Abstract 944: Development of predictive and pharmacodynamic biomarker strategies for GDC-0425, a checkpoint kinase 1 inhibitor, in combination with gemcitabine
Authors: Mahrus Sami , DuPree Kelly , Kowanetz Kaska , Tan Jenille , Tremayne Jarrod , Jakubiak Diana , Haverty Peter , Zhu Yuda , Peale Franklin , Blackwood Elizabeth , Bourgon Richard , Yauch Robert , Lackner Mark , Evangelista Marie 
Published: August 2015

Abstract
GDC-0425 is a potent and selective small molecule inhibitor of checkpoint kinase 1 (Chk1) recently evaluated in the DPM4957g phase I study in combination with the nucleoside analog gemcitabine. The cytotoxic effect of gemcitabine, elicited through the induction of genotoxic stress, is limited by Chk1 activation, which leads to cell cycle arrest and allows time for repair of damaged DNA. Chk1 inhibition by GDC-0425 can convert a genotoxic insult into a cytotoxic event by overriding cell cycle arrest and thereby driving cancer cells into mitotic catastrophe.
A panel of nearly 200 cancer cell lines was screened to evaluate potential benefit of combining GDC-0425 and gemcitabine. Elastic net modeling was applied to cell line data including exome-seq, RNA-seq, DNA copy number, and loss of heterozygosity to perform a broad and unbiased search for predictors of drug activity and synergy. In the model for GDC-0425 and gemcitabine synergy, TP53 mutations were found to be the highest-ranking features, followed by mRNA expression of SLFN11, a gene encoding a putative helicase implicated in sensitizing cells to DNA-damaging agents. Expression levels of several p53-regulated transcripts were also found to be high-ranking features in this model, underscoring the value of p53 pathway functionality as a predictor of synergy between GDC-0425 and gemcitabine.
In consideration of pharmacodynamic (PD) biomarkers, phosphorylated CDK2 (pCDK2) and phosphorylated H2AX (pH2AX), located at proximal and distal points in the Chk1 pathway, respectively, were found to be modulated by GDC-0425 and gemcitabine in cell line and xenograft models in a dose-dependent fashion. The GDC-0425 dose response for these biomarkers correlated with anti-tumor activity.
Finally, to understand why GDC-0425 and gemcitabine synergy is more pronounced in some TP53 mutant cell lines than in others, a screen was performed to evaluate engagement of the Chk1 and p53 pathways in response to gemcitabine in a representative panel of cell lines. Chk1 activation was evaluated using pCDK2, whereas p53 activation was evaluated using expression of known p53 transcriptional targets. Higher synergy was generally observed when gemcitabine activated Chk1 and not p53, regardless of TP53 mutational status.
These studies provide a foundation for predictive and PD biomarker strategies to support the evaluation of GDC-0425 with gemcitabine in early stage clinical trials that are based on markers of p53 pathway functionality and Chk1 pathway modulation.
Citation Format: Sami Mahrus, Kelly DuPree, Kaska Kowanetz, Jenille Tan, Jarrod Tremayne, Diana Jakubiak, Peter Haverty, Yuda Zhu, Franklin Peale, Elizabeth Blackwood, Richard Bourgon, Robert Yauch, Mark Lackner, Marie Evangelista. Development of predictive and pharmacodynamic biomarker strategies for GDC-0425, a checkpoint kinase 1 inhibitor, in combination with gemcitabine. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 944. doi:10.1158/1538-7445.AM2015-944