Identification of ferroptosis related markers by integrated bioinformatics analysis and In vitro model experiments in rheumatoid arthritis
Abstract Background Rheumatoid arthritis (RA) is an autoimmune disease characterized by destructive and symmetrical joint diseases and synovitis. This research attempted to explore the mechanisms involving ferroptosis in RA, and find the biological markers by integrated analysis. Methods Gene expres...
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| Format: | Article |
| Language: | English |
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BMC
2023-01-01
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| Series: | BMC Medical Genomics |
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| Online Access: | https://doi.org/10.1186/s12920-023-01445-7 |
| _version_ | 1811171509061812224 |
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| author | Jinjun Xia Lulu Zhang Tao Gu Qingyang Liu Qiubo Wang |
| author_facet | Jinjun Xia Lulu Zhang Tao Gu Qingyang Liu Qiubo Wang |
| author_sort | Jinjun Xia |
| collection | DOAJ |
| description | Abstract Background Rheumatoid arthritis (RA) is an autoimmune disease characterized by destructive and symmetrical joint diseases and synovitis. This research attempted to explore the mechanisms involving ferroptosis in RA, and find the biological markers by integrated analysis. Methods Gene expression data (GSE55235 and GSE55457) of synovial tissues from healthy and RA individuals were downloaded. By filtering the differentially expressed genes (DEGs) and intersecting them with the 484 ferroptosis-related genes (FRGs), the overlapping genes were identified. After the enrichment analysis, the machine learning-based approaches were introduced to screen the potential biomarkers, which were further validated in other two datasets (GSE77298 and GSE93272) and cell samples. Besides, we also analyze the infiltrating immune cells in RA and their correlation with the biomarkers. Results With the criteria, 635 DEGs in RA were included, and 29 of them overlapped in the reported 484 FRGs. The enrichments of the 29 differentially expressed ferroptosis-related genes indicated that they may involve in the FoxO signaling pathway and inherited metabolic disorder. RRM2, validating by the external datasets and western blot, were identified as the biomarker with the high diagnostic value, whose associated immune cells, such as Neutrophils and Macrophages M1, were also further evaluated. Conclusion We preliminary explored the mechanisms between ferroptosis and RA. These results may help us better comprehend the pathophysiological changes of RA in basic research, and provide new evidences for the clinical transformation. |
| first_indexed | 2024-04-10T17:15:11Z |
| format | Article |
| id | doaj.art-74a8ffac4e1f49a9b5cbc03e4acefd6c |
| institution | Directory Open Access Journal |
| issn | 1755-8794 |
| language | English |
| last_indexed | 2024-04-10T17:15:11Z |
| publishDate | 2023-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Genomics |
| spelling | doaj.art-74a8ffac4e1f49a9b5cbc03e4acefd6c2023-02-05T12:26:31ZengBMCBMC Medical Genomics1755-87942023-01-0116111410.1186/s12920-023-01445-7Identification of ferroptosis related markers by integrated bioinformatics analysis and In vitro model experiments in rheumatoid arthritisJinjun Xia0Lulu Zhang1Tao Gu2Qingyang Liu3Qiubo Wang4Department of Clinical Laboratory, Wuxi 9Th People’s Hospital Affiliated to Soochow UniversityDepartment of Clinical Laboratory, Wuxi 9Th People’s Hospital Affiliated to Soochow UniversityDepartment of Clinical Laboratory, Wuxi 9Th People’s Hospital Affiliated to Soochow UniversityDepartment of Clinical Laboratory, Wuxi 9Th People’s Hospital Affiliated to Soochow UniversityDepartment of Clinical Laboratory, Wuxi 9Th People’s Hospital Affiliated to Soochow UniversityAbstract Background Rheumatoid arthritis (RA) is an autoimmune disease characterized by destructive and symmetrical joint diseases and synovitis. This research attempted to explore the mechanisms involving ferroptosis in RA, and find the biological markers by integrated analysis. Methods Gene expression data (GSE55235 and GSE55457) of synovial tissues from healthy and RA individuals were downloaded. By filtering the differentially expressed genes (DEGs) and intersecting them with the 484 ferroptosis-related genes (FRGs), the overlapping genes were identified. After the enrichment analysis, the machine learning-based approaches were introduced to screen the potential biomarkers, which were further validated in other two datasets (GSE77298 and GSE93272) and cell samples. Besides, we also analyze the infiltrating immune cells in RA and their correlation with the biomarkers. Results With the criteria, 635 DEGs in RA were included, and 29 of them overlapped in the reported 484 FRGs. The enrichments of the 29 differentially expressed ferroptosis-related genes indicated that they may involve in the FoxO signaling pathway and inherited metabolic disorder. RRM2, validating by the external datasets and western blot, were identified as the biomarker with the high diagnostic value, whose associated immune cells, such as Neutrophils and Macrophages M1, were also further evaluated. Conclusion We preliminary explored the mechanisms between ferroptosis and RA. These results may help us better comprehend the pathophysiological changes of RA in basic research, and provide new evidences for the clinical transformation.https://doi.org/10.1186/s12920-023-01445-7Rheumatoid arthritisDifferentially expressed genesFerroptosis-related genesBiomarkers |
| spellingShingle | Jinjun Xia Lulu Zhang Tao Gu Qingyang Liu Qiubo Wang Identification of ferroptosis related markers by integrated bioinformatics analysis and In vitro model experiments in rheumatoid arthritis BMC Medical Genomics Rheumatoid arthritis Differentially expressed genes Ferroptosis-related genes Biomarkers |
| title | Identification of ferroptosis related markers by integrated bioinformatics analysis and In vitro model experiments in rheumatoid arthritis |
| title_full | Identification of ferroptosis related markers by integrated bioinformatics analysis and In vitro model experiments in rheumatoid arthritis |
| title_fullStr | Identification of ferroptosis related markers by integrated bioinformatics analysis and In vitro model experiments in rheumatoid arthritis |
| title_full_unstemmed | Identification of ferroptosis related markers by integrated bioinformatics analysis and In vitro model experiments in rheumatoid arthritis |
| title_short | Identification of ferroptosis related markers by integrated bioinformatics analysis and In vitro model experiments in rheumatoid arthritis |
| title_sort | identification of ferroptosis related markers by integrated bioinformatics analysis and in vitro model experiments in rheumatoid arthritis |
| topic | Rheumatoid arthritis Differentially expressed genes Ferroptosis-related genes Biomarkers |
| url | https://doi.org/10.1186/s12920-023-01445-7 |
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