Correlation of PIK3CA mutation-associated gene expression signature (PIK3CA-GS) with deactivation of the PI3K pathway and with prognosis within the luminal-B ER+ breast cancers

Loi S, Haibe-Kains B, Lallemand F, Pusztai L, Bardelli A, Gillett C, Ellis P, Piccart-Gebhart MJ, Phillips WA, McArthur GA and Sotiriou C


Background: The phosphathidylinositol-3-kinase (PI3K) signaling pathway is frequently deregulated in tumor biology and is an attractive target for cancer therapy. Our aim was to characterize the molecular and clinical outcome effects of PIK3CA mutations in breast cancer (BC).

Methods: We analyzed 173 BC samples for PIK3CA mutations. Corresponding gene expression profiles were used to understand its effects on the PI3K pathway. We validated a PIK3CA-GS in 2 independent BC cohorts (n = 183) with known PIK3CA mutation status and evaluated its correlation with clinical outcome in 1748 BC samples stratified by treatment and subtype.

Results: 26% of BCs had a PIK3CA mutation. Tumors with PIK3CA mutation demonstrated a distinct gene expression signature (p = 0.03 after 1000 perm). In 2 datasets it could discriminate PIK3CA mutation carriers from wild-type (ROC 0.68, 0.71, p = 0.001for both). However, the PIK3CA-GS was correlated with deactivation of the PI3K pathway probably through a negative feedback loop. This observation was supported by: 1) the PIK3CA-GS was significantly correlated with gene expression changes induced by PI3K inhibitors (Connectivity Map, Gene set enrichment analyses) and 2) the PIK3CA-GS was anti-correlated with a GS of PTEN loss (R = -0.3; Saal et al, 2007). Higher levels of the PIK3CA signature were observed in HER-2+ and estrogen receptor positive (ER+), luminal BC subtypes. Whilst there was no association with mutation status alone and prognosis, increasing expression of the PIK3CA-GS (suggesting deactivation) was significantly associated with better clinical outcome in both untreated (p = 0.04) and particularly ER+, luminal-B, tamoxifen only-treated (p = 0.004) BC. Multivariate analysis (HR: 0.4; 95%CI: 0.3–0.7; p = 0.002) confirmed that the PI3KCA-GS provided independent prognostic information.

Conclusions: Paradoxically, the PIK3CA-GS correlates with inhibition of the PI3K pathway in ER+ BC and identifies a subgroup of luminal B BCs with a favorable outcome. The PIK3CA-GS may be a better indicator of PI3K pathway dysfunction than mutation status, potentially indicating patients who may benefit from combined endocrine therapy and PI3K inhibition.