Detection of metallothionein 1G as a methylated tumor suppressor gene in human hepatocellular carcinoma using a novel method of double combination array analysis

Gene expression profiling or karyotyping analysis has made it possible to identify novel genes with altered expressions or copy numbers that have not been previously reported in liver cancer. On the same HCC sample, we performed double array analysis, both expression profiling and karyotyping analysis using a single nucleotide polymorphism (SNP) array in an attempt to find a novel tumor suppressor gene for its prognostic marker. We conducted expression array and SNP chip array using tumor and corresponding non-tumor tissues from the resected liver specimen of a 68-year-old woman who had chronic hepatitis type C. Additionally, we performed quantitative real-time reverse transcription polymerase chain reaction (PCR) and methylation-specific PCR (MSP) for gene detection using specimens from 48 patients with HCC, and investigated their correlation with the prognosis. Metallothionein (MT) 1G gene located on 16q13 showed a decreased expression in tumor tissue. The copy number by SNP chip array revealed no loss of heterozygosity since no deletions were detected in 16q13, and HCC tissue showed AB call in both SNPs next to MT1G. In quantitative real-time PCR using 48 HCC clinical samples, mRNA expression of MT1G decreased significantly compared with that in corresponding non-cancerous liver tissues (p<0.0323). Twenty-nine (60.4%) of 48 HCCs gave a positive result in MSP, indicating a poorer prognosis than the negative group, although the difference was not significant (p<0.0978). Our results indicated that MT1G acts as a tumor suppressor gene in HCC. Moreover, findings suggested that the mechanisms of MT1G silencing are related to promoter hypermethylation.