NF1-mutated melanoma tumors harbor distinct clinical and biological characteristics

Abstract

In general, melanoma can be considered as a UV-driven disease with an aggressive metastatic course and high mutational load, with only few tumors (acral, mucosal, and uveal melanomas) not induced by sunlight and possessing a lower mutational load. The most commonly activated pathway in melanoma is the mitogen-activated protein kinase (MAPK) pathway. However, the prognostic significance of mutational stratification is unclear and needs further investigation. Here, in silico we combined mutation data from 162 melanomas subjected to targeted deep sequencing with mutation data from three published studies. Tumors from 870 patients were grouped according to BRAF, RAS, NF1 mutation or triple-wild-type status and correlated with tumor and patient characteristics. We found that the NF1-mutated subtype had a higher mutational burden and strongest UV mutation signature. Searching for co-occurring mutated genes revealed the RASopathy genes PTPN11 and RASA2, as well as another RAS domain-containing gene RASSF2 enriched in the NF1 subtype after adjustment for mutational burden. We found that a larger proportion of the NF1-mutant tumors were from males and with older age at diagnosis. Importantly, we found an increased risk of death from melanoma (disease-specific survival, DSS; HR, 1.9; 95% CI, 1.21-3.10; P = 0.046) and poor overall survival (OS; HR, 2.0; 95% CI, 1.28-2.98; P = 0.01) in the NF1 subtype, which remained significant after adjustment for age, gender, and lesion type (DSS P = 0.03, OS P = 0.06, respectively). Melanoma genomic subtypes display different biological and clinical characteristics. The poor outcome observed in the NF1 subtype highlights the need for improved characterization of this group.

Keywords: BRAF; NRAS; NF1; melanoma.

Figure 1

Flow‐chart describing the compilation of the cohort and detailed description.

Figure 2

Mutational burden in association with clinical parameters in 864 melanoma tumors. (A) The total number of somatic mutations (coding and non‐coding) was determined for each patient and further correlated to clinical factors such as tumor type, melanoma origin, gender and age. (B–D) Genetic activation of the MAPK pathway in melanoma (n = 870). A schematic overview of selected MAPK mutations in BRAF,RAS and NF1 with each gene was analyzed separately with no consideration of cross gene co‐occurring events (B). The melanoma samples were further classified into mutational subtypes based on hotspot mutations in BRAF (affecting amino acid V600 and/or K601), RAS (Q61, G12, G13) or any non‐synonymous mutation in NF1 (C), and correlated to mutational burden (D). Non‐parametric Kruskal–Wallis and Wilcoxon tests were used to calculate P‐values (A and D).

Figure 3

Mutational processes in melanoma. (A) Heatmap of signature weight values with samples ordered according to genomic subtypes and signature 7 (UV) activity. (B) Boxplot of signature 7 (UV) weight values across the four genomic subtypes. (C) Boxplot of signature 7 (UV) weight values across gene expression subtypes (excluding unclassified cases). Non‐parametric Kruskal–Wallis tests were used to calculate P‐values (B,C).

Figure 4

Five‐year survival analysis of melanomas stratified by the mutational subtypes using the Kaplan–Meier and log‐rank tests to determine (A, C) disease specific survival (DSS) and (B, D) overall survival (OS) in all tumors (A, B) and metastases only (C, D). Survival differences between the genomic groups were estimated using Kaplan–Meier analysis. P‐values have been calculated using the log‐rank test.