Platelets-related signature based diagnostic model in rheumatoid arthritis using WGCNA and machine learning
Background and aimRheumatoid arthritis (RA) is an autoinflammatory disease that may lead to severe disability. The diagnosis of RA is limited due to the need for biomarkers with both reliability and efficiency. Platelets are deeply involved in the pathogenesis of RA. Our study aims to identify the u...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-06-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1204652/full |
| _version_ | 1797796790226911232 |
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| author | Yuchen Liu Yuchen Liu Haixu Jiang Tianlun Kang Xiaojun Shi Xiaoping Liu Chen Li Chen Li Xiujuan Hou Meiling Li Meiling Li |
| author_facet | Yuchen Liu Yuchen Liu Haixu Jiang Tianlun Kang Xiaojun Shi Xiaoping Liu Chen Li Chen Li Xiujuan Hou Meiling Li Meiling Li |
| author_sort | Yuchen Liu |
| collection | DOAJ |
| description | Background and aimRheumatoid arthritis (RA) is an autoinflammatory disease that may lead to severe disability. The diagnosis of RA is limited due to the need for biomarkers with both reliability and efficiency. Platelets are deeply involved in the pathogenesis of RA. Our study aims to identify the underlying mechanism and screening for related biomarkers.MethodsWe obtained two microarray datasets (GSE93272 and GSE17755) from the GEO database. We performed Weighted correlation network analysis (WGCNA) to analyze the expression modules in differentially expressed genes identified from GSE93272. We used KEGG, GO and GSEA enrichment analysis to elucidate the platelets-relating signatures (PRS). We then used the LASSO algorithm to develop a diagnostic model. We then used GSE17755 as a validation cohort to assess the diagnostic performance by operating Receiver Operating Curve (ROC).ResultsThe application of WGCNA resulted in the identification of 11 distinct co-expression modules. Notably, Module 2 exhibited a prominent association with platelets among the differentially expressed genes (DEGs) analyzed. Furthermore, a predictive model consisting of six genes (MAPK3, ACTB, ACTG1, VAV2, PTPN6, and ACTN1) was constructed using LASSO coefficients. The resultant PRS model demonstrated excellent diagnostic accuracy in both cohorts, as evidenced by area under the curve (AUC) values of 0.801 and 0.979.ConclusionWe elucidated the PRSs occurred in the pathogenesis of RA and developed a diagnostic model with excellent diagnostic potential. |
| first_indexed | 2024-03-13T03:38:20Z |
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| id | doaj.art-51253f2053db4659bfb4cdb908c4873a |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-03-13T03:38:20Z |
| publishDate | 2023-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-51253f2053db4659bfb4cdb908c4873a2023-06-23T13:36:49ZengFrontiers Media S.A.Frontiers in Immunology1664-32242023-06-011410.3389/fimmu.2023.12046521204652Platelets-related signature based diagnostic model in rheumatoid arthritis using WGCNA and machine learningYuchen Liu0Yuchen Liu1Haixu Jiang2Tianlun Kang3Xiaojun Shi4Xiaoping Liu5Chen Li6Chen Li7Xiujuan Hou8Meiling Li9Meiling Li10School of Clinical Medicine, Peking Union Medical College, Beijing, ChinaPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaDepartment of Rheumatology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, ChinaDepartment of Rheumatology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, ChinaDepartment of Rheumatology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, ChinaDepartment of Rheumatology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, ChinaPeking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaDepartment of Rheumatology, Fangshan Hospital Beijing University of Chinese Medicine, Beijing, ChinaDepartment of Rheumatology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, ChinaDepartment of Rheumatology, Fuyang Hospital of Anhui Medical University, Fuyang, Anhui, ChinaDepartment of Rheumatology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, ChinaBackground and aimRheumatoid arthritis (RA) is an autoinflammatory disease that may lead to severe disability. The diagnosis of RA is limited due to the need for biomarkers with both reliability and efficiency. Platelets are deeply involved in the pathogenesis of RA. Our study aims to identify the underlying mechanism and screening for related biomarkers.MethodsWe obtained two microarray datasets (GSE93272 and GSE17755) from the GEO database. We performed Weighted correlation network analysis (WGCNA) to analyze the expression modules in differentially expressed genes identified from GSE93272. We used KEGG, GO and GSEA enrichment analysis to elucidate the platelets-relating signatures (PRS). We then used the LASSO algorithm to develop a diagnostic model. We then used GSE17755 as a validation cohort to assess the diagnostic performance by operating Receiver Operating Curve (ROC).ResultsThe application of WGCNA resulted in the identification of 11 distinct co-expression modules. Notably, Module 2 exhibited a prominent association with platelets among the differentially expressed genes (DEGs) analyzed. Furthermore, a predictive model consisting of six genes (MAPK3, ACTB, ACTG1, VAV2, PTPN6, and ACTN1) was constructed using LASSO coefficients. The resultant PRS model demonstrated excellent diagnostic accuracy in both cohorts, as evidenced by area under the curve (AUC) values of 0.801 and 0.979.ConclusionWe elucidated the PRSs occurred in the pathogenesis of RA and developed a diagnostic model with excellent diagnostic potential.https://www.frontiersin.org/articles/10.3389/fimmu.2023.1204652/fullrheumatoid arthritismachine learning (ML)diagnostic modelplateletbioinformatics analysis |
| spellingShingle | Yuchen Liu Yuchen Liu Haixu Jiang Tianlun Kang Xiaojun Shi Xiaoping Liu Chen Li Chen Li Xiujuan Hou Meiling Li Meiling Li Platelets-related signature based diagnostic model in rheumatoid arthritis using WGCNA and machine learning Frontiers in Immunology rheumatoid arthritis machine learning (ML) diagnostic model platelet bioinformatics analysis |
| title | Platelets-related signature based diagnostic model in rheumatoid arthritis using WGCNA and machine learning |
| title_full | Platelets-related signature based diagnostic model in rheumatoid arthritis using WGCNA and machine learning |
| title_fullStr | Platelets-related signature based diagnostic model in rheumatoid arthritis using WGCNA and machine learning |
| title_full_unstemmed | Platelets-related signature based diagnostic model in rheumatoid arthritis using WGCNA and machine learning |
| title_short | Platelets-related signature based diagnostic model in rheumatoid arthritis using WGCNA and machine learning |
| title_sort | platelets related signature based diagnostic model in rheumatoid arthritis using wgcna and machine learning |
| topic | rheumatoid arthritis machine learning (ML) diagnostic model platelet bioinformatics analysis |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1204652/full |
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