Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression.
Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression.
复制标题
DOI：
10.1371/journal.ppat.1005438
复制
发表时间：
2016-02
期刊：
影响因子：
6.7
通讯作者：
Bouchard MJ
中科院分区：
文献类型：
--
作者：
Lamontagne J;Mell JC;Bouchard MJ
在全球范围内，慢性B型肝炎病毒（HBV）感染仍然是原发性肝癌的主要原因。导致HBV相关肝癌发展的机制仍不完全清楚。在某种程度上，这是因为研究受到缺乏有效模型系统的限制，这些模型系统既容易获得又模拟正常肝细胞的细胞环境。此外，许多研究都集中在单一的，特定的因素或途径，可能会受到HBV的影响，没有解决细胞生理学作为一个整体。在这里，我们应用RNA-seq技术来研究转录组范围内HBV介导的基因表达变化，以确定在HBV复制背景下受影响的单一因素和途径以及基因和途径网络。重要的是，这些研究是在培养的原代肝细胞的离体模型中进行的，允许对该模型系统进行转录组学表征，并在生物学相关背景下研究早期HBV介导的效应。我们分析了时间介导的基因表达变化的背景下的差异基因表达，并表明，在HBV复制的背景下，一些基因和细胞通路被改变，包括那些与代谢，细胞周期调控和脂质生物合成。使用多个分析管道以及qRT-PCR和独立的重复RNA-seq分析来鉴定和确认差异表达的基因。我们发现HBV介导的转录组改变可能代表HBV感染后肝细胞的早期变化，提示早期治疗干预的潜在靶点。总的来说，这些研究产生了一个有价值的资源，可用于扩大我们对宿主-病毒相互作用的复杂网络的理解，以及HBV介导的正常肝细胞生理学变化对病毒复制的影响。B型肝炎病毒（HBV）的慢性感染是原发性肝癌的主要全球原因;然而，用于治疗慢性HBV的疗法在范围和功效方面都是有限的。HBV感染导致宿主-病毒相互作用的不完全理解的复杂网络。为了更好地理解这些相互作用，我们在转录组范围内评估了HBV介导的正常肝细胞基因表达的变化。通过鉴定HBV改变的基因表达，我们能够证明HBV影响先前与致癌相关的多种细胞信号通路。由于大多数HBV相关的研究已经调查了肝细胞生理学的晚期变化或在更窄的范围内观察细胞变化，我们的结果代表了识别与HBV复制相关的早期事件的重要进展，HBV相关疾病的发展上游。此外，我们的研究使我们能够表征原代肝细胞培养模型中发生的转录组变化，这是确认这种常用模型系统作为转化细胞系的生物学相关替代品的重要进展。
Globally, a chronic hepatitis B virus (HBV) infection remains the leading cause of primary liver cancer. The mechanisms leading to the development of HBV-associated liver cancer remain incompletely understood. In part, this is because studies have been limited by the lack of effective model systems that are both readily available and mimic the cellular environment of a normal hepatocyte. Additionally, many studies have focused on single, specific factors or pathways that may be affected by HBV, without addressing cell physiology as a whole. Here, we apply RNA-seq technology to investigate transcriptome-wide, HBV-mediated changes in gene expression to identify single factors and pathways as well as networks of genes and pathways that are affected in the context of HBV replication. Importantly, these studies were conducted in an ex vivo model of cultured primary hepatocytes, allowing for the transcriptomic characterization of this model system and an investigation of early HBV-mediated effects in a biologically relevant context. We analyzed differential gene expression within the context of time-mediated gene-expression changes and show that in the context of HBV replication a number of genes and cellular pathways are altered, including those associated with metabolism, cell cycle regulation, and lipid biosynthesis. Multiple analysis pipelines, as well as qRT-PCR and an independent, replicate RNA-seq analysis, were used to identify and confirm differentially expressed genes. HBV-mediated alterations to the transcriptome that we identified likely represent early changes to hepatocytes following an HBV infection, suggesting potential targets for early therapeutic intervention. Overall, these studies have produced a valuable resource that can be used to expand our understanding of the complex network of host-virus interactions and the impact of HBV-mediated changes to normal hepatocyte physiology on viral replication. Chronic infection with the hepatitis B virus (HBV) is the leading global cause of primary liver cancer; however, therapeutics for the treatment of chronic HBV are limited in both scope and efficacy. Infection with HBV results in an incompletely understood, complex network of host-virus interactions. To attempt to better understand these interactions, we assessed HBV-mediated changes to normal hepatocyte gene expression on a transcriptome-wide scale. By identifying gene expression that is altered by HBV, we were able to demonstrate that HBV affects multiple cellular signaling pathways that previously have been associated with carcinogenesis. As most HBV-related studies have investigated either late-stage changes in hepatocyte physiology or looked at cellular changes on a more narrow scale, our results represent an important advancement towards identifying early events associated with HBV replication, upstream of the development of HBV-associated disease. Additionally, our studies allowed us to characterize transcriptome changes that occur in a primary hepatocyte culture model, an important advancement in the confirmation of this commonly used model system as a biologically relevant alternative to transformed cell lines.