title: Genomic landscape of copy number aberrations enables the identification of oncogenic drivers in hepatocellular carcinoma.
abstract: Cancer is a genetic disease with frequent somatic DNA alterations. Studying recurrent copy number aberrations (CNAs) in human cancers would enable the elucidation of disease mechanisms and the prioritization of candidate oncogenic drivers with causal roles in oncogenesis. We have comprehensively and systematically characterized CNAs and the accompanying gene expression changes in tumors and matched nontumor liver tissues from 286 hepatocellular carcinoma (HCC) patients. Our analysis identified 29 recurrently amplified and 22 recurrently deleted regions with a high level of copy number changes. These regions harbor established oncogenes and tumor suppressors, including CCND1 (cyclin D1), MET (hepatocyte growth factor receptor), CDKN2A (cyclin-dependent kinase inhibitor 2A) and CDKN2B (cyclin-dependent kinase inhibitor 2B), as well as many other genes not previously reported to be involved in liver carcinogenesis. Pathway analysis of cis-acting genes in the amplification and deletion peaks implicates alterations of core cancer pathways, including cell-cycle, p53 signaling, phosphoinositide 3-kinase signaling, mitogen-activated protein kinase signaling, Wnt signaling, and transforming growth factor beta signaling, in a large proportion of HCC patients. We further credentialed two candidate driver genes (BCL9 and MTDH) from the recurrent focal amplification peaks and showed that they play a significant role in HCC growth and survival.
  
  
  CONCLUSIONS
  We have demonstrated that characterizing the CNA landscape in HCC will facilitate the understanding of disease mechanisms and the identification of oncogenic drivers that may serve as potential therapeutic targets for the treatment of this devastating disease.
authors.affiliation: Oncology Research Unit, Pfizer Inc, San Diego, CA, USA. Kai.Wang4@pfizer.com
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.forename: Ho Yeong
authors.initials: HY
authors.lastname: Lim
authors.forename: Stephanie
authors.initials: S
authors.lastname: Shi
authors.forename: Jeeyun
authors.initials: J
authors.lastname: Lee
authors.forename: Shibing
authors.initials: S
authors.lastname: Deng
authors.forename: Tao
authors.initials: T
authors.lastname: Xie
authors.forename: Zhou
authors.initials: Z
authors.lastname: Zhu
authors.forename: Yuli
authors.initials: Y
authors.lastname: Wang
authors.forename: David
authors.initials: D
authors.lastname: Pocalyko
authors.forename: Wei Jennifer
authors.initials: WJ
authors.lastname: Yang
authors.forename: Paul A
authors.initials: PA
authors.lastname: Rejto
authors.forename: Mao
authors.initials: M
authors.lastname: Mao
authors.forename: Cheol-Keun
authors.initials: CK
authors.lastname: Park
authors.forename: Jiangchun
authors.initials: J
authors.lastname: Xu
mesh_terms: D063646:Carcinogenesis / Q000235:genetics; D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000473:pathology; D016022:Case-Control Studies; D015815:Cell Adhesion Molecules / Q000235:genetics*; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D056915:DNA Copy Number Variations / Q000235:genetics*; D018450:Disease Progression; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D055106:Genome-Wide Association Study; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics* / Q000473:pathology; D008297:Male; D008565:Membrane Proteins; D008875:Middle Aged; D009363:Neoplasm Proteins / Q000235:genetics*; D009857:Oncogenes / Q000235:genetics; D016601:RNA-Binding Proteins; D014157:Transcription Factors
chemical_list: C111180:BCL9 protein, human; D015815:Cell Adhesion Molecules; C483039:MTDH protein, human; D008565:Membrane Proteins; D009363:Neoplasm Proteins; D016601:RNA-Binding Proteins; D014157:Transcription Factors