Plasticity of Extrachromosomal and IntrachromosomalBRAFAmplifications in Overcoming Targeted Therapy Dosage Challenges

Abstract

Focal amplifications (FA) 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 (MAPKi) resistance that bears BRAFV600 amplifications through either extrachromosomal DNA (ecDNA)/double minutes (DM) or intrachromosomal homogenously staining regions (HSR). Cells harboring BRAFV600E FAs displayed mode switching between DMs and HSRs, from both de novo genetic changes and selection of preexisting 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 proferroptotic drugs, extending the spectrum of ferroptosis sensitivity in MAPKi resistance beyond cases of dedifferentiation. Significance: Understanding the structure and dynamics of oncogene amplifications is critical for overcoming tumor relapse. BRAF amplifications are highly plastic under MAPKi dosage challenges in melanoma, through involvement of de novo genomic alterations, even in the HSR mode. Moreover, BRAF FA-driven, dual MAPKi–resistant cells extend the spectrum of resistance-linked ferroptosis sensitivity. This article is highlighted in the In This Issue feature, p. 873

Ferroptosis turns 10: Emerging mechanisms, physiological functions, and therapeutic applications

“…Aggressive cancers that have undergone epithelial-to-mesenchymal transition are more susceptible to ferroptosis (Viswanathan et al, 2017), and resistance to targeted agents that induce apoptosis is associated with increased sensitivity to ferroptosis (Hangauer et al, 2017). Serine/threonine-protein kinase B-raf (BRAF) amplification is one mechanism that shifts sensitivity from BRAF inhibitors to ferroptosis inducers (Song et al, 2022).…”

Molecular characterization of acquired resistance to KRAS G12C inhibition in gastrointestinal cancers

“…Similar to our ndings, BRAF ampli cation upon RAF inhibitor resistance can be modulated by intermittent treatment 20 . Copy number changes may provide a more rapid means to modulate oncogene activity as we nd that KRAS G12C ampli cation emerges faster than resistance mutations in cell lines and that ampli cation carried on extrachromosomal DNA/double minutes, as seen in the RW7213-R cells, may be quickly lost at times of stress 21 . Our data suggest that this drop in the cell free DNA is likely due to the acquisition of a senescent phenotype in cancer cells, therefore intermittent treatment would probably just favour the survival of KRAS G12C ampli ed cells.…”

Biomolecular Condensation: A New Phase in Cancer Research

“…In this context, DNA translocations that are common in cancer are often associated with the acquisition of superenhancers at driver oncogenes (77). Furthermore, the presence of such IDRs on many TFs across evolution and their frequent shuffling in cancer fusions collectively suggest an important role for IDR-driven phase separation in cancer (82).…”