Analysis in relationships of overlapping genes in systemic sclerosis-associated interstitial lung disease, idiopathic pulmonary fibrosis and pulmonary fibrosis model induced by transforming growth factor-β
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摘要:目的
利用生物信息学技术分析系统性硬化症相关间质性肺病（SSc-ILD）、特发性肺纤维化（IPF）与转化生长因子-β（TGF-β）诱导的肺纤维化模型重叠基因的相关性。
方法通过Gene Expression Omnibus（GEO）数据库获取SSc-ILD、IPF与TGF-β诱导的肺纤维化模型相关基因芯片数据GSE76808、GSE135099。采用R软件对数据进行分析，按照adj.P<0.05和|logFC|>1进行筛选，将筛选得到的基因进行基因交互分析；利用R软件对重叠基因进行基因本体（GO）功能注释、京都基因与基因组百科全书（KEGG）通路富集及可视化；基于String数据库对重叠基因进行蛋白质互作（PPI）分析；应用在线分析工具TISIDB获得hub基因并分析其功能。
结果与健康对照组（NC组）相比，SSc-ILD、IPF、TGF-β诱导的肺纤维化模型中存在差异性表达的基因。在SSc-ILD、IPF、TGF-β诱导的肺纤维化模型均下调的34个重叠基因中存在PPI并获得hub基因ELAVL1。GO富集分析结果表明，ELAVL1基因不仅参与RNA剪接、加工、翻译等多种转录后修饰过程，还在腺苷酸活化蛋白激酶（AMPK）信号通路中存在富集。
结论在SSc-ILD和IPF两种疾病中，AMPK信号可能存在异常，导致TGF-β产生增多，而TGF-β可能通过调控ELAVL1蛋白（HuR）由胞核向胞浆转位，进而参与肺纤维化的调节，但具体机制仍有待进一步验证。
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关键词:
- 转化生长因子-β /
- 系统性硬化症相关间质性肺病 /
- 特发性肺纤维化 /
- 生物信息学分析
Abstract:ObjectiveTo analyze the relationships of overlapping genes in systemic sclerosis-associated interstitial lung disease (SSc-ILD), idiopathic pulmonary fibrosis (IPF) and pulmonary fibrosis model induced by transforming growth factor-β (TGF-β) by using bioinformatics technology.
MethodsRelevant gene chip data GSE76808 and GSE135099 of SSc-ILD, IPF and pulmonary fibrosis model induced by TGF-β were obtained from Gene Expression Omnibus (GEO) database. R software was used to analyze the data, and according to the screening conditions of adj. P<0.05 and |logFC|>1, the screened genes were analyzed by gene interaction; Gene Ontology (GO) function annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and visualization for overlapping genes were performed by using R software; protein-protein interaction (PPI) analysis of overlapping genes was performed based on string database; the hub gene was obtained by analysis tool TISIDB and its function was analyzed.
ResultsCompared with the normal control group (NC group), there were differentially expressed genes in SSc-ILD, IPF and pulmonary fibrosis model induced by TGF-β. There was PPI existed in 34 overlapping genes down-regulated by SSc-ILD, IPF and pulmonary fibrosis model induced by TGF-β, and hub gene ELAVL1 was obtained. GO enrichment analysis results showed that ELAVL1 gene was not only involved in many post-transcriptional modification processes such as RNA splicing, processing and translation, but also enriched in adenylate activated protein kinase (AMPK) signal pathway.
ConclusionIn SSc-ILD and IPF, the AMPK signal may be abnormal, resulting in increasing of TGF-β, and TGF-β may be involved in the regulation of pulmonary fibrosis by regulating the translocation of ELAVL1 protein (HuR) from nucleus to cytoplasm, but the specific mechanism still needs to be further verified.
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图 1 SSc-ILD、IPF、TGF-β诱导的肺纤维化模型中差异性表达的基因
A: 与NC组相比, SSc-ILD中差异性表达的基因; B: 与NC组相比, IPF中差异性表达的基因; C: 与NC组相比, TGF-β诱导的肺纤维化模型中差异性表达的基因。
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图 2 SSc-ILD差异性表达的基因与TGF-β诱导的肺纤维化模型差异性表达的基因中的重叠基因
A、B: 分别为SSc-ILD与TGF-β诱导的肺纤维化模型中高表达、低表达基因的重叠基因韦恩图; C、D: 分别为SSc-ILD与TGF-β诱导的肺纤维化模型中高表达、低表达的重叠基因GO分析结果。
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图 3 IPF差异性表达的基因与TGF-β诱导的肺纤维化模型差异性表达的基因中的重叠基因
A、B: 分别为IPF与TGF-β诱导的肺纤维化模型差异表达基因中的重叠基因韦恩图; C、D: 分别为IPF与TGF-β诱导的肺纤维化模型中上调和下调的重叠基因GO分析结果。
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图 4 SSc-ILD、IPF、TGF-β诱导的肺纤维化模型之间的重叠基因韦恩图
A: SSc-ILD、IPF、TGF-β诱导的肺纤维化模型之间共同上调基因的韦恩图; B: SSc-ILD、IPF、TGF-β诱导的肺纤维化模型之间共同下调基因的韦恩图。
表 1 PPI网络分析中前21个基因
排序 名称 得分 排序 名称 得分 1 ELAVL1 6 10 RAB1A 1 2 JUN 5 10 COX8A 1 3 RBBP4 3 10 NDUFA8 1 3 SPTBN1 3 10 PUM2 1 3 XPO1 3 10 ELF3 1 6 METTL3 2 10 HMG20B 1 6 YTHDC1 2 10 IGFBP4 1 6 PDIA6 2 10 TNFAIP3 1 6 CAPRIN1 2 10 KLF6 1 10 PPIB 1 10 NENF 1 10 CBX1 1 
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表 2 GO分析 ELAVL1 基因
GO号 生物过程 GO号 生物过程 GO号 生物过程 0000375 通过酯交换反应进行RNA剪接 0031047 RNA基因沉默 0048255 mRNA稳定 0000377 通过酯交换反应与凸起的腺苷作为亲核试剂进行RNA剪接 0034248 细胞内酰胺代谢过程的调节 0060147 转录后基因沉默的调控 0000398 通过剪接体进行mRNA剪接 0034249 细胞内酰胺代谢过程的负调控 0060149 转录后基因沉默的负调控 0006397 mRNA加工 0034250 细胞内酰胺代谢过程的正向调控 0060964 miRNA对基因沉默的调控 0006417 调节翻译 0035194 RNA转录后基因沉默 0060965 miRNA对基因沉默的负调控 0008380 RNA剪接 0035195 miRNA的基因沉默 0060966 RNA对基因沉默的调控 0010608 基因表达的转录后调控 0040029 基因表达调控、表观遗传 0060967 RNA对基因沉默的负调控 0016441 转录后基因沉默 0043487 RNA稳定性的调节 0060968 基因沉默的调控 0016458 基因沉默 0043488 mRNA稳定性的调节 0060969 基因沉默的负调控 0017148 翻译的负面调节 0043489 RNA稳定 0070935 3′-UTR介导的mRNA稳定性 0019827 维持干细胞群 0045727 正向调节翻译 0098727 维持细胞数量
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表 3 GO分析 ELAVL1 基因
GO号 分子功能 0003725 结合双链RNA 0003729 结合mRNA 0003730 结合mRNA 3′-UTR 0017091 结合富含AU元素 0035925 结合mRNA 3′-UTR富含AU元素区域
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