Comprehensive copy number profiles of breast cancer cell model genomes - PubMed (original) (raw)

Comprehensive copy number profiles of breast cancer cell model genomes

Ashleen Shadeo et al. Breast Cancer Res. 2006.

Abstract

Introduction: Breast cancer is the most commonly diagnosed cancer in women worldwide and consequently has been extensively investigated in terms of histopathology, immunochemistry and familial history. Advances in genome-wide approaches have contributed to molecular classification with respect to genomic changes and their subsequent effects on gene expression. Cell lines have provided a renewable resource that is readily used as model systems for breast cancer cell biology. A thorough characterization of their genomes to identify regions of segmental DNA loss (potential tumor-suppressor-containing loci) and gain (potential oncogenic loci) would greatly facilitate the interpretation of biological data derived from such cells. In this study we characterized the genomes of seven of the most commonly used breast cancer model cell lines at unprecedented resolution using a newly developed whole-genome tiling path genomic DNA array.

Methods: Breast cancer model cell lines MCF-7, BT-474, MDA-MB-231, T47D, SK-BR-3, UACC-893 and ZR-75-30 were investigated for genomic alterations with the submegabase-resolution tiling array (SMRT) array comparative genomic hybridization (CGH) platform. SMRT array CGH provides tiling coverage of the human genome permitting break-point detection at about 80 kilobases resolution. Two novel discrete alterations identified by array CGH were verified by fluorescence in situ hybridization.

Results: Whole-genome tiling path array CGH analysis identified novel high-level alterations and fine-mapped previously reported regions yielding candidate genes. In brief, 75 high-level gains and 48 losses were observed and their respective boundaries were documented. Complex alterations involving multiple levels of change were observed on chromosome arms 1p, 8q, 9p, 11q, 15q, 17q and 20q. Furthermore, alignment of whole-genome profiles enabled simultaneous assessment of copy number status of multiple components of the same biological pathway. Investigation of about 60 loci containing genes associated with the epidermal growth factor family (epidermal growth factor receptor, HER2, HER3 and HER4) revealed that all seven cell lines harbor copy number changes to multiple genes in these pathways.

Conclusion: The intrinsic genetic differences between these cell lines will influence their biologic and pharmacologic response as an experimental model. Knowledge of segmental changes in these genomes deduced from our study will facilitate the interpretation of biological data derived from such cells.

PubMed Disclaimer

Figures

Figure 1

Figure 1

Comprehensive submegabase-resolution tiling set (SMRT) array comparative genomic hybridization profile of cell line UACC-893. Whole-genome SeeGH karyogram UACC-893. Individual data points denote log2 ratios plotted to corresponding chromosomal location. Log2 ± 0.5 scale bars are included for reference. Displacement of data points to the right and left of the centre line represents gain and loss, respectively. The inset shows a magnified view of complex alteration on chromosome 17q.

Figure 2

Figure 2

Magnified submegabase-resolution tiling set (SMRT) array comparative genomic hybridization profile of the 1p21.1-p11.1 region in MCF-7. Scale bars labelled ± 1 denote log2 ratio scale. Blue highlighted regions indicate the locations of independent amplicons.

Figure 3

Figure 3

Fluorescence in situ hybridization (FISH) analysis in SK-BR-3 and BT-474 cells. (a) SK-BR-3 interphase FISH. Clone RP11-118L18, labeled in spectrum green, is located within a 680 kb amplicon at 3q25.1; clone RP11-419H08, labeled in spectrum red, denotes an unchanged site at 3q11.2. (b) BT-474 interphase FISH. Clone RP11-813P03, labeled in spectrum red, is located at the peak of a 940 kb amplicon at 1q32.1; clone RP11-790I13, labeled in spectrum green, is located within an adjacent unchanged region.

Figure 4

Figure 4

17q SMRT aCGH profile of five cell lines sharing multiple minimum altered regions. Scale bars labelled ± 1 denote log2 ratio scale. Blue highlighted regions indicate the locations of MARs.

Similar articles

Cited by

References

    1. Parkin DM, Bray F, Ferlay J, Pisani P. Global cancer statistics, 2002. CA Cancer J Clin. 2005;55:74–108. - PubMed
    1. Bray F, McCarron P, Parkin DM. The changing global patterns of female breast cancer incidence and mortality. Breast Cancer Res. 2004;6:229–239. doi: 10.1186/bcr932. - DOI - PMC - PubMed
    1. Simpson PT, Reis-Filho JS, Gale T, Lakhani SR. Molecular evolution of breast cancer. J Pathol. 2005;205:248–254. doi: 10.1002/path.1691. - DOI - PubMed
    1. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell. 2000;100:57–70. doi: 10.1016/S0092-8674(00)81683-9. - DOI - PubMed
    1. Garnis C, Buys TP, Lam WL. Genetic alteration and gene expression modulation during cancer progression. Mol Cancer. 2004;3:9. doi: 10.1186/1476-4598-3-9. - DOI - PMC - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources