High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH

Abstract

Chromosomal regions harboring tumor suppressors and oncogenes are often deleted or amplified. Array comparative genomic hybridization detects segmental DNA copy number alterations in tumor DNA relative to a normal control. The recent development of a bacterial artificial chromosome array, which spans the human genome in a tiling path manner with >32,000 clones, has facilitated whole genome profiling at an unprecedented resolution. Using this technology, we comprehensively describe and compare the genomes of 28 commonly used non-small cell lung carcinoma (NSCLC) cell models, derived from 18 adenocarcinomas (AC), 9 squamous cell carcinomas and 1 large cell carcinoma. Analysis at such resolution not only provided a detailed genomic alteration template for each of these model cell lines, but revealed novel regions of frequent duplication and deletion. Significantly, a detailed analysis of chromosome 7 identified 6 distinct regions of alterations across this chromosome, implicating the presence of multiple novel oncogene loci on this chromosome. As well, a comparison between the squamous and AC cells revealed alterations common to both subtypes, such as the loss of 3p and gain of 5p, in addition to multiple hotspots more frequently associated with only 1 subtype. Interestingly, chromosome 3q, which is known to be amplified in both subtypes, showed 2 distinct regions of alteration, 1 frequently altered in squamous and 1 more frequently altered in AC. In summary, our data demonstrate the unique information generated by high resolution analysis of NSCLC genomes and uncover the presence of genetic alterations prevalent in the different NSCLC subtypes.

Characterizing the cancer genome in lung adenocarcinoma

“…Although the overall pattern is broadly consistent with the literature on lung cancer 8,[13][14][15] , our sample size and resolution provide more power to accurately identify and localize both large-scale and focal chromosomal alterations. With respect to large-scale events, no single previous study has identified more than 5 of the gains or 11 of the losses 13,14 (Supplementary Table 2). With respect to focal events, three recent studies 8,14,15 report a total of ,200 events, including 23 of the 31 recurrent focal events observed in our study.…”

“…With respect to large-scale events, no single previous study has identified more than 5 of the gains or 11 of the losses 13,14 (Supplementary Table 2). With respect to focal events, three recent studies 8,14,15 report a total of ,200 events, including 23 of the 31 recurrent focal events observed in our study. The overlap among these three studies is limited to only four events (amplification of EGFR, CCNE1, MDM2 and 8p11, all seen here; Supplementary Table 3 and Supplementary Results).…”

Differential disruption of cell cycle pathways in small cell and non-small cell lung cancer

“…The minimal common alteration within this amplified area in the SCLC cell lines contains only one gene, MAD1L1 (validated by Coe et al, 2006). Although this is a checkpoint gene involved in growth inhibition, its gain has been reported in other cancers (Jin et al, 1999;Tsukasaki et al, 2001;de Leeuw et al, 2004 amplification in the NSCLC samples as well suggests that this gene may play an essential role in the development of lung cancers (Garnis et al, 2006). It is noteworthy that a subset of the genomic similarities between the SCLC and NSCLC cell lines could be the result of adaptation to culturing conditions.…”

“…These arrays contain 97 299 elements representing 32 433 BAC-derived amplified fragment pools spotted in triplicate on two aldehyde-coated glass slides Watson et al, 2004). Array hybridisation was performed as previously described (Coe et al, 2006;Garnis et al, 2006). Briefly, 200 -400 ng of sample and a common reference male genomic DNA (Novagen, Mississauga, ON, Canada) were separately labelled by random priming in the presence of cyanine-5 dCTP or cyanine-3 dCTP (PerkinElmer, Woodbridge, ON, Canada), respectively.…”

“…The data used to generate the frequency diagrams is present in Supplementary Material. The frequency plots and a detailed description of the recurrent regions of alteration specific to these SCLC and NSCLC cell lines have been reported (Coe et al, 2006;Garnis et al, 2006).…”