Identification of biomarkers associated with mitochondrial dysfunction and programmed cell death in chronic obstructive pulmonary disease via transcriptomics
BackgroundResearch has demonstrated that the homeostasis of mitochondria and programmed cell death (PCD) are intimately linked to chronic obstructive pulmonary disease (COPD). Consequently, identifying biomarkers of COPD from mitochondria-related genes (MRGs) and programmed cell death-related genes...
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Frontiers Media S.A.
2025-06-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2025.1567173/full |
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| author | Xiaojuan Yang Yutao Duan Lei Qiu Xia Huang Fei Li |
| author_facet | Xiaojuan Yang Yutao Duan Lei Qiu Xia Huang Fei Li |
| author_sort | Xiaojuan Yang |
| collection | DOAJ |
| description | BackgroundResearch has demonstrated that the homeostasis of mitochondria and programmed cell death (PCD) are intimately linked to chronic obstructive pulmonary disease (COPD). Consequently, identifying biomarkers of COPD from mitochondria-related genes (MRGs) and programmed cell death-related genes (PCD-RGs) is of paramount importance.MethodsDifferentially expressed genes (DEGs) from the GSE42057 dataset and COPD-related genes (COPD-RGs) via weighted gene co-expression network analysis (WGCNA) were intersected with MRGs and PCD-RGs to select candidates. Machine learning identified biomarkers, validated across GSE42057 and GSE94916 datasets. Pathway enrichment, immune infiltration, and drug prediction analyses were performed.ResultsEight candidate genes were derived from intersecting DEGs, COPD-RGs, MRGs, and PCD-RGs. Five biomarkers (BCL2, CCR7, FAM162A, FOXO1, RPS3) were identified, showing consistent dysregulation in COPD. These biomarkers activated the “ribosome” pathway. CCR7 and FOXO1 correlated positively with naïve B cells, while BCL2 negatively correlated with M0 macrophages. BCL2 exhibited strong binding to dolastatin 10, beauvericin, and micellar paclitaxel. RT-qPCR confirmed biomarker expression.ConclusionBCL2, CCR7, FAM162A, FOXO1, and RPS3 are biomarkers for COPD, providing a new breakthrough point for the treatment of this disease. |
| format | Article |
| id | doaj-art-408efe4e6bd4442db250c42d4f47473a |
| institution | DOAJ |
| issn | 1664-8021 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj-art-408efe4e6bd4442db250c42d4f47473a2025-08-20T03:22:08ZengFrontiers Media S.A.Frontiers in Genetics1664-80212025-06-011610.3389/fgene.2025.15671731567173Identification of biomarkers associated with mitochondrial dysfunction and programmed cell death in chronic obstructive pulmonary disease via transcriptomicsXiaojuan Yang0Yutao Duan1Lei Qiu2Xia Huang3Fei Li4Department of Pulmonary and Critical Care Medicine, Shanxi Provincial People’s Hospital, Taiyuan, ChinaRadiology Department, The First People’s Hospital of Jinzhong, Jinzhong, Shanxi, ChinaDepartment of Pulmonary and Critical Care Medicine, Shanxi Provincial People’s Hospital, Taiyuan, ChinaThe Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, ChinaDepartment of Pulmonary and Critical Care Medicine, Shanxi Provincial People’s Hospital, Taiyuan, ChinaBackgroundResearch has demonstrated that the homeostasis of mitochondria and programmed cell death (PCD) are intimately linked to chronic obstructive pulmonary disease (COPD). Consequently, identifying biomarkers of COPD from mitochondria-related genes (MRGs) and programmed cell death-related genes (PCD-RGs) is of paramount importance.MethodsDifferentially expressed genes (DEGs) from the GSE42057 dataset and COPD-related genes (COPD-RGs) via weighted gene co-expression network analysis (WGCNA) were intersected with MRGs and PCD-RGs to select candidates. Machine learning identified biomarkers, validated across GSE42057 and GSE94916 datasets. Pathway enrichment, immune infiltration, and drug prediction analyses were performed.ResultsEight candidate genes were derived from intersecting DEGs, COPD-RGs, MRGs, and PCD-RGs. Five biomarkers (BCL2, CCR7, FAM162A, FOXO1, RPS3) were identified, showing consistent dysregulation in COPD. These biomarkers activated the “ribosome” pathway. CCR7 and FOXO1 correlated positively with naïve B cells, while BCL2 negatively correlated with M0 macrophages. BCL2 exhibited strong binding to dolastatin 10, beauvericin, and micellar paclitaxel. RT-qPCR confirmed biomarker expression.ConclusionBCL2, CCR7, FAM162A, FOXO1, and RPS3 are biomarkers for COPD, providing a new breakthrough point for the treatment of this disease.https://www.frontiersin.org/articles/10.3389/fgene.2025.1567173/fullchronic obstructive pulmonary diseasemitochondriaprogrammed cell deathbiomarkersimmune infiltration |
| spellingShingle | Xiaojuan Yang Yutao Duan Lei Qiu Xia Huang Fei Li Identification of biomarkers associated with mitochondrial dysfunction and programmed cell death in chronic obstructive pulmonary disease via transcriptomics Frontiers in Genetics chronic obstructive pulmonary disease mitochondria programmed cell death biomarkers immune infiltration |
| title | Identification of biomarkers associated with mitochondrial dysfunction and programmed cell death in chronic obstructive pulmonary disease via transcriptomics |
| title_full | Identification of biomarkers associated with mitochondrial dysfunction and programmed cell death in chronic obstructive pulmonary disease via transcriptomics |
| title_fullStr | Identification of biomarkers associated with mitochondrial dysfunction and programmed cell death in chronic obstructive pulmonary disease via transcriptomics |
| title_full_unstemmed | Identification of biomarkers associated with mitochondrial dysfunction and programmed cell death in chronic obstructive pulmonary disease via transcriptomics |
| title_short | Identification of biomarkers associated with mitochondrial dysfunction and programmed cell death in chronic obstructive pulmonary disease via transcriptomics |
| title_sort | identification of biomarkers associated with mitochondrial dysfunction and programmed cell death in chronic obstructive pulmonary disease via transcriptomics |
| topic | chronic obstructive pulmonary disease mitochondria programmed cell death biomarkers immune infiltration |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2025.1567173/full |
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