The identification of key genes and pathways in glioblastoma by bioinformatics analysis.

IF 2.6 Q3 ONCOLOGY Molecular and Cellular Oncology Pub Date : 2023-01-01 DOI:10.1080/23723556.2023.2246657
Zahra Farsi, Najaf Allahyari Fard
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Abstract

GBM is the most common and aggressive type of brain tumor. It is classified as a grade IV tumor by the WHO, the highest grade. Prognosis is generally poor, with most patients surviving only about a year. Only 5% of patients survive longer than 5 years. Understanding the molecular mechanisms that drive GBM progression is critical for developing better diagnostic and treatment strategies. Identifying key genes involved in GBM pathogenesis is essential to fully understand the disease and develop targeted therapies. In this study two datasets, GSE108474 and GSE50161, were obtained from the Gene Expression Omnibus (GEO) to compare gene expression between GBM and normal samples. Differentially expressed genes (DEGs) were identified and analyzed. To construct a protein-protein interaction (PPI) network of the commonly up-regulated and down-regulated genes, the STRING 11.5 and Cytoscape 3.9.1 were utilized. Key genes were identified through this network analysis. The GEPIA database was used to confirm the expression levels of these key genes and their association with survival. Functional and pathway enrichment analyses on the DEGs were conducted using the Enrichr server. In total, 698 DEGs were identified, consisting of 377 up-regulated genes and 318 down-regulated genes. Within the PPI network, 11 key up-regulated genes and 13 key down-regulated genes associated with GBM were identified. NOTCH1, TOP2A, CD44, PTPRC, CDK4, HNRNPU, and PDGFRA were found to be important targets for potential drug design against GBM. Additionally, functional enrichment analysis revealed the significant impact of Epstein-Barr virus (EBV), Cell Cycle, and P53 signaling pathways on GBM.

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胶质母细胞瘤关键基因及通路的生物信息学分析。
GBM是最常见、最具侵袭性的脑肿瘤。世界卫生组织将其列为IV级肿瘤,这是最高级别的肿瘤。预后通常很差,大多数患者只能存活一年左右。只有5%的患者存活超过5年。了解驱动GBM进展的分子机制对于制定更好的诊断和治疗策略至关重要。确定参与GBM发病机制的关键基因对于充分了解该疾病并开发靶向治疗至关重要。本研究从Gene Expression Omnibus (GEO)中获得GSE108474和GSE50161两个数据集,比较GBM和正常样本的基因表达。鉴定并分析差异表达基因(DEGs)。利用STRING 11.5和Cytoscape 3.9.1构建常见上调和下调基因的蛋白-蛋白相互作用(PPI)网络。通过网络分析确定了关键基因。GEPIA数据库用于确认这些关键基因的表达水平及其与生存的关系。使用enrichment服务器对deg进行功能和途径富集分析。共鉴定出698个基因,其中上调基因377个,下调基因318个。在PPI网络中,鉴定出与GBM相关的11个关键上调基因和13个关键下调基因。NOTCH1、TOP2A、CD44、PTPRC、CDK4、HNRNPU和PDGFRA被发现是潜在的抗GBM药物设计的重要靶点。此外,功能富集分析显示eb病毒(EBV)、细胞周期和P53信号通路对GBM有显著影响。
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来源期刊
Molecular and Cellular Oncology
Molecular and Cellular Oncology Biochemistry, Genetics and Molecular Biology-Cancer Research
CiteScore
3.20
自引率
0.00%
发文量
18
期刊介绍: For a long time, solid neoplasms have been viewed as relatively homogeneous entities composed for the most part of malignant cells. It is now clear that tumors are highly heterogeneous structures that evolve in the context of intimate interactions between cancer cells and endothelial, stromal as well as immune cells. During the past few years, experimental and clinical oncologists have witnessed several conceptual transitions of this type. Molecular and Cellular Oncology (MCO) emerges within this conceptual framework as a high-profile forum for the publication of fundamental, translational and clinical research on cancer. The scope of MCO is broad. Submissions dealing with all aspects of oncogenesis, tumor progression and response to therapy will be welcome, irrespective of whether they focus on solid or hematological neoplasms. MCO has gathered leading scientists with expertise in multiple areas of cancer research and other fields of investigation to constitute a large, interdisciplinary, Editorial Board that will ensure the quality of articles accepted for publication. MCO will publish Original Research Articles, Brief Reports, Reviews, Short Reviews, Commentaries, Author Views (auto-commentaries) and Meeting Reports dealing with all aspects of cancer research.
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