Discovering Synergistic Compounds with BYL-719 in PI3K Overactivated Basal-like PDXs

Abstract

Basal-like triple-negative breast cancer (TNBC) tumor cells are difficult to eliminate due to resistance mechanisms that promote survival. While this breast cancer subtype has low PIK3CA mutation rates when compared to estrogen receptor-positive (ER+) breast cancers, most basal-like TNBCs have an overactive PI3K pathway due to gene amplification or high gene expression. BYL-719 is a PIK3CA inhibitor that has been found to have low drug-drug interactions, which increases the likelihood that it could be useful for combinatorial therapy. Alpelisib (BYL-719) with fulvestrant was recently approved for treating ER+ breast cancer patients whose cancer had developed resistance to ER-targeting therapy. In these studies, a set of basal-like patient-derived xenograft (PDX) models was transcriptionally defined with bulk and single-cell RNA-sequencing and clinically actionable mutation profiles defined with Oncomine mutational profiling. This information was overlaid onto therapeutic drug screening results. BYL-719-based, synergistic two-drug combinations were identified with 20 different compounds, including everolimus, afatinib, and dronedarone, which were also found to be effective at minimizing tumor growth. These data support the use of these drug combinations towards cancers with activating PIK3CA mutations/gene amplifications or PTEN deficient/PI3K overactive pathways.

Stratification of Tamoxifen Synergistic Combinations for the Treatment of ER+ Breast Cancer

“…First, bulk RNA sequencing was performed and integrated with The Cancer Genome Atlas (TCGA) transcriptomic data to demonstrate all 20 PDX models were grouped within the expected subtype and distributed throughout the TCGA data ( Figure 2 A). The predicted pathogenicity of missense, frameshift, nonsense, and fusion mutations, as well as CNV, splice variants, and the introduction of stop codons in all PDX models and 14 cell lines, was established using the targeted mutational profiling tool Oncomine v3 ( Figure 2 B) [ 23 ]. The most common mutations were found in TP53, with the second most common being PIK3CA, which has been previously reported for many of these models [ 49 ].…”

“…Preprocessing of bulk RNA-seq data has been described previously [ 23 , 24 ]. Briefly, assessment of sequencing quality was conducted using FastQC v0.11.8 [ 25 ].…”

“…High-throughput screening was performed on PDX and cell line models of ER+ breast cancer using a 516-drug library at 1 μM concentration, as reported previously [ 46 ]. Two biological replicates were averaged, and coefficient of drug interaction (CDI) was calculated for each drug in each model, using the formula CDI = AB/(A × B), where A and B are the viability of tamoxifen and each agent alone, and AB is the viability of the combination [ 23 ].…”

“…In vitro drug screening of PDX cells has been previously described [ 23 , 46 , 47 ]. In brief, single-cell suspensions were plated in 96-well plates at a density of 25,000 cells/well in M87 medium and treated for 72 h. For cell line viability assays, 1250 cells per well were plated in 96-well plates in RPMI-1640 supplemented with GlutaMAX, 10% FBS, and penicillin/streptomycin and allowed to adhere for 24 h. Cells were treated for 72 h, and viability was measured relative to vehicle-treated control using the CellTiter-Glo Luminescent Viability Assay (Promega, Madison, WI, USA), according to the manufacturer’s protocol.…”

Targeting Receptor Tyrosine Kinases as a Novel Strategy for the Treatment of Triple-Negative Breast Cancer

“… 68 In another study, afatinib combined with an inhibitor of PIK3CA induced synergistic growth inhibition in PI3K-overactivated TNBC patient-derived xenografts. 69 The combination of the EGFR inhibitor gefitinib with chemotherapy produced synergistic anticancer activity mediated by cell cycle arrest in TNBC. 70 Besides, the combination of gefitinib with PI3K/AKT inhibitors 71 or autophagy inhibitors 72 induced cytotoxicity in TNBC cell lines and xenograft animal models, respectively.…”