Selection for Targeted Therapy Resistance Indirectly Selects for Cancer Cells with Enhanced Phenotypic Plasticity and Evolvability to Orthogonal Stressors

Resistance to targeted therapies is frequently associated with stem-like features and partial epithelial-to-mesenchymal transition (EMT). Understanding whether these programs directly drive resistance or instead reflect increased phenotypic plasticity is needed to guide strategies for overcoming resistance. Here, we found that resistance to ALK inhibitors (ALKi) in non-small cell lung cancer was associated with increased phenotypic plasticity, reflected in enhanced adaptability to orthogonal stressors and increased metastatic potential, without intrinsic cross-resistance in short-term assays. Computational modeling and experimental validation studies showed that plasticity was progressively enriched over multi-step resistance trajectories. Lineage tracing and clonal analyses revealed a substantial, heritable intra-cell line variability in adaptation potential. High adaptation potential was associated with increased chromatin accessibility at EMT/stemness regulators. Adaptation potential could be enhanced by inducing stemness/EMT programs and suppressed by SOX2 knockdown or epigenetic inhibition, with corresponding effects on resistance. Collectively, these findings indicate that targeted therapy indirectly selects for cells with increased phenotypic plasticity, providing a common basis for the resistance-EMT association and the substrate for multifactorial resistance and metastatic competence. Constraining plasticity could delay resistance and extend response durability.