Plasticity of extrachromosomal and intrachromosomal BRAF amplifications in overcoming targeted therapy dosage challenges.


Focal amplifications (FAs) can mediate targeted therapy resistance in cancer. Understanding the structure and dynamics of FAs is critical for designing treatments that overcome plasticity-mediated resistance. We developed a melanoma model of dual MAPK inhibitor resistance that bears BRAFV600 amplifications through either extrachromosomal DNA/double-minutes (ecDNA/DMs) or intrachromosomal homogenously staining regions (HSRs). Cells harboring BRAFV600E FAs displayed mode switching between DMs and HSRs, from both de novo genetic changes and selection of pre-existing subpopulations. Plasticity is not exclusive to ecDNAs, as cells harboring HSRs exhibit drug addiction-driven structural loss of BRAF amplicons upon dose reduction. FA mechanisms can couple with kinase domain duplications and alternative splicing to enhance resistance. Drug-responsive amplicon plasticity is observed in the clinic, and can involve other MAPK pathway genes, such as RAF1 and NRAS. BRAF FA-mediated dual-MAPKi-resistant cells are more sensitive to pro-ferroptotic drugs, extending the spectrum of ferroptosis sensitivity in MAPKi-resistance beyond cases of dedifferentiation.

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Cancer discovery
  • Publication date 20-12-2021

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