Clinical implication of recurrent copy number alterations in hepatocellular carcinoma and putative oncogenes in recurrent gains on 1q.
To elucidate the pathogenesis of hepatocellular carcinoma (HCC) and develop useful prognosis predictors, it is necessary to identify biologically relevant genomic alterations in HCC. In our study, we defined recurrently altered regions (RARs) common to many cases of HCCs, which may contain tumor-related genes, using whole-genome array-CGH and explored their associations with the clinicopathologic features. Gene set enrichment analysis was performed to investigate functional implication of RARs. On an average, 23.1% of the total probes were altered per case. Mean numbers of altered probes are significantly higher in high-grade, bigger and microvascular invasion (MVI) positive tumors. In total, 32 RARs (14 gains and 18 losses) were defined and 4 most frequent RARs are gains in 1q21.1-q32.1 (64.5%), 1q32.1-q44 (59.2%), 8q11.21-q24.3 (48.7%) and a loss in 17p13.3-p12 (51.3%). Through focusing on RARs, we identified genes and functional pathways likely to be involved in hepatocarcinogenesis. Among genes in the recurrently gained regions on 1q, expression of KIF14 and TPM3 was significantly increased, suggesting their oncogenic potential in HCC. Some RARs showed the significant associations with the clinical features. Especially, the recurrent loss in 9p24.2-p21.1 and gain in 8q11.21-q24.3 are associated with the high tumor grade and MVI, respectively. Functional analysis showed that cytokine receptor binding and defense response to virus pathways are significantly enriched in high grade-related RARs. Taken together, our results and the strategy of analysis will help to elucidate pathogenesis of HCC and to develop biomarkers for predicting behaviors of HCC.
Kim
Tae-Min
TM
Department of Microbiology, The Catholic University of Korea, Seoul, Korea.
Yim
Seon-Hee
SH
Shin
Seung-Hun
SH
Xu
Hai-Dong
HD
Jung
Yu-Chae
YC
Park
Cheol-Keun
CK
Choi
Jong-Young
JY
Park
Won-Sang
WS
Kwon
Mi-Seon
MS
Fiegler
Heike
H
Carter
Nigel P
NP
Rhyu
Mun-Gan
MG
Chung
Yeun-Jun
YJ
D014408:Biomarkers, Tumor / Q000032:analysis; D015153:Blotting, Western; D006528:Carcinoma, Hepatocellular / Q000737:chemistry / Q000235:genetics* / Q000473:pathology*; D045744:Cell Line, Tumor; D002872:Chromosome Deletion; D002878:Chromosomes, Human, Pair 1; D002898:Chromosomes, Human, Pair 8; D006801:Humans; D016547:Kinesins / Q000032:analysis; D008113:Liver Neoplasms / Q000737:chemistry / Q000235:genetics* / Q000473:pathology*; D016254:Mutagenesis, Insertional; D009364:Neoplasm Recurrence, Local / Q000235:genetics*; D015513:Oncogene Proteins / Q000032:analysis; D016133:Polymerase Chain Reaction; D014335:Tropomyosin / Q000032:analysis
D014408:Biomarkers, Tumor; D015513:Oncogene Proteins; C498783:TPM3 protein, human; D014335:Tropomyosin; C502598:KIF14 protein, human; D016547:Kinesins