Fig. 2: Base editing scanning screens identify EGFR variants resistant to first-generation and third-generation TKIs.
From: Multimodal scanning of genetic variants with base and prime editing
a, Overview of the base editing constructs and workflow to identify EGFR variants resistant or sensitive to clinically approved TKIs gefitinib or osimertinib. All-in-one base editing libraries packaged in lentivirus were delivered to MCF10A cells in duplicate. Cells were split into three treatment arms on day 11: nontreated, 0.13 μM gefitinib or 0.3 μM osimertinib and harvested on day 19. b, Scatter plot showing the LFCs of individual sgRNAs along the EGFR protein between nontreated and drug-treated cells for each base editor and drug treatment. LFCs between the plasmid library and nontreated cells on day 19 are shown as color gradients. Background colors represent EGFR domains. c, Scatter plots comparing the LFCs of sgRNAs in cells treated with either gefitinib or osimertinib for each base editor. Nontargeting and essential splice site controls are not shown, neither are sgRNAs with LFCs < −1.5 between plasmid and day 19. d, Three-dimensional structures of the EGFR tyrosine kinase domain in complex with gefitinib (left; Protein Data Bank (PDB) 2ITY) or osimertinib (right; PDB 6JXT) as visualized in ChimeraX. Hits of the respective MCF10A screens are shown in magenta and TKI molecules are shown in gray. aValidation of the Lys852Gly [ABE8e] sgRNA showed that the main variant conferring drug resistance was Lys852Glu (Extended Data Fig. 5d).
