Location-Specific Epigenetic Regulation of the Metallothionein 3 Gene in Esophageal Adenocarcinomas

Metallothionein 3 (MT3) maintains intracellular metal homeostasis and protects against reactive oxygen species (ROS)-induced DNA damage. In this study, we investigated the epigenetic alterations and gene expression of the MT3 gene in esophageal adenocarcinomas (EACs).Using quantitative bisulfite pyrosequencing, we detected unique DNA methylation profiles in the MT3 promoter region. The CpG nucleotides from −372 to −306 from the transcription start site (TSS) were highly methylated in tumor (n = 64) and normal samples (n = 51), whereas CpG nucleotides closest to the TSS (−4 and +3) remained unmethylated in all normal and most tumor samples. Conversely, CpG nucleotides in two regions (from −139 to −49 and +296 to +344) were significantly hypermethylated in EACs as compared to normal samples [FDR<0.001, −log10(FDR)>3.0]. The DNA methylation levels from −127 to −8 CpG sites showed the strongest correlation with MT3 gene expression (r = −0.4, P