Screening of cancer genome has identified numerous genomic loci with copy number changes that may harbor potential driver genes in tumorigenesis. We have performed an integrative analysis of DNA copy numbers and gene expression profiles in hepatocellular carcinoma (HCC) in an attempt to uncover most provable genomic regions of concomitant copy number and transcription alterations. Unbiased screening of these regions identifies 50 potential driver genes with significant prognostic relevance.Our integrative analyses of genomic data also identified novel potential driver genes for HCC development including NCSTN and SCRIB. Particularly, NCSTN, encoding Type I transmembrane glycoprotein, has never been known to be associated with cancers. SCRIB has recently been reported to be associated with human cancers 31, but its oncogenic role has not been fully studied yet. Moreover, our analysis provided a novel notion i.e. a connection of EGFR, AMPK, and mTOR with the 50 genes. Recently, HSF1, one of the 50 genes, was reported to have oncogenic potential, and which function is mediated by mTOR 32 and EGFR 33 signaling. Similarly, we also demonstrated that the oncogenic activity of NCSTN and SCRIB is possibly mediated via the mTOR pathway. From these results, we postulate the existence of a multifaceted association of the 50 driver genes with three signaling pathways in cancer progression, although further elucidation will be necessary. We conclude our data demonstrate that a systems-level integrative analysis of genome scale data independently collected from a small group of patients provide a striking advantage for identifying genes likely to drive neoplastic development in the liver, and provides new biological and clinical insights for the development of novel treatment modalities. To decode the molecular events during early stages of liver carcinogenesis, we performed gene expression profiling on cirrhotic (regenerative) and dysplastic nodules as well as early HCC. Although considerable heterogeneity was observed at the regenerative and dysplastic stages, a clear difference was detected between dysplastic nodules and eHCC which included 460 differentially expressed genes. Functional analysis of the significant gene set identified the MYC oncogene as a plausible driver gene for malignant conversion of the dysplastic nodules. In addition, gene set enrichment analysis (GSEA) revealed a remarkable enrichment of MYC up-regulated gene sets in eHCC versus dysplasia. Presence of the MYC signature significantly correlated with increased expression of CSN5 as well as with the higher overall transcription rate of genes located in the 8q chromosome region. Furthermore, a classifier constructed from MYC target genes could robustly discriminate eHCC from HGDN and LGDN. In conclusion, our study identified unique expression patterns associated with the transition of high-grade dysplastic nodules to early HCC and demonstrated that activation of the MYC transcription signature is critical for the malignant conversion of pre-neoplastic liver lesions. The fifth subunit of COP9 signalosome CSN5 complex targets p53 tumor suppressor for its degradation through the ubiquitin system in coordination with Mdm2. Our recent microarray analysis identified the elevated expression of CSN5 in early HCC as compared to dysplastic stage, implying that CSN5 is one of the early markers of malignant conversion. We have now tested if targeting of CSN5 can affect the course of HCC progression in vitro and in vivo. To inactivate CSN5 gene expression, Huh7 and HepG2 cells were treated with three different siRNAs. The down-regulation of CSN5 in both mRNA and protein level was confirmed by quantitative real-time RT-PCR and Western blotting. Cell growth was analyzed by MTT and FACS analysis, and apoptosis was estimated by ELISA for detection of ssDNA. For in vivo evaluation of CSN5 as a therapeutic target, a bioluminescent Huh7 cell line permanently expressing luciferase was transplanted into the spleen of immunodeficient mice to establish Huh7-luc+ HCC orthotopic xenograft model. Chemically modified CSN5siRNA was systematically delivered to liver through tail vein injection of stable nucleic acid lipid particle (SNALP). Tumor relapses were persistently monitored by bioluminescence imaging, up to 28 days after cell transplantation. Huh7 and HepG2 cells transfected with CSN5-siRNA showed 68% and 77% growth inhibition, respectively, associated with cell-cycle arrest in G1 phase. CSN5-deficient cells also exhibited a 1.8 fold increase in apoptosis as compared with negative control siRNA-treated cells. We also have demonstrated that, when the HCC cells were undergoing apoptotic progression through downregulation of CSN5 protein following the siRNA treatment, the levels of p53, its responder p21 and p27 were restored. CSN5siRNA, a chemically modified variant of CSN5-2siRNA, was selected for in vivo application in terms of growth inhibition of Compared to SNALP-control siRNA treatment, four times injection of SNALP-CSN5siRNA at a dosage of 2 mg/kg effectively suppressed neoplastic growth in the mouse model of metastatic human liver cancer. Taken together, the results suggest that CSN5 is an important regulator of HCC cell growth and survival, and may be an attractive target for treatment of HCC disease. Further, SNALP technology for in vivo delivery of siRNA may be effective in treating human HCC. HCC is a hyper-vascular tumor, and expression of the hypoxia inducible factor (HIF-1alpha) and its target genes is reported to be associated with a poor prognosis phenotype. We have recently characterize the hypoxic gene expression profile from primary mouse hepatocytes and have used it to apply a comparative functional genomics approach to classify 139 human HCC. The mouse hepatocytes were isolated by 2 steps collagenase perfusion of the mouse liver followedby purification in Percoll gradient. Cells were seeded at 3x10 in 10 cm dishes with DMEM/HAMs F-12 medium supplemented with 10%FBS. Hypoxia was induced by culture of cells inside an air-tight chamber with inflow and outflow valves that was infused with a mixture of 1% O2, 5% CO2 and 94% N2.RNA isolation and microarray based global gene expression analysis performed. Mouse hepatocytes under hypoxic conditions over 24 hours revealed more than 1800 significant regulated genes (p less than 0.001). Genes that showed at least 2 fold expression difference between hypoxic and normoxic conditions were selected to define the hypoxia gene expression signature. 504 orthologous genes derived from the hypoxic signature were used to perform hierarchical cluster analysis of 139 human HCC. As a result, two subsets of genes were identified. One subset of 104 genes implicated in cell cycle and apoptosis regulation, blood coagulation and immune response, among other functions, was able to predict HCC with a good prognosis. On the other hand, a subset of 62 genes, some of them involved in cell cycle progression (e.g. Cdk6, Ches1, Ccng1, Ngfb), apoptosis regulation (e.g. Bcl6b, Pik3r1) and angiogenesis (e.g. Vegf, Id3), was able to predict HCC with a poor prognosis. Interestingly, among these 62 genes, we identified some that have already been found to predict poor prognosis in other human cancers. the hypoxia gen [summary truncated at 7800 characters]