Tian Wen, Li Yongsheng, Zhang Jinghua, Li Jijun, Gao Jinghua
Department of Internal Medicine-Oncology, Cangzhou Central Hospital, Cangzhou 061000, Hebei Province, China.
Department of Internal Medicine-Oncology, Cangzhou Central Hospital, Cangzhou 061000, Hebei Province, China.
Gene. 2018 Apr 15;650:7-14. doi: 10.1016/j.gene.2018.01.093. Epub 2018 Jan 31.
Osteosarcoma (OS) is a common primary malignancy in children and adolescents with relative high survival rate after chemotherapy. While, the toxicity of chemotherapy and personalized different response to chemotherapy makes it difficult for the selection of therapeutics and improvement of diagnosis. In this study, we conducted a combined analysis of two types of microarray datasets (gene expression and DNA methylation) from the Gene Expression Omnibus (GEO). Differential methylation sites (DMS) were identified by the IMA package and differential expression genes (DEGs) were screened out via the limma package. A total of 11,242 DMS (corresponding to 3080 genes (DMGs)) and 337 DEGs, with 40 overlaps (OS genes) between DEGs and DMGs, were identified. Enriched functions of OS genes were obtained through the Database for Annotation, Visualization and Integrated Discovery (DAVID). The OS genes were mainly enriched in the biological processes related to inflammatory/immune response and Pertussis pathways and Hematopoietic cell lineage pathways. Besides, OS-specific disease network was obtained, and found that UBS and NRF1 were regulated by multiple OS genes. Kaplan Meier analysis of OS genes identified BHMT2, DOCK2, DNALI1 and RIPK3 as significant OS survival-related genes. SEMA3A and PRAME are included in the 40 OS genes and within the top 10 most up-regulated DEGs. Their expression changes were further validated in U2OS osteosarcoma cell lines and hOB normal cell lines through quantitative PCR (qPCR) and consistent result with microarray analysis was obtained. Based on this study, some novel targets were identified for OS, which would be helpful in its early diagnosis and treatment.
骨肉瘤（OS）是儿童和青少年中常见的原发性恶性肿瘤，化疗后生存率相对较高。然而，化疗的毒性以及对化疗的个性化不同反应使得治疗选择和诊断改善变得困难。在本研究中，我们对来自基因表达综合数据库（GEO）的两种类型的微阵列数据集（基因表达和DNA甲基化）进行了联合分析。通过IMA软件包鉴定差异甲基化位点（DMS），并通过limma软件包筛选差异表达基因（DEG）。共鉴定出11242个DMS（对应3080个基因（DMG））和337个DEG，其中DEG和DMG之间有40个重叠（OS基因）。通过注释、可视化和综合发现数据库（DAVID）获得OS基因的富集功能。OS基因主要富集在与炎症/免疫反应、百日咳途径和造血细胞谱系途径相关的生物学过程中。此外，获得了OS特异性疾病网络，发现UBS和NRF1受多个OS基因调控。对OS基因的Kaplan Meier分析确定BHMT2、DOCK2、DNALI1和RIPK3为与OS生存相关的重要基因。SEMA3A和PRAME包含在40个OS基因中，并且在上调幅度最大的前10个DEG中。通过定量PCR（qPCR）在U2OS骨肉瘤细胞系和hOB正常细胞系中进一步验证了它们的表达变化，并获得了与微阵列分析一致的结果。基于本研究，确定了一些骨肉瘤的新靶点，这将有助于其早期诊断和治疗。
