A three miRNAs signature for predicting the transformation of oral leukoplakia to oral squamous cell carcinoma

Abstract

Oral squamous cell carcinoma (OSCC) remains to be a global health problem. However, the underlying molecular mechanisms regulating the oral leukoplakia (OLK) to OSCC remain poorly known. MicroRNAs (miRNAs) expression profiles of GSE33299 and GSE62809 were downloaded from gene expression omnibus (GEO) respectively. R software and bioconductor packages were used to compare and identify the differentially expressed miRNAs between OLK tissues and OLK transformed OSCC (OLK-OSCC). The target genes of commonly changed miRNAs were then subjected to gene ontology (GO) enrichment analysis, pathway analysis and miRNA-target genes network analysis. The prediction power of commonly changed miRNAs was further tested in an independent cohort. In total, 161 (88 upregulated and 73 downregulated) and 68 (19 upregulated and 49 downregulated) markedly altered miRNAs were identified from GSE33299 and GSE62809 respectively. The downstream targets of these differentially expression miRNAs in the two cohorts shared many top enriched GO and KEGG pathways. A set of three miRNAs signature including miR-129-5p, miR-296-5p and miR-450b-5p was commonly changed in both GSE33299 and GSE62809. Functional analysis revealed that the downstream target genes of the miRNA signature were associates with transcriptional regulation, estrogen signaling pathway, p53 signaling pathway and RIG-I-like receptor signaling pathway. This three-gene signature was further successfully validated in another independent cohort. The expression levels of miR-129-5p and miR-296-5p were significantly downregulated in OLK-OSCC tissues compared to OLK tissues, while miR-450b-5p levels were higher in OLK-OSCC tissues. In addition, this three miRNAs signature could discriminate OLK from OLK-OSCC with high accuracy. In conclusion, our study has identified a three miRNAs signature that might help predict the transformation of OLK to OSCC. Which will provide useful guidance for therapeutic applications.

Keywords: Functional analysis; MicroRNAs; oral leukoplakia; oral squamous cell carcinoma.

Figure 1

Volcano plots of miRNAs between OLK-OSCC tissues and OLK tissues. X-axis indicates the p values (log-scaled), whereas the Y-axis shows the fold change (log-scaled). Each symbol represents a different miRNA, and the red/green color of the symbols categorize the upregulated/downregulated miRNAs.

Figure 2

Heatmaps of the significantly differentially expressed miRNAs between OLK-OSCC tissues and OLK tissues.

Figure 3

Gene ontology and KEGG analyses of the target genes of the differentially expressed miRNAs in GSE33299 and GSE62809.

Figure 4

A set of commonly changed miRNA (miR-129-5p, miR-296-5p and miR-450b-5p) in both GEO studies were identified. The miR-129-5p and miR-296-5p levels were downregulated, while miR-450b-5p levels were upregulated in OLK-OSCC tissues compared to OLK tissues.

Figure 5

Gene ontology and KEGG analyses of the target genes of the three miRNAs signature.

Figure 6

MiRNA-target genes interaction network of the target genes of the three miRNAs signature. The yellow color represented the miRNAs. Red color and green color indicated the upregulated and downregulated target genes respectively.

Figure 7

In the validation study, our results showed that the expression level of miR-129-5p were remarkably lower in OLK-OSCC tissues compared with those in OLK tissues (P = 0.0041) and healthy control (HC) tissues (P < 0.0001). Similarly, miR-296-5p were significantly decreased in OLK-OSCC tissues compared to those in OLK tissues (P = 0.0014) and healthy control (HC) tissues (P = 0.0002). No significance was found between OLK tissues and HC tissues for miR-129-5p and miR-296-5p levels. However, the miR-450b-5p levels were significantly higher in OLK-OSCC tissues compared to OLK (P = 0.0007) and HC tissues (P < 0.0001). The expression level of miR-450b was lower in HC tissues in comparison with OLK tissues (P = 0.0460).

Figure 8

Receiver operating characteristic (ROC) analysis of the three potential miRNAs signature for discriminating OLK from OLK-OSCC.