Investigation of the prognostic biomarkers for thymoma

Abstract Background Thymoma represents the most common anterior mediastinal malignancy and has a close association with autoimmune disease. However, the potential molecular oncogenesis of thymoma has not been fully clarified yet. This study aims to identify hub genes and signaling pathways associated with thymoma to explore the possible pathogenesis of thymoma and analyze their prognostic significance. Results A total of 738 DEGs were screened for subsequent analysis. Functional enrichment analysis emphasizes the important roles of the cell cycle signaling pathway, p53 signaling pathway, and TGF-β signaling pathway in the development of thymoma. Six hub genes had a close connection with prognosis. The relative higher expression of JUN(HR:4.95[1-24.47], p = 0.031) and the lower expression of CDK1(HR:0.17[0.03–0.83], p = 0.015), E2F2(HR:0.16[0.03–0.83], p = 0.015), MCM2(HR:0.16[0.03–0.82], p = 0.014), MKI67(HR:0.18[0.04–0.89], p = 0.02) and TOP2A(HR:0.12[0.02–0.58], p = 0.0018) was associated with a worse OS in thymoma patients. Besides, E2F2 was particularly overexpressed in type B2 thymoma compared with the other subtypes and normal thymus tissue. Immune infiltration analysis indicated that only E2F2 (r=-0.198, p = 3.35E-02) was negatively correlated with tumor purity. Moreover, the expression of CDK1, E2F2, JUN, and MCM2 was significantly correlated with the infiltration of B cells, CD8 + T cells, CD4 + T cells, macrophages, neutrophils, and DCs. Conclusion Among the top 10 hub genes confirmed in thymoma, CDK1, E2F2, MCM2, MKI67, JUN, and TOP2A show prognostic significance and might also play vital roles in immune surveillance and tumor progression. E2F2 might be the potential biomarker for type B2 thymoma.