TargetScan筛选退变椎间盘髓核细胞凋亡相关lncRNA的研究  

Target Scan as a tool in screening of apoptosis related long non-coding RNA in degenerative intervertebral nucleus pulposus cell

作　　者：王毅峰[1,2] 宋庆鑫[1] 黄轩[1] 陈智[1] 于利洪 吴水祥 沈洪兴[1] 

机构地区：[1]第二军医大学长海医院脊柱外科,上海市200433 [2]福建省军区厦门警备区医院,厦门市361004

出　　处：《中国矫形外科杂志》2016年第7期643-647,共5页Orthopedic Journal of China

基　　金：上海市新百人计划项目(编号:XBR201399);长海医院"1255"学科建设计划项目(编号:CH125540200)

摘　　要：[目的]寻找退变椎间盘髓核细胞凋亡相关lncRNA,为髓核细胞凋亡的分子机制研究提供指导。[方法]比较miRNA靶基因预测方法,选择灵敏性和特异性均较高、包含不保守区域分析的Target Scan作为预测工具。基于现有lncRNA的序列信息,运行Target Scan的perl脚本,替换mRNA序列信息为lncRNA的序列信息,寻找miRNA的靶lncRNA。根据Target Scan预测结果,综合评估miRNA结合位点数量,靶lncRNA长度,Context+Score评分等指标,筛选目标lncRNA。[结果]文献回顾发现,hsa-miR-27a-3p是退变椎间盘髓核细胞凋亡的关键分子,退变髓核细胞中共有1 052个lncRNA存在差异表达(Fc值≥2,P<0.05),其中有186个lncRNA表达下调。检索Ensemble数据库、UCSC基因浏览器和miRbase数据库,明确差异表达的lncRNA的序列及定位信息,将序列定位明确的117个表达下调的lncRNA纳入研究,筛选退变髓核细胞差异表达lncRNA中含有hsa-miR-27a-3p结合位点的lncRNA。共有28个差异表达的lncRNA含有47个hsa-miR-27a-3p结合位点,其中,ENST00000486904和ENST00000408017的Context+Score百分位数≥90,ENST00000450202长度为459 bp,含有3个hsa-miR-27a-3p结合位点,ENST00000440936、ENST00000441356、ENST00000455216和ENST00000498840分别含有2个hsa-miR-27a-3p结合位点,可能通过吸附miR-27a在椎间盘退变过程中抑制PI3K介导的髓核细胞凋亡。[结论]应用Target Scan数据库进行生物信息学分析,可以有效预测退变椎间盘髓核细胞凋亡相关lncRNA,为进一步的实验研究提供良好的指导。[Objective] To screen apoptosis related long non-coding RNA in degenerative intervertebral nucleus pulposus cell,and provide guidance for the study of molecular mechanism of apoptosis of nucleus pulposus. [Methods] By comparing the miRNA target prediction methods,Target Scan,with high sensitivity and specificity and analysis of non-conservative region,was chosen as a prediction tool. Based on existing lncRNA sequence information,Target Scan perl script was run by replacing the mRNA sequence information for lncRNA,in order to find the miRNA target lncRNA. According to the result of the Target Scan prediction,comprehensive evaluation of factors including number of binding sites,target lncRNA length,Context ＋Score Score was performed,to screen desired target lncRNA. [Results] Literature review showed that hsa-miR-27a-3p was the key to the apoptosis of nucleus pulposus in the degenerative intervertebral disc,1 052 lncRNA was aberrantly expressed in the degenerative nucleus pulposus（ fold change of 2 or more, P〈0. 05）, of which ENST00000486904 and ENST00000408017 Context ＋ Score percentile were 90 or higher. ENST00000450202,length of 459 bp,contained three hsa-miR-27a-3p binding sites. ENST00000440936,ENST00000441356,ENST00000455216 and ENST00000498840 contained two hsa-miR-27a-3p binding sites respectively. It was speculated that through adsorption of miR-27 a,the apoptosis of nucleus pulposus cells were carried out by inhibition of PI3 K in the process of intervertebral disc degeneration. [Conclusion] Application of Target Scan databases for bioinformatics analysis can effectively predict the apoptosis related lncRNA in the degeneration of intervertebral disc nucleus pulposus cells. The result of this study is going to be a good guidance for further study.

关 键 词：长链非编码RNA 椎间盘退变 细胞凋亡 生物信息学分析 

分 类 号：R681.53[医药卫生—骨科学]