猴空泡病毒40感染 Vero细胞前后长链非编码RNA差异表达及功能分析

Differential expression and functional analysis of long non-coding RNAs before and after infection with simian virus 40 in Vero cells

目的运用二代测序技术检测猴空泡病毒40(SV40)感染非洲绿猴肾细胞(Vero)后细胞内长链非编码RNA(lncRNA)的差异表达情况,并分析差异表达lncRNA的生物学功能,为解析SV40和宿主细胞的互作机制提供新思路。方法用SV40病毒感染Vero细胞,72h后收取样品,与对照组同时使用Trizol法提取RNA,并对其进行二代测序。使用CNCI、CPC和Cufflinks系列软件对来源于Vero细胞的lncRNA进行鉴定,筛选差异表达lncRNA。根据位置关系进行lncRNA靶基因预测,利用GO富集分析和KEGG富集分析进行靶基因功能富集分析。结果SV40感染Vero细胞后,共有274个lncRNA发生显著性差异表达,其中50个表达上调,224个表达下调。GO富集分析显示,差异表达lncRNA靶基因主要与胞内信号转导、染色质沉默、免疫反应、葡萄糖代谢和蛋白磷酸化调控等生物学过程密切相关。KEGG富集分析显示,差异表达lncRNA的靶基因主要富集在Notch信号通路、TGF-β信号通路、mTOR信号通路和抗原加工和呈递等多个信号通路上。结论SV40感染Vero细胞后重塑了Vero细胞的lncRNA表达谱,多个显著差异表达的lncRNA通过Notch、TGF-β、mTOR和抗原加工和呈递等信号通路参与细胞对病毒感染的反应调控。

Objective To analyze the differentially expressed long noncoding RNAs(lncRNAs)in Vero cells infected with monkey vacuolation virus 40(SV40)and to analyze the biological function of the dysregulated lncRNAs.Methods Vero cells were infected with SV40,and the samples were harvested 72 hours post-infection.Total RNA was extracted from infected cells using the Trizol method at the same time as the control group and then sequenced.Software,including CNCI,CPC,and Cufflinks,was used to identify and screen dysregulated lncRNAs from RNA-seq data.Target genes of dysregulated lncRNAs were predicted based on their positional relationships.In addition,target gene function was analyzed using Go and KEGG function enrichment analysis.Results After SV40 infected Vero cells,a total of 274 lncRNAs were differently expressed,50 of which were up-regulated and 224 of which were down-regulated.Go enrichment analysis indicated that the target genes of dysregulated lncRNAs were implicated in intracellular signal transduction,chromatin silencing,immune response,glucose metabolism,and protein phosphorylation.KEGG enrichment analysis indicated that the target genes of dysregulated lncRNAs were mainly enriched in the Notch signaling pathway,TGF-βsignaling pathway,mTOR signaling pathway,and antigen processing and presentation signaling pathway.Conclusion The expression profile of lncRNA in Vero cells was altered upon SV40 infection.Abundant dysregulated lncRNAs were implicated in the notch,TGF-β,mTOR,and antigen processing and presentation signaling pathways,regulating the cellular response to viral infection via the target genes of the dysregulated lncRNAs.