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Liu H, Liu G, Guo R, Li S, Chang T. Identification of Potential Key Genes for the Comorbidity of Myasthenia Gravis With Thymoma by Integrated Bioinformatics Analysis and Machine Learning. Bioinform Biol Insights 2024; 18:11779322241281652. [PMID: 39345724 PMCID: PMC11437577 DOI: 10.1177/11779322241281652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 08/21/2024] [Indexed: 10/01/2024] Open
Abstract
Background Thymoma is a key risk factor for myasthenia gravis (MG). The purpose of our study was to investigate the potential key genes responsible for MG patients with thymoma. Methods We obtained MG and thymoma dataset from GEO database. Differentially expressed genes (DEGs) were determined and functional enrichment analyses were conducted by R packages. Weighted gene co-expression network analysis (WGCNA) was used to screen out the crucial module genes related to thymoma. Candidate genes were obtained by integrating DEGs of MG and module genes. Subsequently, we identified several candidate key genes by machine learning for diagnosing MG patients with thymoma. The nomogram and receiver operating characteristics (ROC) curves were applied to assess the diagnostic value of candidate key genes. Finally, we investigated the infiltration of immunocytes and analyzed the relationship among key genes and immune cells. Results We obtained 337 DEGs in MG dataset and 2150 DEGs in thymoma dataset. Biological function analyses indicated that DEGs of MG and thymoma were enriched in many common pathways. Black module (containing 207 genes) analyzed by WGCNA was considered as the most correlated with thymoma. Then, 12 candidate genes were identified by intersecting with MG DEGs and thymoma module genes as potential causes of thymoma-associated MG pathogenesis. Furthermore, five candidate key genes (JAM3, MS4A4A, MS4A6A, EGR1, and FOS) were screened out through integrating least absolute shrinkage and selection operator (LASSO) regression and Random forest (RF). The nomogram and ROC curves (area under the curve from 0.833 to 0.929) suggested all five candidate key genes had high diagnostic values. Finally, we found that five key genes and immune cell infiltrations presented varying degrees of correlation. Conclusions Our study identified five key potential pathogenic genes that predisposed thymoma to the development of MG, which provided potential diagnostic biomarkers and promising therapeutic targets for MG patients with thymoma.
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Affiliation(s)
- Hui Liu
- Department of Neurology, Xi’an Medical University, Xi’an, Shaanxi, China
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Geyu Liu
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
- Clinical Medicine, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Rongjing Guo
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Shuang Li
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Ting Chang
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
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Álvarez-Velasco R, Gutiérrez-Gutiérrez G, Trujillo JC, Martínez E, Segovia S, Arribas-Velasco M, Fernández G, Paradas C, Vélez-Gómez B, Casasnovas C, Nedkova V, Guerrero-Sola A, Ramos-Fransi A, Martínez-Piñeiro A, Pardo J, Sevilla T, Gómez-Caravaca MT, López de Munain A, Jericó I, Pelayo-Negro AL, Martín MA, Morgado Y, Mendoza MD, Pérez-Pérez H, Rojas-García R, Turon-Sans J, Querol L, Gallardo E, Illa I, Cortés-Vicente E. Clinical characteristics and outcomes of thymoma-associated myasthenia gravis. Eur J Neurol 2021; 28:2083-2091. [PMID: 33721382 DOI: 10.1111/ene.14820] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/26/2021] [Accepted: 03/10/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND AND PURPOSE Prognosis of myasthenia gravis (MG) in patients with thymoma is not well established. Moreover, it is not clear whether thymoma recurrence or unresectable lesions entail a worse prognosis of MG. METHODS This multicenter study was based on data from a Spanish neurologist-driven MG registry. All patients were aged >18 years at onset and had anti-acetylcholine receptor antibodies. We compared the clinical data of thymomatous and nonthymomatous patients. Prognosis of patients with recurrent or nonresectable thymomas was assessed. RESULTS We included 964 patients from 15 hospitals; 148 (15.4%) had thymoma-associated MG. Median follow-up time was 4.6 years. At onset, thymoma-associated MG patients were younger (52.0 vs. 60.4 years, p < 0.001), had more generalized symptoms (odds ratio [OR]: 3.02, 95% confidence interval [CI]: 1.95-4.68, p < 0.001) and more severe clinical forms according to the Myasthenia Gravis Foundation of America (MGFA) scale (OR: 1.6, 95% CI: 1.15-2.21, p = 0.005). Disease severity based on MGFA postintervention status (MGFA-PIS) was higher in thymomatous patients at 1 year, 5 years, and the end of follow-up. Treatment refractoriness and mortality were also higher (OR: 2.28, 95% CI: 1.43-3.63, p = 0.001; hazard ratio: 2.46, 95% CI: 1.47-4.14, p = 0.001). Myasthenic symptoms worsened in 13 of 27 patients with recurrences, but differences in long-term severity were not significant. Fifteen thymomatous patients had nonresectable thymomas with worse MGFA-PIS and higher mortality at the end of follow-up. CONCLUSIONS Thymoma-associated MG patients had more severe myasthenic symptoms and worse prognosis. Thymoma recurrence was frequently associated with transient worsening of MG, but long-term prognosis did not differ from nonrecurrent thymoma. Patients with nonresectable thymoma tended to present severe forms of MG.
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Affiliation(s)
- Rodrigo Álvarez-Velasco
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Department of Medicine, Universitat Autónoma de Barcelona, Barcelona, Spain.,Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Gerardo Gutiérrez-Gutiérrez
- Department of Neurology, Hospital Universitario Infanta Sofía, Universidad Europea de Madrid, San Sebastián de los Reyes, Spain
| | - Juan Carlos Trujillo
- Department of Medicine, Universitat Autónoma de Barcelona, Barcelona, Spain.,Department of Thoracic Surgery, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Elisabeth Martínez
- Department of Thoracic Surgery, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Sonia Segovia
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Marina Arribas-Velasco
- Department of Neurology, Hospital Universitario Infanta Sofía, Universidad Europea de Madrid, San Sebastián de los Reyes, Spain
| | - Guillermo Fernández
- Department of Neurology, Hospital Universitario Infanta Sofía, Universidad Europea de Madrid, San Sebastián de los Reyes, Spain
| | - Carmen Paradas
- Neurology Department, Neuromuscular Disorders Unit, Instituto de Biomedicina de Sevilla, Hospital U. Virgen del Rocío, CSIC, Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Beatriz Vélez-Gómez
- Neurology Department, Neuromuscular Disorders Unit, Instituto de Biomedicina de Sevilla, Hospital U. Virgen del Rocío, CSIC, Universidad de Sevilla, Seville, Spain
| | - Carlos Casasnovas
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Neuromuscular Unit, Neurology Department, Hospital Universitario de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain.,Neurometabolic Diseases Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Velina Nedkova
- Neuromuscular Unit, Neurology Department, Hospital Universitario de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain
| | - Antonio Guerrero-Sola
- Neuromuscular Diseases and ALS Unit, Department of Neurology, Institute of Neurosciences, Hospital Universitario Clínico San Carlos, Madrid, Spain
| | - Alba Ramos-Fransi
- Department of Medicine, Universitat Autónoma de Barcelona, Barcelona, Spain.,Neuromuscular Diseases Unit, Department of Neurology, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Alicia Martínez-Piñeiro
- Department of Medicine, Universitat Autónoma de Barcelona, Barcelona, Spain.,Neuromuscular Diseases Unit, Department of Neurology, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Julio Pardo
- Department of Neurology, Hospital Clínico de Santiago de Compostela, Santiago de Compostela, Spain
| | - Teresa Sevilla
- Neuromuscular Unit, Neurology Department, Hospital Universitari i Politècnic La Fe, Department of Medicine, Universitat de València, and Biomedical Research Institute La Fe (IIS La Fe), Valencia, Spain
| | | | - Adolfo López de Munain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.,Neuromuscular Unit, Hospital Universitario de Donostia. Biodonostia Health Research Institute, University of the Basque Country, Gipuzkoa, Spain
| | - Ivonne Jericó
- Department of Neurology, Complejo Hospitalario de Navarra, IdisNa (Instituto Investigación Sanitaria Navarra), Pamplona, Spain
| | - Ana L Pelayo-Negro
- Department of Neurology, Hospital Universitario Marqués de Valdecilla, University of Cantabria, Santander, Spain
| | | | - Yolanda Morgado
- Department of Neurology, Hospital Universitario de Valme, Seville, Spain
| | - María Dolores Mendoza
- Hospital Universitario de Gran Canaria Doctor Negrín, Las Palmas de Gran Canaria, Spain
| | - Helena Pérez-Pérez
- Department of Neurology, Complejo Hospitalario Universitario de Canarias, Santa Cruz de Tenerife, Spain
| | - Ricard Rojas-García
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Department of Medicine, Universitat Autónoma de Barcelona, Barcelona, Spain.,Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Janina Turon-Sans
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Department of Medicine, Universitat Autónoma de Barcelona, Barcelona, Spain.,Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis Querol
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Department of Medicine, Universitat Autónoma de Barcelona, Barcelona, Spain.,Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Eduard Gallardo
- Department of Medicine, Universitat Autónoma de Barcelona, Barcelona, Spain.,Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Illa
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Department of Medicine, Universitat Autónoma de Barcelona, Barcelona, Spain.,Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Elena Cortés-Vicente
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Department of Medicine, Universitat Autónoma de Barcelona, Barcelona, Spain.,Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
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