Functional and structural analyses of novel Smith-Kingsmore Syndrome-Associated MTOR variants reveal potential new mechanisms and predictors of pathogenicity.

Aaron D Besterman,Mark Nellist,Jonathan A Bernstein,Jeff Abramson,Irma Gutierrez-Mejia,Anja A Kattentidt-Mouravieva,Joshua Sadik,Yvette Van Ierland,Julian A Martinez-Agosto,Peter Elfferich,Thorsten Althoff

doi:10.1371/journal.pgen.1009651

Abstract

Smith-Kingsmore syndrome (SKS) is a rare neurodevelopmental disorder characterized by macrocephaly/megalencephaly, developmental delay, intellectual disability, hypotonia, and seizures. It is caused by dominant missense mutations in MTOR. The pathogenicity of novel variants in MTOR in patients with neurodevelopmental disorders can be difficult to determine and the mechanism by which variants cause disease remains poorly understood. We report 7 patients with SKS with 4 novel MTOR variants and describe their phenotypes. We perform in vitro functional analyses to confirm MTOR activation and interrogate disease mechanisms. We complete structural analyses to understand the 3D properties of pathogenic variants. We examine the accuracy of relative accessible surface area, a quantitative measure of amino acid side-chain accessibility, as a predictor of MTOR variant pathogenicity. We describe novel clinical features of patients with SKS. We confirm MTOR Complex 1 activation and identify MTOR Complex 2 activation as a new potential mechanism of disease in SKS. We find that pathogenic MTOR variants disproportionately cluster in hotspots in the core of the protein, where they disrupt alpha helix packing due to the insertion of bulky amino acid side chains. We find that relative accessible surface area is significantly lower for SKS-associated variants compared to benign variants. We expand the phenotype of SKS and demonstrate that additional pathways of activation may contribute to disease. Incorporating 3D properties of MTOR variants may help in pathogenicity classification. We hope these findings may contribute to improving the precision of care and therapeutic development for individuals with SKS.

Highlights

The PI3K/AKT/MTOR signaling pathway plays a central role in cellular growth and neurodevelopment
Smith-Kingsmore Syndrome is a rare disease caused by damage in a gene named MTOR that is associated with excessive growth of the head and brain, delays in development and deficits in intellectual functioning
We describe new medical findings in these patients that may be common in Smith-Kingsmore Syndrome more broadly

Summary

Introduction

The PI3K/AKT/MTOR signaling pathway plays a central role in cellular growth and neurodevelopment. Germline and somatic variants in genes within this signaling pathway, including PTEN, PIK3CA, PIK3R2, and AKT3, have been implicated in overgrowth and neurodevelopmental disorders (NDD), characterized by the excess growth of the body and/or brain, depending on the specific distribution and degree of activation of the variant [1,2]. Activating missense variants in MTOR have been implicated in a range of overgrowth disorders that can strongly impact neurodevelopment [3]. The phenotypic impact of MTOR variants depends largely on the degree of activation and somatic distribution of the variant [1]. Germline and somatic mosaic MTOR pathogenic variants [5] cause Smith-Kingsmore Syndrome (SKS), which is characterized by macrocephaly/megalencephaly, developmental delay, intellectual disability, hypotonia, and seizures [3]

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