Identification of Multiple Mechanisms of Resistance to Vemurafenib in a Patient with BRAFV600E-Mutated Cutaneous Melanoma Successfully Rechallenged after Progression

Abstract

Purpose: To investigate the mechanism(s) of resistance to the RAF-inhibitor vemurafenib, we conducted a comprehensive analysis of the genetic alterations occurring in metastatic lesions from a patient with a BRAF V600E -mutant cutaneous melanoma who, after a first response, underwent subsequent rechallenge with this drug. Experimental Design: We obtained blood and tissue samples from a patient diagnosed with a BRAF V600E -mutant cutaneous melanoma that was treated with vemurafenib and achieved a near-complete response. At progression, he received additional lines of chemo/immunotherapy and was successfully rechallenged with vemurafenib. Exome and RNA sequencing were conducted on a pretreatment tumor and two subcutaneous resistant metastases, one that was present at baseline and previously responded to vemurafenib (PV1) and one that occurred de novo after reintroduction of the drug (PV2). A culture established from PV1 was also analyzed.Results: We identified two NRAS-activating somatic mutations, Q61R and Q61K, affecting two main subpopulations in the metastasis PV1 and a BRAF alternative splicing, involving exons 4-10, in the metastasis PV2. These alterations, known to confer resistance to RAF inhibitors, were tumor-specific, mutually exclusive, and were not detected in pretreatment tumor samples. In addition, the oncogenic PIK3CA H1047R mutation was detected in a subpopulation of PV1, but this mutation did not seem to play a major role in vemurafenib resistance in this metastasis.Conclusions: This work describes the coexistence within the same patient of different molecular mechanisms of resistance to vemurafenib affecting different metastatic sites. These findings have direct implications for the clinical management of BRAF-mutant melanoma.

BRAF Fusion as a Novel Mechanism of Acquired Resistance to Vemurafenib in BRAFV600E Mutant Melanoma

“…Of note, this patient did experience some clinical benefit, although brief in duration, upon rechallenge with a BRAF inhibitor after progression on immunotherapy. This result suggests that rechallenge with BRAF/MEK inhibitors may be of benefit in the setting of interval progression of kinase inhibitor therapy, as has been reported by others (30)(31)(32).…”

Tumor Evolution as a Therapeutic Target

“…In patients with CRC who became resistant to cetuximab or panitumumab and showed emergence of a KRAS-mutated cell population, the interruption of therapy or treatment with a different class of compounds (e.g., a VEGF inhibitor) correlated with a reduction of KRASmutant allelic fraction in plasma, as assessed with liquid biopsy (18,116). In a patient-derived xenograft model of melanoma displaying resistance to BRAF inhibition, intermittent dosing of vemurafenib led to long-term control of tumor growth, unlike continuous treatment (117), in line with the observation of responses upon rechallenge in patients with melanoma with acquired resistance to BRAF inhibitors (118,119).…”

BRAF Inhibitor Resistance Mechanisms in Metastatic Melanoma: Spectrum and Clinical Impact

“…For instance, only one of the two phenotypically distinct nodules within a vemurafenib-resistant tumor (patient 24) contained mutant N-RAS. Similarly, two subclonal N-RAS mutations were identified within a single vemurafenib-resistant metastasis (42), and multiple mechanisms of resistance were detected, but did not coexist, in single-cell derived dabrafenib-resistant melanoma clones (43).…”

“…Several investigators have reported heterogeneity of BRAF inhibitor resistance mechanisms in subcutaneous and nodal melanoma metastases (12,39,42). These data indicate that selecting an effective secondary treatment, after progression on BRAF inhibitor therapy, based on the examination of a single progressing biopsy is unlikely to be effective.…”