Rapamycin-regulated gene expression signature determines prognosis in breast cancer.

Abstract

Abstract Abstract #3072 Background: Mammalian target of rapamycin (mTOR) is a serine/threonine kinase involved in multiple intracellular signaling pathways promoting tumor growth. mTOR is aberrantly activated in a significant portion of breast cancers and is a promising target for treatment. Rapamycin and its analogues are in clinical trials for breast cancer treatment. Patterns of gene expression (metagenes) may also be used to simulate a biologic process or effects of a drug treatment. In this study, we tested the hypothesis that the gene-expression signature regulated by rapamycin could predict disease outcome for patients with breast cancer.
 Methods: MDA-MB-468 breast cancer cell line is triple negative and PTEN null. Sensitivity of MDA-MB-468 breast cancer cell line to rapamycin was determined by in vitro growth assays and in vivo tumor studies. Total RNA was extracted from cell lines treated with rapamycin or DMSO for 24 hours and xenografts treated with DMSO or rapamycin for 1 or 22 days. Total RNA was used for expression profiling and hybridized to Affymetrix HG-U133 Plus 2.0 arrays. We used two well-described primary breast cancer datasets of 251 (Miller et al, Proc. Natl. Acad. Sci. USA 2005;102:13550) and 286 (Wang et al, Lancet. 2005;365:671) patients from the public domain and assessed the prognostic capability of rapamycin-regulated gene expression signatures.
 Results: Colony formation and sulforhodazine B (IC50 < 1 nM) assays, and xenograft animals showed that MDA-MB-468 cells were sensitive to treatment with rapamycin. The comparison of in vitro and in vivo gene expression data identified a 31-gene expression signature that was up- regulated by rapamycin treatment in vitro as well as in vivo (FDR of 0.1). From the 31 genes on HG-U133 Plus 2.0 array, 20 that were included on HG-U133A array were used for analysis. In the Miller dataset, rapamycin metagene index (RMI) did not correlate with tumor size or lymph node status. High (0.75 percentile) RMI was significantly associated with longer survival (P=0.015). On multivariate analysis, RMI (P=0.029), tumor size (P=0.015) and lymph node status (P=0.001) were prognostic. In the Wang dataset, RMI predicted time to disease relapse (P=0.009).
 Conclusion: Rapamycin-regulated gene expression signature predicts clinical outcome in breast cancer. This supports the central role of mTOR signaling in breast cancer biology and provides further impetus to pursue mTOR-targeted therapies for breast cancer treatment. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 3072.