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  • Oncogenomics
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Gene expression profiling of breast cell lines identifies potential new basal markers

Oncogene volume 25, pages 2273–2284 (2006)Cite this article

Abstract

A better molecular characterization of breast cell lines (BCL) may help discover new markers to apply to tumour samples. We performed gene and protein expression profiling of 31 BCL using whole-genome DNA microarrays and immunohistochemistry (IHC) on ‘cell microarrays’ (CMA), respectively. Global hierarchical clustering discriminated two groups of BCL: group I corresponded to luminal cell lines, group II to basal and mesenchymal cell lines. Correlations with centroids calculated from a published ‘intrinsic 500-gene set’ assigned 15 cell lines as luminal, eight as basal and four as mesenchymal. A set of 1.233 genes was differentially expressed between basal and luminal samples. Mesenchymal and basal subtypes were rather similar and discriminated by only 227 genes. The expression of 10 proteins (CAV1, CD44, EGFR, MET, ETS1, GATA3, luminal cytokeratin CK19, basal cytokeratin CK5/6, CD10, and ERM protein moesin) encoded by luminal vs basal discriminator genes confirmed the subtype classification and the validity of the identified markers. Our BCL basal/luminal signature correctly re-classified the published series of tumour samples that originally served to identify the molecular subtypes, suggesting that the identified markers should be useful for tumour classification and might represent promising targets for disease management.

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Acknowledgements

We are grateful to F Birg, D Maraninchi, C Mawas, A Puisieux and P Viens for discussions and encouragements. This work has been supported by Inserm, Institut Paoli-Calmettes, and grants from Ligue Nationale Contre le Cancer (Label) and Ministries of Health and Research (Cancéropôle PACA).

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Author notes

  1. E Charafe-Jauffret and C Ginestier: These authors contributed equally to this work.

Authors and Affiliations

  1. Marseille Cancer Institute, Laboratory of Molecular Oncology, Inserm/Institut Paoli-Calmettes, Marseille, France

    E Charafe-Jauffret, C Ginestier, F Monville, P Finetti, J Adélaïde, N Cervera, S Fekairi, J Jacquemier, D Birnbaum & F Bertucci

  2. Department of BioPathology, Institut Paoli-Calmettes, Marseille, France

    E Charafe-Jauffret, L Xerri & J Jacquemier

  3. Université de la Méditerranée, UFR de Médecine, Marseille, France

    E Charafe-Jauffret, L Xerri & F Bertucci

  4. Department of Medical Oncology, Marseille Cancer Institute, UMR599 Inserm/Institut Paoli-Calmettes, Marseille, France

    F Bertucci

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  1. E Charafe-Jauffret
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Correspondence to D Birnbaum.

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Supplementary Information accompanies the paper on Oncogene website (http://www.nature.com/onc)

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Charafe-Jauffret, E., Ginestier, C., Monville, F. et al. Gene expression profiling of breast cell lines identifies potential new basal markers. Oncogene 25, 2273–2284 (2006). https://doi.org/10.1038/sj.onc.1209254

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