Transient Splicing-Associated Isoform Remodeling Defines Early MAPKi Resistance Adaptation in Melanoma

Abstract

A long-standing question in targeted therapy resistance is how tumor cells rapidly enter drug-tolerant states before stable resistance emerges. In BRAF-mutant melanoma, early adaptation to MAPK inhibitor (MAPKi) therapy is accompanied by profound phenotypic plasticity, yet the molecular mechanisms that enable this transition remain poorly understood. Here, we show that MAPKi adaptation is characterized by a transient transcript isoform remodeling that is largely invisible to conventional gene-expression analysis. We integrated and analyzed multiple different datasets, including bulk and single-cell RNA-seq datasets from melanoma cell lines, murine models, patient-derived xenografts and patient tumors, spanning no-treatment, on-treatment/minimal residual disease, and acquired-resistant states. We find that differential transcript usage peaks during the adaptive on-treatment phase and then is markedly attenuated when resistance was established. These dynamics were conserved across experimental systems and supported by independent exon-usage analyses. Notably, most genes undergoing differential transcript usage showed no corresponding change in total gene expression, and genes with isoform-level changes more strongly highlighted MAPKi resistance-associated pathways, including PI3K/AKT/mTOR and receptor tyrosine kinase signaling. Further, classifiers trained on cell-line transcript-usage features identified the adaptive state more accurately than gene-expression-based models in independent PDX and patient datasets. Interestingly, MAPKi-associated isoform changes recapitulated melanoblast-associated developmental splicing programs and were linked to a few key splicing regulators. Together, these findings identify an underappreciated regulatory layer connecting drug tolerance, developmental plasticity, and acquired resistance. Beyond the current context, our results suggest that comprehensively tracking isoform and splicing alterations may potentially advance our understanding of the emergence of treatment resistance in additional indications and treatment regimes.