Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics

• Published in: PeerJ (San Francisco, CA) CA), 2023-10, Vol.11, p.e16122-e16122, Article e16122
• Main Authors: Teng, Da, Chen, Hongping, Jia, Wenjuan, Ren, Qingmiao, Ding, Xiaoning, Zhang, Lihui, Gong, Lei, Wang, Hua, Zhong, Lin, Yang, Jun
• Format: Article
• Language: English
• Subjects: Atherosclerosis; Bioinformatics; Cardiology; Cardiovascular disease (CVD); Cell Biology; Cell differentiation; Development and progression; Foam cells; Gene expression; Genes; Genomes; Genomics; Lipid metabolism; Lipids; Molecular Biology; Pathology; Protein-protein interactions
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.16122

Background Foam cells play crucial roles in all phases of atherosclerosis. However, until now, the specific mechanisms by which these foam cells contribute to atherosclerosis remain unclear. We aimed to identify novel foam cell biomarkers and interventional targets for atherosclerosis, characterizing their potential mechanisms in the progression of atherosclerosis. Methods Microarray data of atherosclerosis and foam cells were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expression genes (DEGs) were screened using the "LIMMA" package in R software. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Ontology (GO) annotation were both carried out. Hub genes were found in Cytoscape after a protein-protein interaction (PPI) enrichment analysis was carried out. Validation of important genes in the GSE41571 dataset, cellular assays, and tissue samples. Results A total of 407 DEGs in atherosclerosis and 219 DEGs in foam cells were identified, and the DEGs in atherosclerosis were mainly involved in cell proliferation and differentiation. CSF1R and PLAUR were identified as common hub genes and validated in GSE41571. In addition, we also found that the expression of CSF1R and PLAUR gradually increased with the accumulation of lipids and disease progression in cell and tissue experiments. Conclusion CSF1R and PLAUR are key hub genes of foam cells and may play an important role in the biological process of atherosclerosis. These results advance our understanding of the mechanism behind atherosclerosis and potential therapeutic targets for future development.