Gene Expression Signatures of PI3K Signaling Are Associated with Low ER Levels and the Luminal B Subtype in Breast Cancer Cell Lines and Human Tumors, and in Patients Predicts Poor Outcome.
Authors: C. Creighton, X. Fu, X. Fu, S. Hilsenbeck, S. Hilsenbeck, C. Osborne, C. Osborne, B. Hennessy, G. Mills, A. Lee, A. Lee, R. Schiff, R. Schiff
Journal: Cancer Research (2009)

Abstract Background: Accumulating evidence suggests that both levels and activity of ER and progesterone receptor (PR) are dramatically influenced by growth factor receptor (GFR) signaling pathways, and that this crosstalk is a major determinant of both breast cancer (BC) progression and response to therapy. The phosphatidylinositol 3-kinase (PI3K) pathway, a key mediator of GFR signaling, is one of the most altered pathways in BC. We thus examined whether deregulated PI3K signaling in luminal ER+ breast tumors is associated with ER level and activity, molecular subtype, and outcome.Materials and Methods: To directly test for an association between ER levels and PI3K activation in BC, we defined a PI3K transcriptional signature as the set of genes either induced or repressed by PI3K inhibitors in the public Connectivity Map (CMap) expression profile dataset (www.broad.mit.edu/cmap). Using this signature, we assigned a PI3K activation score to each ER+ human breast tumor from two independent expression profile datasets (van de Vijver et al., n=226; Loi et al., n=348). Furthermore, within a broad panel of luminal BC cell lines, we compared the gene signature-based CMap PI3K score with a proteomic (Reversed Phase Proteomic Array, RPPA)-based PI3K score (which relied on protein measurement for PI3K signaling intermediates). We also compared the CMap-derived PI3K activation scores with scores based on a signature of PTEN loss in human breast tumors (Saal et al.), and on a signature of Akt activation in a transgenic mouse model (Majumder et al.).Results: Within ER+ tumors, ER mRNA level was negatively associated with the CMap PI3K activation score (van de Vijver: Pearson's rs=-0.32, p&amp;lt;1E-06; Loi: rs=-0.18, p&amp;lt;0.002). PI3K activation scores based on CMap, Saal, or Majumder gene signatures were highly correlated with each other (van de Vijver rs=0.65-0.71). When scoring for luminal B versus luminal A molecular subtypes, CMap PI3K scores were associated with the more aggressive luminal B subtype (van de Vijver rs=0.75, p&amp;lt;1E-40). High PI3K activation scores were associated with poorer outcome in ER+ tumors treated or untreated with tamoxifen (tamoxifen treated: Loi p=0.02, n=263; van de Vijver p=0.05, n=34, log-rank statistic). Analysis of 18 previously identified luminal BC cell lines showed a significant association between PI3K activation at the genomic and proteomic levels (rs=0.47, p&amp;lt;0.02) and, as in the clinical tumors, there was a strong and significant association between PI3K activation and the luminal B subtype.Discussion: Our data suggest that luminal B tumors have hyperactive GFR/PI3K signaling associated with lower ER levels, which has been correlated with resistance to endocrine therapy. Targeting PI3K in these tumors might reverse loss of ER expression and signaling and restore hormonal sensitivity. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 31.