Functional characterization of the 9q34.13 locus identifies RAPGEF1 as modulating risk for melanoma and nevi via RAS activation

Genome-wide association studies identified a melanoma- and nevus count-associated locus on chromosome band 9q34.13. Fine-mapping and melanocyte expression data collectively suggest two potential causal genes with opposite association with risk: higher levels of Rap guanine nucleotide exchange factor 1 (<i>RAPGEF1</i>) and lower levels of uridine-cytidine kinase 1 (<i>UCK1</i>). Colocalization analyses and conditional TWAS suggest multiple causal <i>cis</i>-regulatory sequence variants in partial linkage disequilibrium (LD) to each other. Melanocyte capture-HiC and CRISPR-inhibition demonstrated regulatory interactions between fine-mapped variants and the <i>RAPGEF1</i> and <i>UCK1</i> promoters. Focusing on <i>RAPGEF1</i>, we demonstrate <i>RAPGEF1</i> expression promotes melanocyte growth and drives malignant transformation of human immortalized melanocytes. Following treatment with human EGF, <i>RAPGEF1</i> overexpression activated both RAP1 and RAS. Further, we show <i>RAPGEF1</i> expression is significantly enriched in melanomas lacking strongly activating RAS-MAPK mutations, suggesting that <i>RAPGEF1</i> may promote oncogenic RAS-MAPK signaling in melanomas. Furthermore, in these tumors, we provide preliminary evidence to support the prognostic relevance of <i>RAPGEF1</i> expression in patients lacking <i>RAS</i> or <i>BRAF</i> mutations. Together with other recent studies, these data suggest that germline variation influencing RAS activation may play a key role in nevus development and melanoma risk.