Analysis and Experimental Validation of Rheumatoid Arthritis Innate Immunity Gene CYFIP2 and Pan-Cancer
Rheumatoid arthritis (RA) is a chronic, heterogeneous autoimmune disease. Its high disability rate has a serious impact on society and individuals, but there is still a lack of effective and reliable diagnostic markers and therapeutic targets for RA. In this study, we integrated RA patient informati...
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| Format: | Article |
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Frontiers Media S.A.
2022-07-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2022.954848/full |
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| author | ZhenYu Zhao ShaoJie He XinCheng Yu XiaoFeng Lai Sheng Tang El Akkawi Mariya M. MoHan Wang Hai Yan XingQi Huang Shan Zeng DingSheng Zha |
| author_facet | ZhenYu Zhao ShaoJie He XinCheng Yu XiaoFeng Lai Sheng Tang El Akkawi Mariya M. MoHan Wang Hai Yan XingQi Huang Shan Zeng DingSheng Zha |
| author_sort | ZhenYu Zhao |
| collection | DOAJ |
| description | Rheumatoid arthritis (RA) is a chronic, heterogeneous autoimmune disease. Its high disability rate has a serious impact on society and individuals, but there is still a lack of effective and reliable diagnostic markers and therapeutic targets for RA. In this study, we integrated RA patient information from three GEO databases for differential gene expression analysis. Additionally, we also obtained pan-cancer-related genes from the TCGA and GTEx databases. For RA-related differential genes, we performed functional enrichment analysis and constructed a weighted gene co-expression network (WGCNA). Then, we obtained 490 key genes by intersecting the significant module genes selected by WGCNA and the differential genes. After using the RanddomForest, SVM-REF, and LASSO three algorithms to analyze these key genes and take the intersection, based on the four core genes (BTN3A2, CYFIP2, ST8SIA1, and TYMS) that we found, we constructed an RA diagnosis. The nomogram model showed good reliability and validity after evaluation, and the ROC curves of the four genes showed that these four genes played an important role in the pathogenesis of RA. After further gene correlation analysis, immune infiltration analysis, and mouse gene expression validation, we finally selected CYFIP2 as the cut-in gene for pan-cancer analysis. The results of the pan-cancer analysis showed that CYFIP2 was closely related to the prognosis of patients with various tumors, the degree of immune cell infiltration, as well as TMB, MSI, and other indicators, suggesting that this gene may be a potential intervention target for human diseases including RA and tumors. |
| first_indexed | 2024-12-10T16:58:02Z |
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| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-12-10T16:58:02Z |
| publishDate | 2022-07-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Immunology |
| spelling | doaj.art-6f2e0b0575ce4191b369879130d0f88a2022-12-22T01:40:40ZengFrontiers Media S.A.Frontiers in Immunology1664-32242022-07-011310.3389/fimmu.2022.954848954848Analysis and Experimental Validation of Rheumatoid Arthritis Innate Immunity Gene CYFIP2 and Pan-CancerZhenYu Zhao0ShaoJie He1XinCheng Yu2XiaoFeng Lai3Sheng Tang4El Akkawi Mariya M.5MoHan Wang6Hai Yan7XingQi Huang8Shan Zeng9DingSheng Zha10Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, ChinaDepartment of Orthopaedics, Panyu Hospital of Chinese Medicine, Guangzhou, ChinaDepartment of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, ChinaDepartment of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, ChinaDepartment of Orthopedics, The Sixth Affiliated Hospital, South China University of Technology, Foshan, ChinaDepartment of Plastic and Reconstructive Surgery, ZhuJiang Hospital of Southern Medical University, GuangZhou, ChinaDepartment of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, ChinaDepartment of Medicine, Flushing Hospital Medical Center, Flushing, NY, United StatesDepartment of Neurosurgery , General Hospital of Tianjin Medical University, ChinaDepartment of Rheumatology, The First Affiliated Hospital, Jinan University, Guangzhou, ChinaDepartment of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, ChinaRheumatoid arthritis (RA) is a chronic, heterogeneous autoimmune disease. Its high disability rate has a serious impact on society and individuals, but there is still a lack of effective and reliable diagnostic markers and therapeutic targets for RA. In this study, we integrated RA patient information from three GEO databases for differential gene expression analysis. Additionally, we also obtained pan-cancer-related genes from the TCGA and GTEx databases. For RA-related differential genes, we performed functional enrichment analysis and constructed a weighted gene co-expression network (WGCNA). Then, we obtained 490 key genes by intersecting the significant module genes selected by WGCNA and the differential genes. After using the RanddomForest, SVM-REF, and LASSO three algorithms to analyze these key genes and take the intersection, based on the four core genes (BTN3A2, CYFIP2, ST8SIA1, and TYMS) that we found, we constructed an RA diagnosis. The nomogram model showed good reliability and validity after evaluation, and the ROC curves of the four genes showed that these four genes played an important role in the pathogenesis of RA. After further gene correlation analysis, immune infiltration analysis, and mouse gene expression validation, we finally selected CYFIP2 as the cut-in gene for pan-cancer analysis. The results of the pan-cancer analysis showed that CYFIP2 was closely related to the prognosis of patients with various tumors, the degree of immune cell infiltration, as well as TMB, MSI, and other indicators, suggesting that this gene may be a potential intervention target for human diseases including RA and tumors.https://www.frontiersin.org/articles/10.3389/fimmu.2022.954848/fullrheumatoid arthritisCYFIP2GEOWGCNApan-cancerST8SIA1 |
| spellingShingle | ZhenYu Zhao ShaoJie He XinCheng Yu XiaoFeng Lai Sheng Tang El Akkawi Mariya M. MoHan Wang Hai Yan XingQi Huang Shan Zeng DingSheng Zha Analysis and Experimental Validation of Rheumatoid Arthritis Innate Immunity Gene CYFIP2 and Pan-Cancer Frontiers in Immunology rheumatoid arthritis CYFIP2 GEO WGCNA pan-cancer ST8SIA1 |
| title | Analysis and Experimental Validation of Rheumatoid Arthritis Innate Immunity Gene CYFIP2 and Pan-Cancer |
| title_full | Analysis and Experimental Validation of Rheumatoid Arthritis Innate Immunity Gene CYFIP2 and Pan-Cancer |
| title_fullStr | Analysis and Experimental Validation of Rheumatoid Arthritis Innate Immunity Gene CYFIP2 and Pan-Cancer |
| title_full_unstemmed | Analysis and Experimental Validation of Rheumatoid Arthritis Innate Immunity Gene CYFIP2 and Pan-Cancer |
| title_short | Analysis and Experimental Validation of Rheumatoid Arthritis Innate Immunity Gene CYFIP2 and Pan-Cancer |
| title_sort | analysis and experimental validation of rheumatoid arthritis innate immunity gene cyfip2 and pan cancer |
| topic | rheumatoid arthritis CYFIP2 GEO WGCNA pan-cancer ST8SIA1 |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2022.954848/full |
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