Expression and Methylation of Tumor Suppressor Gene DKK3 in Nasopharyngeal Carcinoma: A Datamining Study

Abstract

Objectives: To study the relationship between the expression level of tumor suppressor gene DKK3 in nasopharyngeal carcinoma tissues and the methylation of the promoter region, and to explore the methylation of DKK3 gene promoter as a potential epigenetic intervention target for nasopharyngeal carcinoma. Methods: First, download the nasopharyngeal carcinoma expression profile chip, RNA-Seq sequencing and methylation chip data from the GEO database, use the R software to analyze the difference of DKK3 expression and promoter methylation in nasopharyngeal carcinoma and adjacent tissues and normal control tissues; then, select cancer tissue specimens and corresponding adjacent tissue specimens from 50 patients with nasopharyngeal carcinoma, use RT-PCR to detect the mRNA expression of DKK3 gene and methylation-specific PCR (MSP) to detect the promoter methylation level, and analyze the relationship between the two. Results: The mRNA level of DKK3 gene was found significantly down-regulated (|log2FC|> 1.0) by three different expression profiling platforms of AffymetrixU133 Plus2.0, IlluminaHiSeq 2000 and 4000. Methylation chip analysis found that the methylation status of 4 CpG sites in nasopharyngeal carcinoma tissues was significantly higher than that of normal control tissues. 2 CpG sites in nasopharyngeal carcinoma tissues was significantly higher than that of adjacent tissues (GSE62336). Conclusions: Hypermethylation in the promoter region caused down-regulation of the tumor suppressor gene DKK3 expression in nasopharyngeal carcinoma tissues, which was a potential target for epigenetic intervention.