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

Abstract

Background Long intergenic non-coding RNAs (lincRNAs) are capable of regulating several tumours, while competitive endogenous RNA (ceRNA) networks are of great significance in revealing the biological mechanism of tumours. Here, we aimed to study the ceRNA network of lincRNA in glioblastoma (GBM). Methods We obtained GBM and normal brain tissue samples from TCGA, GTEx, and GEO databases, and performed weighted gene co-expression network analysis and differential expression analysis on all lincRNA and mRNA data. Subsequently, we predicted the interaction between lincRNAs, miRNAs, and target mRNAs. Univariate and multivariate Cox regression analyses were performed on the mRNAs using CGGA data, and a Cox proportional hazards regression model was constructed. The ceRNA network was further screened by the DEmiRNA and mRNA of Cox model. Results A prognostic prediction model was constructed for patients with GBM. We assembled a ceRNA network consisting of 18 lincRNAs, 6 miRNAs, and 8 mRNAs. Gene Set Enrichment Analysis was carried out on four lincRNAs with obvious differential expressions and relatively few studies in GBM. Conclusion We identified four lincRNAs that have research value for GBM and obtained the ceRNA network. Our research is expected to facilitate in-depth understanding and study of the molecular mechanism of GBM, and provide new insights into targeted therapy and prognosis of the tumour.

WASF3 overexpression affects the expression of circular RNA hsa-circ-0100153, which promotes breast cancer progression by sponging hsa-miR-31, hsa-miR-767-3p, and hsa-miR-935

“…The interactions with a strong correlation threshold of r > 0.85 or r < −0.85 and a CP-value <0.05 were selected to establish the ceRNA network. The Cytoscape 3.9.1 software was used to visualize the ceRNA network [ 34 , 35 ].…”

Crosstalk between SOX Genes and Long Non-Coding RNAs in Glioblastoma

“…Sets of lncRNAs related to the immune system [ 149 , 150 ], autophagy [ 151 ], EMT [ 152 ], pyroptosis [ 153 ], ferroptosis [ 154 ], and lncRNAs with methylated promoters [ 155 ] have been explored to develop reliable and biologically relevant lncRNA signatures for predicting survival of patients with GBM. To acquire better insights into the biological function of lncRNA signatures and molecular mechanisms/pathways through which they exert their function in GBM, a growing amount of research is focused on in silico functional analyses to establish lncRNA-miRNA-mRNA-associated ceRNA regulatory networks in GBM [ 156 , 157 , 158 , 159 , 160 ]. Peng et al constructed a ceRNA co-expression network consisting of two lncRNAs (NORAD, XIST), five miRNAs (miR-3613, miR-371, miR-373, miR-32, miR-92), and two mRNAs (LYZ, PIK3AP1), which might serve as a prognostic biomarker in GBM [ 157 ].…”

Long, Noncoding RNA Dysregulation in Glioblastoma

“…Comprehensive analyses of these networks have yielded intricate maps of coexpression variation in RNA species that affect up to 60 mRNAs. Although these intricate networks have yet to inform GBM biology, they have demonstrated utility in stratifying patient survival, thus serving as potential prognostic biomarkers [116,117]. Utilizing these networks to inform GBM biology and better understand the malignant transformation of tumor cells may benefit from leveraging atlases of neurodevelopmental gene expression programs in relevant cell types, particularly radial glia and intermediate progenitors [118].…”