Mutations in <i>DZIP1</i> and <i>XYLT1</i> are associated with nonsyndromic early onset high myopia in the Korean population

Mutations in <i>DZIP1</i> and <i>XYLT1</i> are associated with nonsyndromic early onset high myopia in the Korean populatio

Frequent Amplification of CENPF, GMNN and CDK13 Genes in Hepatocellular Carcinomas

<div><p>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 <em>CENPF</em> (centromere protein F/mitosin), <em>GMNN</em> (geminin, DNA replication inhibitor), <em>CDK13</em> (cyclin-dependent kinase 13), and <em>FAM82B</em> (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 <em>CENPF</em>, <em>GMNN</em>, and <em>CDK13</em> were highly oncogenic whereas <em>FAM82B</em> was not. Interestingly, the oncogenic activity of these genes (excluding <em>FAM82B</em>) was highly correlated with gene-copy numbers in tumor samples (correlation coefficient, r>0.423), indicating that amplifications of <em>CENPF</em>, <em>GMNN</em>, and <em>CDK13</em> genes are tightly linked and coincident in tumors. Furthermore, we confirmed that <em>CDK13</em> gene copy number was significantly associated with clinical onset age in patients with HCC (<em>P = </em>0.0037). Taken together, our results suggest that coincidently amplified <em>CDK13</em>, <em>GMNN</em>, and <em>CENPF</em> genes can play a role as common cancer-driver genes in human cancers.</p> </div

Detection of four amplified genes with high mRNA expression common to both liver and colon cancer.

<p>Among 35 amplified genes in HCC, 8 genes were initially selected as HCC-specifically amplified and overexpressed genes and then four genes (<i>CENPF</i>, <i>GMNN</i>, <i>CDK13</i>, and <i>FAM82B</i>) were ultimately selected as amplified and overexpressed cancer genes common to both liver and colon cancer.</p

Detection of amplifed genes common to both liver and colon cancer.

<p>Identification of overlapping amplified and overexpressed genes in liver (n = 8 genes) and colon cancer (n = 76 genes) pinpointed <i>CENPF</i>, <i>GMNN</i>, <i>CDK13</i>, and <i>FAM82</i> as candidate cancer genes.</p

Screening of gene amplification in primary tumor tissues and a panel of human cancer cell lines.

<p>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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043223#s4" target="_blank">Materials and Methods</a>. 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).</p

Oncogenic effects of <i>CENPF</i>, <i>GMNN</i> and <i>CDK13</i> after stable transfection in NIH3T3 cells.

<p>Clonogenic assays and invasion assays were performed using stably transfected NIH3T3 cells with <i>CENPF</i>, <i>GMNN</i>, <i>CDK13</i> or <i>FAM82B</i> 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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043223#s4" target="_blank">Materials and Methods</a>. Data representing means and standard deviations of triplicate experiments are shown for (C) clonogenic assays and (D) invasion assays as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043223#s4" target="_blank">Materials and Methods</a> (*<i>P<</i>0.05, **<i>P</i><0.01 versus control group; t-test).</p

Selection of eight amplified genes with high mRNA expression from among 35 genomically amplified genes in primary HCC tissues.

<p>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.</p

Association of <i>CDK13</i> gene amplification with clinical onset of cancer in HCC patients.

<p>Mean age of clinical onset is indicated by horizontal bars. The statistical significance of differences was determined by ANOVA.</p