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Exploring the pathogenesis of osteomyelitis accompanied by diabetic foot ulcers using microarray data analysis
Although numerous studies have shown distinctive similarities between osteomyelitis and diabetic foot ulcers (DFU), the common pathogenesis of both is not fully understood. The current research focuses on an in-depth study of the molecular and pathway mechanisms involved in the complication of these...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Lippincott Williams & Wilkins
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10615496/ https://www.ncbi.nlm.nih.gov/pubmed/37904457 http://dx.doi.org/10.1097/MD.0000000000033962 |
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author | Fan, Pan Ye, Huanhuan Zhu, Chenhua Xie, Hu |
author_facet | Fan, Pan Ye, Huanhuan Zhu, Chenhua Xie, Hu |
author_sort | Fan, Pan |
collection | PubMed |
description | Although numerous studies have shown distinctive similarities between osteomyelitis and diabetic foot ulcers (DFU), the common pathogenesis of both is not fully understood. The current research focuses on an in-depth study of the molecular and pathway mechanisms involved in the complication of these 2 diseases. We downloaded clinical information on osteomyelitis (GSE30119) and DFU (GSE29221) from the GEO database, along with gene expression matrices. Differentially expressed genes (DEGs) among normal individuals and patients with osteomyelitis; normal individuals and patients with DFU were identified by R software, and thus common DEGs were confirmed. We then analyzed these differential genes, including the functional pathway analysis, protein–protein interaction (PPI), modules and hub genes establishment, and transcription factor regulatory networks. We identified 109 common DEGs (46 up-regulated and 63 down-regulated genes) for subsequent analysis. The results of PPI network and the functional pathway analysis revealed the importance of immune response and inflammatory response in both diseases. Among them, chemokines and cytokines were found to be closely related to both osteomyelitis and DFU. In addition, the tumor necrosis factor (TNF) pathway and Staphylococcus aureus infection were found to have more significant roles too. The 12 most essential key genes were later screened by cytoHubba, including matrix metalloproteinases (MMP) 1, MMP3, MMP9, IL8, C-X-C chemokine receptor (CXCR) 2, C-X-C motif chemokine ligand (CXCL) 9, CXCL10, CXCL13, FCGR3B, IL1B, LCN2, S100A12. CXCL10, and MMP1 were validated using the least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE) algorithms. Osteomyelitis and DFU share similar molecular and pathway mechanisms. These common key genes and pathways may provide new directions toward the future study of osteomyelitis and DFU. |
format | Online Article Text |
id | pubmed-10615496 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Lippincott Williams & Wilkins |
record_format | MEDLINE/PubMed |
spelling | pubmed-106154962023-10-31 Exploring the pathogenesis of osteomyelitis accompanied by diabetic foot ulcers using microarray data analysis Fan, Pan Ye, Huanhuan Zhu, Chenhua Xie, Hu Medicine (Baltimore) 4300 Although numerous studies have shown distinctive similarities between osteomyelitis and diabetic foot ulcers (DFU), the common pathogenesis of both is not fully understood. The current research focuses on an in-depth study of the molecular and pathway mechanisms involved in the complication of these 2 diseases. We downloaded clinical information on osteomyelitis (GSE30119) and DFU (GSE29221) from the GEO database, along with gene expression matrices. Differentially expressed genes (DEGs) among normal individuals and patients with osteomyelitis; normal individuals and patients with DFU were identified by R software, and thus common DEGs were confirmed. We then analyzed these differential genes, including the functional pathway analysis, protein–protein interaction (PPI), modules and hub genes establishment, and transcription factor regulatory networks. We identified 109 common DEGs (46 up-regulated and 63 down-regulated genes) for subsequent analysis. The results of PPI network and the functional pathway analysis revealed the importance of immune response and inflammatory response in both diseases. Among them, chemokines and cytokines were found to be closely related to both osteomyelitis and DFU. In addition, the tumor necrosis factor (TNF) pathway and Staphylococcus aureus infection were found to have more significant roles too. The 12 most essential key genes were later screened by cytoHubba, including matrix metalloproteinases (MMP) 1, MMP3, MMP9, IL8, C-X-C chemokine receptor (CXCR) 2, C-X-C motif chemokine ligand (CXCL) 9, CXCL10, CXCL13, FCGR3B, IL1B, LCN2, S100A12. CXCL10, and MMP1 were validated using the least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE) algorithms. Osteomyelitis and DFU share similar molecular and pathway mechanisms. These common key genes and pathways may provide new directions toward the future study of osteomyelitis and DFU. Lippincott Williams & Wilkins 2023-10-27 /pmc/articles/PMC10615496/ /pubmed/37904457 http://dx.doi.org/10.1097/MD.0000000000033962 Text en Copyright © 2023 the Author(s). Published by Wolters Kluwer Health, Inc. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the Creative Commons Attribution License 4.0 (CCBY) (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | 4300 Fan, Pan Ye, Huanhuan Zhu, Chenhua Xie, Hu Exploring the pathogenesis of osteomyelitis accompanied by diabetic foot ulcers using microarray data analysis |
title | Exploring the pathogenesis of osteomyelitis accompanied by diabetic foot ulcers using microarray data analysis |
title_full | Exploring the pathogenesis of osteomyelitis accompanied by diabetic foot ulcers using microarray data analysis |
title_fullStr | Exploring the pathogenesis of osteomyelitis accompanied by diabetic foot ulcers using microarray data analysis |
title_full_unstemmed | Exploring the pathogenesis of osteomyelitis accompanied by diabetic foot ulcers using microarray data analysis |
title_short | Exploring the pathogenesis of osteomyelitis accompanied by diabetic foot ulcers using microarray data analysis |
title_sort | exploring the pathogenesis of osteomyelitis accompanied by diabetic foot ulcers using microarray data analysis |
topic | 4300 |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10615496/ https://www.ncbi.nlm.nih.gov/pubmed/37904457 http://dx.doi.org/10.1097/MD.0000000000033962 |
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