Fig. 2: Variants modulating drug sensitivity cluster into four functional classes.
From: Base editing screens define the genetic landscape of cancer drug resistance mechanisms
a, Variants conferring resistance or sensitivity to the MEK inhibitor, trametinib, in HT-29 cells. Comparison of gRNA z-scores for the control treated arm versus plasmid library, and the drug-treated arm versus plasmid library is shown. b, Variants conferring resistance to the combination of BRAF and EGFR inhibitors, dabrafenib and cetuximab, in HT-29 cells. Comparison of gRNA z-scores for the control treated arm versus plasmid library, and the drug-treated arm versus plasmid library is shown. c, Crystal structure of the complex of EGFR and cetuximab (PDB 1yy9)82, and MEK1 and trametinib (PDB 7jur)83, highlights canonical drug resistance variants discovered in base editor screens predicted to disrupt drug binding. d, Cell growth of base-edited HT-29 cells harboring canonical and drug-addiction drug-resistance variants. Cells were left untreated or treated with trametinib (3 nM) or the combination of dabrafenib (80 nM) and cetuximab (1 µg ml−1), and cell proliferation was monitored using an incucyte. Data represent the mean ± s.d. of biological triplicates and are representative of two independent experiments. e, Western blotting of WT HT-29 ABE cells and cells harboring drug-resistance mutations activating the MAPK signaling pathway. Cells were treated with the combination of dabrafenib (80 nM) and cetuximab (1 µg ml−1) or DMSO as a control for 24 h before analysis. f, β-galactosidase staining for senescent cells; β-galactosidase positive senescent foci (blue) are indicated with arrows. HT-29 cells were treated with the combination of dabrafenib (80 nM) and cetuximab (1 µg ml−1) or DMSO as a control for 48 h before analysis. Representative images are shown for the drug addiction variant MAP2K1 Y130C. Scale bar, 500 µm. Predicted amino acid editing consequences are labeled for drug resistance screens and genotyped edits are shown in d, e and f. Data are the average of two independent experiments performed on separate days, or representative of two independent experiments (e and f). See also Extended Data Figs. 2 and 3.
