Classification of glioma based on prognostic alternative splicing

Abstract

BackgroundPreviously 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.MethodsUsing 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.ResultsWe 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.ConclusionA 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.

Network pharmacological systems study of Huang‑Lian‑Tang in the treatment of glioblastoma multiforme

“…GBM may develop rapidly from undiagnosed, less malignant precursor lesions or may progress slowly from preexisting low-grade glioma (31). In spite of the progress in the treatment of GBM, including chemotherapy, the prognosis remains poor (32,33). Therefore, it is necessary to identify potential pathways for the development of this cancer type and to prevent the occurrence of GBM.…”

Development of a nomogram for prognostic prediction of lower‐grade glioma based on alternative splicing signatures

“…23 In glioma, the study of AS events is still in the initial stage, but the relationship between AS events and the prognosis of glioma patients has been analyzed. 13 Chai et al proposed a new classification of LGG based on AS events. 24 The above studies demonstrate that AS events play a crucial role in tumors.…”

“…In recent years, with the establishment of a tumor database, the bioinformatics analysis between AS events and the outcome of cancer patients has also become a research hotspot. 13 Although this research continues to emerge, an effective and practical prediction model for LGG patient prognosis based on AS events has not yet been established. Therefore, in this study, bioinformatics analysis technology was used to comprehensively and deeply analyze the clinical information and Splice-Seq information of LGG patients in The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.…”

“…Considering the broad implications of AS, an increasing number of studies have explored AS events as a prognostic biomarker for cancer patients. In recent years, with the establishment of a tumor database, the bioinformatics analysis between AS events and the outcome of cancer patients has also become a research hotspot 13 . Although this research continues to emerge, an effective and practical prediction model for LGG patient prognosis based on AS events has not yet been established.…”

Expression profile of SYNE3 and bioinformatic analysis of its prognostic value and functions in tumors

“…Combined with our survival analysis, tumor-promoting functions of miRNAs displayed more obvious in KIRC, CESC, LUAD and HNSC. While for LGG, there might be other mechanisms related to its heterogeneity [ 35 ], unique progressive features or micro-environment, causing a contrary result.…”