Functional Classification of the ATM Variant c.7157C>A and In Vitro Effects of Dexamethasone.

Sara Biagiotti,Marco Malatesta,Mattia Paolo Aliano,Silvia Soddu,Caterina Caputi,Giulia Federici,Mauro Magnani,Ambra Barone,Luciana Chessa,Vincenzo Leuzzi

doi:10.3389/fgene.2021.759467

Abstract

Most of the ATM variants associated with Ataxia Telangiectasia are still classified as variants with uncertain significance. Ataxia Telangiectasia is a multisystemic disorder characterized by “typical” and “atypical” phenotypes, with early-onset and severe symptoms or with late-onset and mild symptoms, respectively. Here we classified the c.7157C > A ATM variant found in homozygosity in two brothers of Lebanese ethnicity. The brothers presented with an atypical phenotype, showing less than 50% of the positive criteria considered for classification. We performed several in silico analyses to predict the effect of c.7157C > A at the DNA, mRNA and protein levels, revealing that the alteration causes a missense substitution in a highly conserved alpha helix in the FAT domain. 3D structural analyses suggested that the variant might be pathogenic due to either loss of activity or to a structural damage affecting protein stability. Our subsequent in vitro studies showed that the second hypothesis is the most likely, as indicated by the reduced protein abundance found in the cells carrying the variant. Moreover, two different functional assays showed that the mutant protein partially retains its kinase activity. Finally, we investigated the in vitro effect of Dexamethasone showing that the drug is able to increase both protein abundance and activity. In conclusion, our results suggest that the c.7157C > A variant is pathogenic, although it causes an atypical phenotype, and that dexamethasone could be therapeutically effective on this and possibly other missense ATM variants.

Highlights

Ataxia Telangiectasia (AT) is a rare autosomal recessive disorder caused by biallelic mutations in the ATM gene (Savitsky et al, 1995)
The Lebanese family was identified through analysis of the fulllength ATM gene in the older child, who first reported difficulties in gait and posture; a written informed consent was obtained from the father for the use of clinical data and for the use of cell lines already deposited in the cell bank for further investigation
Similar analysis was repeated after 48 h of stimulation confirming the induction, which was maximum at 24 h (Supplementary Figure S1). These results suggest that DEX is able to increase the expression of ATM-A2386E protein, rising the protein level to about 39 and 60% compared to the basal level of the Wild-type ATM (WT-ATM) control

Summary

Introduction

Ataxia Telangiectasia (AT) is a rare autosomal recessive disorder caused by biallelic mutations in the ATM gene (Savitsky et al, 1995). Based on the type of mutation and the functionality of the resulting protein, ATM variants are classified into benign, mildly pathogenic, pathogenic, or variant with uncertain significance (VUS) when their consequences on the phenotype are not clear. Patients with AT carrying typical ATM variants have a severe clinical picture characterized by early onset ataxia before 8 years, loss of the ability to walk, oculomotor apraxia and ocular telangiectasia before the age of 15, and clinical immunodeficiency with IgA deficiency in 60% of cases (Fievet et al, 2019). AT patients with atypical variants show a less severe phenotype with late-onset ataxia after 8 years, loss of ability to walk after 15 years, and non-manifest immunodeficiency (Fievet et al, 2019)

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Conclusion