Abstract P6-05-09: Development of a predictive biomarker gene expression signature for the PIK3CA inhibitor, GDC-0032, in breast cancer cells
Authors: Savage H , O'Brien C , Spoerke J , Huw L , Wallin J , Friedman L , Lackner MR , Wilson TR 
Published: August 2014

Abstract
Introduction
The PI3-Kinase pathway is one of the most commonly mutated pathways in cancer and plays a major role in cell proliferation and survival. Mutations in PIK3CA, the gene encoding the p110 subunit of PI3K, are among the most common alterations in breast cancer, occurring in approximately 45% of luminal A, 30% of luminal B, 30% of HER2 positive and 8% of triple negative breast cancers. Additional pathway activating alterations include loss of PTEN, AKT mutations and overexpression of PIK3CA and HER2. Development of a pharmacodynamic biomarker is challenging with the more isoform specific PI3K inhibitors as multiple upstream pathways can funnel into common downstream immunohistochemical evaluable endpoints. In addition, phosphorylated epitopes are often labile and do not always lend themselves to immunohistochemical evaluation in the clinical setting. GDC-0032, which is currently under clinical investigation, is a class I PI3K inhibitor with 30-fold less inhibition on PI3K beta relative to PI3K alpha, and the development of a predictive and on-study pharmacodynamic signature may prove informative as compared to traditional IHC endpoints.
Methods
We screened a panel of 53 breast cancer cell lines, incorporating all subtypes, to GDC-0032 using the cell proliferation assay cell titer glo. To determine if there was a relationship between pathway activation and sensitivity to GDC-0032, we correlated response to PIK3CA mutations, loss of PTEN and HER2 overexpression. Using RNA sequencing, we compared the baseline gene expression between the sensitive and refractory cell lines. Next, to identify an on-study pharmacodynamic gene expression signature, we treated both sensitive and refractory cell lines with GDC-0032 and ran an in-house custom designed 800 gene NanoString breast cancer gene set that incorporated published PI3K pathway signatures, intrinsic subtyping genes and immunological related genes. Finally, the GDC-0032 signature was applied to a set of 160 FFPE breast cancer samples and overlaid with relevant biomarkers.
Results and Conclusions
Sensitivity to GDC-0032 correlated strongly with PI3K pathway activation including PIK3CA mutations and HER2 overexpression in breast cancer cells. Comparing baseline whole genome RNA expression of GDC-0032 sensitive and refractory cell lines, we identified 293 genes that were differentially expressed. Applying a more stringent statistical cutoff (greater than 2 fold difference and t-test less than 0.01) refined the gene list to 51 genes, which defined the baseline GDC-0032 sensitivity signature. Applying the 800 gene breast cancer NanoString panel to a set of 160 FFPE breast cancer samples, the GDC-0032 sensitivity signature correlated with luminal status and was enriched in PIK3CA mutant tumors. In conclusion, our in-house designed GDC-0032 sensitivity signature correlated strongly with PIK3CA mutations in clinical specimens. However the lack of complete correlation may identify tumors that have an activated PI3K pathway outside of PIK3CA mutations and/or HER2 amplification that may derive clinical benefit from GDC-0032.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-05-09.