Revisiting the UK Genetic Severity Score for NF2: a proposal for the addition of a functional genetic component

Abstract

BackgroundNeurofibromatosis type 2 (NF2) is an autosomal dominant disorder characterised by the development of multiple schwannomas, especially on vestibular nerves, and meningiomas. The UK NF2 Genetic Severity Score (GSS) is useful to predict the progression of the disease from germline NF2 pathogenic variants, which allows the clinical follow-up and the genetic counselling offered to affected families to be optimised.Methods52 Spanish patients were classified using the GSS, and patients’ clinical severity was measured and compared between GSS groups. The GSS was reviewed with the addition of phenotype quantification, genetic variant classification and functional assays of Merlin and its downstream pathways. Principal component analysis and regression models were used to evaluate the differences between severity and the effect of NF2 germline variants.ResultsThe GSS was validated in the Spanish NF2 cohort. However, for 25% of mosaic patients and patients harbouring variants associated with mild and moderate phenotypes, it did not perform as well for predicting clinical outcomes as it did for pathogenic variants associated with severe phenotypes. We studied the possibility of modifying the mutation classification in the GSS by adding the impact of pathogenic variants on the function of Merlin in 27 cases. This revision helped to reduce variability within NF2 mutation classes and moderately enhanced the correlation between patient phenotype and the different prognosis parameters analysed (R2=0.38 vs R2=0.32, p>0001).ConclusionsWe validated the UK NF2 GSS in a Spanish NF2 cohort, despite the significant phenotypic variability identified within it. The revision of the GSS, named Functional Genetic Severity Score, could add value for the classification of mosaic patients and patients showing mild and moderate phenotypes once it has been validated in other cohorts.

Antisense oligonucleotides targeting exon 11 are able to partially rescue the Neurofibromatosis Type 2 phenotype in vitro

“…Functionality of Merlin-e11 was studied in primary fibroblasts harbouring a heterozygous truncating variant in exon 11: one from an adult patient (Patient_ES11_1) and another from a paediatric patient (Patient_ES11_2) (Table S1). Given the complexity of determining differences in severity in the phenotype from studying the signalling pathways in which Merlin is involved [29], physiological read outs were assessed. Due to the role of Merlin in cytoskeletal organization [38,39], Merlin-e11’s functional activity was first tested through actin immunofluorescence.…”

“…The genotype-phenotype correlation of NF2 has long been studied [22][23][24][25][26][27][28][29][30]. For NF2, it is well reported that nonsense variants and large deletions, which account for around 30% of cases, are associated with severe manifestations of the disease, whereas missense, or in-frame variants present a milder form of NF2.…”

“…For NF2, it is well reported that nonsense variants and large deletions, which account for around 30% of cases, are associated with severe manifestations of the disease, whereas missense, or in-frame variants present a milder form of NF2. Besides, about 25% of the point mutations affect the correct splicing of the NF2 gene, and this mechanism is associated with a variable severity of the disease [27,29,31]. The well-known association between the genetic variant type and disease severity may constitute an opportunity to develop personalized gene therapies based on the specific variant of the NF2 gene.…”

Skin lesions in neurofibromatosis type 2: diagnostic and prognostic significance of cutaneous (plexiform) schwannomas

“…Genetic testing of blood, or tissue when available, was performed using a custom NGS Panel (I2HCP), which comprises 135 genes associated with cancer predisposition syndromes and RASopathies, 23 as described by Catasus et al 7 Patients were grouped into 6 classes using the FGSS, which predicts clinical phenotype based on the type of mutation detected, ranging from class 1 (less severe) to class 6 (most severe) (Table S1). Patients were also grouped according to phenotype severity scores calculated using well-known prognostic markers 24,25 at the time of evaluation, as described by Catasus et al 7 Phenotype severity was classified into 4 categories, where group 1 represented the most severe form of disease and group 4 the less severe (Table S2).…”

Re‐evaluation of missense variant classifications in NF2

“…Further disease‐specific guidelines are currently in development through ClinGen and other curation networks, which incorporate additional disease‐associated features into variant classification; for example, loss of heterozygosity (LOH) and retention of a missense variant in a tumor would be informative for NF2 variant classification. Recently proposed improvements in NF2 genetic severity scores suggest incorporation of merlin functional assays conducted in patient fibroblasts (Catasús et al, 2021), this evidence would be similarly valuable for NF2 variant interpretation.…”