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

Xiaolong Zhu,Tianbing Chen,Kun Lv,Xingwei Wu,Hui Yang,Lan Jiang

doi:10.1186/s12935-020-01488-1

Xiaolong Zhu, Tianbing Chen + Show 4 more

Open Access

https://doi.org/10.1186/s12935-020-01488-1

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Abstract

BackgroundGlioblastoma 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.MethodsIn 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.ResultsIn 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.ConclusionThe 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.

Highlights

Glioblastoma multiforme (GBM) is the most seriously brain tumor with extremely poor prognosis
Screening differentially expressed Long noncoding RNA (lncRNA), miRNAs and mRNAs Firstly, the genome wide mRNA and lncRNA expression profiles in GBM were analyzed in GSE51146 dataset by GEO2R
Co‐expression analysis of lncRNA and mRNA To explore biologic function of lncRNAs and mRNAs in GBM, we need to define the regulatory relationship between lncRNAs and mRNAs

Summary

Introduction

Glioblastoma multiforme (GBM) is the most seriously brain tumor with extremely poor prognosis. Our research focus on the differentially expressed long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs in GBM and the role of competitive endogenous RNAs (ceRNAs) network in the pathogenesis and prognosis of GBM. The miRNA, a single chain ncRNAs of around 22 nucleotides in length, influence the gene expression by binding to the 3′-UTR of their respective target genes [9]. They are key regulators that mediate tumor development and pathology, such as proliferation, transcription, post-transcriptional modifications, invasion, apoptosis, and cell metabolism [10]. The functions of lncRNAs and miRNA in gene expression regulation are not well characterized

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