Temporal gene expression patterns (Next Generation Sequencing) in liver tumourigenesis of hepatocyte-specific deletion of shp2 and/or pten

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to reveal dynamics of liver tumourigenesis in different mouse model and identify some key regulators that control HCC initiation or progression. We also try to define a index based on transcriptome of samples to quantify tumor development stage. Methods: mRNA profiles of wild-type (WT), hepatocyte-specific shp2 deletion (Shp2-/-) mice (SKO), hepatocyte-specific pten deletion (Pten-/-) mice (PKO), and hepatocyte-specific shp2 and pten deletion mice (DKO) were generated by deep sequencing. The sequence reads that passed quality filters were mapped to Mouse genome using STAR, and mRNA profiles were obtained using cuffdiff. Results: quality control of mRNA profiles showed that the data captured key features of phenotypes. Significantly changed genes, pathways, biolgocial processes, ligand and receptor, epigenetic regulators et al of SKO, PKO, DKO mice at different ages were obtained. Temporal gene expression patterns during liver tumorigenesis in SKO, PKO and DKO mice were obtained. Conclusions: Our study represents the first detailed analysis of temporal transcriptomes during liver tumourigenesis, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comprehensive investigations of expression profiles. mRNA profiles of wild-type (WT), hepatocyte-specific shp2 deletion (Shp2-/-) mice (SKO), hepatocyte-specific pten deletion (Pten-/-) mice (PKO), and hepatocyte-specific shp2 and pten deletion mice (DKO) were generated by deep sequencing, with replicates, using Illumina.研究目的：下一代测序（Next-generation Sequencing，NGS）彻底革新了细胞通路的系统层面分析。本研究旨在揭示不同小鼠模型中肝脏肿瘤发生的动态过程，筛选调控肝细胞癌（Hepatocellular Carcinoma, HCC）起始与进展的关键调控因子，并尝试基于样本转录组构建可量化肿瘤发展阶段的指标。研究方法：通过深度测序获取野生型（WT）、肝细胞特异性shp2基因敲除（Shp2-/-）小鼠（SKO）、肝细胞特异性pten基因敲除（Pten-/-）小鼠（PKO）以及肝细胞特异性shp2与pten双敲除小鼠（DKO）的mRNA表达谱。对通过质量过滤的测序读段，使用STAR软件比对至小鼠基因组，并通过cuffdiff工具得到mRNA表达谱。研究结果：mRNA表达谱的质量控制结果显示，本数据集捕获了表型的关键特征。本研究获取了不同周龄SKO、PKO、DKO小鼠中存在显著差异的基因、通路、生物学过程、配体与受体以及表观遗传调控因子等组学信息；同时解析了SKO、PKO、DKO小鼠肝脏肿瘤发生过程中的时序基因表达模式。研究结论：本研究是首个基于RNA测序（RNA-seq）技术、带有生物学重复的肝脏肿瘤发生时序转录组详细分析。本研究报道的优化数据分析流程可为表达谱的全面研究提供参考框架。本研究通过Illumina平台结合深度测序并设置生物学重复，获取了野生型（WT）、肝细胞特异性shp2基因敲除（Shp2-/-）小鼠（SKO）、肝细胞特异性pten基因敲除（Pten-/-）小鼠（PKO）以及肝细胞特异性shp2与pten双敲除小鼠（DKO）的mRNA表达谱。