Identification of potential common genetic modifiers of neurofibromas: a genome wide association study in 1,333 neurofibromatosis type 1 patients

Neurofibromatosis type 1 (NF1) is characterized by the highly variable and unpredictable development of benign peripheral nerve sheath tumors named cutaneous (cNFs), subcutaneous (scNFs), and plexiform (pNFs) neurofibromas.A significant genetic component in the variability of neurofibroma incidence was evidenced, but without the influence of the causative NF1 gene pathogenic variant. To identify neurofibroma modifier genes, a NF1 patient database was developed.All patients were phenotypically evaluated by a medical practitioner using a standardized questionnaire and the causal NF1 variant identified. We enrolled 1,333 NF1 patients who were genotyped for more than 7 million common variants.Genome-wide association case-only study identified a significant association in 9q21.33 for the pNFs phenotype in the discovery cohort. Twelve, three, and four regions suggestive of association at the 10-6 threshold were identified for pNFs, cNFs, and scNFs, respectively. Evidence of replication was observed for four, two, and six loci, including 168 candidate modifier protein-coding genes. Among the candidate modifier genes, some were implicated in the RAS-MAPK pathway, cell cycle control, and myelination. Using an original CRISPR/Cas9-based functional assay, we confirmed GAS1 and SPRED2 as pNFs and scNFs candidate modifiers, as their inactivation specifically affected NF1-mutant Schwann cells growth.Our study may shed new light on the pathogenesis of NF1-associated neurofibromas and will hopefully contribute to the development of personalized care for this deleterious and life-threatening condition.