大鼠脊髓损伤后差异表达基因的筛选与分析

Screening and analyzing differentially expressed genes in rats after spinal cord injury

摘要:

目的： 通过对大鼠脊髓损伤（spinal cord injury，SCI）相关基因芯片进行生物信息学分析，为阐明继发性SCI的分子机制提供新思路。方法： 首先从GEO数据库下载大鼠SCI的mRNA表达谱数据集GSE464和GSE45006，利用R语言limma包筛选损伤和正常脊髓的差异表达基因（differential expression genes，DEGs）并取交集。然后进行GO、KEGG及GSEA分析。随后使用STRING在线工具和Cytoscape软件构建蛋白-蛋白互作（protein-protein interaction，PPI）网络并将其进行可视化，利用cytoHubba插件选择hub基因。最后使用GOSemSim包预测hub基因编码蛋白间的相互作用。结果： 共筛选出226个DEGs。功能注释及通路富集分析显示，DEGs主要涉及细胞对炎症的反应、离子的调节、再生及修复等生物学过程（biological process，BP）；主要参与突触前膜、轴突末端、神经元投射终点站等细胞组分（cellular component，CC）；介导ATP磷酸化、细胞骨架的结构组成、与钙依赖蛋白结合等分子功能（molecular function，MF）。富集的通路主要有TNF、AGE-RAGE、NF-κB和Toll样受体等信号通路。共获得10个hub基因，分别为Tubb5、Prkcd、Anxa2、Gns、Fabp5、Ctsc、Lyz2、Gusb、Vat1和Grn，并且与SCI密切相关，其中Prkcd、Ctsc、Vat1、Gns和Lyz2基因在SCI中缺乏相关研究，值得进一步研究。结论： 本研究鉴定了可能参与继发性SCI的hub基因和信号通路，为继发性SCI的分子机制提供了新的理论依据。

Abstract:

Objective: To perform a bioinformatics analysis of the gene chip associated with spinal cord injury (SCI) in rats, so as to provide new ideas for clarifying the molecular mechanism of secondary SCI. Methods: Firstly, data sets GSE464 and GSE45006 of rat SCI mRNA expression profile were downloaded from the GEO database. The R language limma package was used to screen differential expression genes (DEGs) of injured and normal spinal cord and obtain the intersection. Then GO, KEGG and GSEA analyses were performed. Subsequently, the STRING online tool and Cytoscape software were used to construct and visualize a protein-protein interaction (PPI) network, and the cytoHubba plug-in was used to select the hub gene. Finally, the GOSemSim package was used to predict interactions between proteins encoded by the hub gene. Results: A total of 226 DEGs were screened. Functional annotation and pathway enrichment analysis showed that DEGs were mainly involved in biological processes (BP), which contained response of cells to inflammation, regulation of ions, regeneration and repair; mainly participated in the main cellular components (CC) including presynaptic membrane, axonal ends and neuron projection endpoints; mediated the molecular function (MF): ATP phosphorylation, structural composition of the cytoskeleton, and binding to calcium-dependent proteins. Enriched pathways were mainly TNF, AGE-RAGE, NF-κB and Toll-like receptors. A total of 10 hub genes were obtained, namely Tubb5, Prkcd, Anxa2, Gns, Fabp5, Ctsc, Lyz2, Gusb, Vat1, and Grn, and were closely related with SCI. Among them, Prkcd, Ctsc, Vat1, Gns and Lyz2 genes in SCI lacked studies, and were worthy of further study. Conclusion: This study identifies hub genes and signaling pathways that may be involved in secondary SCI, and provides a new theoretical basis for the molecular mechanism of secondary SCI.