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Identification of miRNAs as promising biomarkers for diagnosis with combined analysis of mRNA transcriptome using next-generation sequencing in glioblastoma patients

ABSTRACT: Applying Next Generation Sequencing technique we compared the mRNA expression pattern of tumor tissue sample of 5 GPs and peritumoral region of 5 lower grade (I-II) Glioma patients, serving as control group. To determine the difference on mRNA expresion level between GBM and control cases, we performed cluster analysis on the NGS dataset of 6 replicates for each of the two goups of samples with iDEP 96 software. In order to characterize the extent of up- or downregulation, log2FC values were calculated using the iDEP.96 web tool applying the DESeq2 algorithm. On the base of that 6125 known mRNAs were identified to be differentially expressed using a threshold of false discovery rate (FDR) <0.05 and fold-change> 2 during the analysis. Among them, 2253 mRNAs were upregulated (log2FC > 2) and 3872 mRNAs were downregulated (log2FC < -2) with biological revelance in tissue samples comparing with the control samples. To validate our results obtained by NGS, seven upregulated mRNAs: E2F2, HOXD13, VEGFA, CDC45, AURKB, HOXC10, MYBL2 and seven downregulated mRNAs:FABP6, PRLHR, NEUROD6, CBLN1, HRH3, HCN1, RELN were chosen for RT-qPCR analysis. As the result of that E2F2, HOXD13, VEGFA, CDC45, AURKB, HOXC10, MYBL2 was significantly upregulated while FABP6, PRLHR, NEUROD6, CBLN1, HRH3, HCN1, RELN was significantly downregulated, compared with those in the control samples.

ORGANISM(S): Homo sapiens

PROVIDER: GSE285290 | GEO | 2025/04/02

REPOSITORIES: GEO

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Project description:Expression data from the hippocampus of epileptic mice carrying two different pathogenic de novo mutations in the hyperpolarization-activated, cyclic nucleotide-gated, non-selective cation channel gene Hcn1 (p.G391D in human corresponding to G380D in mouse; p.M153I in human corresponding to M142I in mice) in comparison to wildtype controls. De novo mutations in voltage- and ligand-gated channels have been associated with an increasing number of cases of developmental and epileptic encephalopathies, which often fail to respond to classic antiseizure medications. Here, we examine two knock-in mouse models replicating de novo mutations in the HCN1 voltage-gated channel gene, p.G391D and p.M153I (Hcn1G380D/+ and Hcn1M142I/+ in mouse), associated with severe drug-resistant neonatal- and childhood-onset epilepsy, respectively. Heterozygous mice from both lines displayed spontaneous generalized tonic-clonic seizures. Animals replicating the p.G391D variant had an overall more severe phenotype, with pronounced alterations in the levels and distribution of HCN1 protein, including disrupted targeting to the axon terminals of basket cell interneurons. In line with clinical reports from patients with pathogenic HCN1 sequence variations, administration of the antiepileptic Na+ channel antagonists lamotrigine and phenytoin resulted in the paradoxical induction of seizures in both mouse lines, consistent with an effect to further impair inhibitory neuron function. We also show that these variants can render HCN1 channels unresponsive to classic antagonists, indicating the need to screen mutated channels to identify novel compounds with diverse mechanism of action. Our results underscore the need to tailor effective therapies for specific channel gene variants, and how strongly validated animal models may provide an invaluable tool towards reaching this objective. This dataset contains a comparison of the gene expression profile of the hippocampus of epileptic mice carrying either the pathogenic G380D (GD) variant (Hcn1GD/+ mice), or the M142I (MI) variant (Hcn1MI/+ mice) in Hcn1 in comparison to wildtype (WT) controls (Hcn1+/+ mice).

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Identification of miRNAs as promising biomarkers for diagnosis with combined analysis of mRNA transcriptome using next-generation sequencing in glioblastoma patients

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