Plasticity of Extrachromosomal and Intrachromosomal BRAF Amplifications in Overcoming Targeted Therapy Dosage Challenges

Kai Song, Jenna K. Minami, Arthur Huang, Siavash R. Dehkordi, Shirley H. Lomeli, Jens Luebeck, Mark H. Goodman, Gatien Moriceau, Oscar Krijgsman, Prashanthi Dharanipragada, Trevor Ridgley, William P. Crosson, Jesus Salazar, Eli Pazol, Gabriel Karin, Rachana Jayaraman, Nikolas G. Balanis, Salwan Alhani, Kyle Sheu, Johanna Ten HoeveAmelia Palermo, Stephen E. Motika, T. Niroshi Senaratne, Kim H. Paraiso, Paul J. Hergenrother, P. Nagesh Rao, Asha S. Multani, Daniel S. Peeper, Vineet Bafna, Roger S. Lo, Thomas G. Graeber

Research output: Contribution to journalArticlepeer-review


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 inhibi-tor (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 resist-ance. 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.

Original languageEnglish (US)
Pages (from-to)1046-1069
Number of pages24
JournalCancer Discovery
Issue number4
StatePublished - Apr 1 2022

ASJC Scopus subject areas

  • Oncology


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