@article{e06a4e2ebe3f4ca38215e18836623c10,
title = "Plasticity of Extrachromosomal and Intrachromosomal BRAF Amplifications 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 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.",
author = "Kai Song and Minami, {Jenna K.} and Arthur Huang and Dehkordi, {Siavash R.} and Lomeli, {Shirley H.} and Jens Luebeck and Goodman, {Mark H.} and Gatien Moriceau and Oscar Krijgsman and Prashanthi Dharanipragada and Trevor Ridgley and Crosson, {William P.} and Jesus Salazar and Eli Pazol and Gabriel Karin and Rachana Jayaraman and Balanis, {Nikolas G.} and Salwan Alhani and Kyle Sheu and {Ten Hoeve}, Johanna and Amelia Palermo and Motika, {Stephen E.} and Senaratne, {T. Niroshi} and Paraiso, {Kim H.} and Hergenrother, {Paul J.} and Rao, {P. Nagesh} and Multani, {Asha S.} and Peeper, {Daniel S.} and Vineet Bafna and Lo, {Roger S.} and Graeber, {Thomas G.}",
note = "Funding Information: NIH awards P30 CA016042 and 5P30 AI028697, and by the JCCC, the UCLA AIDS Institute, the David Geffen School of Medicine at UCLA, the UCLA Chancellor{\textquoteright}s Office, and the UCLA Vice Chancellor{\textquoteright}s Office of Research. Next-generation sequencing was performed at the Technology Center for Genomics and Bioinformatics at UCLA. CGH and low-pass WGS were performed at PacGenomics. Bionano optical mapping assemblies were provided by Andy Pang from Bionano Genomics, Inc. Metabolomics was performed at the UCLA Metabolomics Center supported by the NIH Shared Instrumentation grant S10 OD016387 (T.G. Graeber). A subset of the results shown here are in part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga. Funding Information: T.G. Graeber is supported by the NIH NCI P01 CA168585 and R01 CA222877, the Melanoma Research Alliance (MRA; Team Science Award 691165), the UCLA SPORE in Prostate Cancer (NIH NCI P50 CA092131), the W.M. Keck Foundation, and the UCLA Eli and Edythe Broad Center of Regenerative Medicine, and Stem Cell Research Hal Gaba Director?s Fund for Cancer Stem Cell Research. R.S. Lo is supported by the NIH (1R01CA176111A1, 1R21CA21591001, R21CA25583701, and 1P01CA168585), the MRA (Team Science Award 691165), the V Foundation for Cancer Research (Translational Award), Mary Tanner and Maurizio Grimaldi, and the Ressler Family Foundation. V. Bafna, J. Luebeck, and S.R. Dehkordi were supported in part by grants from the NIH (U24CA264379 and R01GM114362). K.H. Paraiso is a postdoctoral fellow supported by the UCLA Tumor Cell Biology Training Program (USHHS Ruth L. Kirschstein Institutional National Research Service Award # T32 CA009056). G. Moriceau is supported by the NIH (1P01CA168585) and the MRA (Young Investigator Award). P. Dharanipragada and A. Palermo are supported by Jonsson Comprehensive Cancer Center (JCCC) postdoctoral fellowships. FISH microscopy was performed at the Advanced Light Microscopy/Spec-troscopy Laboratory and the Leica Microsystems Center of Excellence at the California NanoSystems Institute at UCLA with funding support from NIH Shared Instrumentation Grant S10OD025017 and NSF Major Research Instrumentation grant CHE-0722519. Flow cytometry was performed in the UCLA JCCC and Center for AIDS Research Flow Cytometry Core Facility that is supported by NIH awards P30 CA016042 and 5P30 AI028697, and by the JCCC, the UCLA AIDS Institute, the David Geffen School of Medicine at UCLA, the UCLA Chancellor?s Office, and the UCLA Vice Chancel-lor?s Office of Research. Next-generation sequencing was performed at the Technology Center for Genomics and Bioinformatics at UCLA. CGH and low-pass WGS were performed at PacGenomics. Bionano optical mapping assemblies were provided by Andy Pang from Bionano Genomics, Inc. Metabolomics was performed at the UCLA Metabolomics Center supported by the NIH Shared Instrumentation grant S10 OD016387 (T.G. Graeber). A subset of the results shown here are in part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga. Funding Information: T.G. Graeber is supported by the NIH NCI P01 CA168585 and R01 CA222877, the Melanoma Research Alliance (MRA; Team Science Award 691165), the UCLA SPORE in Prostate Cancer (NIH NCI P50 CA092131), the W.M. Keck Foundation, and the UCLA Eli and Edythe Broad Center of Regenerative Medicine, and Stem Cell Research Hal Gaba Director{\textquoteright}s Fund for Cancer Stem Cell Research. R.S. Lo is supported by the NIH (1R01CA176111A1, 1R21CA21591001, R21CA25583701, and 1P01CA168585), the MRA (Team Science Award 691165), the V Foundation for Cancer Research (Translational Award), Mary Tanner and Maurizio Grimaldi, and the Ressler Family Foundation. V. Bafna, J. Luebeck, and S.R. Dehkordi were supported in part by grants from the NIH (U24CA264379 and R01GM114362). K.H. Paraiso is a postdoctoral fellow supported by the UCLA Tumor Cell Biology Training Program (USHHS Ruth L. Kirschstein Institutional National Research Service Award # T32 CA009056). G. Moriceau is supported by the NIH (1P01CA168585) and the MRA (Young Investigator Award). P. Dharanipragada and A. Palermo are supported by Jonsson Comprehensive Cancer Center (JCCC) postdoctoral fellowships. FISH microscopy was performed at the Advanced Light Microscopy/Spectroscopy Laboratory and the Leica Microsystems Center of Excellence at the California NanoSystems Institute at UCLA with funding support from NIH Shared Instrumentation Grant S10OD025017 and NSF Major Research Instrumentation grant CHE-0722519. Flow cytometry was performed in the UCLA JCCC and Center for AIDS Research Flow Cytometry Core Facility that is supported by Publisher Copyright: {\textcopyright} 2021 American Association for Cancer Research.",
year = "2022",
month = apr,
day = "1",
doi = "10.1158/2159-8290.CD-20-0936",
language = "English (US)",
volume = "12",
pages = "1046--1069",
journal = "Cancer Discovery",
issn = "2159-8274",
publisher = "American Association for Cancer Research Inc.",
number = "4",
}