Genome-wide analysis of stepwise hepatocarcinogenesis using next generation sequencer.

Early hepatocellular carcinoma (HCC) originates from the hepatocytes of chronic liver disease and develops into classical HCC. To identify sequential genomic changes in multistep hepatocarcinogenesis, we analyzed fusion genes and mutations using next generation sequencer about 40 early and 80 advanced HCCs. First, exome sequence showed that base sequence aberrations were more frequent in advanced HCC than early HCC, and mutations including TP53 (24%), CTNNB1 (24%), and ARID1A (16%) were recurrently observed in both early and advanced HCCs. Consistent with our previous report homozygous deletions near CSMD1 and CDKN2A were also found in 8 and 5 cases, respectively, only in advanced HCC. Next, we detected 4 types of fusion gene, including interchromosomal (translocation), intrachromosomal (deletion), intrachromosomal (translocation), and inversion by RNA sequencing. We also found that every HCC harbored 2 to 5 fusion genes, which were more frequent in advanced than early HCC, although there were no recurrent rearrangements in neither advanced nor early HCCs. Especially chromathripsis, in which 10 to 100 rearrangements were localized in the specific genomic regions and genomic features imply chromosome breaks occur in one-off crisis, was the event observed only in advanced HCC. Taken together, genomic changes were more frequent in advanced HCC, suggesting early HCC originates in the chronic liver disease and progresses into advanced HCC with genomic aberrations.