Table 1.
Tumor-promoting genes identified by the oncogenomic cDNA screen
| Tumor Promoting Genes | Chromosomal Location | Focal Amplicon Frequency | Gain Frequency | RNA/DNA Correl. | Biochemical Function(s) | Average Tumor Volume |
|---|---|---|---|---|---|---|
| FNDC3B* | 3q26.31 | 3% | 19% | 0.14 | Unknown | 0.59 ± 0.16 |
| IRF4 | 6p25.3 | 6% | 37% | 0.21 | Transcription factor | 0.14 ± 0.04 |
| CLIC1 | 6p21.33 | 3% | 31% | 0.29 | Chloride channel | 0.30 ± 0.11 |
| POLR1C* | 6p21.1 | 6% | 32% | 0.40 | RNA Pol I and III subunit | 0.15 ± 0.03 |
| MET | 7q31.2 | 3% | 23% | 0.40 | Receptor tyrosine kinase | 1.09 ± 0.23 |
| ZCCHC7* | 9p13.2 | 2% | 9% | 0.09 | Unknown | 0.72 ± 0.13 |
| MRPL41* | 9q34.3 | 5% | 10% | 0.46 | Mitochondrial ribosomal protein | 0.85 ± 0.19 |
| MRPS2* | “ | “ | 10% | 0.53 | Mitochondrial ribosomal protein | 0.13 ± 0.02 |
| PMPCA* | “ | “ | 10% | 0.50 | Mitochondrial peptidase | 1.23 ± 0.10 |
| RHOD* | 11q13.1 | 5% | 12% | 0.53 | Rho GTPase | 0.76 ± 0.18 |
| CCS* | “ | “ | 12% | 0.33 | Copper chaperone | 0.67 ± 0.061 |
| CCND1 | 11q13.3 | 14% | 20% | 0.65 | Activates CDK4/6 and ER | 0.98 ± 0.33 |
| FGF19 | “ | “ | 20% | 0.68 | Ligand for FGFR4 | 0.53 ± 0.23 |
| CDK4 | 12q14.1 | 3% | 13% | 0.25 | Cell cycle serine kinase | 2.43 ± 0.78 |
| TSPAN31* | “ | “ | 13% | 0.05 | Unknown | 0.71 ± 0.25 |
| HCK | 20q11.21 | 2% | 34% | 0.22 | Src-like tyrosine kinase | 1.70 ± 0.16 |
| POFUT1* | “ | “ | 34% | 0.27 | Glycosyltransferase | 0.78 ± 0.24 |
| PIM2 | Xp11.23 | 3% | 17% | -0.10 | Serine-threonine kinase | 0.96 ± 0.41 |
Properties of the 18 genes (out of 124) that scored positive for tumorigenicity in the oncogenomic cDNA screen. Asterisks by the gene name indicate that the gene has not previously been reported to possess tumor-promoting activity. The chromosomal location was determined using the UCSC Genome Browser website. The focal amplicon frequency represents the percentage of HCC samples that harbored a focal amplicon (< 10 Mb) containing the specified gene. Gain frequency represents the percentage of samples harboring either focal amplification or wider amplification. The Pearson’s correlation coefficient of mRNA expression and DNA copy number was determined as described in the text. Biochemical functions were obtained from literature searching, and the mean tumor volume and standard error was determined using the subcutaneous assay (n = 8) as described in the text. See also Figure S1.