Adaptive drug resistance in melanoma is characterised by lipidome remodelling while maintaining cell membrane biophysical properties

Abstract

Aim: Cancer drug resistance is driven by dynamic, systems-level adaptations, including cellular state transitions, epigenetic reprogramming, metabolic rewiring, and proteome remodelling. Lipid metabolic reprogramming is increasingly recognised as a contributor to resistance through alterations in the membrane composition and has been hypothesised to promote resistance by increasing membrane rigidity and limiting drug permeability. Here we tested this hypothesis in melanoma using a cell state-resolved multi-omics approach.

Methods: We combined lipidomics, surface-resolved phospholipid profiling, live-cell biophysical measurements, and whole-cell proteomics to characterise plasma membrane composition and function across drug-naïve, drug-tolerant persister, and permanently drug-resistant states in BRAF^V600E metastatic melanoma cells treated with dabrafenib.

Results: Lipidomic analyses revealed membrane remodelling, particularly in the drug-tolerant state, including altered fatty acid chain unsaturation, and increased cholesterol (Chol) and sphingomyelin levels. All cell states retained surface exposure of negatively charged phosphatidylserine and phosphatidylinositol. Despite compositional changes typically associated with membrane rigidification, plasma membrane fluidity and tension remain conserved across all resistance states. Proteomic analysis further revealed coordinated regulation of lipid metabolic pathways, including Chol homeostasis and sphingolipid turnover, indicating that lipid-metabolic adaptation supports survival under drug pressure without substantially altering membrane biophysical properties.

Conclusion: These findings show that lipid metabolic rewiring supports drug tolerance while conserving core membrane features. By resolving resistance-associated changes across both molecular and biophysical layers, this study identifies shared plasma membrane features and vulnerabilities across heterogeneous melanoma cell populations, supporting the application of membrane-active therapeutic agents and of combination strategies targeting lipid-metabolic adaptations to delay or prevent resistance.

Keywords

Proteome / metabolomics / membrane lipids / glycerophospholipids / cholesterol / leaflet asymmetry / lipid metabolism / phospholipase digestion

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