Cell viability assay

For all epistasis analysis, APE1 was depleted first, followed by ALC1. 1000 SUM149PT cells in a volume of 100 μl were plated into each well of 96-well clear bottom plates on Day 0. On Day 1, 100 μl of 2X drug dilution was added to cells in technical replicates. While other drugs were retained, MMS-treated cells were released into fresh media after 24 h. Seven days post drug addition, the media was replaced with phenol red-free DMEM (Thermo Scientific, 31053028) supplemented with 10% BCS, 1x penicillin-streptomycin, 2 mM l-glutamine freshly reconstituted with resazurin (Sigma 199303) to a final concentration of 10 ug/mL. Cells were then incubated for 3–4 h at 37 °C or until the media in solvent-treated wells developed a pink color. Fluorescence was measured at 560 nm excitation and 590 nm emission using the SoftMax Pro 6.4 software on the SpectraMax i3x microplate reader. For UWB1.289, OVSAHO, and MDA-MB-436 cell lines, cells were plated in solid white flat bottom plates and viability assessment was performed CellTiter Glo 2.0 Assay (Promega, PRG9242). When plotting the survival curves, the fluorescence/luminescence of the drug-treated population was normalized to solvent-exposed cells. The data were fitted to a curve in GraphPad Prism using the following equation: y = min+ (max-min)/1 + 10^logEC50-x.