摘要
目的基于生物信息学方法分析小鼠脑出血组织的基因表达,探讨影响脑出血疾病发生发展的差异表达基因及用于疾病治疗的药物预测。方法从基因表达综合(GEO)下载GSE216607和GSE200575进行分析,获得基因表达谱,筛选差异表达基因(DEGs)(P<0.05,|log FC|≥2),两者取交集。接着利用基因本体(GO)、京都基因和基因组数据库(KEGG)富集分析对目标基因的信号通路进行富集分析。然后通过STRING数据库构建蛋白质相互作用(PPI)网络。最后通过Cytoscape软件中筛选hub基因,对hub基因进行实时荧光定量聚合酶链式反应(RT-qPCR)验证,将关键基因导入Coremine Medical数据库映射出具有潜在治疗作用的药物。利用UCSC数据库联合JASPAR数据库预测差异表达基因相关的转录因子(TF)。结果共鉴定出81个上调的DEGs,GO富集分析显示其参与了白细胞迁移、细胞因子活性等。并且KEGG富集分析中显示与细胞因子信号通路、白细胞介素(IL)-17信号通路、肿瘤坏死因子(TNF)信号通路等信号通路有关。通过PPI网络最终筛选出5个hub基因IL-1β、趋化因子配体2(CCL2)、C-X-C基序趋化因子配体1(CXCL1)、金属蛋白酶组织抑制因子1(TIMP1)、丝氨酸蛋白酶抑制因子E1(SERPINE1)。RT-qPCR表明与假手术组(Sham)组比较,脑出血模型组小鼠脑组织中IL-1β、CCL2、CXCL1、TIMP1、SERPINE1的mRNA含量均明显上升(P<0.05)。Coremine Medical筛选出的人参花、人参芦、人参叶、人参、茶树根等中药可能作为脑出血潜在的分子药物来源,并且筛选出马卡因、阿朴天仙子碱、灌木远志酮A、花生四烯酸、胡萝卜苷、β-谷甾醇、豆甾醇、吉九里香碱、谷甾醇、9,12,15-二十二碳三烯醇、顺式-11,14,17-二十碳三烯酸甲酯等分子可能是治疗脑出血的潜在分子药物。结论IL-1β、CCL2、CXCL1、TIMP1、SERPINE1等基因在脑出血后表达存在差异,可能参与了脑出血后的病理机制,并且马卡因、阿朴天仙子碱、灌木远志酮A、花生四烯酸、胡萝卜苷、β-谷甾醇、豆甾醇、吉九里香碱、谷甾醇、9,12,15-二十二碳三烯醇、顺式-11,14,17-二十碳三烯酸甲酯等分子可能是治疗脑出血的潜在药物分子。
Objective To analyze the gene expression of mouse intracranial hemorrhage(ICH)tissues based on bioinformatics methods,and to explore the differentially expressed genes(DEGs)affecting ICH development and drug prediction for disease treatment.Methods Gene expression profiles were obtained by downloading GSE216607 and GSE200575 from the Gene Expression Omnibus(GEO)for analysis,and DEGs were screened(P<0.05,|logFC|≥2),which were taken to be intersected.Then the signaling pathways of the target genes were enriched using gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG).Next the protein-protein interaction(PPI)network was constructed by Search Tool for the Retrieval of Interacting Genes/Proteins(STRING)database.Finally,the hub genes were screened in Cytoscape software,and real-time quantitative polymerase chain reaction(RT-qPCR)was performed to validate the hub genes,and the key genes were imported into Coremine Medical database to map out the drugs with potential therapeutic effects.Transcription factors(TFs)associated with DEGs were predicted using the University of California,Santa Cruz Genomics Institute(UCSC)Genome Browser Database in conjunction with the JASPAR database,a database of transcription factor binding profiles.Results A total of 81 up-regulated DEGs were identified,and GO enrichment analysis results showed that they were involved in leukocyte migration,cytokine activity and so on.Moreover,KEGG enrichment analysis results showed that they were related to cytokine signaling pathway,IL-17 signaling pathway,tumor necrosis factor(TNF)signaling pathway and other signaling pathways.Five hub genes,interleukin-1 beta(IL-1β),chemokine(C-C motif)ligand 2(CCL2),C-X-C motif chemokine ligand 1(CXCL1),tissue inhibitor of metalloproteinases 1(TIMP1),and Serpin family E member 1(SERPINE1),were finally screened by PPI network.RT-qPCR showed that the mRNA content of IL-1β,CCL2,CXCL1,TIMP1,and SERPINE1 were significantly increased in the brain tissues of mice in the ICH model group when compared with the Sham group(P<0.05).The herbal medicines such as ginseng flower,ginseng lu,ginseng leaf,ginseng,and tea tree root,which were screened by Coremine Medical,may serve as potential source of molecular drugs for ICH,and screened molecules such as Inermin,Aposiopolamine,Frutinone A,arachidonate,alexandrin_qt,beta-sitosterol,Stigmasterol,Girinimbin,sitosterol,9,12,15-docosatrienol,icosa-11,14,17-trienoic acid methyl ester as potential molecular drugs for the treatment of ICH.Conclusion Genes such as IL-1β,CCL2,CXCL1,TIMP1,and SERPINE1 are involved in the pathological mechanisms following intracranial hemorrhage,and that Inermin,Aposiopolamine,Frutinone A,arachidonate,alexandrin_qt,beta-sitosterol,Stigmasterol,Girinimbin,sitosterol,9,12,15-docosatrienol,and icosa-11,14,17-trienoic acid methyl ester may be potential molecular drugs for the treatment of ICH.
作者
刘建
杨莎
曾宇
孔卓
王方
张继勤
王超
谭赢
LIU Jian;YANG Sha;ZENG Yu;KONG Zhuo;WANG Fang;ZHANG Jiqin;WANG Chao;TAN Ying(Department of Neurosurgery,Guizhou Provincial People's Hospital,Guiyang,Guizhou 550005,China;Department of Anesthesiology,Guizhou Provincial People's Hospital,Guiyang,Guizhou 550005,China;Graduate School of Zunyi Medical University,Zunyi,Guizhou 563099,China;School of Medicine of Guizhou University,Guiyang,Guizhou550025,China;Graduate School of Guizhou Medical University,Guiyang,Guizhou550004,China;Shanghai Children's Medical Center Guizhou Hospital,Guiyang,Guizhou 550081,China)
出处
《安徽医药》
2025年第10期2090-2095,I0005,I0006,共8页
Anhui Medical and Pharmaceutical Journal
基金
国家自然科学基金项目(82360376)。
关键词
脑出血
差异表达基因
hub基因
富集分析
中药
转录因子
Intracranial hemorrhage
Differentially expressed gene
Hub gene
Enrichment analysis
Traditional Chinese medicine
Transcription factors
