Abstract 2029: Precision therapeutic combinations are synergistic against triple negative breast cancer using compensatory pathways
Authors: Solzak Jeffrey P. , Hancock Brad , Paul Robin , Kiel Patrick , Skaar Todd , Schneider Bryan , Radovich Milan 
Published: July 2017

Abstract
Introduction: Triple negative breast cancer (TNBC) accounts for 15% of all breast cancer cases in the United States, and despite its lower incidence, contributes to a disproportionately higher rate of morbidity and mortality compared to other breast cancer subtypes. No FDA-approved targeted therapies are currently available. It has been hypothesized that drug combinations could potentially be chosen based on a tumor harboring two or more druggable genomic mutations. However, previously published data has noted that single agent treatment can change the genomic landscape and may be responsible for the lack of synergy of dual genomic drug targeting. Herein we show that targeting a compensatory pathway after treatment with a genomically-directed agent, results in synergistic combinations and can outperform choosing two drugs a priori based on genomic mutations.
Methods: Nine TNBC cell lines were chosen based on the presence of two or more clinically actionable genomics targets. Drug combinations based on targeting two genomic mutations were chosen using DNA-seq data from CCLE and a board consisting of oncologists and researchers. Compensatory therapies were found using RNA-seq data from untreated versus single-agent treated TNBC cell lines. The merged transcript RPKMs were transformed and analyzed for differential expression. Statistically significant genes were imported into Ingenuity Pathway Analysis (IPA) to identify therapeutics based on compensatory targets using the Causal Network Analysis and Upstream Regulator functions. Cell viability was assessed via Celltiter-Fluor. Synergy of the combinations was calculated using the Chou-Talalay method.
Results: Using two-drug combinations based on genomic mutations alone in all nine cell lines resulted only in additive or antagonistic responses. However, using RNA-seq data of each cell line treated with one genomically-directed agent, IPA analysis identified several compensatory targets that were upregulated or activated. Treating each cell line in combination with one genomically-directed agent plus one compensatory agent resulted in a striking increase in synergy. To understand why targeting compensatory pathways was superior to targeting two genomic mutations, we re-evaluated the RNA-seq data. This analysis revealed that treatment with the first genomically-directed agent, in many cases, resulted in down-regulation or inactivation of the second genomic-target. This may explain the lack of synergy when targeting cells with two drugs based only on genomic mutations.
Conclusion: Targeting TNBC cell lines based on drug combinations informed by compensatory pathways results in significant synergy and is superior to choosing drug combinations based on genomic alterations alone.
Citation Format: Jeffrey P. Solzak, Brad Hancock, Robin Paul, Patrick Kiel, Todd Skaar, Bryan Schneider, Milan Radovich. Precision therapeutic combinations are synergistic against triple negative breast cancer using compensatory pathways [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2029. doi:10.1158/1538-7445.AM2017-2029