Comprehensive transcriptomic characterization of two melanoma cell lines with acquired dual resistance to BRAF and MEK inhibitors: toward understanding and reversing therapy resistance

To elucidate the molecular mechanisms underlying acquired resistance to dual BRAF and MEK inhibition, we performed transcriptomic profiling of two melanoma cell lines, Hs294T and WM9, rendered resistant to the combination of vemurafenib and cobimetinib.RNA-seq analysis revealed distinct resistance-associated gene expression signatures in each model, with only partial overlap, suggesting divergent adaptive responses to the same therapeutic pressure. Both resistant cell lines exhibited strong upregulation of extracellular matrix compo-nents, epithelial-mesenchymal transition (EMT) markers, and chemokine signaling genes, along with repression of melanocytic lineage markers. Inference of transcription factor and kinase activity uncovered line-specific regulatory rewiring, including activa-tion of MYOCD, SMAD3, and TP53, and suppression of immune regulators such as RFX5 and RFXANK. Network-based analysis identified key resistance hubs - IL6, FN1, COL1A1, and EGFR. WM9 cells showed broader transcriptional reprogramming and prominent engagement of inflammatory and immune-related pathways. At the same time, Hs294T resistance was marked by a more restricted program focused on stromal remodeling and impaired antigen presentation. RNA-seq profiling of Hs294T and WM9 cell lines with acquired dual resistance to to the combination of vemurafenib and cobimetinib and their respective controls (sensitive cells). Each group contained three biological replicates, resulting in six samples per cell line and twelve samples in total.