Screening Key Genes of Ferroptosis in Atherosclerosis Based on GEO Database Bioinformatics and Experimental Validation
10.3969/j.issn.1671-7414.2024.05.021
- VernacularTitle:基于GEO数据库生物信息学筛选动脉粥样硬化铁死亡关键基因和实验验证
- Author:
Xing WEI
1
;
Qianying CHEN
;
Houwen GONG
;
Fengcheng XU
;
Liming HAN
;
Bin GE
;
Dacai GONG
Author Information
1. 成都医学院第三附属医院/成都市郫都区人民医院检验科,成都 611730
- Keywords:
bioinformatics;
ferroptosis;
atherosclerosis;
differentially expressed genes;
qRT-PCR
- From:
Journal of Modern Laboratory Medicine
2024;39(5):112-119
- CountryChina
- Language:Chinese
-
Abstract:
Objective To screen key genes for ferroptosis in atherosclerosis(AS)using bioinformatics methods and analyze the biological functions of key genes to gain an in-depth understanding of the pathogenesis of AS.Methods AS gene expression profile chip dataset GSE100927 was downloaded from the Gene Expression Omnibus(GEO)database.P＜0.05 and|logFC＞1|were used as the conditions to screen the differential genes of AS.These genes were intersected with ferroptosis gene dataset to screen out the genes related to AS ferroptosis.Gene ontology(GO)functional annotation and enrichment analysis of Kyoto Encyclopedia of Genes and Genomes(KEGG)were carried out.The STRING online analysis tool combined with Cytoscape visualization software was subsequently used to mine genes that play a key role in the biological process of AS,and the AS dataset GSE9874 was used as the verification set to verify the expression of key genes.Blood samples from 30 confirmed AS patients in the cardiovascular department of our hospital from January to March 2023 were collected as the experimental group,while blood samples from 20 healthy volunteers were collected as the control group.Sample RNA was extracted,and quantitative real time polymerase chain reaction(qRT-PCR)was used to verify the selected genes.Results A total of 10 differential genes related to ferroptosis were screened by bioinformatics method.GO functional enrichment analysis showed that differential genes were mainly involved in inflammation,apoptosis,oxidative stress and other biological processes,while KEGG pathway enrichment analysis showed that differential genes were mainly involved in ferroptosis,HIF-1 signaling pathway,and leukocyte migration pathway through endothelial cells.Seven key modules of gene construction were screened out through the protein interaction network,which were FTL,SLC40A1,CYBB,NCF2,HMOX1,DPP4 and ALOX5.GSE9874 was used for verification,and 5 key genes including ALOX5,DPP4,FTL,SLC40A1 and NCF2 were finally screened out.The expression detection of key genes in clinical samples by qRT-PCR showed that compared with the control group,the up-regulated genes in blood of AS group were DPP4(t=1.795,P=0.046),FTL(t=2.218,P=0.029)and SLC40A1(t=2.859,P=0.009),and the down-regulated genes were ALOX5(t=8.039,P＜0.001)and NCF2(t=11.867,P＜0.001),and the differences were significant.The experimental results were consistent with the results of bioinformatics analysis.Subgroup analysis showed that DPP4 expression in plaque group was higher than that in intima thickening group,and the difference was significant(t=2.843,P=0.036).Conclusion The key genes of ferroptosis screened by bioinformatics are AS,ALOX5,DPP4,FTL,SLC40A1 and NCF2,which may be potential targets for the diagnosis and treatment of AS,providing new ideas for the clinical diagnosis and treatment of AS.
