TERT, BRAF, and NRAS Mutational Heterogeneity between Paired Primary and Metastatic Melanoma Tumors

Abstract

Mutational heterogeneity can contribute to therapeutic resistance in solid cancers. In melanoma, the frequencies of intertumoral and intratumoral heterogeneity are controversial. We examined mutational heterogeneity within individual patients with melanoma using multiplatform analysis of commonly mutated driver and nonpassenger genes. We analyzed paired primary and metastatic tumors from 60 patients and multiple metastatic tumors from 39 patients whose primary tumors were unavailable (n ¼ 271 tumors). We used a combination of multiplex SNaPshot assays, Sanger sequencing, mutation-specific PCR, or droplet digital PCR to determine the presence of BRAF V600 , NRAS Q61 , TERT e124C>T , and TERT e146C>T mutations. Mutations were detected in BRAF (39%), NRAS (21%), and/or TERT (78%). Thirteen patients had TERT mutant discordant tumors; seven of these had a single tumor with both TERT e124C>T and TERT e146C>T mutations present at different allele frequencies. Two patients had both BRAF and NRAS mutations; one had different tumors and the other had a single tumor with both mutations. One patient with a BRAF mutant primary lacked mutant BRAF in at least one of their metastases. Overall, we identified mutational heterogeneity in 18 of 99 patients (18%). These results suggest that some primary melanomas may be composed of subclones with differing mutational profiles. Such heterogeneity may be relevant to treatment responses and survival outcomes.

SnapshotDx Quiz: November 2020

“…The article by Chang et al (2020) and other previously published reports support the concept of subclones within melanoma tumors, although they raise questions regarding the truncal nature of BRAF mutations in all cases. Examples of patients who appear to acquire BRAF mutations after the development of metastases have been described because they were not detected in the paired primary tumors from the same patients (Chang et al, 2020). Although initially considered to be consistent with a tumor evolution model characterized by the acquisition of mutations, because of lack of sampling of mutant cells in the primary tumor, this finding raises the possibility that BRAF mutations are not necessarily truncal mutations in all cases.…”

“…MBC is negative for melanocytic markers, including MART-1, S100, and SOX10 stains. Chang et al (2020), the absence of a presumed truncal driver mutation among one or more metastatic tumors arising from a primary mutation may be due to which of the following?…”

“…In the current model of branched evolution used to describe melanoma, clones stem from a driver or truncal mutation such as BRAF, and subclones (i.e., branches) are defined by the acquisition of subsequent mutations such as TERT (Davis et al, 2017;Shain et al, 2015). The article by Chang et al (2020) and other previously published reports support the concept of subclones within melanoma tumors, although they raise questions regarding the truncal nature of BRAF mutations in all cases. Examples of patients who appear to acquire BRAF mutations after the development of metastases have been described because they were not detected in the paired primary tumors from the same patients (Chang et al, 2020).…”

“…In the article by Chang et al (2020), mutational heterogeneity was observed in the three most commonly mutated genes in melanoma. According to the authors, the results suggest that known driver mutations may be subclonal in primary www.jidonline.org e123 melanomas, although likely in a minority of cases.…”

“…b. An undiagnosed second primary tumor: To address the concern regarding second-order primary melanomas, the authors of the study obtained the tumor samples from a prospective clinical-pathologic biorepository that included complete clinical data and protocol-driven follow-up and included second primary tumors in the few patients in whom they occurred (Chang et al, 2020). The authors found BRAF, NRAS, and TERT mutational heterogeneity in 7%, 3%, and 13% of these patients, respectively.…”