Potential biomarkers and their regulatory relationships in laryngeal squamous cell carcinoma with lymph node metastasis revealed by integrating mRNA, microRNA and long non-coding RNA profiles

Mechanisms about regulation of mRNAs, microRNAs (miRNAs), and long non-coding RNAs (lncRNA) in cervical lymph node metastatic laryngeal squamous cell carcinoma (LSCC) remained unclear. Two sets of three microarrays of mRNA, miRNA and lncRNA in fresh surgical LSCC samples were established, respectively from three paired tumor and adjacent normal mucosa epithelial tissues in cN + (Positive metastasis of cervical lymph node) patients, and three paired tumor and adjacent normal tissues in cN0 (non-cervical lymph node metastatic) patients. Bioinformatic methods including differentiation analysis and enrichment analysis were recruited to identify crucial mRNAs, miRNAs and lncRNAs. Pearson Correlation Coefficients, TargetScan 6.2 and Miranda software were used to establish lncRNA-mRNA, miRNA-mRNA and lncRNA-miRNA regulatory networks. Venn analysis was performed to select specific integrated network for cervical lymph node metastatic LSCC. In total, 2253/600 differentially expressed (DE)-mRNAs, 45/34 DE-miRNAs and 71/48 DE-lncRNAs were identified as specific for lymph node metastatic/non-metastatic LSCC samples. Cell cycle and proteasome pathways were over-represented for specific mRNAs in lymph node metastatic samples. In the interacted networks, PVT1 was associated with the downregulated hsa-miR-1207-5p and the upregulated G6PD, which was predicted targeted by hsa-miR-1207-5p; whereas LOC157273 was closely related to the downregulated hsa-miR-145-5p and upregulated CDK4, SEH1L and SMC1A, which were predicted targeted by hsa-miR-145-5p. Several important mRNAs (G6PD, SMC1A and CDK4), miRNAs (miR-1207-5p and hsa-miR-145-5p) and lncRNAs (PVT1 and LOC157273) were identified as potential biomarkers for lymph node metastatic LSCC diagnosis. Additionally, PVT1 might regulate miR-1207-5p, whose potential target was G6PD; and SMC1A and CDK4 might be targets of hsa-miR-145-5p.