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A comparative study of genome-wide SNP, CGH microarray and protein expression analysis to explore genotypic and phenotypic mechanisms of acquired antiestrogen resistance in breast cancer

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Abstract

Allelic imbalance is a common feature of many malignancies. We have measured allelic imbalance in genomic DNA from the breast cancer cell lines T47D, MDA-MB-231, two antiestrogen sensitive (MCF7N and MCF7L) and two resistant MCF7 cell lines (MMU2 and LCC9) using single nucleotide polymorphism (SNP) oligonucleotide microarrays. DNA from MCF7L and MMU2 cells was also analysed by comparative genome hybridisation (CGH) to compare with SNP microarray data. Proteins previously determined to be involved in disease progression were quantified by Western blot and compared to array data. The SNP and CGH array both detected cytogenetic abnormalities commonly found in breast cancer: amplification of chromosomes 11q13–14.1, 17q and 20q containing cyclin D1, BCAS1 and 3 (Breast Cancer Amplified Sequence) and AIB1 (Amplified in Breast cancer) genes; losses at 6q, 9p and X chromosomes, which included ERα (Estrogen Receptor alpha) and p16 INK4A genes. However the SNP chip array data additionally identified regions of loss of heterozygosity (LOH) followed by duplication of the remaining allele-uniparental disomy (UPD). Good concordance between SNP arrays and CGH analyses was observed, however there was poor correlation between gene copy number and protein levels between the cell lines. There were reductions in ERα, cyclin D1 and p27 protein levels whilst p21 protein levels were elevated in antiestrogen resistant MCF7 cell lines. Although protein levels varied there was no difference in gene copy number. This study shows SNP and CGH array analysis are powerful tools for analysis of allelic imbalance in breast cancer. However, the antiestrogen resistant phenotype was likely to be due to changes in gene expression and protein degradation rather than in altered gene copy number.

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Acknowledgements

Special thanks to Lynne Minto for isolating DNA and Drs Caroline Witton and John Bartlett for facilitating the CGH. We gratefully acknowledge Dr Robert Clarke (Georgetown University) for the gift of LCC9 cells. We are also grateful for financial support for this work from the following sources: The Breast Cancer Campaign, Yorkshire Cancer Research, Cancer Research UK and the Leukaemia Research Fund.

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Authors and Affiliations

  1. Northern Institute for Cancer Research, Paul O’ Gorman Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK

    Neil Johnson, Nicola J. Curtin & Andrew G. Hall

  2. Leeds Institute for Molecular Medicine, University of Leeds, Leeds, UK

    Valerie Speirs

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  1. Neil Johnson
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  2. Valerie Speirs
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  3. Nicola J. Curtin
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  4. Andrew G. Hall
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Correspondence to Nicola J. Curtin.

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Johnson, N., Speirs, V., Curtin, N.J. et al. A comparative study of genome-wide SNP, CGH microarray and protein expression analysis to explore genotypic and phenotypic mechanisms of acquired antiestrogen resistance in breast cancer. Breast Cancer Res Treat 111, 55–63 (2008). https://doi.org/10.1007/s10549-007-9758-6

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  • DOI: https://doi.org/10.1007/s10549-007-9758-6

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