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Chromosomal Alterations in Hepatocellular Carcinoma Cell Lines Detected by Comparative Genomic Hybridization
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Sang Jin Park, Mahn Joon Ha, Hugh Chul Kim, Hyon Ju Kim
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Cancer Res Treat. 2002;34(3):175-185. Published online June 30, 2002
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DOI: https://doi.org/10.4143/crt.2002.34.3.175
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 Abstract
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- PURPOSE
There have only been a few cytogenetic studies of hepatocellular carcinoma (HCC), and so far, no consistent specific chromosomal abnormalities have been described.
Here, we have used comparative genomic hybridization (CGH), a powerful molecular cytogenetic technique for detecting changes of the copy number throughout the genome, to screen for genetic alterations in HCC cell lines. The CGH results were compared with those derived from G-banding and chromosome painting.
MATERIALS AND METGODS: Conventional cytogenetic analyses were performed on five HCC cell lines, SNU-354, SNU-368, SNU-387, SNU-449 and SNU-475, using a G- banding staining technique. In CGH, equal amounts of differently labeled DNA from the cell lines, and normal reference DNA, were hybridized simultaneously to normal metaphase chromosomes.
They were visualized by different fluorochromes, and the signal intensities quantified separately as gray levels along the single chromosomes. The over- and under-represented DNA segments were determined by computation of ratio images and average ratio profiles. To confirm the CGH results, florescence in situ hybridization (FISH), with chromosome specific painting, was performed using indirectly labeled chromosome specific paints.
RESULTS
Complex unbalanced chromosomal aberrations, which could not be identified reliably by conventional cytogenetics in HCC cell lines, were successfully resolved by CGH analysis. CGH results were validated using FISH with chromosome specific probes. In HCC cell lines, gains in DNA copy number were more common than losses. The most prominent changes were gains of 1q12- qter (80% of cases), 1q41-qter (100%), 7 (80%), 8q12-qter (60%), 8q23-qter (80%) and 20q12-qter (60%). Recurrent losses were mapped on 4q13-qter (60%), 16q12-qter (60%), 16q21-qter (80%), 13q12-q14.2 (60%) and Yq11.2 (100%). All four male HCC cell lines showed loss or rearrangement of the Y chromosome.
CONCLUSION
Conventional cytogenetics, CGH and FISH using painting probes, represent complementary approaches that, when employed in combination, could greatly facilitate the comprehensive analysis of chromosomal imbalances in HCC cell lines. Our results suggest the existence of an oncogene, or protooncogenes, on chromosome 1q41-qter, and the tumor suppressor genes on Yq11.2, that play a role in the development and/or progression of hepatocellular carcinogenesis.
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Determination of Chromosomal Alterations in Nasal NK/T-cell Lymphomas by DOP-PCR and Comparative Genomic Hybridization
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Sang Jin Park, Mahn Joon Ha, Hyon Ju Kim, Kwang Hwa Park, Hyun Soo Kim, Woo Ik Yang, Hugh Chul Kim
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J Korean Cancer Assoc. 2000;32(3):578-586.
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Abstract
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- PURPOSE
Because of difficulty of obtaining metaphase cells from tumor specimens, there are only a few cytogenetic studies in nasal NK/T-cell lymphomas, and so far no consistent specific chromosomal abnormalities have been described. In this study, we have used degenerate oligonucleotide primed PCR (DOP-PCR) and comparative genomic hybridization (CGH) to deter mine chromosomal alterations from 6 nasal NK/T-cell lymphoma tissues dissected from formalin- fixed paraffin-embedded slide sections.
MATERIALS AND METHODS
For the isolation of tumor DNA, four 7-micrometer-thick tissue sections from each sample were dewaxed and rehydrated, and areas of high tumor cell content (more than 60%) were dissected and pooled into a tube. Normal DNA was prepared from the peripheral blood of a healthy volunteer. Tumor DNA was labeled with biotin-16-dUTP by DOP-PCR and normal DNA was labeled with digoxigenin-dUTP using a nick translation kit. In CGH, equal amounts of differently labeled DNA from the tumors and normal reference DNA were hybridized simul taneously to normal metaphase chromosomes. They were visualized by different fluordegrees Chromes, and the signal intensities were quantitated separately as gray levels for each chromosome. The over- and underrepresented DNA segments were determined by computation of image ratios and average ratio profiles.
RESULTS
Our results show that gains of DNA copy number were more prevalence than DNA losses. The most commonly observed gains were mapped to chromosomal regions of 1p32.2 ter,19 and 20 in 4 of 6 cases (67%). The other frequent gains were found on chromosomes 12q in 3 of 6 cases. The most frequent loss was detected on 6q in 4 of 6 cases(67%), and less fre quently observed on 13q21.1 q34 and 13q14 q34.
CONCLUSION
These genomic changes found in specific chromosomal regions are likely to harbor genes of importance in nasal NK/T-cell lymphomagenesis, therefore such cytogenetic mapping of genomic imbalance may be of value for further molecular delineation of NK/T-cell lymphoma.
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Chromosomal Alterations in Gastric Cancer Cell Lines Detected by Comparative Genomic Hybridization
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Mahn Joon Ha, Sang Jin Park, Hyun Woong Kang, Hyon Ju Kim, Hugh Chul Kim
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J Korean Cancer Assoc. 1999;31(2):219-229.
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Abstract
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- PURPOSE
There are only a few cytogenetic studies in gastric cancer and so far no consistent specific chromosomal abnormalities have been described. In this study, we have used comparative genomic hybridization (CGH), a powerful molecular cytogenetic technique for detecting changes of the copy number throughout the genome, to screen for genetic alterations in gastric cancer cell lines. The CGH results were compared with those derived from G-banding and chromosome painting.
MATERIALS AND METHODS
Conventional cytogenetic analysis was performed on five human gastric cancer cell lines, AGS, SNU-1, SNU-16, SNU-620, and SNU-719, by a G-banding staining technique. In CGH, equal amounts of differently labeled DNA from the cell lines and normal reference DNA were hybridized simultaneously to normal metaphase chromosomes. They were visualized by different fluorochromes, and the signal intensities were quantitated separately as gray levels along the single chromosomes. The over- and under- represented DNA segments were determined by computation of ratio images and average ratio profiles. To confirm the CGH results, fluorescence in situ hybridization (FISH) with chromosome specific painting was performed using indirectly labeled chromosome specific paints.
RESULTS
Complex unbalanced chromosomal aberrations that could not be identified reliably by conventional cytogenetics in gastric cancer cell lines were successfully resolved by CGH analysis. CGH results were validated by using FISH with chromosome specific probes. In gastric cancer cell lines, gains of DNA copy number were more common than losses. Gains were detected on 1p, 1q, 2p, 3q, 6p, 7q, 10q, 11p, and 19q, and losses were observed on 4p, 4q, 5q, 12p, 12q, and 18q. Interestingly, all the five gastric cancer cell lines tested showed gain of DNA copy number on the chromosome 20, suggesting an existence of oncogene.
CONCLUSION
Conventional cytogenetics, CGH, and FISH using painting probes represent complementary approaches that, when employed in combination, could greatly facilitate the comprehensive analysis of chromosomal imbalances in gastric cancer cell lines. Our results suggest the existence of an oncogene or oncogenes on chromosome 20 that play a role in the development and/or the progression of gastric carcinogenesis.
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KCA
