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Identification of potential driver genes in human liver carcinoma by genomewide screening

 Hyun Goo Woo  ;  Eun Sung Park  ;  Ju-Seog Lee  ;  Yun-Han Lee  ;  Tsuyoshi Ishikawa  ;  Yoon Jun Kim  ;  Snorri S. Thorgeirsson 
 CANCER RESEARCH, Vol.69(9) : 4059-4066, 2009 
Journal Title
Issue Date
Carcinoma, Hepatocellular/genetics* ; Carcinoma, Hepatocellular/pathology ; Comparative Genomic Hybridization ; DNA, Neoplasm/genetics ; Gene Dosage ; Genome, Human ; Humans ; Liver Neoplasms/genetics* ; Liver Neoplasms/pathology ; Prognosis ; Transcription, Genetic
Genomic copy number aberrations and corresponding transcriptional deregulation in the cancer genome have been suggested to have regulatory roles in cancer development and progression. However, functional evaluation of individual genes from lengthy lists of candidate genes from genomic data sets presents a significant challenge. Here, we report effective gene selection strategies to identify potential driver genes based on systematic integration of genome scale data of DNA copy numbers and gene expression profiles. Using regional pattern recognition approaches, we discovered the most probable copy number-dependent regions and 50 potential driver genes. At each step of the gene selection process, the functional relevance of the selected genes was evaluated by estimating the prognostic significance of the selected genes. Further validation using small interference RNA-mediated knockdown experiments showed proof-of-principle evidence for the potential driver roles of the genes in hepatocellular carcinoma progression (i.e., NCSTN and SCRIB). In addition, systemic prediction of drug responses implicated the association of the 50 genes with specific signaling molecules (mTOR, AMPK, and EGFR). In conclusion, the application of an unbiased and integrative analysis of multidimensional genomic data sets can effectively screen for potential driver genes and provides novel mechanistic and clinical insights into the pathobiology of hepatocellular carcinoma.
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5. Research Institutes (연구소) > Institute for Medical Convergence (연의-생공연 메디컬융합연구소) > 1. Journal Papers
Yonsei Authors
Park, Eun Sung(박은성)
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