Search for potential target genes in dexamethasone-induced open-angle glaucoma by bioinformatics
10.3760/cma.j.cn115989-20211214-00683
- VernacularTitle: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
- Author:
Liling LIU
1
;
Deling LI
;
Weiting ZENG
;
Xinyi ZHANG
;
Jiangang XU
;
Minbin YU
Author Information
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
- Keywords:
Dexamethasone;
Glaucoma, open-angle;
Trabecular meshwork;
Differentially expressed genes;
Myofibroblast;
Bioinformatics;
In vitro experiment
- From:
Chinese Journal of Experimental Ophthalmology
2023;41(2):127-133
- CountryChina
- Language:Chinese
-
Abstract:
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 cells to myofibroblasts transition after dexamethasone treatment.
