Methylation profile analysis of dna repair genes in hepatocellular carcinoma with ms-mlpa

Hepatocellular carcinoma (HCC) is one of the rare tumours with well-defined major risk factors. Frequently seen factors include environmental agents like Hepatitis B and C, alcohol, aflatoxins and other etiological agents. The multifactorial etiology of HCC can be explained by its complex molecular pathogenesis. A wide range of genetic changes; including gene expression changes, mutations, and loss of heterozygosity and promoter hypermethylation; has been reported in HCC. In the current study, the methylation status of seven genes involved in DNA repair mechanisms, namely MLH1, PMS2, MSH6, MSH2, MGMT, MSH3 and MLH3, was investigated in tumour samples from HCC patients, using the methylation specific – multiplex ligation dependent probe amplification (MS-MLPA) method and the results were correlated with clinical findings. The most common etiological factor in these cases was the presence of hepatitis B alone (47.2%). Among the 56 cases that were studied, promoter methylation was detected in at least one of the genes in 27 (48.2%) cases, only in one gene in 13 (23.2%) cases and in more than one gene in 14 (25%) cases. Only in one (1.8%) patient, methylation was detected in all of the genes studied. Of the seven genes investigated, methylation was most frequently observed in MSH3, with 14 (25%) cases. Methylation of at least one gene was significantly more frequent in patients with single tumours than multifocal tumours. There were significant differences regarding hepatitis B status, Child class, tumour number, grade and TNM stage in cases where PMS2 methylation was detected. These results suggest that methylation of genes involved in mismatch repair may be responsible in the pathogenesis of HCC and evaluating changes in multiple genes in these pathways simultaneously would be more informative. Despite being a robust and relatively inexpensive method, the MS-MLPA assay could be more extensively applied with improvements in the currently intricate data analysis component.