Increase In DNA Copy Number Research Articles

Retention of polysomy at 9p23-24 during karyotypic evolution in human breast cancer cell line COLO 824

Somatic genetic alterations of 9p have been seen in a wide range of human cancers, including breast cancer. Loss of heterozygosity analysis of primary breast cancer tumors has revealed a high frequency of deletion of DNA from 9p21-22 encompassing the MTSI (P16/CDKN2A) gene. We report the approximately tenfold increase in copy number of DNA from 9p23-24, which is far distal to P16/CDKN2A in female breast cancer cell line COLO 824, as revealed by fluorescence in situ hybridization, comparative genomic hybridization, and microsatellite analysis. Amplification of DNA has been reported previously to encompass multiple sites of the genome of the breast cancer cell, but increase in DNA copy number has not been seen in distal 9p.

Presence of High-Level DNA Copy Number Gains in Gastric Carcinoma and Severely Dysplastic Adenomas but Not in Moderately Dysplastic Adenomas

Our aim was to investigate the presence of DNA copy number changes in gastric adenomas and to identify the changes that may play a role in gastric carcinogenesis. DNA copy number changes in 16 patients with gastric adenoma and in 22 tumors from patients with intestinal type gastric carcinomas were studied by using comparative genomic hybridization. DNA copy number changes were found in 44% of the adenoma cases and in 86% of the intestinal type gastric carcinomas. On average, gains were more common than losses (0.9 vs. 0.5 in adenomas and 4.1 vs. 1.8 in carcinomas). In adenomas, the most common gains involved chromosome 8 in 3 cases, and gain of chromosome 7 and 20q was detected in 2 cases. The most frequent losses were observed at 5q (three times). Only adenomas with severe dysplasia showed high-level amplifications that were detected at chromosome 13, 17cen–q22, and 20q12–ter. In gastric cancer, the most common gains were detected at 20q (55%), 17q12–q21 (41%), and 8q (41%), and the most common losses were detected at 18q (41%) and 4q (32%). High-level amplifications were observed at 20q (3 tumors), 17cen–q21 (3 tumors), 2p (1 tumor), and 18q (1 tumor). These findings suggest that the progression of dysplasia is associated with higher levels of DNA copy number increase (e.g., the gains at 17q and 20q), which were typically observed in the intestinal type gastric cancer. Furthermore, the results support the hypothesis that adenoma precedes cancer.

Preferential oxidation of cardiac mitochondrial DNA following acute intoxication with doxorubicin

The purpose of this investigation was to determine whether acute doxorubicin intoxication causes a preferential accumulation of 8-hydroxydeoxyguanosine (8OHdG) adducts to mitochondrial DNA (mtDNA) as opposed to nuclear DNA (nDNA), particularly in cardiac tissue. Adult male rats received a single i.p. bolus of doxorubicin (15 mg/kg) and were killed 1–14 days later. Acute intoxication with doxorubicin caused a 2-fold greater increase in 8OHdG adducts to mtDNA compared to nDNA, the concentration of adducts to both nDNA and mtDNA being 20%–40% greater for heart as opposed to liver. For both tissues, the relative abundance of adducts was highest at the earliest time-point examined (24 h) and decreased to control values by 2 weeks. The temporal dilution of 8OHdG adducts was not the result of cell hyperplasia and was only partially due to amplification of the mitochondrial genome, most probably via an increase in DNA copy number rather than a stimulation of mitochondrial biogenesis.

Identification of novel regions of altered DNA copy number in small cell lung tumors

Identification of the genetic alterations that occur in tumors is an important approach to understanding tumorigenesis. We have used comparative genomic hybridization (CGH), a novel molecular cytogenetic method, to identify the gross DNA copy number changes that commonly occur in small cell lung cancer (SCLC). We analyzed ten SCLC tumors (seven primary tumors and three metastases) from eight patients. We found frequent increases in DNA copy number on chromosome arms 5p, 8q, 3q, and Xq and frequent decreases in copy number on chromosome arms 3p, 17p, 5q, 8p, 13q, and 4p. The increase in copy number at 8q24 (MYC) and decreases at 17p13 (TP53), 13q14 (RB), and 3p have previously been identified in SCLC with other methods. Many of the other regions in which we detected common copy number changes have not been reported to be regions of common alteration in SCLC tumors. Comparison of copy number changes between a primary tumor and a metastasis from the same patient showed that they were more closely related to each other than to any of the other tumors. The results of direct CGH analysis of SCLC tumors reported here confirm the existence of copy number changes that we identified previously by using cell lines.

Differential oncogene amplification in tumor cells from a patient treated with cisplatin and 5-fluorouracil

Peritoneal cells were derived from a patient (PK) with adenocarcinoma of the colon during the course of cisplatin/ 5-fluorouracil ( 5-FUra) treatment. Resistance to cisplatin and 5-FUra, characterized by a lack of response to chemotherapy and continued growth of the tumor, was concomitantly associated with a 2–4-fold increase in DNA copy number for dTMP synthase and dihydrofolate reductase. There was a corresponding amplification in DNA copy number of the c- myc ( 2×), H-ras ( 4×), and c- fos ( 15×) oncogenes. Cytogenetic studies revealed an iso ( 13q) chromosome, but failed to show any double minutes or homogeneously staining regions. In addition, drug-resistant tumor cells from PK and another patient (HG) displayed enhanced expression of dTMP synthase, c- fos and DNA polymerase β when compared to normal colon tissue and the HCT 8 human colon carcinoma cell line. These results suggest that elevated oncogene DNA and gene expression may be involved in the development of cisplatin resistance.

Plastid Transcription Activity and DNA Copy Number Increase Early in Barley Chloroplast Development

Plastid transcription activity and DNA copy number were quantified during chloroplast development in the first foliage leaf in dark-grown and illuminated barley (Hordeum vulgare L.) seedlings. Primary foliage leaves of seedlings given continuous illumination from 2 days post-imbibition reached a final mean length of 15 centimeters at 6.5 days, whereas primary leaves of dark-grown seedlings required 7 days to reach a similar length. Dividing cells were observed in the basal 0.5 to 1 centimeter of primary leaves until 5.5 days post-imbibition. Plastids isolated from cells located in the basal meristem of 4-day-old seedlings were small ( approximately 2 micrometers in diameter), exhibited low transcription activity and contained approximately 130 copies of plastid DNA per organelle. Cell size increased from 18 to 60 micrometers in a 1 to 3 centimeter region located adjacent to the leaf basal meristem. In this region, transcriptional activity per plastid increased 10-fold and DNA copy number increased from 130 to 210. Plastid transcriptional activity declined rapidly in illuminated plants with increasing leaf cell age and plastid DNA copy number also declined but with a slower time course. In dark-grown seedlings, plastid transcriptional activity declined more slowly than in illuminated plants while DNA copy number remained constant with increasing cell age. These data show that plastid transcriptional activity and DNA copy number increase early in chloroplast development and that transcriptional activity per DNA template varies up to 5-fold during barley leaf biogenesis.