Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme

Abstract

Background: Glioblastoma multiforme (GBM) is the most seriously brain tumor with extremely poor prognosis. Recent research has demonstrated that competitive endogenous RNA (ceRNA) network which long noncoding RNAs (lncRNAs) act as microRNA (miRNA) sponges to regulate mRNA expression were closely related to tumor development. However, the regulatory mechanisms and functional roles of ceRNA network in the pathogenesis of GBM are remaining poorly understood. Methods: In this study, we systematically analyzed the expression profiles of lncRNA and mRNA (GSE51146 dataset) and miRNA (GSE65626 dataset) from GEO database. Then, we constructed a ceRNA network with the dysregulated genes by bioinformatics methods. The TCGA and GSE4290 dataset were used to confirm the expression and prognostic value of candidate mRNAs. Results: In total, 3413 differentially expressed lncRNAs and mRNAs, 305 differentially expressed miRNAs were indentified in GBM samples. Then a ceRNA network containing 3 lncRNAs, 5 miRNAs, and 60 mRNAs was constructed. The overall survival analysis of TCGA databases indicated that two mRNAs (C1s and HSD3B7) were remarkly related with the prognosis of GBM. Conclusion: The ceRNA network may increase our understanding to the pathogenesis of GBM. In general, the candidate mRNAs from the ceRNA network can be predicted as new therapeutic targets and prognostic biomarkers for GBM.

Machine learning for the micropeptide encoded by LINC02381 regulates ferroptosis through the glucose transporter SLC2A10 in glioblastoma

“…We have been working on basic research on gliomas and anti-tumor medicinal plants, including gene clusters, tumor markers [8], and noncoding RNA-based translational medicine research [9]. For example, we identified the potential role of SRY-Box Transcription Factor 6 (SOX6) in GBM [10]; and analyzed the gene set of mitochondrial metabolism-related genes and discovered the importance of Annexin A2 (ANXA2), S100 Calcium Binding Protein A11 (S100A11), and Tubulin Beta 6 Class V (TUBB6) as prognostic factors for GBM [11].…”

Long intergenic noncoding RNA 00665 promotes proliferation and inhibits apoptosis in colorectal cancer by regulating miR-126-5p

“…MicroRNAs (miRNAs) are considered short ncRNA fragments and negatively regulate gene transcript function. Studies have proven that lncRNAs regulate mRNA expression through their miRNA sponge, named the competitive endogenous RNA (ceRNA) network, and this function is closely related to tumor development [ 8 ]. Thus, we proposed to investigate the ceRNA network in CRC in this study.…”

Comprehensive analysis of ceRNA network related to lincRNA in glioblastoma and prediction of clinical prognosis

“…Additionally, its related ceRNA network has been shown to play a role in the progression of kidney cancer [ 19 ]. At present, there are few studies on the ceRNA network in glioblastoma, conducted mainly for a single database and with a small sample, and there are fewer prognostic prediction analyses [ 20 , 21 ]. In their study, Liu et al used two databases to construct a ceRNA network for GBM, but did not incorporate WGCNA analysis, nor did they systematically construct a prognostic prediction model [ 22 ].…”