1. ¹Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
2. ²National Centre of Competence in Research (NCCR) Molecular Oncology, Swiss Institute for Experimental Cancer Research (ISREC), Epalinges, Switzerland
3. ³Hôpitaux Universitaires de Genève, Geneva, Switzerland
4. ⁴for the Swiss Group for Clinical Cancer Research (SAKK), Bern, Switzerland
5. ⁵European Organisation for Research and Treatment of Cancer (EORTC), Brussels, Belgium
6. ⁶Centre René Huguenin, St-Cloud, France
7. ⁷Centre René Gauducheau, Nantes, France
8. ⁸Institut Jules Bordet, Brussels, Belgium
9. ⁹Institut Bergonié, Bordeaux, France
10. ¹⁰for the Swedish Breast Cancer Group (SweBCG), Karolinska Institute, Stockholm, Sweden
11. ¹¹for the Anglo-Celtic Cooperative Oncology Group (ACCOG), Edinburgh University, Edinburgh, UK
12. ¹²Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland

Correspondence: R Iggo, E-mail: richard.iggo@isrec.ch

Received 29 September 2004; Revised 7 January 2005; Accepted 27 January 2005; Published online 9 May 2005.

Abstract

Previous microarray studies on breast cancer identified multiple tumour classes, of which the most prominent, named luminal and basal, differ in expression of the oestrogen receptor gene (ER). We report here the identification of a group of breast tumours with increased androgen signalling and a 'molecular apocrine' gene expression profile. Tumour samples from 49 patients with large operable or locally advanced breast cancers were tested on Affymetrix U133A gene expression microarrays. Principal components analysis and hierarchical clustering split the tumours into three groups: basal, luminal and a group we call molecular apocrine. All of the molecular apocrine tumours have strong apocrine features on histological examination (P=0.0002). The molecular apocrine group is androgen receptor (AR) positive and contains all of the ER-negative tumours outside the basal group. Kolmogorov–Smirnov testing indicates that oestrogen signalling is most active in the luminal group, and androgen signalling is most active in the molecular apocrine group. ERBB2 amplification is commoner in the molecular apocrine than the other groups. Genes that best split the three groups were identified by Wilcoxon test. Correlation of the average expression profile of these genes in our data with the expression profile of individual tumours in four published breast cancer studies suggest that molecular apocrine tumours represent 8–14% of tumours in these studies. Our data show that it is possible with microarray data to divide mammary tumour cells into three groups based on steroid receptor activity: luminal (ER+ AR+), basal (ER- AR-) and molecular apocrine (ER- AR+).