Integrating bioinformatics and experimental validation to Investigate IRF1 as a novel biomarker for nucleus pulposus cells necroptosis in intervertebral disc degeneration
Abstract Intervertebral disc degeneration (IDD) is a prevalent spinal disorder and the principal cause of lower back pain (LBP). Diverse forms of programmed cell death (PCD) have been identified as the key phenotypes of the disease and have the potential to serve as new indicators for the diagnosis...
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Nature Portfolio
2024-12-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-024-81681-8 |
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| author | Kaisheng Zhou Shaobo Wu Zuolong Wu Rui Ran Wei Song Hao Dong Haihong Zhang |
| author_facet | Kaisheng Zhou Shaobo Wu Zuolong Wu Rui Ran Wei Song Hao Dong Haihong Zhang |
| author_sort | Kaisheng Zhou |
| collection | DOAJ |
| description | Abstract Intervertebral disc degeneration (IDD) is a prevalent spinal disorder and the principal cause of lower back pain (LBP). Diverse forms of programmed cell death (PCD) have been identified as the key phenotypes of the disease and have the potential to serve as new indicators for the diagnosis and prognosis of IDD. However, the mechanism underlying necroptosis in IDD remains unclear. This study aimed to identify novel biomarkers that promote nucleus pulposus cell necroptosis in IDD using bioinformatic analysis and experimental validation. We analyzed multiple datasets of IDD from the Gene Expression Omnibus (GEO) database to identify necroptosis-related IDD differential genes (NRDEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed, followed by logistic least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive (SVM) algorithms to identify key genes. Gene set enrichment analysis (GSEA) and logistic regression analysis were used to ascertain the potential functions of these genes and to identify key genes, respectively. We then constructed mRNA-miRNA, mRNA-TF, mRNA-drug, and functional similarity gene interaction networks for the seven key genes identified. We used IDD clinical samples and necroptotic cell model to validate our findings. Immunohistochemical staining, RT-qPCR, and western blotting results indicated that IRF1 may be a hub necroptosis-related gene. To further elucidate the function of IRF1, we constructed IRF1 knockdown and overexpression models, which revealed that IRF1 promotes necroptosis in rat nucleus pulposus cells, increases mitochondrial ROS levels, and decreases ATP levels. These findings provide new insights into the development of necroptosis in IDD and, for the first time, validate the role of IRF1 as a novel biomarker for the diagnosis and treatment of IDD. |
| format | Article |
| id | doaj-art-9580f2acd17d47b0aa48aab9983b6621 |
| institution | OA Journals |
| issn | 2045-2322 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-9580f2acd17d47b0aa48aab9983b66212025-08-20T02:31:03ZengNature PortfolioScientific Reports2045-23222024-12-0114112110.1038/s41598-024-81681-8Integrating bioinformatics and experimental validation to Investigate IRF1 as a novel biomarker for nucleus pulposus cells necroptosis in intervertebral disc degenerationKaisheng Zhou0Shaobo Wu1Zuolong Wu2Rui Ran3Wei Song4Hao Dong5Haihong Zhang6Department of Orthopaedics, Lanzhou University Second HospitalDepartment of Orthopaedics, Lanzhou University Second HospitalDepartment of Orthopaedics, Lanzhou University Second HospitalDepartment of Orthopaedics, Lanzhou University Second HospitalDepartment of Orthopaedics, Lanzhou University Second HospitalDepartment of Orthopaedics, Lanzhou University Second HospitalDepartment of Orthopaedics, Lanzhou University Second HospitalAbstract Intervertebral disc degeneration (IDD) is a prevalent spinal disorder and the principal cause of lower back pain (LBP). Diverse forms of programmed cell death (PCD) have been identified as the key phenotypes of the disease and have the potential to serve as new indicators for the diagnosis and prognosis of IDD. However, the mechanism underlying necroptosis in IDD remains unclear. This study aimed to identify novel biomarkers that promote nucleus pulposus cell necroptosis in IDD using bioinformatic analysis and experimental validation. We analyzed multiple datasets of IDD from the Gene Expression Omnibus (GEO) database to identify necroptosis-related IDD differential genes (NRDEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed, followed by logistic least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive (SVM) algorithms to identify key genes. Gene set enrichment analysis (GSEA) and logistic regression analysis were used to ascertain the potential functions of these genes and to identify key genes, respectively. We then constructed mRNA-miRNA, mRNA-TF, mRNA-drug, and functional similarity gene interaction networks for the seven key genes identified. We used IDD clinical samples and necroptotic cell model to validate our findings. Immunohistochemical staining, RT-qPCR, and western blotting results indicated that IRF1 may be a hub necroptosis-related gene. To further elucidate the function of IRF1, we constructed IRF1 knockdown and overexpression models, which revealed that IRF1 promotes necroptosis in rat nucleus pulposus cells, increases mitochondrial ROS levels, and decreases ATP levels. These findings provide new insights into the development of necroptosis in IDD and, for the first time, validate the role of IRF1 as a novel biomarker for the diagnosis and treatment of IDD.https://doi.org/10.1038/s41598-024-81681-8IRF1NecroptosisIntervertebral disc degenerationNucleus pulposusBiomarker |
| spellingShingle | Kaisheng Zhou Shaobo Wu Zuolong Wu Rui Ran Wei Song Hao Dong Haihong Zhang Integrating bioinformatics and experimental validation to Investigate IRF1 as a novel biomarker for nucleus pulposus cells necroptosis in intervertebral disc degeneration Scientific Reports IRF1 Necroptosis Intervertebral disc degeneration Nucleus pulposus Biomarker |
| title | Integrating bioinformatics and experimental validation to Investigate IRF1 as a novel biomarker for nucleus pulposus cells necroptosis in intervertebral disc degeneration |
| title_full | Integrating bioinformatics and experimental validation to Investigate IRF1 as a novel biomarker for nucleus pulposus cells necroptosis in intervertebral disc degeneration |
| title_fullStr | Integrating bioinformatics and experimental validation to Investigate IRF1 as a novel biomarker for nucleus pulposus cells necroptosis in intervertebral disc degeneration |
| title_full_unstemmed | Integrating bioinformatics and experimental validation to Investigate IRF1 as a novel biomarker for nucleus pulposus cells necroptosis in intervertebral disc degeneration |
| title_short | Integrating bioinformatics and experimental validation to Investigate IRF1 as a novel biomarker for nucleus pulposus cells necroptosis in intervertebral disc degeneration |
| title_sort | integrating bioinformatics and experimental validation to investigate irf1 as a novel biomarker for nucleus pulposus cells necroptosis in intervertebral disc degeneration |
| topic | IRF1 Necroptosis Intervertebral disc degeneration Nucleus pulposus Biomarker |
| url | https://doi.org/10.1038/s41598-024-81681-8 |
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