MiR-330-3p and miR-485-5p as biomarkers for glioblastoma: An integrated bioinformatics and experimental study. (June 2021)

• Record Type: Journal Article
• Authors: Rahmati, Yazdan; Alivand, Mohammadreza; Mollanoori, Hasan
• Is Part Of: Computational biology and chemistry. Volume 92(2021)
• Publication Date: 2021-06
• Subjects: GBM glioblastoma multiforme -- WGCNA weighted gene co-expression network analysis -- DEGs differentially expressed genes -- RT-PCR real-time polymerase chain reaction -- AUC area under ROC curve -- GEO gene expression omnibus -- Limma linear models for microarray data -- TOM tozpological overlap matrix -- GS gene significance -- MM module membership -- ROC curve receiver operating characteristic curve -- TCGA the cancer genome atlas -- DEMs differentially expressed miRNAs; Glioblastoma -- Real-time PCR -- ROC curve -- WGCNA -- TCGA -- Serum samples -- Tumor samples; Chemistry -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; Biochemistry -- Data processing; Biology -- Data processing; Molecular biology -- Data processing; Periodicals; Electronic journals; 542.85
• DOI: 10.1016/j.compbiolchem.2021.107458
• Languages: English
• ISSNs: 1476-9271

Abstract

Graphical abstract: Highlights: Our results showed that has-mir-330−3p and has-mir-485−5p could be potential biomarkers in GBM. This study is one of the first attempts to construct a miRNA-target genes network using WGCNA and limma packages. Abstract: Glioblastoma Multiforme (GBM) is the most common, invasive, and malignant primary brain tumor with a poor prognosis and a median survival of 12–15 months. This study tried to identify the most significant miRNA biomarkers in both tissue and serum samples of GBM. GSE25632 was employed from gene expression omnibus and using WGCNA package, association of miRNA networks and clinical data was explored and brown and green modules identified as the most relevant modules. Independently, Limma package was utilized to identify differentially expressed miRNAs (DEMs) in GSE25632 by cutoff l o g F C > 2 and P.value < 0.05. By merging the results of Limma and WGCNA, the miRNAs that were in brown and green modules and had mentioned cutoff were selected as hub miRNAs. Performing enrichment analysis, Pathways in cancer, Prostate cancer, Glioma, p53 signaling pathway, and Focal adhesion were identified as the most important signaling pathways. Based on miRNA- target genes, has-mir-330−3p and has-mir-485−5p were identified as core miRNAs. The expression level of core miRNAs was validated by GSE90604, GSE42657, and GSE93850. We evaluated the expression level of common target genes of two detected core genes based on GSE77043, GSE42656, GSE22891, GSE15824, and GSE122498. The ability of detected miRNAs to discriminate GBM from healthy controls was assessed by area under the curve (AUC) using the ROC curve analysis. Based on TCGA database, we tested the prognostic significance of miRNAs using overall survival analysis. We evaluated the expression level of the miRNAs in tissue of 83 GBM patients and also non-tumoral adjacent (as control) tissues. We used serum samples of 34 GBM patients to evaluate the expression levels of the hub miRNAs compare to the controls. Our results showed that has-mir-330−3p and has-mir-485−5p could be potential biomarkers in GBM.