Department of Neurosurgery, Ningbo First Hospital, Ningbo, Zhejiang, China.
Department of Neurosurgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China.
Mol Biol Rep. 2023 May;50(5):4285-4299. doi: 10.1007/s11033-023-08371-y. Epub 2023 Mar 14.
Glioblastoma multiforme (GBM) is the most prevalent and malignant intracranial tumor with significant features of dismal prognosis and limited therapeutic solutions. Consequently, the present studies are committed to exploring potential biomarkers through bioinformatics analysis, which may serve as valuable prognostic predictors or novel therapeutic targets and provide new insights into the pathogenesis of GBM.
We filtered overlapping differentially expressed genes (DEGs) based on expression profilings from three GBM microarray datasets (GSE116520, GSE4290 and GSE68848) and combined RNA sequencing data from The Cancer Genome Atlas and the Genotype-Tissue Expression databases. Hub genes were prioritized from DEGs after performing protein-protein interaction (PPI) network analysis and weighted gene co-expression network analysis (WGCNA). This was followed by survival analysis to identify potential biomarkers among hub genes. Ultimately, the distributions of gene expressions, genetic alterations, upstream regulatory mechanisms and enrichments of gene functions of the identified biomarkers were analysed on public databases. QRT-PCR, immunohistochemical staining and western blotting was also used to confirm the gene expression patterns in GBM and normal brain tissues. CCK-8 assay clarified the effects of the genes on GBM cells.
A total of 322 common DEGs were determined and nine genes were subsequently considered as hub genes by the combination of PPI network analysis and WGCNA. Only SLC12A5 had prognostic significance, which was deficient in GBM whereas especially enriched in normal neural tissues. SLC12A5 overexpression would inhibit cell proliferation of U251MG. Genetic alterations of SLC12A5 were rarely seen in GBM patients, and there was no apparent association existed between SLC12A5 expression and DNA methylation. SLC12A5 was prominently involved in ion transport, synapse and neurotransmitter.
SLC12A5 shows promise to function as a novel effective biomarker for GBM and deserves further systematic research.
多形性胶质母细胞瘤（GBM）是最常见和恶性的颅内肿瘤，具有预后不良和治疗方法有限的显著特征。因此，目前的研究致力于通过生物信息学分析来探索潜在的生物标志物，这些标志物可能作为有价值的预后预测因子或新的治疗靶点，并为 GBM 的发病机制提供新的见解。
我们基于三个 GBM 微阵列数据集（GSE116520、GSE4290 和 GSE68848）的表达谱和癌症基因组图谱和基因型组织表达数据库中的 RNA 测序数据，筛选出重叠的差异表达基因（DEGs）。在进行蛋白质-蛋白质相互作用（PPI）网络分析和加权基因共表达网络分析（WGCNA）后，从 DEGs 中优先选择枢纽基因。然后进行生存分析，以确定枢纽基因中的潜在生物标志物。最终，在公共数据库中分析鉴定生物标志物的基因表达、遗传改变、上游调控机制和基因功能富集情况。还使用 QRT-PCR、免疫组织化学染色和 Western blot 来确认 GBM 和正常脑组织中基因的表达模式。CCK-8 测定法阐明了基因对 GBM 细胞的影响。
确定了 322 个共同的 DEGs，然后通过 PPI 网络分析和 WGCNA 的组合，确定了 9 个基因作为枢纽基因。只有 SLC12A5 具有预后意义，它在 GBM 中缺乏，而在正常神经组织中特别丰富。SLC12A5 的过表达会抑制 U251MG 细胞的增殖。SLC12A5 的遗传改变在 GBM 患者中很少见，并且 SLC12A5 表达与 DNA 甲基化之间没有明显的关联。SLC12A5 主要参与离子转运、突触和神经递质。
SLC12A5 有望成为 GBM 的一种新型有效生物标志物，值得进一步进行系统研究。
