Comprehensive copy number profiles of breast cancer cell model genomes

Breast cancer is the most prevalent cancer worldwide and is the second leading cause of cancer-related deaths in women in North America [1, 2]. It is a complex disease in which multiple genetic factors can combine to drive pathogenesis [3‐5]. Changes in copy numbers of genes such as ERBB2 and c-MYC have been extensively documented in breast cancer and are present in model cell lines [6‐9]. Amplified (and overexpressed) genes are prime therapeutic targets as for example, the use of the drug trastuzumab against ERBB2 has been shown to improve breast cancer survival rates alone or in combination with other treatments [10‐12].

Strategies to detect gene copy number alterations will facilitate the identification of novel molecular targets. Previous studies with 10-megabase (Mb) resolution conventional metaphase comparative genomic hybridization (CGH) have identified gross regions of recurrent chromosomal aberrations in multiple breast cancer cell lines including loci within chromosomes 1q, 8q, 11q13, 17q and 20q13. Many of these alterations proved to be relevant because they were also present in primary tumors investigated [13‐15]. Recent advances in array CGH have greatly improved the resolution of this technology, enabling the detection of segmental copy losses and gains [16, 17]. Regional genomic arrays, providing contiguous or tiling coverage of a locus of interest, have been constructed for the fine mapping of commonly altered regions in breast cancer (such as 20q13) [18‐20]. Whole chromosome arrays have been used to provide information at 500 kb intervals. For example, a chromosome 17 array was used to identify 13 regions of change present in breast cancer cell line models and primary breast cancers [21]. Similarly, a genome-wide array containing nearly 2,500 bacterial artificial chromosome (BAC) clones with a resolution at about 1.4 Mb was used to illustrate the detection of copy number alterations (CNAs) in various breast cancer cell lines [22]. Recently, a separate study using an array of 422 genomic loci detected frequent alterations at 1, 6, 7p, 9, 11q, 12q, 17, 20q and 22q in archival breast cancer specimens [23]. cDNA arrays have also detected DNA copy changes of amplicons containing ERRB2 on 17q [24‐27]. More recently, a cDNA array containing 6,691 mapped human genes was used to explore the relationship between copy number alteration and gene expression changes in breast tumors and cell lines [28]. While large-insert clone megabase-interval CGH arrays and cDNA arrays provide a robust platform for the rapid survey of tumor genomes, valuable information could be overlooked as a result of their limited resolution. It is clear that a more detailed description of breast tumor genomes would require re-examination with a higher-resolution array platform.

Genetic, biochemical and pharmacologic studies of breast cancer have been greatly dependent on several commonly used model breast cancer cell lines: MCF-7, BT-474, SK-BR-3, T-47D, UACC-893, MDA-MB-231 and ZR-75-30. That is, a summation of studies involving at least one of these seven cell lines produces over 13,500 hits on Medline. These cells are known to harbor gross chromosomal aberrations; measuring the precise segmental copy number status across their entire genome may uncover novel discrete changes. In the current study we expanded the use of array CGH to survey the genomes of these breast cancer cells at unprecedented detail with a recently developed whole-genome tiling path array that covered the genome with 32,433 overlapping BAC clones [29]. Analysis at this resolution has led to the identification of novel features in these genomes and to the delineation of segmental genetic alterations that have escaped detection by conventional molecular cytogenetic techniques and previous marker-based or interval array CGH analysis.

We examined the genomes of seven commonly used breast cancer cell models in unprecedented detail for segmental copy number status, cataloging the boundaries of gains and losses throughout these genomes. In addition, we demonstrated that copy number alteration of multiple genetic loci involved in the EGF family of pathways is common in these cell lines, which suggests that disruption of this frequently dysregulated pathway in breast cancer may occur at several points in the signaling cascade and that several disruptions may occur in combination.

Furthermore, because these cell lines serve as models for studying the molecular biology of breast cancer, it is essential to take into account the potential influence of genetic alterations when interpreting biological data. For example, using these lines to study the EGF family of pathways, multiple endogenous genetic alterations may have a role in biochemical and biological observations. Our work provides a comprehensive list of high-level segmental gains and losses for each genome, providing a database of copy number alterations as a resource for breast cancer research with these cell lines.