Abstract 3502: Selective targeting of CTNBB1-, KRAS- or MYC-driven cell growth by combinations of existing drugs

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Abstract Purpose: Combination therapy plays an important role in achieving durable responses in anticancer therapy. Ideally, compound combinations work synergistically in cancer cells and not in non-malignant cells. Here we present a rational approach for identifying pairs of selective inhibitors that show a synergistic interaction only in specific genetic backgrounds, i.e. mutated in the CTNNB1 (β-catenin) or KRAS genes, or expressing amplified MYC. Experimental Procedures: We have established a panel of sixty six genetically well-characterized cell lines that represents the most frequently occurring oncogenic drivers in cancer (1). A collection of more than 100 inhibitors targeting all important oncogenic signaling pathways, including many kinase and epigenetic regulators, was profiled in a subset of forty four cell lines, generating highly reproducible and high-quality cell proliferation data. The inhibitor response was correlated to the genetic background of the cell lines by Anova analysis (1). Compounds that targeted similar subsets of cell lines, were tested in combination for synergistic interaction, using in vitro proliferation assays with equipotent mixtures, followed by curve shift analysis, isobolograms and combination index scoring. The approach was validated by showing that the MEK inhibitor trametinib and the BRAF inhibitor dabrafenib, which are targeted to BRAF-mutant cell lines, show synergistic interaction in this subpopulation, and not in other cell line types. Results: For all inhibitors, the drug response in cell line panel (Oncolines™) was analyzed. Notably, the Wnt-pathway inhibitor ICG-001 and the MEK inhibitor trametinib were shown to preferentially inhibit CTNNB1-mutated cancer cell lines. Neratinib, a spectrum selective EGFR inhibitor, and GSK-1070916, an Aurora kinase inhibitor, were shown to target MYC-amplified cell lines. The ERBB2 inhibitor TAK-165 and trametinib targeted KRAS mutant cell lines. These compounds thus show a pharmacological synthetic lethal effect. Subsequent combination studies showed synergy on cell proliferation in a high number of cases. ICG-001 works synergistically with trametinib in a CTNNB1-mutant colon cell line, and not in CTNNB1-wild type colon cell lines. Neratinib and GSK-1070916 work synergistically in MYC-amplified cell lines and not in non-MYC-amplified lines. Conclusions: Pharmacogenomic analysis of single agent responses identified compounds that preferentially inhibit the growth of cell lines harbouring mutant CTNNB1 or KRAS, or amplified MYC. Synergy studies in the pertinent genetic background identified new combinations of existing drugs with enhanced targeting of CTNNB1-mutated or MYC-amplified cancer cell lines. Our approach can efficiently discover novel drug combinations that target cancer genes more selectively and more potently.