Integrated Analysis of Competing Endogenous RNAs Network Reveals Potential Signatures in Osteosarcoma Development

Abstract

The purpose of this work was to extract key players such as mRNAs and long non-coding RNA (lncRNAs) in the etiopathogenesis of osteosarcoma (OS). The sequencing analyses (mRNAs and lncRNAs) of OS were conducted followed by differentially expressed mRNAs and lncRNAs (DEmRNAs and DElncRNAs) identification between U-2OS cells with has-miR-590-5p overexpression and negative control cells. Following this, the co-expression and functional enrichment analyses of DEmRNAs and DElncRNAs were carried out. Also, the miRNAs-DElncRNAs-DEmRNAs regulatory network was constructed with DElncRNAs-miRNAs and DElncRNAs-DEmRNAs pairs after the target gene analysis of miRNA. In addition, the ceRNA-has-miR-590-5p was further extracted based on the has-miR-590-5p-DElncRNAs and DElncRNAs-DEmRNAs interactions. Finally, the results of the bioinformatics analysis was verified by reverse-transcription polymerase chain reaction (RT-PCR). Totally, 980 DEmRNAs (539 up-regulated DEmRNAs and 441 down-regulated DEmRNAs) and 682 DElncRNAs (352 up-regulated DElncRNAs and 330 down-regulated DElncRNAs) were extracted between cells with hsa-miR-590-5p overexpression and normal cells. The functional analyses suggested that up-regulated genes were significantly enriched in several GO terms such as signal transduction and cytokine-cytokine receptor interaction pathway while down-regulated genes ( SCUBE3, HIST1H4E and EDIL3) were associated with calcium ion binding, cell surface function and nucleosome assembly. Additionally, the miRNAs-DEmRNAs-DEmRNAs network represented 220 pairs among 41 miRNAs, 38 DElncRNAs and 61 DEmRNAs. Furthermore, the ceRNA-hsa-miR-590-5p network consisted of 70 interaction pairs including hsa-miR-590-5p- SCUBE3-CTB-113D17.1, hsa-miR-590-5p- EDIL3-CTB-113D17.1 and hsa-miR-590-5p- HIST1H4E-CTB-113D17.1) among hsa-miR-590-5p, 30 DEmRNAs and 4 down-regulated DElncRNAs. Meanwhile, the RT-PCR results incidated that compared with the blank (KB) and negative control (NC) group, the mRNA expression of SCUBE3, HIST1H4E, and EDIL3 were significantly descreased in mimics group (P value <0.05). The lncRNA CTB-113D17.1 might implicate with OS development probably via serving as a hsa-miR-590-5p sponge to regulate gene targets ( SCUBE3, EDIL3 and HIST1H4E), which will facilitate the deep understandings of OS progression.