High resolution analysis of genomic aberrations by metaphase and array comparative genomic hybridization identifies candidate tumour genes in lung cancer cell lines
Introduction
Lung cancer is a common malignancy that develops through different carcinogenic pathways in non-smokers and smokers but the genetic targets involved are incompletely understood. Tumours result from clonal expansion of cells carrying a variety of genomic aberrations. The identification of recurrent chromosomal gains or losses is a useful approach to detect loci harbouring oncogenes and tumour suppressor genes (TSG). These aberrations have been conventionally detected by cytogenetics and, more recently, by molecular approaches such as metaphase comparative genomic hybridization (CGH) and array CGH. In this study, we have characterized the genomic aberrations of three locally established lung adenocarcinoma (AD) cell lines from patients with different smoking history by metaphase and array CGH. Candidate tumour loci were then validated by fluorescence in situ hybridization. By consideration of the functional roles of genes contained within these loci, candidate tumour genes were selected and their expression levels in the AD cell lines and 27 independent resected primary lung AD were evaluated by real-time quantitative PCR.
Section snippets
Cancer cell lines
Three cancer cell lines were established from patients with primary lung AD after obtaining institutional review board approval and informed consent. Chemotherapy or radiotherapy had not been given prior to obtaining the cells for culture. HKULC1 was established from the malignant pericardial effusion fluid of a 63-year-old female non-smoker with stage IIIB disease; HKULC2 and HKULC3 were from the pleural fluids of a 65-year-old male smoker with stage IV disease, and a 38-year-old woman with
Genomic aberrations by metaphase CGH
Results of metaphase CGH analysis of the three cell lines are shown in the ideogram in Fig. 1. A common DNA loss that involved all three cell lines was observed at 18q22-qter. Recurrent changes involving two cell lines were observed for gain of whole chromosome 7, 17q arm, segments of 8q, and loss of entire arms of 8p and 17p. The two cell lines from non-smokers showed fewer changes with longer segments of chromosomal gains or losses, involving eight chromosomes in HKULC3 and three in HKULC1.
Discussion
Cancers develop through cumulative genomic mutations and rearrangements. A number of tumour-related genes have been identified by their location within regions of DNA alterations and corresponding deregulated expression [3], [4]. In this study, regions of genomic imbalances in lung cancer cell lines were identified by metaphase and array CGH, followed by expression analysis of selected candidate tumour genes from the aberrant sites by qRT-PCR. Three cell lines derived from adenocarcinomas of
Acknowledgements
We would like to thank Fanny Lai-Fun Fung for her expert technical support. This study was supported by grants from the Research Grants Council of the Hong Kong Special Administrative Region (HKU7310/01M, 7486/03M, 7468/04).
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