Identification and functional assays of single-nucleotide variants of opsins genes in melanocytic tumors

Epidermal melanocytes sense solar light via the opsin-coupled signaling pathway which is involved in a range of biological functions, including regulating pigmentation, proliferation, apoptosis, and tumorigenesis. However, it remains unclear whether there are genetic variants within these opsins that affect opsin protein structure and function, and further melanocyte biological behaviors. Here, we examined single-nucleotide variants (SNVs) of five opsin (RGR, OPN1SW, OPN2, OPN4, and OPN5) genes in MM (malignant melanoma; n = 76) and MN (melanocytic nevi; n = 157), using next-generation sequencing. The effects of these pathogenic single-nucleotide variants (SNVs) on opsin structure and function were further investigated using molecular dynamics (MD) simulations, dynamic cross-correlation (DCC), and site-directed mutagenesis. In total, 107 SNV variants were identified. Of these variants, 14 nonsynonymous SNVs (nsSNVs) of opsin genes were detected, including three mutations in the RGR gene, three mutations in the OPN1SW gene, two mutations in the OPN2 gene, and six mutations in the OPN4 gene. The effect of these missense mutations on opsin function was then assessed using eight prediction tools to estimate the potential impact of an amino acid substitution. The impact of each nsSNV was investigated using MD simulations and DCC analysis. Furthermore, we performed in vitro fluorescence calcium imaging to assess the functional properties of nsSNV proteins using a site-directed mutagenesis method. Taken together, these results revealed that p.A103V (RGR), p.T167I (RGR), p.G141S (OPN1SW), p.R144C (OPN1SW), and p.S231F (OPN4) had more deleterious effects on protein structure and function among the 14 nsSNVs. Opsin gene alterations showed the low frequency of missense mutations in melanocytic tumors, and although rare, some mutations in these opsin genes disrupt the canonical function of opsin. Our findings provide new insight into the role of opsin variants in the loss of function.