Original articleGenome signatures of colon carcinoma cell lines
Introduction
Tumor cell lines are an important resource in the role of understanding cancer initiation and progression. For most studies using cancer cell lines, information regarding their genomes is relevant, sometimes indispensable, to understand the biological events behind carcinogenesis. This is because they have chromosomal changes with potential effect at the molecular level, such as altered gene expression and regulation. Thus, it is surprising that many cell lines are left undefined with regard to their genomic profile, either by conventional karyotyping or fluorescence in situ hybridization (FISH)-based screening techniques. The combined use of karyotyping and molecular cytogenetic techniques is even more unusual, despite of the fact that the complexity of genomic rearrangements often requires such an approach to be able to describe it accurately.
Although the introduction of banding techniques [1] enabled the identification of chromosomes and chromosomal rearrangements, some marker chromosomes remain unidentified in complex karyotypes. Two main FISH-based screening techniques are now used to complement conventional karyotyping. The first technique, comparative genomic hybridization (CGH), gives an average genomic profile of copy number gains and losses for all chromosomes in a single experiment, but it is unable to provide information on balanced chromosomal rearrangements [2]. The second methodology, based on simultaneous painting of all chromosomes, of which spectral karyotyping (SKY) [3] and multicolor fluorescence in situ hybridization (M-FISH) [4] are the most commonly used variants, is ideal for detecting interchromosomal rearrangements, but somewhat less effective for intrachromosomal changes.
The genetic aberrations in primary colorectal carcinomas are, as in many other human cancers, numerous and non-random [5], [6]. The majority of primary colorectal carcinomas develops through the chromosome instability cell line (CIN) pathway and is characterized by aneuploidy with the presence of many numerical and structural cytogenetic abnormalities. About 15% show near-diploid indices but exhibit genome-wide instability at the nucleotide level. This is caused by a defect in the mismatch repair system that gives rise to the microsatellite instability (MSI) phenotype [7], [8], [9], [10], which is also characteristic of 90% of tumors from patients with the hereditary non polyposis colon cancer syndrome (HNPCC) [11], [12].
Here, we describe the genomic profiles of 20 colon cancer cell lines (11 with microsatellite stable (MSS) and 9 with MSI phenotype), combining the results obtained by 3 screening techniques. Some of the cell lines have not previously been cytogenetically described, and others are completely described for the first time in this study. The large differences in the genomic profiles among cell lines from the same tumor type demonstrate the importance of this knowledge when using cell lines as experimental tools. In addition, we add data from previous publications of CGH for colon cancer cell lines since the initial publication of this method [2]. For the commonly used colon cancer cell lines within our dataset, we also compare previously published karyotypes and identify the “core aberrations” for each cell line.
Section snippets
Materials and methods
Twenty different colon cancer cell lines, and 2 variants from 3 of them were included in this study. Information regarding their origin, TP53 mutation, and MSI statuses is presented in Table 1 and in Gayet et al. [13]. Nine cell lines are known to exhibit MSI and 2 of these had a TP53 mutation. None of the MSI cell lines showed loss of heterozygosity at chromosome arm 17p. The remaining 11 cell lines were MSS and 10 of these had both a TP53 point mutation and loss of heterozygosity (LOH) of 17p
Results
Various genetic characteristics of the 20 colon cancer cell lines analyzed in the present study are summarized in Table 1. The copy number changes and karyotypes of each cell line are presented in Table 2.
Combination of genome screening methods
The combination of conventional G-banding, CGH, and M-FISH used in this study proved effective for characterizing the tumor genomic profiles. We took advantage of the particular strengths of each technique to obtain a detailed picture of the chromosomal changes that characterize this panel of 20 colon cancer cell lines. Whereas CGH only detects net gains and losses of chromosomes, we were able to identify structural aberrations such as translocations by G-banding and M-FISH analysis. For
Conclusions
Here, we present a genetic study of 20 cell lines and a review of relevant data from other sources. We emphasize the importance of using complementary genome screening techniques and show that the combination of CGH, G-banding, and M-FISH is an effective way to characterize the genomic profiles of tumor cell lines. We provide a combined reference for some of the most commonly used colon cancer cell lines. In addition, copy number profiles are presented for the first time for most of the cell
Acknowledgments
Thanks to Nicholas M. Luscombe at the Department of Molecular Biophysics and Biochemistry at Yale University for critically reading the manuscript. K.K. is a research fellow funded by a grant from the Norwegian Cancer Society A95068 (RAL).
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