Dynamic evolution of clonal composition and neoantigen landscape in recurrent metastatic melanoma with a rare combination of driver mutations.

In melanoma, initiating oncogenic mutations in BRAF or NRAS are detected in premalignant lesions that accumulate additional mutations and genomic instability as the tumour evolves to the metastatic state. Here we investigate evolution of clonal composition and neoantigen landscape in an atypical melanoma displaying recurrent cutaneous lesions over a 6-year period without development of extra-cutaneous metastases. Whole exome sequencing of 4 cutaneous lesions taken over the 6-year period identified a collection of single nucleotide variants (SNVs) and small insertions and deletions (Indels) shared amongst all tumours along with progressive selection of subclones displaying fewer SNVs. Later tumours also displayed lower neoantigen burden compared to early tumours suggesting that clonal evolution was at least in part driven by counter selection of subclones with high neoantigen burdens. Amongst the selected mutations are a missense mutation in MAP2K1 (F53Y) and an inversion on chromosome 7 generating a AKAP9-BRAF fusion. The mutant proteins cooperatively activate the MAP kinase signalling pathway confirming they are potential driver mutations of this tumour. We hence describe the long-term genetic evolution of cutaneous metastatic melanoma characterised by an unexpected phenotypic stability and neoantigen driven clonal selection.