The Driverless Triple-Wild-Type (BRAF, RAS, KIT) Cutaneous Melanoma: Whole Genome Sequencing Discoveries

Malignant melanoma of the skin develops primarily, but not exclusively, on UV-exposed skin, where the most frequent histological forms are superficial spreading and nodular melanomas. In these tumors in the vaste majority of cases (similar to 80%), the driver oncogenes are mutant BRAF, RAS and KIT. The genetic makeup of the triple-wild-type melanoma (BRAF, NRAS and NF1) has been known for some time, but those studies grouped together rare histopathological versions with common ones, as well as mucosal and even uveal ones. Here we used whole genome sequencing to genetically characterize the triple-wild-type melanoma (TWM), termed here as BRAF, RAS and KIT wild type, using the most common histological forms and excluding rare ones. All these tumors except one were UV-induced. In this driverless setting, we revealed rare oncogenic drivers known from melanoma or other cancer types and identified rare actionable tyrosine kinase mutations in NTRK1/3, RET and VEGFR1. Mutations of TWM identified genes involved in antitumor immunity, Ca++ and BMP signaling. Even with this comprehensive genomic approach, cases remained driverless in several instances, suggesting that unrecognized drivers are hiding among passenger mutations. The genetic makeup of the triple-wild-type melanoma (BRAF, NRAS and NF1) has been known for some time, but those studies grouped together rare histopathological versions with common ones, as well as mucosal and even uveal ones. Here we used whole genome sequencing to genetically characterize the triple-wild-type melanoma (TWM), termed here as BRAF, RAS and KIT wild type (the most frequent oncogenic drivers of skin melanoma), using the most common histological forms and excluding rare ones. All these tumors except one were clearly induced by UV based on the mutational signature. The tumor mutational burden was low in TWM, except in the NF1 mutant forms, and a relatively high frequency of elevated LOH scores suggested frequent homologue recombination deficiency, but this was only confirmed by the mutation signature in one case. Furthermore, all these TWMs were microsatellite-stabile. In this driverless setting, we revealed rare oncogenic drivers known from melanoma or other cancer types and identified rare actionable tyrosine kinase mutations in NTRK1, RET and VEGFR1. Mutations of TWM identified genes involved in antitumor immunity (negative and positive predictors of immunotherapy), Ca++ and BMP signaling. The two regressed melanomas of this cohort shared a 17-gene mutation signature, containing genes involved in antitumor immunity and several cell surface receptors. Even with this comprehensive genomic approach, a few cases remained driverless, suggesting that unrecognized drivers are hiding among passenger mutations.

Automated summary

Malignant melanoma of the skin, primarily on UV-exposed skin, is commonly associated with mutant BRAF, RAS, and KIT oncogenes. The genetic makeup of triple-wild-type melanoma (BRAF, NRAS, and NF1) has been studied before, but with mixed rare and common histopathological subtypes. In this study, whole genome sequencing was used to characterize triple-wild-type melanoma, excluding rare histopathological subtypes. Unrecognized drivers were identified among passenger mutations in some cases.