Genotypic analysis of esophageal squamous cell carcinoma by molecular cytogenetics and real-time quantitative polymerase chain reaction

  • Authors:
    • Chueh-Chuan Yen
    • Yann-Jang Chen
    • Kai-Hsi Lu
    • Jiun-Yi Hsia
    • Jung-Ta Chen
    • Cheng-Po Hu
    • Po-Min Chen
    • Jin-Hwang Liu
    • Tzeon-Jye Chiou
    • Wei-Shu Wang
    • Muh-Hwa Yang
    • Ta-Chung Chao
    • Chi-Hung Lin
  • View Affiliations

  • Published online on: October 1, 2003     https://doi.org/10.3892/ijo.23.4.871
  • Pages: 871-881
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Abstract

We performed an integrated cytogenetic study using a combination of comparative genomic hybridization (CGH), spectral karyotyping (SKY) and fluorescence in situ hybridization (FISH) to analyze chromosomal aberrations associated with 8 human esophageal squamous cell carcinoma (EC-SCC) cell lines, and used real-time quantitative PCR (Q-PCR) to study the copy number changes of two candidate genes of chromosome 3q, PIK3CA and TP63, in 20 primary tumors of EC-SCC. The pooled CGH results revealed frequent gain abnormalities on chromosome arms 1p, 1q, 3q, 5p, 6p, 7p, 7q, 8q, 9q, 11q, 12p, 14q, 15q, 16p, 16q, 17q, 18p, 19q, 20q, 22q, and Xq, while frequent losses were found on 3p, 4, 5q, 6q, 7q, 9p, and 18q. SKY detected 195 translocations, 13 deletions and 2 duplications. Among the 374 breakpoints, most clustered at the centromeric regions, such as 8q10, 13q10, 7q10, 9q10, 14q10, 15q10, 16q10, 21q10, and 22q10, but also at other regions, including 3q (3q21, 3q22, 3q25), 7p (7p22, 7p14, 7p12), 7q (7q21, 7q31, 7q32), 8q (8q21.1, 8q23), 11q (11q21, 11q24), 13q (13q14) and 18q (18q21). There was a good correlation between the number of aberrations identified by CGH and SKY (r=0.667; p=0.035). Combined CGH and SKY analyses indicated that chromosomes 3, 7, 9, 11, 14, 16, 18, 19, 20, and 22 harbored higher frequency of chromosomal aberrations than expected. FISH using BAC clones containing oncogene PIK3CA and TP63 found that both genes were amplified in 6 and 5 cell lines, respectively. Q-PCR analysis of primary tumors revealed amplification of PIK3CA and TP63 in 100% and 80% of the cases. Average copy number of PIK3CA per haploid genome was greater than that of TP63 (6.27 vs 2.73), and the difference showed statistical significance (p<0.001). Combination of CGH, SKY and FISH could reveal detailed chromosomal changes associated with esophageal cancer cells, and Q-PCR could assess the change of the candidate genes in clinical samples in a high throughput way.

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October 2003
Volume 23 Issue 4

Print ISSN: 1019-6439
Online ISSN:1791-2423

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Spandidos Publications style
Yen C, Chen Y, Lu K, Hsia J, Chen J, Hu C, Chen P, Liu J, Chiou T, Wang W, Wang W, et al: Genotypic analysis of esophageal squamous cell carcinoma by molecular cytogenetics and real-time quantitative polymerase chain reaction. Int J Oncol 23: 871-881, 2003
APA
Yen, C., Chen, Y., Lu, K., Hsia, J., Chen, J., Hu, C. ... Lin, C. (2003). Genotypic analysis of esophageal squamous cell carcinoma by molecular cytogenetics and real-time quantitative polymerase chain reaction. International Journal of Oncology, 23, 871-881. https://doi.org/10.3892/ijo.23.4.871
MLA
Yen, C., Chen, Y., Lu, K., Hsia, J., Chen, J., Hu, C., Chen, P., Liu, J., Chiou, T., Wang, W., Yang, M., Chao, T., Lin, C."Genotypic analysis of esophageal squamous cell carcinoma by molecular cytogenetics and real-time quantitative polymerase chain reaction". International Journal of Oncology 23.4 (2003): 871-881.
Chicago
Yen, C., Chen, Y., Lu, K., Hsia, J., Chen, J., Hu, C., Chen, P., Liu, J., Chiou, T., Wang, W., Yang, M., Chao, T., Lin, C."Genotypic analysis of esophageal squamous cell carcinoma by molecular cytogenetics and real-time quantitative polymerase chain reaction". International Journal of Oncology 23, no. 4 (2003): 871-881. https://doi.org/10.3892/ijo.23.4.871