Overview: 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.
UCLA researchers led by Professor Thomas Graeber have 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.
Related publications (by the inventors only): Song K, Minami JK, Huang A, Dehkordi SR, Lomeli SH, Luebeck J, Goodman MH, Moriceau G, Krijgsman O, Dharanipragada P, Ridgley T, Crosson WP, Salazar J, Pazol E, Karin G, Jayaraman R, Balanis NG, Alhani S, Sheu K, Ten Hoeve J, Palermo A, Motika SE, Senaratne TN, Paraiso KH, Hergenrother PJ, Rao PN, Multani AS, Peeper DS, Bafna V, Lo RS, Graeber TG. Plasticity of Extrachromosomal and Intrachromosomal BRAF Amplifications in Overcoming Targeted Therapy Dosage Challenges. Cancer Discov. 2022 Apr 1;12(4):1046-1069. doi: 10.1158/2159-8290.CD-20-0936. PMID: 34930786; PMCID: PMC9192483.