<p>Identification of Novel lncRNA Markers in Glioblastoma Multiforme and Their Clinical Significance: A Study Based on Multiple Sequencing Data</p>

Abstract

Background: Long non-coding RNAs (lncRNAs) have been verified to have a vital role in the progression of glioblastoma multiforme (GBM). Our research was about to identify the potential lncRNAs which was closely associated with the pathogenesis and prognosis of glioblastoma multiforme. Methods: All RNA sequence profiling data from patients with GBM were obtained from The Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA). Differently expressed genes identified from GBM and control samples were used to construct competing endogenous RNA (ceRNA) network and perform corresponding functional enrichment analysis. Univariate Cox regression followed by lasso regression and multivariate Cox was used to validate independent lncRNA factors and construct a risk prediction model. Quantitative polymerase chain reaction (qPCR) was performed to verify the expression levels of potential lncRNA biomarkers in human GBM clinical specimens. A gene set enrichment analysis (GSEA) was subsequently conducted to explore potential signaling pathways in which critical lncRNAs may be involved. Moreover, nomogram plot was applied based on our prediction model and significant clinical covariates to visualize the prognosis of GBM patients. Results: A total of 2023 differentially expressed genes (DEGs) including 56 lncRNAs, 1587 message RNAs (mRNAs) and 380 other RNAs were included. Based on predictive databases, 16lncRNAs, 32 microRNAs (miRNAs) and 99 mRNAs were used to construct a ceRNA network. Moreover, we performed a novel risk prediction model with 5 potential prognostic lncRNAs, in which 4 of them were newly identified in GBM, to predict the prognosis of GBM patients. Finally, a nomogram plot was constructed to illustrate the potential relationship between the prognosis of GBM and our risk prediction model and significant clinical covariates. Conclusion: In this study, we identified 4 novel potential lncRNA biomarkers and constructed a prediction model of GBM prognosis. A simple-to-use nomogram was provided for further clinical application.

A Five Immune-Related lncRNA Signature as a Prognostic Target for Glioblastoma

“…Normalized RNA-seq data with the estimation of Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) of glioblastoma patients and the corresponding clinical information were acquired from TCGA database ( https://portal.gdc.cancer.gov/ , RRID: SCR_003193). The exclusion criteria were as follows: 1) samples with unknown survival information; 2) samples with OS less than 30 days, who died because of nonneoplastic factors, such as myocardial infarction, hemorrhage, and severe infection ( Cheng et al, 2015 ; Li and Guo, 2020 ). A total of 151 TCGA glioblastoma samples were included for the subsequent analysis, that were randomly split up into the training set and the validation set.…”

[Retracted] Establishment and External Validation of a Hypoxia‐Derived Gene Signature for Robustly Predicting Prognosis and Therapeutic Responses in Glioblastoma Multiforme

“…Through survival package [17], univariate cox regression analysis was presented for screening prognosis-related genes in the hypoxia-relevant coexpression module in TCGA dataset. A LASSO prognostic model was then established utilizing glmnet package [4]. Using survival package, risk score was determined in line with the expression value and LASSO regression coefficient of each candidate gene.…”

“…Patients who develop GBM have the median survival rate of <1 year and high death risks [2]. Numerous studies have developed genomic models for risk stratification and prognosis prediction of GBM [4][5][6]. Nevertheless, because of technical problems such as limited sample size and individual heterogeneity, most models possess limited reproducibility and none of them have been applied in clinical routine practice.…”

<p>LncRNA RNF144A-AS1 Promotes Bladder Cancer Progression via RNF144A-AS1/miR-455-5p/SOX11 Axis</p>

“…10 RNF144A-AS1 was also identified in glioblastoma multiforme and served as a potential lncRNA biomarker. 11 However, only a few studies have reported its role in BC progression. One report suggested RNF144A-AS1 as a prognostic factor for BC using the least absolute shrinkage and selection operation Cox regression.…”