猪成纤维细胞敲减卵泡抑素基因后的生物信息学分析

Bioinformatics Analysis of Porcine Fibroblasts After Follistatin Gene Knock-down

在哺乳动物中,卵泡抑素(follistatin,FST)不仅参与生殖调控,还与肌肉生长、脂肪沉积等显著相关。为了探究该基因在成纤维细胞中的生物学功能,本研究利用二代测序技术对敲减FST基因的猪成纤维细胞进行转录组测序,筛选差异表达基因,并利用在线生物学软件对差异基因进行GO功能注释及生物学通路富集分析。结果发现,敲减FST基因后共有370个基因显著上调,287个基因显著下调。与细胞增殖、凋亡相关的HOXA6、PARP14、ZBP1、NDUFB9、RAB13、FAM83D、THBS1和BTF3基因以及与疾病相关的ZNF354C、RNF213、IFIT1、CCL5和VPS13C基因均发生了显著变化。这些差异基因共得到51个GO功能注释,生物过程分类下的生物调节、细胞过程、代谢过程、单一生物过程和细胞组分分类下的细胞器、细胞区域、细胞及分子功能分类下的黏合条目下聚集的差异基因数量最多,均>200个。共发现12条显著富集的通路,包括3条与细胞增殖相关的通路(p53信号通路、细胞周期和真核生物中核糖体的生物发生),4条与疾病相关的通路(阿尔茨海默氏病、沙门氏菌感染、亨廷顿病和非小细胞肺癌),2条与肌肉收缩相关的通路(血管平滑肌收缩和心肌收缩)以及泛素介导的蛋白水解作用、肌动蛋白细胞骨架的调节和缝隙连接通路。以上研究结果表明,在成纤维细胞中敲减FST基因后,与细胞增殖分化和部分疾病相关的基因和生物学通路被显著富集,暗示FST基因在成纤维细胞的创伤修复过程中发挥重要的作用。

In mammals,follistatin(FST)is not only involved in reproductive regulation,but also significantly associated with muscle growth and fat deposition.In order to explore the biological function of this gene in fibroblasts,the second generation sequencing technique was used to sequence the transcriptome of pig fibroblasts with FST gene knock-down and screen the differentially expressed genes.GO functional annotation and pathway enrichment analysis were carried out using on-line biological software.The results showed that 370 genes were significantly up-regulated and 287 genes were significantly down-regulated after FST gene knockdown.There were significant changes in HOXA6,PARP14,ZBP1,NDUFB9,RAB13,FAM83D,THBS1 and BTF3 genes associated with cell proliferation and apoptosis,as well as disease-related genes ZNF354C,RNF213,IFIT1,CCL5 and VPS13C.51 GO terms were clustered for these differential genes.Biological regulation,cellular process,metabolic process and single-organism process were screened under biological process.Organelle,cell part and cell were screened under cellular component.Binding terms were screened under molecular function.These terms were all including more than 200 differential genes.12 significantly enriched pathways were identified,including 3 pathways related to cell proliferation,such as p53 signal pathway,cell cycle and ribosome biogenesis in eukaryotes,4 pathways were related to disease,such as Alzheimer’s disease,Salmonella infection,Huntington’s disease and non-small cell lung cancer,2 pathways were related to muscle contraction,such as vascular smooth muscle contraction,cardiac muscle contraction.In addition,there were ubiquitin mediated proteolysis,regulation of actin cytoskeleton and gap junction pathways.The results indicated that after FST gene knockdown in fibroblasts,genes and biological pathways related to cell proliferation,differentiation and some diseases were significantly enriched,suggesting that FST gene played an important role in wound repair process of fibroblasts.