Targeted Genetic Screen in Amyotrophic Lateral Sclerosis Reveals Novel Genetic Variants with Synergistic Effect on Clinical Phenotype

Johnathan Cooper-Knock, Henry Robins, Isabell Niedermoser, Matthew Wyles, Paul R Heath, Adrian Higginbottom, Theresa Walsh, Mbombe Kazoka, Paul G Ince, Guillaume M Hautbergue, Christopher J McDermott, Janine Kirby, Pamela J Shaw, Project MinE ALS Sequencing Consortium

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Abstract

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.

Original languageEnglish
Pages (from-to)370
JournalFrontiers in Molecular Neuroscience
Volume10
DOIs
Publication statusPublished - 2017
Externally publishedYes

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Amyotrophic Lateral Sclerosis
Phenotype
RNA-Binding Proteins
Mutation
Prions
Genes
Carrier Proteins
DNA Sequence Analysis
Age of Onset
Disease Progression

Keywords

  • Journal Article

Cite this

Cooper-Knock, J., Robins, H., Niedermoser, I., Wyles, M., Heath, P. R., Higginbottom, A., ... Project MinE ALS Sequencing Consortium (2017). Targeted Genetic Screen in Amyotrophic Lateral Sclerosis Reveals Novel Genetic Variants with Synergistic Effect on Clinical Phenotype. Frontiers in Molecular Neuroscience, 10, 370. https://doi.org/10.3389/fnmol.2017.00370

Targeted Genetic Screen in Amyotrophic Lateral Sclerosis Reveals Novel Genetic Variants with Synergistic Effect on Clinical Phenotype. / 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.

In: Frontiers in Molecular Neuroscience, Vol. 10, 2017, p. 370.

Research output: Contribution to journalArticle

Cooper-Knock, J, Robins, H, Niedermoser, I, Wyles, M, Heath, PR, Higginbottom, A, Walsh, T, Kazoka, M, Ince, PG, Hautbergue, GM, McDermott, CJ, Kirby, J, Shaw, PJ & Project MinE ALS Sequencing Consortium 2017, 'Targeted Genetic Screen in Amyotrophic Lateral Sclerosis Reveals Novel Genetic Variants with Synergistic Effect on Clinical Phenotype', Frontiers in Molecular Neuroscience, vol. 10, pp. 370. https://doi.org/10.3389/fnmol.2017.00370
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. / Targeted Genetic Screen in Amyotrophic Lateral Sclerosis Reveals Novel Genetic Variants with Synergistic Effect on Clinical Phenotype. In: Frontiers in Molecular Neuroscience. 2017 ; Vol. 10. pp. 370.
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AU - Niedermoser, Isabell

AU - Wyles, Matthew

AU - Heath, Paul R

AU - Higginbottom, Adrian

AU - Walsh, Theresa

AU - Kazoka, Mbombe

AU - Ince, Paul G

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N2 - 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.

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