A novel germline NF1 splicing variant drives the onset of an anorectal mucosal melanoma in a patient with a stable and durable nivolumab response

Objective. Neurofibromatosis type-1 (NF1) patients rarely develop mucosal melanomas. We report a rare form of anorectal mucosal melanoma (ARMM) in an NF1 syndromic patient profiled for genomics and transcriptomics to assess the determinants of the response to nivolumab.

Methods. Primary melanoma and metastases were analyzed with targeted sequencing and gene expression profile (tGEP). We applied in silico (cBioPortal and predictor tools) and in vitro (hybrid minigene) approaches to confirm the variant pathogenicity.

Results. We detected the novel c.4269+2_4269+3delTG germline splicing variant in NF1, which proved to be pathogenic by the minigene assay showing an aberrant splicing. The tumor showed a copy-number (CN) neutral loss of heterozygosity for the WT allele, and both ARMM and metastases carried several CN gains associated with NF1-driven carcinogenesis and very low mutation burden. The tGEP analysis unveiled a macrophagic infiltration, with a pro-inflammatory M1-type polarization, in the context of lack of PD-L1 expression.

Conclusions. The response to nivolumab in a germline NF1-driven ARMM case seems independent from levels of TMB and PD-L1 expression and may be mediated by inflammatory response induced by M1-polarized macrophages.