Classification of glioma based on prognostic alternative splicing

• Main Authors: Yaomin Li, Zhonglu Ren, Yuping Peng, Kaishu Li, Xiran Wang, Guanglong Huang, Songtao Qi, Yawei Liu
• Format: Article
• Language: English
• Published: BMC 2019-11-01
• Series: BMC Medical Genomics
• Subjects: Glioma; Glioblastoma; Alternative splicing; Prognosis; Classification
• Online Access: http://link.springer.com/article/10.1186/s12920-019-0603-7

Abstract Background Previously developed classifications of glioma have provided enormous advantages for the diagnosis and treatment of glioma. Although the role of alternative splicing (AS) in cancer, especially in glioma, has been validated, a comprehensive analysis of AS in glioma has not yet been conducted. In this study, we aimed at classifying glioma based on prognostic AS. Methods Using the TCGA glioblastoma (GBM) and low-grade glioma (LGG) datasets, we analyzed prognostic splicing events. Consensus clustering analysis was conducted to classified glioma samples and correlation analysis was conducted to characterize regulatory network of splicing factors and splicing events. Results We analyzed prognostic splicing events and proposed novel splicing classifications across pan-glioma samples (labeled pST1–7) and across GBM samples (labeled ST1–3). Distinct splicing profiles between GBM and LGG were observed, and the primary discriminator for the pan-glioma splicing classification was tumor grade. Subtype-specific splicing events were identified; one example is AS of zinc finger proteins, which is involved in glioma prognosis. Furthermore, correlation analysis of splicing factors and splicing events identified SNRPB and CELF2 as hub splicing factors that upregulated and downregulated oncogenic AS, respectively. Conclusion A comprehensive analysis of AS in glioma was conducted in this study, shedding new light on glioma heterogeneity and providing new insights into glioma diagnosis and treatment.