Extended Data Fig. 6: Lung cancer targeted therapies induce APOBEC3A expression.

a, mRNA expression of APOBEC family genes in response to osimertinib. PC9 cells were treated with 1 μM osimertinib for up to 14 days and gene expression was determined by quantitative RT-PCR. Data are expressed as log₂ fold change (FC) relative to untreated control. b, mRNA expression levels (CPM: counts per million) of APOBEC family genes determined by RNA-seq in EGFR-mutant NSCLC cell lines treated with 300 nM gefitinib for 0, 1 and 14 days. Data correspond to BioProject ID PRJNA941908 (ref. ⁶⁴) c, Schema for allele specific droplet digital PCR assay for quantifying A3A editing at the DDOST hairpin hotspot (adapted from Jalili et al.¹⁸). d, e, Expression of A3A or A3B in PC9 with Tet-On flag-tagged wild-type A3A^WT/A3B^WT or catalytic inactive mutant A3A^E72A/A3B^E255Q constructs. Cells were treated with 200 ng/mL doxycycline (DOX) treatment for 72 h. Protein expression was confirmed by western blot (d). mRNA expression levels were determined by quantitative RT-PCR (e). Data are expressed as relative to untreated control (mean ± s.d. of 3 biological replicates, two-sided Student’s t-test). f, DDOST mRNA editing in PC9 cells overexpressing wild-type A3A^WT/A3B^WT and catalytic inactive A3A^E72A/A3B^E255Q mutants. Cells were treated with 200 ng/mL DOX treatment for 72 h. DDOST editing was determined by ddPCR assay (mean ± s.d. of 3 biological replicates, two-sided Student’s t-test). g, Change of tumor volume in EGFR-mutant NSCLC xenograft models treated with osimertinib at the time of harvesting minimal residual disease (MRD) for DDOST hairpin hotspot analysis in Fig. 2c. h, Top edited hairpin hotspot sites (supported by at least 2 edited reads) in PC9 cells in ApoTrack mRNA-seq analysis in Fig. 2e. The majority are predicted to be synonymous mutations. None of the missense mutations have been reported to be recurrently mutated in cancer.