Abstract PD3-04: PAK-1 amplified breast cancer cell lines are preferentially sensitive to PAK inhibition with G-5555

The small GTP-binding proteins Rac1 and Cdc42 stimulate activity of the serine/threonine kinase p21-activated kinase-1 (PAK-1) to drive growth factor signaling networks and Ras-driven tumorigenesis. Genomic amplification and over-expression of PAK1 are prevalent in luminal breast cancer and correlate with poor clinical outcome. Here we use a novel and selective small molecule inhibitor, G-5555, of the group I PAKs (PAK1, 2, and 3) to evaluate the importance of PAK1 in promoting growth of PAK1 amplified breast cancer cells. Cell lines with amplification of PAK1 were found to be more sensitive to PAK1 inhibition than non-amplified cell lines. Additionally, reverse phase protein array (RPPA) was used to assess the effects of PAK1 inhibition on a wide range of signaling pathways in both amplified and non-amplified cell lines. Reduced levels of phosphorylation of MEK S298 was observed in all cell lines exposed to G-5555 irrespective of amplification status, consistent with PAK1 inhibition in these cell lines. However, modulation of this downstream PAK1 substrate did not correlate with inhibition of cell proliferation or induction of cell death. Cell lines that showed inhibition of proliferation in response to G-5555 also showed enhanced levels of cell death along with apoptosis. Moreover, G-5555 reduced tumor growth in the PAK1 amplified MDA-MB-175 xenograft tumor model. Finally, we compared the in vitro activity of G-5555 with palbociclib, a recently approved inhibitor of the cyclin-dependent kinases CDK4 and CDK6, in PAK1 amplified luminal breast cancer cell lines. Our data supports PAK1 as an attractive target in PAK1 amplified cells and tumors and suggests that inhibiting PAK1 rather than CDK4/6 in this context may be a more attractive therapeutic strategy.

Citation Format: Ong CC, Blackwood E, Jakubiak D, Daemen A, Ramaswamy S, Heise C, Schmidt M, Sanders L, Wilson TR, Huw L, Ndubaku C, Rudolph J, Hoeflich KP, Friedman L, O'Brien T. PAK-1 amplified breast cancer cell lines are preferentially sensitive to PAK inhibition with G-5555. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr PD3-04.

Abstract P6-05-09: Development of a predictive biomarker gene expression signature for the PIK3CA inhibitor, GDC-0032, in breast cancer cells

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.

Abstract P6-05-12: Comprehensive molecular analysis of estrogen receptor positive breast cancer to determine clinically actionable alterations

Introduction.

Understanding the genetic landscape of estrogen receptor positive breast caner is critical for defining clinically actionable alleles that may be targeted using next generation biologics. PIK3CA mutations have previously been reported to be the most common mutation within estrogen receptor positive breast cancer, however the overlap and mutual exclusivity with other key driving alleles is poorly understood, especially how these biomarkers change following treatment failure. We custom designed a mutation, copy number variation and RNA expression panels to profile biomarkers from low quality formalin fixed paraffin embedded extracted material. Data relating to key pathways, such as PI3K and immune modulatory pathways, and overlap with other biomarkers will be presented.

Methods.

Formalin fixed paraffin embedded material was available from 195 primary cases and 95 paired metastatic estrogen receptor positive breast cancer patients. Samples were assayed for the expression of PTEN by IHC, hotspot mutations in 11 oncogenic driving genes using Q-PCR based technology, copy number alterations in 42 genes using Q-PCR based technology and RNA expression using a custom designed 400 breast cancer specific NanoString gene panel.

Results.

PTEN loss, as defined by H-score of 0, was found in 4.5% of primary samples and in 4.3% of metastatic samples. PIK3CA mutations were found in 43% of primary samples and in 38% of metastatic samples and were largely found to be mutually exclusive with PTEN loss. AKT1 mutations were found in 5.4% of primary samples and in 4.1% of metastatic samples. Less frequent mutations in KRAS (7.0%) and BRAF (1.7%) were found in the primary sample, and some were co-existing with PIK3CA mutations. Copy number gains were found in CCND1 (23.5%), ZNF703 (19.5%), FGFR1 (16.8%) and PAK1 (11.4%) and were largely concordant with the paired metastatic sample. Analysis with clinical outcome is ongoing.

Conclusions.

PIK3CA was the most frequently altered gene detected and was mutually exclusive with other key driving mutations within the PI3K pathway (AKT1 and PTEN). A strong concordance was observed between genetic alterations found in the primary sample and the paired metastatic sample. Mutations and expression gains within clinically actionable targets were found less frequently, but may provide alternative treatment strategies for these patients following failure of endocrine therapy.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-05-12.