Identification of immune infiltration-related biomarkers in carotid atherosclerotic plaques
Abstract Atherosclerosis is a chronic lipid-driven inflammatory response of the innate and adaptive immune systems, and it is responsible for several cardiovascular ischemic events. The present study aimed to determine immune infiltration-related biomarkers in carotid atherosclerotic plaques (CAPs)....
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-40530-w |
| _version_ | 1797559767754866688 |
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| author | Kai Zheng Wentao Yang Shengxing Wang Mingsheng Sun Zhenyi Jin Wangde Zhang Hualiang Ren Chunmin Li |
| author_facet | Kai Zheng Wentao Yang Shengxing Wang Mingsheng Sun Zhenyi Jin Wangde Zhang Hualiang Ren Chunmin Li |
| author_sort | Kai Zheng |
| collection | DOAJ |
| description | Abstract Atherosclerosis is a chronic lipid-driven inflammatory response of the innate and adaptive immune systems, and it is responsible for several cardiovascular ischemic events. The present study aimed to determine immune infiltration-related biomarkers in carotid atherosclerotic plaques (CAPs). Gene expression profiles of CAPs were extracted from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between the CAPs and control groups were screened by the “limma” package in R software. Immune cell infiltration between the CAPs and control groups was evaluated by the single sample gene set enrichment analysis. Key infiltrating immune cells in the CAPs group were screened by the Wilcoxon test and least absolute shrinkage and selection operator regression. The weighted gene co-expression network analysis was used to identify immune cell-related genes. Hub genes were identified by the protein–protein interaction (PPI) network. Receiver operating characteristic curve analysis was performed to assess the gene’s ability to differentiate between the CAPs and control groups. Finally, we constructed a miRNA-gene-transcription factor network of hub genes by using the ENCODE database. Eleven different types of immune infiltration-related cells were identified between the CAPs and control groups. A total of 1,586 differentially expressed immunity-related genes were obtained through intersection between DEGs and immune-related genes. Twenty hub genes were screened through the PPI network. Eventually, 7 genes (BTK, LYN, PTPN11, CD163, CD4, ITGAL, and ITGB7) were identified as the hub genes of CAPs, and these genes may serve as the estimable drug targets for patients with CAPs. |
| first_indexed | 2024-03-10T17:50:01Z |
| format | Article |
| id | doaj.art-8c9270d759f34621807f2335e3920b63 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-10T17:50:01Z |
| publishDate | 2023-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-8c9270d759f34621807f2335e3920b632023-11-20T09:23:19ZengNature PortfolioScientific Reports2045-23222023-08-0113111510.1038/s41598-023-40530-wIdentification of immune infiltration-related biomarkers in carotid atherosclerotic plaquesKai Zheng0Wentao Yang1Shengxing Wang2Mingsheng Sun3Zhenyi Jin4Wangde Zhang5Hualiang Ren6Chunmin Li7Department of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical UniversityDepartment of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical UniversityDepartment of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical UniversityDepartment of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical UniversityDepartment of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical UniversityDepartment of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical UniversityDepartment of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical UniversityDepartment of Vascular Surgery, Beijing Chaoyang Hospital, Capital Medical UniversityAbstract Atherosclerosis is a chronic lipid-driven inflammatory response of the innate and adaptive immune systems, and it is responsible for several cardiovascular ischemic events. The present study aimed to determine immune infiltration-related biomarkers in carotid atherosclerotic plaques (CAPs). Gene expression profiles of CAPs were extracted from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between the CAPs and control groups were screened by the “limma” package in R software. Immune cell infiltration between the CAPs and control groups was evaluated by the single sample gene set enrichment analysis. Key infiltrating immune cells in the CAPs group were screened by the Wilcoxon test and least absolute shrinkage and selection operator regression. The weighted gene co-expression network analysis was used to identify immune cell-related genes. Hub genes were identified by the protein–protein interaction (PPI) network. Receiver operating characteristic curve analysis was performed to assess the gene’s ability to differentiate between the CAPs and control groups. Finally, we constructed a miRNA-gene-transcription factor network of hub genes by using the ENCODE database. Eleven different types of immune infiltration-related cells were identified between the CAPs and control groups. A total of 1,586 differentially expressed immunity-related genes were obtained through intersection between DEGs and immune-related genes. Twenty hub genes were screened through the PPI network. Eventually, 7 genes (BTK, LYN, PTPN11, CD163, CD4, ITGAL, and ITGB7) were identified as the hub genes of CAPs, and these genes may serve as the estimable drug targets for patients with CAPs.https://doi.org/10.1038/s41598-023-40530-w |
| spellingShingle | Kai Zheng Wentao Yang Shengxing Wang Mingsheng Sun Zhenyi Jin Wangde Zhang Hualiang Ren Chunmin Li Identification of immune infiltration-related biomarkers in carotid atherosclerotic plaques Scientific Reports |
| title | Identification of immune infiltration-related biomarkers in carotid atherosclerotic plaques |
| title_full | Identification of immune infiltration-related biomarkers in carotid atherosclerotic plaques |
| title_fullStr | Identification of immune infiltration-related biomarkers in carotid atherosclerotic plaques |
| title_full_unstemmed | Identification of immune infiltration-related biomarkers in carotid atherosclerotic plaques |
| title_short | Identification of immune infiltration-related biomarkers in carotid atherosclerotic plaques |
| title_sort | identification of immune infiltration related biomarkers in carotid atherosclerotic plaques |
| url | https://doi.org/10.1038/s41598-023-40530-w |
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