Abstract P1-10-03: Precision therapeutic combinations are synergistic against triple negative breast cancer using compensatory pathways
Authors: Solzak J , Hancock B , Paul R , Radovich M 
Published: February 2018

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. In an effort to treat TNBC, a cancer that has no targeted therapies, many have chosen to experiment with combinations of drugs that are chosen for their genomic expression or “hard targets”. It has been previously noted however, that single agent therapeutics can change the genomic landscape of both mice and human cells and may be responsible for resistance. Here we show that targeting a compensatory pathway after treatment with a single therapy, results in synergistic combinations and can outperform the choice of hard target therapies.
Methods: Eight TNBC cell lines were chosen based on their abundance of clinically actionable targets. The primary hard target combinations were chosen using data from TCGA and a board consisting of oncologists and researchers at Indiana University School of Medicine. Compensatory therapies were found using RNA sequencing data from untreated versus single therapeutic 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 either therapeutics or genomic targets using the Causal network analysis and Upstream regulator functions. All drug combinations were tested in their respective cell lines and cell viability was assessed via Celltiter-Fluor. Synergy of the combinations was calculated using the Chou-Talalay method.
Results: Using genomically chosen hard targets for drug combinations, all eight cell lines displayed additive or antagonistic results except low nanomolar doses for the MDA-MB-231 cell line. Dosing of MDA-MB-231s with Debrafinib and Pazopanib however, turned highly antagonistic as dosing increased. Using next-generation RNA sequencing data of TNBCs, IPA analysis identified several compensatory targets for each cell line when treated with one of the primary genomically driven drug at its IC50. Using dose escalation of the new drugs with a single hard target drug, we found that each compensatory combination displayed a striking increase in synergy across all TNBC cell lines treated when compared to their original hard target combination.
Conclusion: RNA sequencing of TNBC cells lines treated with single therapies chosen by actionable genomic landscape has revealed compensatory pathways, indicating further druggable targets. These compensatory pathways have been observed to more efficacious in treating TNBC cell lines. Using therapeutics that are either FDA approved or in clinical trials we have found that each compensatory combination shows a higher level of synergy across all cell lines. These data show that choosing a secondary therapy based on compensatory pathways may outperform hard target combinations in the clinic.
Citation Format: Solzak J, Hancock B, Paul R, Radovich M. Precision therapeutic combinations are synergistic against triple negative breast cancer using compensatory pathways [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-10-03.