摘要
【目的】研究小鼠肠I/R损伤早期肠黏膜中长链非编码RNA(lncRNA)的变化,建立差异表达的lncRNA表达谱及功能角色,并对lncRNA和凋亡相关基因进行编码-非编码基因共表达(CNC)生物信息学分析。【方法】采用lncRNA芯片高通量筛选小鼠肠I/R损伤早期肠黏膜中差异lncRNA的变化并用qRT-PCR验证芯片重复性,通过对与lncRNA同时差异表达的mRNA进行基因本体论(GO)富集分析,重点分析凋亡相关功能。最后,挑选差异变化的已知凋亡相关基因的mRNA,通过CNC分析计算出与之显著相关的IncRNA-mRNA关系对,构建差异lncRNA和凋亡mRNA共表达网络。【结果】与假手术组相比,肠I/R后小鼠肠上皮细胞lncRNA表达谱发生了显著变化,其中表达上调的lncRNA有1 503个,表达下调的lncRNA有2 099个(Fold change≥2,P<0.05)。同时,1 528个mRNA表达上调,1 630个mRNA表达下调(Fold change≥2,P<0.05)。GO分析富集指数得出,参与调控的功能最主要与脂代谢过程、氧化还原反应、应激反应、凋亡过程、程序性细胞死亡、细胞周期、炎症反应、内皮细胞分化增殖、组织重构、MAPK、Wnt、血管内皮生长因子信号通路等有关。"凋亡"相关的子条目在上调和下调的GO分子功能条目注释中以不同形式多次富集,且排在前列。最后生物信息学分析发现,凋亡相关mRNA与差异表达的lncRNA存在着显著的共表达网络关系。【结论】本研究筛选出小鼠肠I/R损伤早期肠黏膜差异变化的lncRNA,建立并初步验证了差异lncRNA表达谱,生物信息学分析得出调控"凋亡"相关过程是其重要的生物学功能,大量的差异lncRNA与凋亡基因确实存在高度的共表达关系,为后继研究提供了基础和方向。
【Objective】To investigate the lncRNA expression profile and potential roles in mouse intestinal mucosa after I/R treatment and explore the co-expression relationship between dysregulated lncRNA and apoptotic mRNA at the early stage of reperfusion.【Methods】 The expression profiles of lncRNA were obtained using microarray and some lncRNA were further validated by quantitative real-time polymerase chain reaction(qRT-PCR). Gene ontology(GO)analyses were performed to determine closely related biological functions,especially apoptosis-related functions. Finally,the known apoptosis-related mRNA with obviously changes were selected to construct the co-expression network of the dysregulated lncRNA and their correlated apoptotic mRNA,and were analyzed by CNC analysis to calculate the significant correlation of IncRNA-mRNA pairs.【Results】Compared with sham operation group,the expression profile of R was significantly changed,including 1 503 up-regulated lncRNAs and 2 099 down regulated in I/R group,while 1 630 mRNA were down-regulated(fold-change≥2.0,P<0.05). GO enrichment analysis showed that the main functions involved in regulation were lipid metabolism,redox reaction,stress reaction,apoptosis process,programmed cell death,cell cycle,inflammatory response,endothelial cell differentiation and proliferation,tissue remodeling,MAPK,Wnt,vascular endothelial growth factor signaling pathway and so on. Apoptosis-related subitems were enriched in the up-and down-regulated annotations of GO molecular function in different forms,which were in the forefront. There was a significant co-expression relationship between apoptosis-related mRNA and dysregulated lncRNA.【Conclusion】In this study,we established and preliminarily validated the expression profiles of the differentially expressed lncRNA at the early stage of reperfusion in mouse intestinal ischemia injury. Bioinformatics analysis showed that the important biological function of dysregulated lncRNA was the regulation of apoptosis-related processes,and a large number of those lncRNA were indeed highly co-expressed with apoptotic genes,which would provide a basis and direction for future research.
引文
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