Construction of microRNA-messenger networks for human osteosarcoma

Osteosarcoma is the most common bone tumor in children and young adults. Although the microRNAs (miRNA) expression analyses of osteosarcoma have been performed previously, the construction of miRNA-messenger RNA (mRNA) networks for osteosarcoma is needed. This study aimed to identify osteosarcoma-related miRNAs through analyzing the microarray datasets and to construct the regulatory network of miRNA-mRNA for human osteosarcoma. The datasets were extracted from the Gene Expression Omnibus and the differentially expressed miRNAs were screened through the limma package in Bioconductor. Genes targeted by the differentially expressed miRNAs were screened out by using the Miranda, MirTarget2, PicTar, PITA, and TargetScan databases. The predicted target genes were further analyzed by Gene Ontology and pathway enrichment analysis and a regulatory network of differentially expressed miRNAs and their target osteosarcoma-associated genes was constructed. A total of 36 downregulated miRNAs and 182 upregulated miRNAs were identified in osteosarcoma samples compared with normal samples and 397 target genes for upregulated miRNAs and 222 target genes for downregulated miRNAs were obtained. The enriched pathways for target genes of differentially expressed miRNAs included transcriptional misregulation in cancer, the AMPK signaling pathway, and MAPK signaling pathway. In the regulatory network, has-miR-199a-5p targeted the highest number of genes and nemo-like kinase (NLK) was targeted by five miRNAs (hsa-miR-140-5p, hsa-miR-107, hsa-miR-324-5p, hsa-miR-199a-5p, and hsa-miR-28-5p). The has-miR-324-5p targets NLK, TGFB2, and PPARG. These miRNAs and their target genes may serve as potential therapeutic targets of osteosarcoma.

骨肉瘤是儿童和青少年中最常见的骨肿瘤。尽管先前已经对骨肉瘤进行了微小RNA（miRNA）表达分析，但仍需要构建骨肉瘤的miRNA - 信使RNA（mRNA）网络。本研究旨在通过分析微阵列数据集来识别与骨肉瘤相关的miRNA，并构建人类骨肉瘤的miRNA - mRNA调控网络。数据集从基因表达综合数据库（Gene Expression Omnibus）中提取，通过Bioconductor中的limma软件包筛选出差异表达的miRNA。利用Miranda、MirTarget2、PicTar、PITA和TargetScan数据库筛选出差异表达miRNA所靶向的基因。对预测的靶基因进一步进行基因本体论（Gene Ontology）和通路富集分析，并构建差异表达miRNA及其靶向的骨肉瘤相关基因的调控网络。与正常样本相比，在骨肉瘤样本中总共鉴定出36个下调的miRNA和182个上调的miRNA，并且获得了上调miRNA的397个靶基因和下调miRNA的222个靶基因。差异表达miRNA的靶基因富集的通路包括癌症中的转录失调、AMPK信号通路和MAPK信号通路。在调控网络中，has - miR - 199a - 5p靶向的基因数量最多，类Nemo激酶（NLK）被5个miRNA（hsa - miR - 140 - 5p、hsa - miR - 107、hsa - miR - 324 - 5p、hsa - miR - 199a - 5p和hsa - miR - 28 - 5p）靶向。has - miR - 324 - 5p靶向NLK、TGFB2和PPARG。这些miRNA及其靶基因可能作为骨肉瘤潜在的治疗靶点。