Targeted genetic screen in Amyotrophic lateral sclerosis reveals novel genetic variants with synergistic effect on clinical phenotype

• Published in: Frontiers in molecular neuroscience Vol. 10; p. 370
• Main Authors: Cooper-Knock, Johnathan, Robins, Henry, Niedermoser, Isabell, Wyles, Matthew, Heath, Paul R., Higginbottom, Adrian, Walsh, Theresa, Kazoka, Mbombe, Ince, Paul G., Hautbergue, Guillaume M., McDermott, Christopher J., Kirby, Janine, Shaw, Pamela J., Project MinE ALS Sequencing Consortium, de Carvalho, Mamede, Pinto, Susana
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers 09-11-2017; Frontiers Research Foundation; Frontiers Media S.A
• Subjects: Amyotrophic Lateral Sclerosis; C9ORF72; Consortia; Deoxyribonucleic acid; DNA; DNA sequencing; Genes; Genetic diversity; Genetic screening; Genomes; Genotype & phenotype; Genotypes; Hypotheses; Mutation; Neuroscience; Oligogenic inheritance; Pathogenesis; Patients; Phase transitions; Phenotypes; Proteins; Ribonucleic acid; RNA; RNA binding proteins; RNA-binding protein; United Kingdom > UK; oligogenic inheritance; C9ORF72; amyotrophic lateral sclerosis; DNA sequencing; RNA binding proteins
• ISSN: 1662-5099; 1662-5099
• DOI: 10.3389/fnmol.2017.00370

Copyright © 2017 Cooper-Knock, Robins, Niedermoser, Wyles, Heath, Higginbottom, Walsh, Kazoka, Project MinE ALS Sequencing Consortium, Ince, Hautbergue, McDermott, Kirby and Shaw. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Amyotrophic lateral sclerosis (ALS) is underpinned by an oligogenic rare variant architecture. Identified genetic variants of ALS include RNA-binding proteins containing prion-like domains (PrLDs). We hypothesized that screening genes encoding additional similar proteins will yield novel genetic causes of ALS. The most common genetic variant of ALS patients is a G4C2-repeat expansion within C9ORF72. We have shown that G4C2-repeat RNA sequesters RNA-binding proteins. A logical consequence of this is that loss-of-function mutations in G4C2-binding partners might contribute to ALS pathogenesis independently of and/or synergistically with C9ORF72 expansions. Targeted sequencing of genomic DNA encoding either RNA-binding proteins or known ALS genes (n = 274 genes) was performed in ALS patients to identify rare deleterious genetic variants and explore genotype-phenotype relationships. Genomic DNA was extracted from 103 ALS patients including 42 familial ALS patients and 61 young-onset (average age of onset 41 years) sporadic ALS patients; patients were chosen to maximize the probability of identifying genetic causes of ALS. Thirteen patients carried a G4C2-repeat expansion of C9ORF72. We identified 42 patients with rare deleterious variants; 6 patients carried more than one variant. Twelve mutations were discovered in known ALS genes which served as a validation of our strategy. Rare deleterious variants in RNA-binding proteins were significantly enriched in ALS patients compared to control frequencies (p = 5.31E-18). Nineteen patients featured at least one variant in a RNA-binding protein containing a PrLD. The number of variants per patient correlated with rate of disease progression (t-test, p = 0.033). We identified eighteen patients with a single variant in a G4C2-repeat binding protein. Patients with a G4C2-binding protein variant in combination with a C9ORF72 expansion had a significantly faster disease course (t-test, p = 0.025). Our data are consistent with an oligogenic model of ALS. We provide evidence for a number of entirely novel genetic variants of ALS caused by mutations in RNA-binding proteins. Moreover we show that these mutations act synergistically with each other and with C9ORF72 expansions to modify the clinical phenotype of ALS. A key finding is that this synergy is present only between functionally interacting variants. This work has significant implications for ALS therapy development.
We acknowledge grants from EU Framework 7 (Euro-Motor), and the JPND/MRC SOPHIA, STRENGTH and ALS-CarE projects. JC-K holds a NIHR Clinical Lectureship and PS is supported as an NIHR Senior Investigator. This work was also supported by the NIHR Sheffield Biomedical Research Centre and the Sheffield NIHR Clinical Research Facility.