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

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, characterizi...

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Autores principales: Teng, Da, Chen, Hongping, Jia, Wenjuan, Ren, Qingmiao, Ding, Xiaoning, Zhang, Lihui, Gong, Lei, Wang, Hua, Zhong, Lin, Yang, Jun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10557941/
https://www.ncbi.nlm.nih.gov/pubmed/37810795
http://dx.doi.org/10.7717/peerj.16122
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author Teng, Da
Chen, Hongping
Jia, Wenjuan
Ren, Qingmiao
Ding, Xiaoning
Zhang, Lihui
Gong, Lei
Wang, Hua
Zhong, Lin
Yang, Jun
author_facet Teng, Da
Chen, Hongping
Jia, Wenjuan
Ren, Qingmiao
Ding, Xiaoning
Zhang, Lihui
Gong, Lei
Wang, Hua
Zhong, Lin
Yang, Jun
author_sort Teng, Da
collection PubMed
description 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.
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spelling pubmed-105579412023-10-07 Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics Teng, Da Chen, Hongping Jia, Wenjuan Ren, Qingmiao Ding, Xiaoning Zhang, Lihui Gong, Lei Wang, Hua Zhong, Lin Yang, Jun PeerJ Bioinformatics 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. PeerJ Inc. 2023-10-03 /pmc/articles/PMC10557941/ /pubmed/37810795 http://dx.doi.org/10.7717/peerj.16122 Text en ©2023 Teng et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Teng, Da
Chen, Hongping
Jia, Wenjuan
Ren, Qingmiao
Ding, Xiaoning
Zhang, Lihui
Gong, Lei
Wang, Hua
Zhong, Lin
Yang, Jun
Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics
title Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics
title_full Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics
title_fullStr Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics
title_full_unstemmed Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics
title_short Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics
title_sort identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10557941/
https://www.ncbi.nlm.nih.gov/pubmed/37810795
http://dx.doi.org/10.7717/peerj.16122
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