Plasticity of extrachromosomal and intrachromosomal BRAF amplifications in overcoming targeted therapy dosage challenges
Focal amplifications (FAs) resulting in copy number gain of targeted genomic regions can mediate targeted therapy resistance. Understanding the structure, plasticity and vulnerability of FAs is critical for designing treatments that overcome such resistance. Here we developed a combined BRAF plus MEK inhibitor resistance melanoma model that bears high mutant BRAF amplifications through two modes of FAs: extrachromosomal double minutes (ecDNA/DMs) and intrachromosomal homogenously staining regions (HSRs), and investigated FA structure and dynamics in the context of drug resistance plasticity. We found that cells harboring BRAF 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 also exhibit copy number and length changes through structural loss of amplicon repeats that allow them to respond to dose reduction and recover from drug addiction. DM and HSR mechanisms can couple with other BRAF genomic changes, such as kinase domain duplications and alternative splicing, to enhance therapy resistance. Amplicon plasticity is observed in other MAPK pathway genes, such as RAF1 and NRAS, and occurs in clinical cases of therapy resistance. We found that BRAF FA-induced dual MAPKi-resistant cells are more sensitive to pro-ferroptotic drugs, which extends the spectrum of melanoma resistance-derived ferroptosis sensitivity beyond cases of dedifferentiation.