BRAF Fusion as a Novel Mechanism of Acquired Resistance to Vemurafenib in BRAF Mutant Melanoma

Purpose: Many patients with BRAF mutant melanoma treated with BRAF inhibitors experience a rapid response, but ultimately develop resistance. Insight into the mechanism of resistance is critical for development of more effective treatment strategies. Experimental Design: Comprehensive genomic profiling of serial biopsies was performed in a patient with a BRAF mutant metastatic melanoma who developed resistance to vemurafenib. An AGAP3–BRAF fusion gene, identified in the vemurafenib-resistant tumor, was expressed in BRAF melanoma cell lines, and its effect on drug sensitivity was evaluated. Results: Clinical resistance to vemurafenib in a melanoma harboring a BRAF mutation was associated with acquisition of an AGAP3–BRAF fusion gene. Expression of the AGAP3– BRAF fusion in BRAF mutant melanoma cells induced vemurafenib resistance; however, these cells remained relatively sensitive to MEK inhibitors. The patient experienced clinical benefit following treatment with the combination of a BRAF and a MEK inhibitor. Rebiopsy of the tumor at a later time point, after BRAF and MEK inhibitors had been discontinued, showed loss of the AGAP3–BRAF fusion gene. Mixing experiments suggest that cells harboring both BRAF and AGAP3– BRAF only have a fitness advantage over parental BRAF cells during active treatment with a BRAF inhibitor. Conclusions: We report acquisition of a BRAF fusion as a novel mechanism of acquired resistance to vemurafenib in a patient with melanoma harboring a BRAF mutation. The acquisition and regression of clones harboring this fusion during the presence and absence of a BRAF inhibitor are consistent with rapidly evolving clonal dynamics in melanoma. Clin Cancer Res; 23(18); 5631–8. 2017 AACR. Introduction BRAF mutations are found in approximately half of malignant melanomas (1–3). These activating mutations in the MAPK/ERK pathway drive tumor progression, survival, and metastasis by promoting cell-cycle progression, facilitating escape from apoptosis, and abrogating immune destruction (4). The development of selective BRAF inhibitors, including vemurafenib and dabrafenib, was a landmark in the treatment of melanoma and has led to significant improvements in clinical response rate (RR), progression-free survival (PFS), and overall survival (OS), compared with chemotherapy for patients with BRAF-mutant melanoma (5, 6). Although an initial reduction in tumor volume is observed in the majority of patients with BRAF mutant melanoma treated with BRAF inhibitors, clinical resistance associated with progression of disease develops in most patients and limits the long-term utility of these agents. This has led to the clinical investigation and approval of combination BRAF and MEK inhibitor therapy (dabrafenib plus trametinib; vemurafenib plus combimetinib) that is associated with superior RR, PFS, and OS compared with BRAF inhibitor monotherapy (7–9). Several mechanisms of acquired resistance to vemurafenib have been identified and these include secondary NRAS mutations (10), mutations in ARAF and CRAF (11), amplification of BRAF (12), activation of other prosurvival signaling pathways, including the phosphoinositide-3-kinase (PI3K) pathway (11), and amplification of upstream receptor tyrosine kinases such as MET (13). To date, over a dozen acquired mechanisms of resistance are described and, often, multiple mechanisms of Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey. Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey. Rutgers Ernest Mario School of Pharmacy, Piscataway Township, New Jersey. Department of Radiology, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey. Foundation Medicine, Inc. Cambridge, Massachusetts. Central Comprehensive Cancer Centre, Central District, Hong Kong. Department Obstetrics/Gynecology and Reproductive Sciences, Division of Gynecologic Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey. Developmental Therapeutics/Phase I Program, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey. Note: Supplementary data for this article are available at Clinical Cancer Research Online (http://clincancerres.aacrjournals.org/). Corresponding Authors: Shridar Ganesan, Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, NewBrunswick, NJ 08903. Phone: 732-235-5211; Fax: 732-235-5331; E-mail: ganesash@cinj.rutgers.edu; and Janice M. Mehnert, 195 Little Albany Street, New Brunswick, New Jersey 08903. Phone: 732-2358945; Fax: 732-235-8094; E-mail: mehnerja@cinj.rutgers.edu doi: 10.1158/1078-0432.CCR-16-0758 2017 American Association for Cancer Research. Clinical Cancer Research www.aacrjournals.org 5631 on May 17, 2021. © 2017 American Association for Cancer Research. clincancerres.aacrjournals.org Downloaded from Published OnlineFirst May 24, 2017; DOI: 10.1158/1078-0432.CCR-16-0758