High-throughput sequencing identifies 3 novel susceptibility genes for hereditary melanoma

Cutaneous melanoma is one of the most aggressive human cancers due to its high invasiveness. Germline mutations in high-risk melanoma susceptibility genes have been associated with development hereditary melanoma; however, most genetic culprits remain elusive. To unravel novel susceptibility genes for hereditary melanoma, we performed whole exome sequencing (WES) on eight patients with multiple primary melanomas, high number of nevi, and negative for high and intermediate-risk germline mutations. Thirteen new potentially pathogenic variants were identified after bioinformatics analysis and validation. CDH23, ARHGEF40, and BRD9 were identified as the most promising susceptibility genes in hereditary melanoma. In silico analysis of CDH23 and ARHGEF40 variants provided clues for altered protein structure and function associated with the identified mutations. Then, we also evaluated the clinical value of CDH23, ARHGEF40, and BRD9 expression in sporadic melanoma by using the TCGA dataset (n = 461). No differences were observed in BRD9 expression between melanoma and normal skin samples, nor with melanoma stage, whereas ARHGEF40 was found overexpressed, and CDH23 was downregulated and its loss was associated with worse survival. Altogether, these results reveal three novel genes with clinical relevance in hereditary and sporadic melanoma.The authors are thankful for the collaboration of all departments involved from IPOLFG, Lisboa, Portugal. F.P. received a grant from National Funds through the Foundation for Science and Technology (FCT), reference SFRH/BPD/115730/2016. The authors are thankful for the financial support to Liga Portuguesa Contra o Cancro, Núcleo Regional Sul (LPCC-NRS), IPOLFG, TVI (Televisão Independente) and iNOVA4Health Research Unit (LISBOA-01-0145-FEDER-007344), co-funded by FCT/Ministério da Ciência e do Ensino Superior, through national funds, and FEDER under the PT2020 Partnership Agreement