Fig. 3: Base editing scanning screens identify unique and shared drug-resistant variants between cell lines harboring WT EGFR and EGFRΔGlu746–Ala750.
From: Multimodal scanning of genetic variants with base and prime editing
a, Diagram showing combined ABE8e and BE3.9max screen hits along the EGFR protein in PC-9 cells. Hits are defined as sgRNAs with LFCs > −1.5 between plasmid and day 19 and LFC > 0.75 between nontreated and EGF-deprived cells. b, Scatter plots comparing the LFCs of sgRNAs in MCF10A (WT EGFR) and PC-9 (EGFRΔGlu746–Ala750) cell lines treated with gefitinib or osimertinib. sgRNAs with LFC < −1.5 between plasmid and day 19 in PC-9 cells are shown in gray. Nontargeting and essential splice site controls are not shown. c,d, EGFR-targeted amplicon sequencing data for individual sgRNA validation in PC-9 cells. PC-9 cells were infected with sgRNAs Ile853Val;Thr854Ala [ABE8e] (c) or Leu1038Leu;Exon 25 + 1 [BE3.9max] (d) in three biological replicates and later split into control and treatment arms with gefitinib or osimertinib. The percentages of reads corresponding to the four most represented alleles at each target site are shown for nontreated and drug-treated cells. Nucleotide sequences represent the coding DNA strand and amino acid sequences correspond to the annotated EGFR residues. Black and red squares denote WT EGFR and splice donor sites, respectively. Holm-adjusted P values are shown for two-sided t-tests. Asterisks within barplots in d refer to the stop codon. aValidation of the Lys852Gly [ABE8e] sgRNA showed that the main variant conferring drug resistance was Lys852Glu (Extended Data Fig. 8d).
