Diao Chunyu, Xi Yong, Xiao Tao
Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China.
Department of Orthopedics, Tongchuan People's Hospital, Tongchuan, Shaanxi 727000, P.R. China.
Oncol Lett. 2018 Mar;15(3):2789-2794. doi: 10.3892/ol.2017.7649. Epub 2017 Dec 19.
Osteosarcoma (OS) is an invasive malignant neoplasm of the bones. The present study identified and analyzed key genes associated with OS. Expression profiling of the dataset GSE49003, which included 6 metastatic and 6 non-metastatic OS cell lines and was obtained from the Gene Expression Omnibus, was performed. Following data preprocessing, the differentially expressed genes (DEGs) were selected using the limma package in R. Subsequently, bidirectional hierarchical clustering using the pheatmap package in R and an unpaired Students' t-test was performed for the DEGs. Based on the Search Tool for the Retrieval of Interacting Genes database and Cytoscape software, a protein-protein interaction (PPI) network for the DEGs was constructed. Using Database for Annotation, Visualization and Integrated Discovery software and the Kyoto Encyclopedia of Genes and Genomes Orthology Based Annotation System server, functional and pathway enrichment analyses were performed for the DEGs corresponding to the proteins of the network. In addition, the transcription factors (TFs) and CpG islands of the gene promoter were searched for using the TRANSFAC database and CpG Island Searcher software, respectively. A total of 323 DEGs were identified between the metastatic and non-metastatic samples. In the PPI network, upregulated epidermal growth factor receptor (EGFR) exhibits a high degree and was therefore highly interconnected with other proteins. Enrichment analysis revealed that EGFR was enriched in cytoskeleton organization, organic substance response and the signaling pathway of focal adhesion. The TFs early growth response 1, nuclear factor-κB complex subunits, peroxisome proliferator activated receptor α, signal transducer and activator of transcription 3 and MYC proto-oncogene were identified in the EGFR promoter region. Furthermore, multiple CpG islands, starting from the 400 bp of the EGFR promoter sequence, were predicted. Methylated modification of the CpG islands in the EGFR promoter may help to regulate EGFR expression. The TFs identified in the EGFR promoter may function in the progression of OS.
骨肉瘤（OS）是一种侵袭性骨恶性肿瘤。本研究鉴定并分析了与骨肉瘤相关的关键基因。对数据集GSE49003进行了表达谱分析，该数据集包含6个转移性和6个非转移性骨肉瘤细胞系，取自基因表达综合数据库（Gene Expression Omnibus）。经过数据预处理后，使用R语言中的limma软件包筛选出差异表达基因（DEGs）。随后，使用R语言中的pheatmap软件包进行双向层次聚类，并对DEGs进行非配对学生t检验。基于检索相互作用基因数据库（Search Tool for the Retrieval of Interacting Genes database）和Cytoscape软件，构建了DEGs的蛋白质-蛋白质相互作用（PPI）网络。使用注释、可视化和综合发现数据库（Database for Annotation, Visualization and Integrated Discovery software）软件和基于京都基因与基因组百科全书直系同源注释系统（Kyoto Encyclopedia of Genes and Genomes Orthology Based Annotation System）服务器，对与网络中蛋白质相对应的DEGs进行功能和通路富集分析。此外，分别使用TRANSFAC数据库和CpG岛搜索软件（CpG Island Searcher software）搜索基因启动子的转录因子（TFs）和CpG岛。在转移性和非转移性样本之间共鉴定出323个DEGs。在PPI网络中，上调的表皮生长因子受体（EGFR）具有较高的度数，因此与其他蛋白质高度相互连接。富集分析显示，EGFR在细胞骨架组织、有机物反应和粘着斑信号通路中富集。在EGFR启动子区域鉴定出转录因子早期生长反应1、核因子-κB复合体亚基、过氧化物酶体增殖物激活受体α、信号转导和转录激活因子3以及MYC原癌基因。此外，从EGFR启动子序列的400 bp处开始预测了多个CpG岛。EGFR启动子中CpG岛的甲基化修饰可能有助于调节EGFR的表达。在EGFR启动子中鉴定出的转录因子可能在骨肉瘤的进展中发挥作用。
