Analysis of long noncoding gene expression and its interactions with protein-coding genes in vascular endothelial cells in keloids
Abstract Objectives The purpose of this study was to determine the relationship between protein-coding RNA (messenger RNA, mRNA) and long noncoding RNA (lncRNA) expressed in vascular endothelial cells (VECs) in keloids by reanalyzing Gene Expression Omnibus (GEO) microarray chip data. Materials and...
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BMC
2025-02-01
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| Series: | European Journal of Medical Research |
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| Online Access: | https://doi.org/10.1186/s40001-025-02271-6 |
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| author | Yunxiang Luo Zi Ye Yi Li Chau Wei Wong Shuqia Xu Yu Deng Zhicheng Su Xueqing Li Yingxiong Huang Bing Han |
| author_facet | Yunxiang Luo Zi Ye Yi Li Chau Wei Wong Shuqia Xu Yu Deng Zhicheng Su Xueqing Li Yingxiong Huang Bing Han |
| author_sort | Yunxiang Luo |
| collection | DOAJ |
| description | Abstract Objectives The purpose of this study was to determine the relationship between protein-coding RNA (messenger RNA, mRNA) and long noncoding RNA (lncRNA) expressed in vascular endothelial cells (VECs) in keloids by reanalyzing Gene Expression Omnibus (GEO) microarray chip data. Materials and methods The GSE121618 database and clinical information of these samples were downloaded and reanalyzed by the R language package. Expression differences in mRNA and lncRNA between keloids and normal skin were calculated. GO/KEGG enrichment analysis was conducted to determine the function of these genes, and an interaction network of lncRNAs–mRNAs was constructed. Magnetic Sorting of VECs and qRT-PCR were used to verify these bioinformatic results. Results The expression of three hundred and five mRNAs in the keloid group was significantly different from that in the normal group, and 98 lncRNAs were different, 21 of which were upregulated and 118 of which were downregulated. The hub relationship between the upregulated lncRNA‒mRNA interaction was lncRNA LINC01546–RASAL3/COL13A1, while the downregulated hub was lncRNA LOC101929787–PRKAA2/KRT71/SSTR1. qPCR verification result showed no obvious statistical differences. Conclusions Through the in-depth mining of keloid microarray data using bioinformatic methods, we speculated that VECs can affect the development and progression of keloids by epigenomic regulation via lncRNA‒mRNA interactions. |
| format | Article |
| id | doaj-art-0c45ed5228cc4cd5a8961b19ce5ee522 |
| institution | Kabale University |
| issn | 2047-783X |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | European Journal of Medical Research |
| spelling | doaj-art-0c45ed5228cc4cd5a8961b19ce5ee5222025-02-09T12:26:43ZengBMCEuropean Journal of Medical Research2047-783X2025-02-0130111110.1186/s40001-025-02271-6Analysis of long noncoding gene expression and its interactions with protein-coding genes in vascular endothelial cells in keloidsYunxiang Luo0Zi Ye1Yi Li2Chau Wei Wong3Shuqia Xu4Yu Deng5Zhicheng Su6Xueqing Li7Yingxiong Huang8Bing Han9Department of Plastic Surgery, The First Affiliated Hospital of Sun Yat-sen UniversityDepartment of Emergency, The First Affiliated Hospital of Sun Yat-sen UniversityDepartment of Emergency, The First Affiliated Hospital of Sun Yat-sen UniversityDepartment of Plastic Surgery, The First Affiliated Hospital of Sun Yat-sen UniversityDepartment of Plastic Surgery, The First Affiliated Hospital of Sun Yat-sen UniversityDepartment of Plastic Surgery, The First Affiliated Hospital of Sun Yat-sen UniversityDepartment of Plastic Surgery, The First Affiliated Hospital of Sun Yat-sen UniversityDepartment of Plastic Surgery, The First Affiliated Hospital of Sun Yat-sen UniversityDepartment of Emergency, The First Affiliated Hospital of Sun Yat-sen UniversityScar and Wound Treatment Department, Plastic Surgery Hospital, Chinese Academy of Medical Science, Peking Union Medical CollegeAbstract Objectives The purpose of this study was to determine the relationship between protein-coding RNA (messenger RNA, mRNA) and long noncoding RNA (lncRNA) expressed in vascular endothelial cells (VECs) in keloids by reanalyzing Gene Expression Omnibus (GEO) microarray chip data. Materials and methods The GSE121618 database and clinical information of these samples were downloaded and reanalyzed by the R language package. Expression differences in mRNA and lncRNA between keloids and normal skin were calculated. GO/KEGG enrichment analysis was conducted to determine the function of these genes, and an interaction network of lncRNAs–mRNAs was constructed. Magnetic Sorting of VECs and qRT-PCR were used to verify these bioinformatic results. Results The expression of three hundred and five mRNAs in the keloid group was significantly different from that in the normal group, and 98 lncRNAs were different, 21 of which were upregulated and 118 of which were downregulated. The hub relationship between the upregulated lncRNA‒mRNA interaction was lncRNA LINC01546–RASAL3/COL13A1, while the downregulated hub was lncRNA LOC101929787–PRKAA2/KRT71/SSTR1. qPCR verification result showed no obvious statistical differences. Conclusions Through the in-depth mining of keloid microarray data using bioinformatic methods, we speculated that VECs can affect the development and progression of keloids by epigenomic regulation via lncRNA‒mRNA interactions.https://doi.org/10.1186/s40001-025-02271-6KeloidLncRNABioinformaticGEO databaseVascular endothelial cell |
| spellingShingle | Yunxiang Luo Zi Ye Yi Li Chau Wei Wong Shuqia Xu Yu Deng Zhicheng Su Xueqing Li Yingxiong Huang Bing Han Analysis of long noncoding gene expression and its interactions with protein-coding genes in vascular endothelial cells in keloids European Journal of Medical Research Keloid LncRNA Bioinformatic GEO database Vascular endothelial cell |
| title | Analysis of long noncoding gene expression and its interactions with protein-coding genes in vascular endothelial cells in keloids |
| title_full | Analysis of long noncoding gene expression and its interactions with protein-coding genes in vascular endothelial cells in keloids |
| title_fullStr | Analysis of long noncoding gene expression and its interactions with protein-coding genes in vascular endothelial cells in keloids |
| title_full_unstemmed | Analysis of long noncoding gene expression and its interactions with protein-coding genes in vascular endothelial cells in keloids |
| title_short | Analysis of long noncoding gene expression and its interactions with protein-coding genes in vascular endothelial cells in keloids |
| title_sort | analysis of long noncoding gene expression and its interactions with protein coding genes in vascular endothelial cells in keloids |
| topic | Keloid LncRNA Bioinformatic GEO database Vascular endothelial cell |
| url | https://doi.org/10.1186/s40001-025-02271-6 |
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