椎间盘退变纤维环及髓核异常表达基因的比较及生物信息学分析

目的:通过对已公开发表的基因芯片表达谱数据进行研究,探究椎间盘退变过程中纤维环与髓核组织的基因表达差异,并采用生物信息学方法对差异进行分析。方法:经GEO数据库选取两组椎间盘退变相关的基因芯片表达谱数据GSE23130及GSE67567,GSE23130所研究标本来源于正常及退变纤维环组织,GSE67567标本来源于正常及退变髓核组织。对上述数据系列进行质量分析,GSE23130及GSE67567各有10例样本数据被纳入实验。采用Gene Spring 13.0软件对GSE23130正常及退变纤维环间差异表达基因及GSE67567正常及退变髓核间差异表达基因分别进行筛选,利用KEGG PATHWAY和DAVID功能注释簇集分析分别对GSE23130及GSE67567上调及下调基因进行生物信息学分析。结果:GSE23130及GSE67567各筛选出差异表达基因3182个和3017个,其中135个基因在上述两个基因表达谱数据中均存在差异表达。针对两组数据进行的KEGG PATHWAY分析发现TGF-beta signaling pathway和regulation of apoptosis等数个相同的生物学通路及DAVID功能注释簇集;此外,还发现了数个与GSE23130及GSE67567单独相关的DAVID功能注释簇集。结论:椎间盘退变过程中纤维环及髓核组织内基因表达情况存在差异,两种组织内发生的生物过程不尽相同。某些生物学过程在两种组织内均出现异常改变,这些生物学过程中的异常变化可能是椎间盘退变的关键环节,值得进行深入研究。

Comparison and Bioinformatics Analysis of the Aberrantly Expressed Genes between Degenerated Annulus Fibrous and Nucleus Pulpous

ABSTRACT Objective: In this paper, two released microarray datasets were employed for the comparison of the gene expression profiles between annulus fibrous and nucleus pulpous in intervertebral disc degeneration (IDD). Several bioinformatics analysis were also applied for the differentially expressed genes. Methods: Two IDD related microarray datasets GSE23130 and GSE67567 were selected from the Gene Expression Omnibus. Samples of GSE23130 were derived from normal and degenerated annulus fibrous. GSE67567 samples were collected from normal and degenerative nucleus pulpous tissue. Quality filtering were applied for the data series. 10 samples of GSE23130 and GSE67567 were included respectively in the current study. GeneSpring 13.0 software were applied to screen the differentially expressed genes in GSE23130 and GSE67567 respectively. KEGG PATHWAY analysis and DAVID functional annotation clustering analysis were performed for the up-regulated and down-regulated genes respectively in two datasets. Results: While 3,182 and 3,017 differentially expressed genes were found in GSE23130 and GSE67567 respectively, only 135 of which were both differentially expressed in two datasets. Several KEGG biological pathways such as hsa03040:Spliceosome and hsa04350:TGF-beta signaling pathway and a number of DAVID functional annotation clusters such as nuclear lumen and the regulation of apoptosis were both noted in GSE23130 and GSE67567. However, several DAVID functional annotation clusters were also found relative to GSE23130 and GSE67567 respectively alone. Conclusion: The current study showed differences of gene expression profile between annulus fibrous and nucleus pulpous in IDD. Subsequent bioinformatics analysis indicated that biological processed in the two tissue were not all the same. Biological processes which were aberrantly changed in both tissue might be the key links in IDD deserved further investigating.