我们进行了无偏倚的全基因组筛选，以确定生产性HCV感染所需的宿主因子。我们采用了两部分筛选方案，以确定参与整个病毒生命周期的宿主因子，从病毒进入到感染性病毒的产生。随后进行验证筛选，以尽量减少潜在的脱靶效应。初步筛选鉴定出512个基因，验证法鉴定出262个。我们确定了238个宿主易感因子（hsf）和24个宿主耐药因子（hrf），其中大多数以前与HCV无关。在这262个被证实的病毒中，有45个针对的是晚期病毒感染。对这些宿主基因和其他已发表数据库的综合生物信息学分析揭示了HCV对细胞过程和分子功能的广泛而复杂的依赖性，也暗示了调节HCV感染的新的细胞信号通路。