Genetic/epigenetic effects in NF1 microdeletion syndrome: beyond the haploinsuffi-ciency, looking at the contribution of not deleted genes

NF1 microdeletion syndrome, accounting for 5-11% of NF1 patients, is characterized by a more severe phenotype compared to patients carrying intragenic NF1 mutation. Despite 70% of NF1 microdeletion patients presents the same 1.4 Mb type-I deletion, they show variable expressivity. The contribution of different pathogenic mechanisms, besides haploinsufficiency of some genes included in the deletion interval, is expected. We verified the occurrence of position effect, pseudo-dominance and variants in possible modifier genes in 22 type-I NF1 microdeletion patients. The expression dysregulation of genes flanking the deletion assessed by qRT-PCR shows position effect of 17q11.2 deleted region, with alterations of Topological Associating Domains and changes of chromatin interactions by 4C-seq analysis, not only in the region flanking the deletion, but also in the deletion interval, on the homologous chromosome. Interestingly, hypo-expression of ZNF207 flanking gene, associated to an altered differentiation of ectoderm, could have a role in cutaneous and neurological NF1 clinical traits. While haploinsufficiency and position effect should account for pathognomonic clinical signs, the variable phenotype should be correlated to variants with a genetic modifier significance. By targeted NGS analysis, we identified two likely pathogenic rare variants in RAF1 and RASA1 genes, possibly contributing to incidental phenotypic features like tumor development. This pivotal study, based on a wide analysis of both genetic and epigenetic effects of 17q11.2 microdeletion, provides new insights on the comprehension of NF1 microdeletion syndrome pathogenesis. This approach can be applied to unravel the pathomechanisms of microdeletion syndromes, improving precision medicine, prognosis and follow up for patients.