Genome-wide analysis of stepwise hepatocarcinogenesis using next generation sequencer
Yutaka Midarikawa1, 2, Shogo Yamamoto2, Hiroki Ueda2, Kotaro Sonoda2, Shingo Tsuji2, Kenji Tatsuno2, Tatsuhiro Shibata3, Kyle Covington4, David A. Wheeler4, Tadatoshi Takayama1, Hiroyuki Aburatani2
1Nihon univ. Tokyo, Japan; 2Tokyo Univ. Tokyo, Japan; 3National Cancer Center, Tokyo, Japan; 4Baylor College of Medicine, Houston, TX
Early hepatocellular carcinoma (HCC) consists of small hepatocytes with little cellular atypia but with structural atypia. This type of very well-differentiated cancerous tissue is usually characterized by indistinct margins and many portal tracts within the tumor, and is clinically detected as hypovascular tumor by imaging modalities. Early HCC usually becomes hypervascular over time and develops into classical HCC. To identify sequential genomic changes in multistep hepatocarcinogenesis, we analyzed fusion genes and mutations using next generation sequencer and methylation status of CpG islands using 450K array about 40 early and 96 advanced HCCs. First, exome sequence showed that base sequence aberrations were more frequent in advanced HCC than early HCC (307. 5 vs 90. 5 genes per tumor). Mutations including p53 (30. 0% vs 41. 6%) and WNT signaling pathways (27. 5% vs 30. 2%) were recurrently observed in both early and advanced HCCs. On the other hand, mutations in chromatin remodeling genes were more frequently observed in advanced HCC (19. 7%) than early HCC (5. 0%). Consistent with our previous report homozygous deletions near CSMD1 and CDKN2A were also found in 8 and 3 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 oneoff crisis, was the event observed only in advanced HCC. Finally, we integrated methylation status of CpG core and expression data from RNA sequencing and identified silenced genes by promoter methylation through stepwise hepatocarcinogenesis. Taken together, genomic aberrations including mutation, expression alteration, rearrangement, and methylation status were more frequent in advanced HCC, suggesting early HCC originates in the chronic liver disease and progresses into advanced HCC with accumulation of such genomic aberrations.
Hiroyuki Aburatani - Grant/Research Support: Takeda Pharmaceuticals, Forerunner Pharma Research
The following people have nothing to disclose: Yutaka Midorikawa, Shogo Yamamoto, Hiroki Ueda, Kotaro Sonoda, Shingo Tsuji, Kenji Tatsuno, Tatsuhiro Shibata, Kyle Covington, David A. Wheeler, Tadatoshi Takayama