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. 2012;7(8):e43223.
doi: 10.1371/journal.pone.0043223. Epub 2012 Aug 13.

Frequent amplification of CENPF, GMNN and CDK13 genes in hepatocellular carcinomas

Hye-Eun Kim  1 , Dae-Ghon Kim, Kyung Jin Lee, Jang Geun Son, Min-Young Song, Young-Mi Park, Jae-Jung Kim, Sung-Won Cho, Sung-Gil Chi, Hyun Sub Cheong, Hyoung Doo Shin, Sang-Wook Lee, Jong-Keuk Lee
Affiliations

Frequent amplification of CENPF, GMNN and CDK13 genes in hepatocellular carcinomas

Hye-Eun Kim et al. PLoS One. 2012.

Abstract

Genomic changes frequently occur in cancer cells during tumorigenesis from normal cells. Using the Illumina Human NS-12 single-nucleotide polymorphism (SNP) chip to screen for gene copy number changes in primary hepatocellular carcinomas (HCCs), we initially detected amplification of 35 genes from four genomic regions (1q21-41, 6p21.2-24.1, 7p13 and 8q13-23). By integrated screening of these genes for both DNA copy number and gene expression in HCC and colorectal cancer, we selected CENPF (centromere protein F/mitosin), GMNN (geminin, DNA replication inhibitor), CDK13 (cyclin-dependent kinase 13), and FAM82B (family with sequence similarity 82, member B) as common cancer genes. Each gene exhibited an amplification frequency of ~30% (range, 20-50%) in primary HCC (n = 57) and colorectal cancer (n = 12), as well as in a panel of human cancer cell lines (n = 70). Clonogenic and invasion assays of NIH3T3 cells transfected with each of the four amplified genes showed that CENPF, GMNN, and CDK13 were highly oncogenic whereas FAM82B was not. Interestingly, the oncogenic activity of these genes (excluding FAM82B) was highly correlated with gene-copy numbers in tumor samples (correlation coefficient, r>0.423), indicating that amplifications of CENPF, GMNN, and CDK13 genes are tightly linked and coincident in tumors. Furthermore, we confirmed that CDK13 gene copy number was significantly associated with clinical onset age in patients with HCC (P = 0.0037). Taken together, our results suggest that coincidently amplified CDK13, GMNN, and CENPF genes can play a role as common cancer-driver genes in human cancers.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. SNP-based detection of gene amplification in 12 paired primary HCC tissues using a Human NS-12K SNP chip.
Gene amplification was detected based on genotype intensities that were more than 1.5-fold higher in tumor samples (shown in red dots) than in normal samples (shown in blue dots) in each genotype group (X-axis), with manual confirmation of intensity and the images of genotype cluster plots (A). A total of 90 normal genome samples isolated from the blood of healthy individuals were used as controls (shown in gray dots) for comparison. The samples showing gene amplification were marked with green circle in the genotype cluster images. The numbers shown inside genotype cluster plots indicate the numbers of genotype for specific SNP. Y-axis and X-axis indicate the signal intensity and genotype group, respectively. Using the Human NS-12K SNP chip, a total of 35 genomically amplified genes were initially identified in primary HCC samples (B). A detailed gene list is presented in Table S1.
Figure 2
Figure 2. Selection of eight amplified genes with high mRNA expression from among 35 genomically amplified genes in primary HCC tissues.
Human NS-12K SNP chip genotyping experiments was performed using cDNA templates derived from two hepatoma cell lines. Each dot indicates a single DNA sample; samples tested: 12 normal tissue gDNAs (blue), 12 tumor tissue gDNAs (red), two HCC cell line gDNAs (black), and two HCC cell line cDNAs (green). The numbers shown inside genotype cluster plots indicate the numbers of genotype for specific SNP. In addition, high mRNA expression (shown in green dots) was detected with high signal intensity in the genotype cluster plots. Y-axis and X-axis indicate the signal intensity and genotype group, respectively.
Figure 3
Figure 3. Detection of amplifed genes common to both liver and colon cancer.
Identification of overlapping amplified and overexpressed genes in liver (n = 8 genes) and colon cancer (n = 76 genes) pinpointed CENPF, GMNN, CDK13, and FAM82 as candidate cancer genes.
Figure 4
Figure 4. Detection of four amplified genes with high mRNA expression common to both liver and colon cancer.
Among 35 amplified genes in HCC, 8 genes were initially selected as HCC-specifically amplified and overexpressed genes and then four genes (CENPF, GMNN, CDK13, and FAM82B) were ultimately selected as amplified and overexpressed cancer genes common to both liver and colon cancer.
Figure 5
Figure 5. Screening of gene amplification in primary tumor tissues and a panel of human cancer cell lines.
The number of gene copies in primary liver tumor tissues (n = 57) and colon tumor tissues (n = 12) was examined using the TaqMan Copy Number Assay System, as described in Materials and Methods. All paired nontumor tissues had a normal number of gene copies (2 copies) in both HCC and colorectal cancer patients. However, a various numbers of gene copies, especially gene amplification, were detected in the primary liver tumor tissues (A) and colon tumor tissues (B). In addition, copy numbers were also examined in a panel of human cancer cell lines (n = 70) (C).
Figure 6
Figure 6. Correlation of gene copy number between four amplified genes in primary HCC tissues and various cancer cell lines.
Pearson Correlation coefficients and P-values were determined as described in the Materials and Methods. Above the diagonal indicates primary HCC tissues (n = 57 primary tumor tissues) and below the diagonal indicates various cancer cell lines (n = 70 cancer cell lines from nine different cancer types).
Figure 7
Figure 7. Oncogenic effects of CENPF, GMNN and CDK13 after stable transfection in NIH3T3 cells.
Clonogenic assays and invasion assays were performed using stably transfected NIH3T3 cells with CENPF, GMNN, CDK13 or FAM82B gene. The images of clonogenic assays (A) and migration assays (B) in a representative experiment were taken at day 14 and 24 h after treatment, respectively, as described in Materials and Methods. Data representing means and standard deviations of triplicate experiments are shown for (C) clonogenic assays and (D) invasion assays as described in Materials and Methods (*P<0.05, **P<0.01 versus control group; t-test).
Figure 8
Figure 8. Association of CDK13 gene amplification with clinical onset of cancer in HCC patients.
Mean age of clinical onset is indicated by horizontal bars. The statistical significance of differences was determined by ANOVA.
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References

    1. Albertson DG, Collins C, McCormick F, Gray JW (2003) Chromosomal aberrations in solid tumors. Nature Genet 34: 369–376. - PubMed
    1. Stratton MR, Campbell PJ, Futreal PA (2009) The cancer genome. Nature 458: 719–724. - PMC - PubMed
    1. Medina PP, Castillo SD, Blanco S, Sanz-Garcia M, Largo C, et al. (2009) The SRY-HMG box gene, SOX4, is a target of gene amplification at chromosome 6p in lung cancer. Hum Mol Genet 18: 1343–1352. - PubMed
    1. Liu W, Chang B, Sauvageot J, Dimitrov L, Gielzak M, et al. (2006) Comprehensive assessment of DNA copy number alterations in human prostate cancers using Affymetrix 100K SNP mapping array. Genes Chromosomes Cancer 45: 1018–1032. - PubMed
    1. Santarius T, Shipley J, Brewer D, Stratton MR, Cooper CS (2010) A census of amplified and overexpressed human cancer genes. Nature Rev Cancer 10: 59–64. - PubMed

MeSH terms

Grants and funding

This work was supported by a grant (#0720200) from the National R&D Program for Cancer Control, Ministry of Health & Welfare, Republic of Korea, and a grant (No. 2010-419) from the Asan Institute for Life Sciences, Seoul, Korea. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.