Isolation of NotI clusters hypomethylated in HBV-integrated hepatocellular carcinomas by two-dimensional electrophoresis.

To examine genetic and epigenetic alterations associated with HBV integration in hepatocarcinogenesis, we compared genomic DNA profiles of primary hepatocellular carcinomas (HCCs) and cell lines that either contained or did not contain integrated HBV. To accomplish this, we carried out Restriction Landmark Genomic Scanning (RLGS), a two-dimensional system that displays 2000-3000 Not I landmark sites in a single gel electrophoresis experiment. We identified one Not I landmark spot that showed high signal intensity in HBV-integrated cell lines or in primary HCCs, but not in HCCs or tumor-cell lines free of HBV integration. Cloning of this spot revealed that it consisted of a Not I cluster sequence enriched with CpG dinucleotides. This sequence, hypomethylated in association with HBV integration, was found in the peri-centromeric region of human acrochromosomes. The results demonstrate that epigenetic changes at specific sequences in the genome occur in association with HBV integration during the process of hepatocarcinogenesis.