Association between SNAP25 and human glioblastoma multiform: a comprehensive bioinformatic analysis
Association between SNAP25 and human glioblastoma multiform: a comprehensive bioinformatic analysis
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SNAP25 与人多形性胶质母细胞瘤之间的关联：综合生物信息学分析
DOI：
10.1042/bsr20200516
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发表时间：
2020-05
影响因子：
4
通讯作者：
You Yongping
中科院分区：
文献类型：
--
作者：
Yu Cheng;Yin Jianxing;Wang Xiefeng;Chen Lijiu;Wei Yutian;Lu Chenfei;You Yongping
背景：多形性胶质母细胞瘤（GBM）是一种最常见的侵袭性恶性脑肿瘤。近年来，靶向治疗在GBM治疗中的应用越来越广泛。方法：本研究从gene expression omnibus （GEO）下载GSE22866。基因组和临床数据来自TCGA。鉴定差异表达基因（DEGs），并使用clusterprofiler进行功能分析。然后，利用“WGCNA”包构建deg共表达网络。接下来，使用Search Tool for Retrieval of Interacting Genes Database （STRING）评估蛋白质-蛋白质相互作用（PPI），筛选Cytoscape中的hub模块。绘制了维恩图，以显示PPI网络和TCGA中重叠的轮毂deg。采用单因素和多因素Cox比例风险回归分析预测每位患者的风险评分。hub基因的验证在其他数据库中完成。结果：deg的功能分析证实了deg参与生长因子结合和门控通道活性。在10个与GBM相关的模块中，红色模块与GBM的相关性最强。VAMP2作为最亲密的蛋白被过滤掉。对PPI网络和TCGA进行了综合分析。最终，SNAP25被鉴定为与GBM预后正相关的真正枢纽基因。结果经GEPIA、ONCOMINE数据库和qRT-PCR验证。结论：SNAP25可能作为GBM抑制因子和GBM治疗的生物标志物。
Abstract Background: Glioblastoma multiforme (GBM) is a most common aggressive malignant brain tumor. In recent years, targeted therapy has been increasingly applied in GBM treatment. Methods: In the present study, GSE22866 was downloaded from gene expression omnibus (GEO). The genomic and clinical data were obtained from TCGA. The differentially expressed genes (DEGs) were identified and functional analysis was performed using clusterprofiler. Then, the co-expression network for the DEGs was established using the “WGCNA” package. Next, the protein–protein interaction (PPI) was assessed using Search Tool for the Retrieval of Interacting Genes Database (STRING) and hub modules in Cytoscape were screened. The Venn diagram was plotted to showcase the overlapped hub DEGs in PPI network and TCGA. Univariate and multivariate Cox proportional hazards regression analyses were performed to predict the risk score of each patient. Validations of the hub gene were completed in other databases. Results: Functional analysis of the DEGs verified the involvement of DEGs in growth factor binding and gated channel activity. Among the 10 GBM-related modules, the red one displayed the strongest tie with GBM. VAMP2 was filtered out as the most intimate protein. The PPI network and TCGA were comprehensively analyzed. Finally, SNAP25 was identified as a real hub gene positively correlated with GBM prognosis. The result was validated by GEPIA, ONCOMINE database and qRT-PCR. Conclusions: SNAP25 might act as a GBM suppressor and a biomarker in GBM treatment.
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影响因子：
158.5
作者：
Stupp, R;Mason, WP;Ryan, G
通讯作者：
Ryan, G
影响因子：
14.9
作者：
Kanehisa M;Goto S;Sato Y;Furumichi M;Tanabe M
通讯作者：
Tanabe M
影响因子：
14.9
作者：
Ritchie ME;Phipson B;Wu D;Hu Y;Law CW;Shi W;Smyth GK
通讯作者：
Smyth GK
影响因子：
5.4
作者：
Zhang Y;Xu J;Zhu X
通讯作者：
Zhu X
GEPIA：用于癌症和正常基因表达谱和交互式分析的网络服务器。
影响因子：
14.9
作者：
Tang Z;Li C;Kang B;Gao G;Li C;Zhang Z
通讯作者：
Zhang Z