Gene expression profile identifies potential biomarkers for human intervertebral disc degeneration.
Gene expression profile identifies potential biomarkers for human intervertebral disc degeneration.
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基因表达谱识别人类椎间盘退变的潜在生物标志物
DOI：
10.3892/mmr.2017.7741
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发表时间：
2017-12
影响因子：
3.4
通讯作者：
Feng SQ
中科院分区：
文献类型：
--
作者：
Guo W;Zhang B;Li Y;Duan HQ;Sun C;Xu YQ;Feng SQ
本研究旨在通过生物信息学分析基因芯片数据，揭示椎间盘退变（IDD）发病机制的潜在相关基因。比较IDD患者和对照组椎间盘两个区域的基因表达谱。GSE 70362包含两组基因表达谱，16个来自IDD患者的髓核（NP）样品和8个来自对照的髓核（NP）样品，以及16个来自IDD患者的纤维环（AF）样品和8个来自对照的纤维环样品，从Gene Expression Omnibus数据库下载。共93和114个差异表达基因（DEG），分别在NP和AF样品中，使用Limma软件包的R编程环境。基因本体（GO）功能富集分析表明DEG在IDD中可能参与细胞粘附、生物粘附和细胞外基质组织化等多个过程。使用京都基因和基因组百科全书（KEGG）进行的途径富集分析表明，所鉴定的DEG可能参与粘着斑和p53信号通路。进一步的分析显示，在两个区域（NP和AF）之间观察到35个共同的DEG，这可能进一步受到WebGestalt检索的6簇microRNA（miRNAs）的调控。通过GO功能和KEGG途径富集分析对DEG-miRNA调控网络中的基因进行了注释，其中细胞外基质组织化是最重要的生物学过程被破坏，粘着斑是最重要的失调途径。此外，蛋白质相互作用网络模块的结果表明，炎症细胞因子干扰素信号转导参与IDD。这些发现不仅可以促进对IDD发病机制的理解，而且还可以确定这种疾病的新的潜在生物标志物。
The present study aimed to reveal the potential genes associated with the pathogenesis of intervertebral disc degeneration (IDD) by analyzing microarray data using bioinformatics. Gene expression profiles of two regions of the intervertebral disc were compared between patients with IDD and controls. GSE70362 containing two groups of gene expression profiles, 16 nucleus pulposus (NP) samples from patients with IDD and 8 from controls, and 16 annulus fibrosus (AF) samples from patients with IDD and 8 from controls, was downloaded from the Gene Expression Omnibus database. A total of 93 and 114 differentially expressed genes (DEGs) were identified in NP and AF samples, respectively, using a limma software package for the R programming environment. Gene Ontology (GO) function enrichment analysis was performed to identify the associated biological functions of DEGs in IDD, which indicated that the DEGs may be involved in various processes, including cell adhesion, biological adhesion and extracellular matrix organization. Pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) demonstrated that the identified DEGs were potentially involved in focal adhesion and the p53 signaling pathway. Further analysis revealed that there were 35 common DEGs observed between the two regions (NP and AF), which may be further regulated by 6 clusters of microRNAs (miRNAs) retrieved with WebGestalt. The genes in the DEG-miRNA regulatory network were annotated using GO function and KEGG pathway enrichment analysis, among which extracellular matrix organization was the most significant disrupted biological process and focal adhesion was the most significant dysregulated pathway. In addition, the result of protein-protein interaction network modules demonstrated the involvement of inflammatory cytokine interferon signaling in IDD. These findings may not only advance the understanding of the pathogenesis of IDD, but also identify novel potential biomarkers for this disease.
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影响因子：
4.6
作者：
Kazezian Z;Gawri R;Haglund L;Ouellet J;Mwale F;Tarrant F;O'Gaora P;Pandit A;Alini M;Grad S
通讯作者：
Grad S
影响因子：
2.9
作者：
Bian DL;Wang XM;Huang K;Zhai QX;Yu GB;Wu CH
通讯作者：
Wu CH
microRNA分析：方法和考虑因素。
DOI：
10.1038/nrg3198
发表时间：
2012-04-18
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
Pritchard CC;Cheng HH;Tewari M
通讯作者：
Tewari M
影响因子：
14.9
作者：
Ritchie ME;Phipson B;Wu D;Hu Y;Law CW;Shi W;Smyth GK
通讯作者：
Smyth GK
影响因子：
5.4
作者：
He, Jiaxuan;Xue, Rongliang;Wei, Haidong
通讯作者：
Wei, Haidong