Original article
Genome signatures of colon carcinoma cell lines

https://doi.org/10.1016/j.cancergencyto.2004.03.014Get rights and content

Abstract

In cancer biology, cell lines are often used instead of primary tumors because of their widespread availability and close reflection of the in vivo state. Cancer is a genetic disease, commonly caused by small- and large-scale DNA rearrangements. Therefore, it is essential to know the genomic profiles of tumor cell lines to enable their correct and efficient use as experimental tools. Here, we present a comprehensive study of the genomic profiles of 20 colon cancer cell lines combining conventional karyotyping (G-banding), comparative genomic hybridization (CGH), and multicolor fluorescence in situ hybridization (M-FISH). Major differences between the microsatellite instability (MSI) and chromosome instability (CIN) cell lines are shown; the CIN cell lines exhibited complex karyotypes involving many chromosomes (mean: 8.5 copy number changes), whereas the MSI cell lines showed considerably fewer aberrations (mean: 2.6). The 3 techniques complement each other to provide a detailed picture of the numerical and structural chromosomal changes that characterize cancer cells. Therefore, 7 of the cell lines (Colo320, EB, Fri, IS2, IS3, SW480, and V9P) are here completely karyotyped for the first time and, among these, 5 have not previously been cytogenetically described. By hierarchical cluster analysis, we show that the cell lines are representative models for primary carcinomas at the genome level. We also present the genomic profiles of an experimental model for tumor progression, including 3 cell lines (IS1, IS2, and IS3) established from a primary carcinoma, its corresponding liver- and peritoneal metastasis from the same patient. To address the question of clonality, we compared the genome of 3 common cell lines grown in 2 laboratories. Finally, we compared all our results with previously published CGH data and karyotypes of colorectal cell lines. In conclusion, the large variation in genetic complexity of the cell lines highlights the importance of a comprehensive reference of genomic profiles for investigators engaged in functional studies using these research tools.

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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