Identification of biomarkers associated with the recurrence of osteosarcoma using ceRNA regulatory network analysis.

Abstract

The aim of the present study was to identify the important mRNAs, micro (mi)RNAs and long non-coding (lnc)RNAs that are associated with osteosarcoma recurrence. The GSE3905 dataset, which contains two sub-datasets (GSE39040 and GSE39055), was downloaded from the Gene Expression Omnibus (GEO). Prognosis-associated RNAs were identified by performing Cox regression univariate analysis and were subsequently used to construct a competing endogenous (ce)RNA regulatory network for Gene Set Enrichment Analysis (GSEA). Kaplan-Meier survival analysis was used to determine the associations between expression levels and survival prognosis. In addition, another independent miRNA profile, GSE79181, was downloaded from GEO for validation. Among the differentially expressed RNAs, 417 RNAs (5 lncRNAs, 19 miRNAs, and 393 mRNAs) were observed to be associated with prognosis. The GSEA for the ceRNA regulatory network revealed that ‘Mitogen-activated protein kinase (MAPK) signaling pathway’, ‘Chemokine signaling pathway’ and ‘Spliceosome’ were markedly associated with osteosarcoma. In addition, three lncRNAs [long intergenic non-protein coding RNA 28 (LINC00028), LINC00323, and small nucleolar RNA host gene 1 (SNHG1)] and two miRNAs (hsa-miR-124 and hsa-miR-7) regulating three mRNAs [Ras-related protein Rap-1b (RAP1B), activating transcription factor 2 (ATF2) and protein phosphatase Mg2+/Mn2+ dependent 1B (PPM1B)] participated in the MAPK signaling pathway. The Kaplan-Meier survival analysis also demonstrated that samples with lower expression levels of LINC00323 and SNHG1 had better prognosis, and samples with increased expression levels of LINC00028, hsa-miR-124 and hsa-miR-7 had better prognosis. Overexpression of RAP1B, ATF2 and PPM1B was positively associated with osteosarcoma recurrence. The roles of hsa-miR-124 and hsa-miR-7 in osteo-sarcoma recurrence were also validated using GSE79181. Thus, in conclusions, the three lncRNAs (LINC00028, LINC00323 and SNHG1), two miRNAs (hsa-miR-124 and hsa-miR-7) and three mRNAs (RAP1B, ATF2, and PPM1B) were associated with osteosarcoma recurrence.