转移性骨肉瘤的分子特征:差异表达基因、转录因子和微小RNA
Molecular characterization of metastatic osteosarcoma: Differentially expressed genes, transcription factors and microRNAs.
作者信息
Heng Lisong, Jia Zhen, Bai Jie, Zhang Kun, Zhu Yangjun, Ma Jianbing, Zhang Jun, Duan Honghao
机构信息
Department of Orthopedics and Traumatology, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710054, P.R. China.
Department of Endocrinology, Xi'an No. 1 Hospital, Xi'an, Shaanxi 710002, P.R. China.
出版信息
Mol Med Rep. 2017 May;15(5):2829-2836. doi: 10.3892/mmr.2017.6286. Epub 2017 Mar 3.
The present study aimed to understand the molecular mechanisms underlying osteosarcoma metastasis. Microarray dataset GSE49003 was downloaded from the Gene Expression Omnibus database and used for analysis. Raw expression data were preprocessed using the preprocessCore, impute and aggregate packages in R. Differentially expressed genes (DEGs) between metastatic and non‑metastatic osteosarcoma cell lines were screened using the limma package following exclusion of DEGs with a higher significance in intra‑groups compared with inter‑groups using the genefilter package. Enrichment analysis was performed on DEGs using TargetMine, followed by identification of transcription factors (TFs) and microRNAs (miRNAs). Regulatory networks were constructed using Cytoscape software. A total of 248 upregulated and 208 downregulated genes were obtained. The upregulated genes were significantly enriched in the following pathways: Downregulation of transforming growth factor β (TGF‑β) receptor signaling and TGF‑β receptor signaling activates SMADs; these upregulated genes included protein phosphatase 1, regulatory subunit 15A, transforming growth factor, β receptor II and ubiquitin carboxyl‑terminal hydrolase L5. In addition, some upregulated genes were enriched in lung cancer disease ontology, including epidermal growth factor receptor (EGFR), insulin‑like growth factor 2 mRNA binding protein 3 (IGF2BP3), runt‑related transcription factor 3 (RUNX3) and secreted frizzled‑related protein 1 (SFRP1). Conversely, the downregulated genes were significantly enriched in extracellular matrix‑associated pathways or functions, such as collagen, type XII, α 1; collagen, type I, α 1; collagen, type IV, α 1; and collagen, type V, α 1. In addition, some downregulated genes were significantly enriched in the TGF‑β signaling pathway, including bone morphogenetic protein 4, inhibitor of DNA binding 3 and SMAD family member 6. A total of 10 TFs and 84 miRNAs (e.g. miR-21-5p) were deemed to be associated with DEGs. In conclusion, DEGs enriched in the downregulation of TGF‑β receptor signaling, TGF‑β receptor signaling activates SMADs and TGF‑β signaling pathways, as well as the extracellular matrix may be implicated in the progression of osteosarcoma metastasis. Dysregulated EGFR, IGF2BP3, RUNX3 and SFRP1 may contribute to the metastasis of osteosarcoma to the lungs. In addition, screened TFs and miR-21-5p may be associated with metastasis via target genes.
本研究旨在了解骨肉瘤转移的分子机制。从基因表达综合数据库下载微阵列数据集GSE49003并用于分析。使用R语言中的preprocessCore、impute和aggregate软件包对原始表达数据进行预处理。在使用genefilter软件包排除组内差异表达基因(DEG)比组间差异更显著的情况后,使用limma软件包筛选转移和非转移骨肉瘤细胞系之间的DEG。使用TargetMine对DEG进行富集分析,随后鉴定转录因子(TF)和微小RNA(miRNA)。使用Cytoscape软件构建调控网络。共获得248个上调基因和208个下调基因。上调基因在以下通路中显著富集:转化生长因子β(TGF-β)受体信号通路下调以及TGF-β受体信号通路激活SMAD;这些上调基因包括蛋白磷酸酶1调节亚基15A、转化生长因子β受体II和泛素羧基末端水解酶L5。此外,一些上调基因在肺癌疾病本体中富集,包括表皮生长因子受体(EGFR)、胰岛素样生长因子2 mRNA结合蛋白3(IGF2BP3)、 runt相关转录因子3(RUNX3)和分泌型卷曲相关蛋白1(SFRP1)。相反,下调基因在细胞外基质相关通路或功能中显著富集,如 XII型胶原α1链、I型胶原α1链、IV型胶原α1链和V型胶原α1链。此外,一些下调基因在TGF-β信号通路中显著富集,包括骨形态发生蛋白4、DNA结合抑制因子3和SMAD家族成员6。共10个TF和84个miRNA(如miR-21-5p)被认为与DEG相关。总之,富集于TGF-β受体信号通路下调、TGF-β受体信号通路激活SMAD以及TGF-β信号通路以及细胞外基质中的DEG可能与骨肉瘤转移进展有关。EGFR、IGF2BP3、RUNX3和SFRP1失调可能导致骨肉瘤转移至肺部。此外,筛选出的TF和miR-21-5p可能通过靶基因与转移相关。