Abstract B21: Enhanced understanding of drug responses and drug-drug interactions in triple negative breast cancer cells with a multiplexed cell viability and cell death readout
Authors: Gautam Prson , Karhinen Leena , Szwajda Agnieszka , Jha Sawan Kumar , Yadav Bhagwan , Aittokallio Tero , Wennerberg Krister 
Published: May 2016

Triple negative breast cancers (TNBC) are a heterogeneous group of cancers that remain a considerable clinical challenge with no known effective targeted therapy, limiting the therapies to cytotoxic chemotherapy, radiation and surgery. Molecular sub-classifications of TNBC have been established but none of these define therapy. With an aim to establish potential novel stratified therapeutic strategies to target TNBC, we applied the Drug Sensitivity and Resistance Testing (DSRT) (Pemovska et al., Cancer Discov. 2013) chemo-sensitivity profiling approach in which the responses of cells to 304 approved and investigational oncology drugs were explored. We studied a diverse panel of 15 TNBC cell lines in an attempt to functionally classify the TNBCs. To go beyond standard growth inhibition drug sensitivity testing we utilized a multiplexed cell viability and cytotoxicity readout allowing us to differentiate between cytostatic and cytotoxic drug responses.

Evaluating both types of drug responses, several discoveries were made: First, the multiplexed viability and cytotoxicity readout identified several drug classes that previously had been assumed to have cytotoxic effects based on their strong effects on cell viability but in fact only showed cytostatic effects in most cells. Drug classes exhibiting this type of response included anti-mitotics, mTOR, CDK, metabolic inhibitors, as well as many targeted agents selectively inhibiting oncogenically activated pathways in individual cell lines. Second, within the responses to these broad cytostatic-acting classes of drugs, there were subsets of the cell lines that responded by cell death, suggesting that these cell lines may represent the TNBC subtypes that might best respond to the drugs in the clinic. To explore this further, we tested whether the cytostatic vs. cytotoxic responses could be linked to expression of protein biomarkers using a published TNBC cell line reverse-phase protein array data set (Daemen et al, Genome Biol. 2013). This led to the identification of potential predictive biomarkers such as PAI-1, MAPK phosphatase and Notch-3 levels linking to toxic responses to mitotic and proteasome inhibitors, suggesting that these could be explored as predictors for clinical responses for the drugs. Third, drug response based clustering of cell lines was very distinctive to transcriptomics based TNBC subgroups and recurrent mutation patterns, highlighting the considerable challenges in converting genetic and transcriptomic data to therapeutic responses. Fourth, the cytotoxicity readout highlighted effective synergistic drug combinations that were not apparent using cell viability readouts. For instance, we identified selective synergistic combinations of the MEK inhibitor trametinib with PARP inhibitors or the tyrosine kinase inhibitor ponatinib in DU4475 cells; as well as of the rapamycin analog everolimus with the ATP-competitive mTOR inhibitor dactolisib in several mTOR addicted cell lines.

In conclusion, we showed that tracking drug-induced toxic responses in drug sensitivity testing and drug combination evaluation provides novel critical information on drug vulnerabilities. This argues that high throughput chemo-sensitivity profiling of cancer need to go beyond the current standard cell viability testing.

Citation Format: Prson Gautam, Leena Karhinen, Agnieszka Szwajda, Sawan Kumar Jha, Bhagwan Yadav, Tero Aittokallio, Krister Wennerberg. Enhanced understanding of drug responses and drug-drug interactions in triple negative breast cancer cells with a multiplexed cell viability and cell death readout. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B21.