DNA base lesion-containing G-quadruplex mediates transcriptome reprogramming in EGFR-TKI resistance of non-small cell lung cancer

Cancer cells, such as non-small cell lung cancer (NSCLC) cells, exhibit remarkable phenotypic plasticity and undergo epigenetic reprogramming, characteristics that enable them to evade targeted therapies. However, how NSCLC cells use epigenetic regulatory mechanisms (including endogenous DNA base damage) to drive transcriptome reprogramming and develop resistance to EGFR-tyrosine kinase inhibitor (EGFR-TKI) therapy remains unclear. We employed an integrated multi-omics approach in erlotinib-sensitive and resistant NSCLC cells, including genome-wide mapping of abasic sites (AP sites) via Single-Strand Break Mapping at Nucleotide Genome Level-AP (SSiNGLe-AP), characterization of binding landscapes of 8-Oxoguanine DNA Glycosylase 1 (OGG1), Apurinic/Apyrimidinic Endonuclease 1 (APE1), and genome-wide profiling of G-quadruplex (G4) structures by Cleavage Under Targets and Tagmentation sequencing (CUT&Tag-seq). Combined with RNA-seq and ATAC-seq analysis, we performed functional validation using overexpression, RNAi, qPCR, western blot, immunofluorescence, sphere formation, and flow cytometry. High-resolution microscopy revealed that oxidized base lesions and repair complexes orchestrated the spatiotemporal dynamics of G4 structures. Co-localization of G4 structures with CpG islands (CGIs) was assessed by Whole-Genome Bisulfite Sequencing (WGBS). Finally, the therapeutic relevance of targeting this pathway was evaluated using a mouse xenograft model treated with APE1 inhibitors. We identified the DNA base lesion repair proteins OGG1 and APE1 as key mediators of transcriptional reprogramming that promote cancer cell plasticity and resistance to EGFR-TKIs. Mechanistically, genome-wide profiling revealed their dynamic redistribution to specific genomic loci in resistant cells. Beyond canonical repair, APE1 stabilizes G4 structures at the promoters of epithelial-mesenchymal transition (EMT) and stemness-associated genes, facilitating their transcriptional activation. This APE1-driven, G4-dependent transcriptional program occurs preferentially at hypomethylated CGIs, revealing a mechanism by which DNA secondary structures shape the epigenetic landscape to promote cellular plasticity. Our study elucidates a novel pathway in which OGG1/APE1-mediated processing of oxidative damage orchestrates a G4-dependent transcriptional program to drive EMT and stemness in EGFR-TKI-resistant NSCLC. The therapeutic potential of targeting this axis is demonstrated by the efficacy of BER inhibitors in suppressing tumor growth in vivo, establishing APE1-G4 targeting as a promising anti-resistance strategy.