生物信息学方法对地塞米松致开角型青光眼潜在靶基因的确定和分析  

Search for potential target genes in dexamethasone-induced open-angle glaucoma by bioinformatics

作　　者：刘丽玲 李德玲 曾伟婷 张心怡 徐建刚[1] 余敏斌[1] Liu Liling;Li Deling;Zeng Weiting;Zhang Xinyi;Xu Jiangang;Yu Minbin(State Key Laboratory of Ophthalmology,Zhongshan Ophthalmic Center,Sun Yat-sen University,Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science,Guangzhou 510060,China)

机构地区：[1]中山大学中山眼科中心、眼科学国家重点实验室、广东省眼科视觉科学重点实验室,广州510060

出　　处：《中华实验眼科杂志》2023年第2期127-133,共7页Chinese Journal Of Experimental Ophthalmology

摘　　要：目的利用生物信息学方法寻找地塞米松致开角型青光眼的潜在靶基因。方法在GEO数据库检索激素类青光眼相关数据集,选取数据集GSE16643、GSE37474和GSE124114,采用GEO2R分析,对GSE37474和GSE124114差异表达数据进行GSEA分析,并对3个数据集差异表达数据绘制Venn图取3个交集数据集,通过基因本体论(GO)/京都基因与基因组百科全书(KEGG)对交集基因注释和富集分析并比对GTEx Portal的正常组织,通过STRING得到对应的蛋白网络,最后将找到的候选基因在UCSC和JASPAR上查找转录因子。将人眼原代小梁细胞分为地塞米松组和对照组,分别用500 nmol/L地塞米松2 ml和等体积乙醇溶液培养7 d,采用Western blot法检测小梁细胞中BDKRB1和TAGLN蛋白表达。结果GSEA分析GSE37474和GSE124114数据集差异基因在补体和凝血级联通路富集;3个数据集共有的基因有89个,通过GO分析发现这些基因主要是调控细胞外基质胶原形成,GO分析得分最高、含有胶原的细胞外基质的基因在GTEx Portal找到与成纤维细胞有关。通过STRING蛋白互作网络分析关键基因簇发现,ACTA2、MYL9、TAGLN、LMOD1间关系密切。UCSC和JASPAR上查找到BDKRB1、NID1、MFGE8和TAGLN的转录因子SP1。地塞米松组BDKRB1和TAGLN蛋白相对表达量分别为1.32±0.14和0.44±0.09,明显高于对照组的1.00±0.00和0.20±0.10,差异均有统计学意义(t=-3.61、2.89,均P<0.05)。结论生物信息法分析表明地塞米松作用于小梁细胞后转录因子SP1是开角型青光眼发生的靶基因,主要参与小梁细胞向肌成纤维细胞转化过程调节。Objective To predict potential target genes in dexamethasone-induced open-angle glaucoma via bioinformatics technology.Methods The GEO datasets GSE16643,GSE37474,and GSE124114 were used to analyze the differentially expressed genes by GEO2R.Gene Set Enrichment Analysis(GSEA)was performed on the differentially expressed genes between GSE37474 and GSE124114.Intersection of the three datasets were displayed by Venn diagram.The annotation and enrichment analysis of the intersection genes were performed through Gene Ontology(GO)/Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis and then were compared with normal tissue in GTEx Portal database.The corresponding protein interaction network was obtained by STRING.Finally,the candidate genes were searched for their transcription factors in UCSC and JASPAR.Primary human trabecular cells were divided into dexamethasone group and control group,treated with 2 ml 500 nmol/L dexamethasone and the same amount of ethanol,respectively.The expression of BDKRB1 and TAGLN in trabecular cells was detected by Western blot.Results Differential genes between GSE37474 and GSE124114 datasets enriched in complement and coagulation cascade by GSEA.There were 89 intersecting genes of the three datasets.These genes mainly regulated the formation of extracellular matrix by GO analysis.The gene with the highest enrichment score and collagen-containing extracellular matrix was found to be associated with fibroblasts in GTEx Portal database.ACTA2,MYL9,TAGLN,and LMOD1 were closely related in STRING protein-protein interaction network.Transcription factor SP1 in UCSC and JASPAR according to related genes,BDKRB1,NID1,MFGE8 and TAGLN.The relative expression levels of BDKRB1 and TAGLN proteins were 1.32±0.14 and 0.44±0.09 in dexamethasone group,respectively,which were significantly higher than 1.00±0.00 and 0.20±0.10 in the control group,respectively(t=-3.61,2.89;both at P<0.05).Conclusions Bioinformatics analysis showed that transcription factor SP1 may play a role in human trabecular meshwork

关 键 词：地塞米松 开角型青光眼 小梁网 差异表达基因 肌成纤维细胞 生物信息学 体外实验 

分 类 号：R775[医药卫生—眼科]