Exploring NEK1 genetic variability in Italian amyotrophic lateral sclerosis patients

Abstract

Background: Mutations in NEK1, encoding for a serine/threonine kinase which regulates several biological processes, are associated with amyotrophic lateral sclerosis (ALS).

Methods: NEK1 was analysed by amplicon deep sequencing in a cohort of 1016 Italian sporadic and familial ALS patients previously screened for C9orf72, SOD1, TARDBP and FUS mutations.

Results: We identified 28 rare NEK1 variants in 29 patients (2.85%) of whom 20/782 were sporadic (2.5%), 6/107 familial (5%) and 3/127 of unknown aetiology (2.3%). Variants were classified as pathogenic (P; n = 1), likely pathogenic (LP; n = 6 in 7 patients) and of unknown significance (VUS; n = 21) according the American College of Medical Genetics and Genomics criteria. Notably, 64% of the identified variants (18/28, including 4 LP and 14 VUS) were novel. Among the 29 patients with rare NEK1 variants, 7 (of whom 5 were familial cases) had additional variants in one of the four main ALS causative genes. Moreover, 23 patients carried the already reported NEK1 p.Arg261His risk variant (VUS) alone or in addition to SOD1 mutations (n = 1) or C9orf72 repeat expansion (n = 2) and to the NEK1 p.Asp128Val variant (n = 1). Genotype-phenotype correlation analysis showed no significant differences in age at onset or survival in NEK1 variant carriers, independently on the variant type. No flail arm phenotype, but atypical features, including sensory symptoms, were present in NEK1 carriers.

Conclusion: Our study further expands NEK1 genetic variability by identifying novel rare variants and confirming ALS oligogenic nature since 19.6% of NEK1 patients also carried mutations in one of the four main ALS-associated genes.

Keywords: NEK1; ALS; Genetic screening; IPSC; Oligogenicity.

Fig. 1

Schematic representation of the NEK1 protein structure where coloured boxes represent functional protein domains. All the identified variants in our ALS cohort are reported in black if they were previously reported or in blue if they are novel. The number in each lollipop indicates the count of cases in our cohort with the respective variant

Fig. 2

Genotype–phenotype correlations for a age at onset among patients with NEK1 LoF (n = 7), missense (n = 18), the risk p.Arg261His (n = 20) variants and without any NEK1 variant (n = 743) (Kruskal–Wallis chi-squared = 2.9245, p value = 0.4034) and for b survival among patients with NEK1 LoF (n = 3), missense (n = 9), the risk p.Arg261His variant (n = 11) and without NEK1 variants (n = 418) (Log-rank p value = 0.066)