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Hoolachan JM, McCallion E, Sutton ER, Çetin Ö, Pacheco-Torres P, Dimitriadi M, Sari S, Miller GJ, Okoh M, Walter LM, Claus P, Wood MJA, Tonge DP, Bowerman M. A transcriptomics-based drug repositioning approach to identify drugs with similar activities for the treatment of muscle pathologies in spinal muscular atrophy (SMA) models. Hum Mol Genet 2024; 33:400-425. [PMID: 37947217 PMCID: PMC10877467 DOI: 10.1093/hmg/ddad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/08/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a genetic neuromuscular disorder caused by the reduction of survival of motor neuron (SMN) protein levels. Although three SMN-augmentation therapies are clinically approved that significantly slow down disease progression, they are unfortunately not cures. Thus, complementary SMN-independent therapies that can target key SMA pathologies and that can support the clinically approved SMN-dependent drugs are the forefront of therapeutic development. We have previously demonstrated that prednisolone, a synthetic glucocorticoid (GC) improved muscle health and survival in severe Smn-/-;SMN2 and intermediate Smn2B/- SMA mice. However, long-term administration of prednisolone can promote myopathy. We thus wanted to identify genes and pathways targeted by prednisolone in skeletal muscle to discover clinically approved drugs that are predicted to emulate prednisolone's activities. Using an RNA-sequencing, bioinformatics, and drug repositioning pipeline on skeletal muscle from symptomatic prednisolone-treated and untreated Smn-/-; SMN2 SMA and Smn+/-; SMN2 healthy mice, we identified molecular targets linked to prednisolone's ameliorative effects and a list of 580 drug candidates with similar predicted activities. Two of these candidates, metformin and oxandrolone, were further investigated in SMA cellular and animal models, which highlighted that these compounds do not have the same ameliorative effects on SMA phenotypes as prednisolone; however, a number of other important drug targets remain. Overall, our work further supports the usefulness of prednisolone's potential as a second-generation therapy for SMA, identifies a list of potential SMA drug treatments and highlights improvements for future transcriptomic-based drug repositioning studies in SMA.
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Affiliation(s)
- Joseph M Hoolachan
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Eve McCallion
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Emma R Sutton
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Özge Çetin
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Paloma Pacheco-Torres
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, AL910 9AB, United Kingdom
| | - Maria Dimitriadi
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, AL910 9AB, United Kingdom
| | - Suat Sari
- Department of Pharmaceutical Chemistry, Hacettepe University, Ankara, 06100, Turkey
- School of Chemical and Physical Sciences, Lennard-Jones Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Gavin J Miller
- School of Chemical and Physical Sciences, Lennard-Jones Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
- Centre for Glycoscience, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Magnus Okoh
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Lisa M Walter
- SMATHERIA gGmbH – Non-Profit Biomedical Research Institute, Feodor-Lynen-Straße 31, 30625, Hannover, Germany
- Centre of Systems Neuroscience (ZSN), Hannover Medical School, Bünteweg 2, 30559, Hannover, Germany
| | - Peter Claus
- SMATHERIA gGmbH – Non-Profit Biomedical Research Institute, Feodor-Lynen-Straße 31, 30625, Hannover, Germany
- Centre of Systems Neuroscience (ZSN), Hannover Medical School, Bünteweg 2, 30559, Hannover, Germany
| | - Matthew J A Wood
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe, Headington Oxford, OX3 9DU, United Kingdom
| | - Daniel P Tonge
- School of Life Sciences, Huxley Building, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Melissa Bowerman
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, United Kingdom
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Pagnamenta AT, Kaiyrzhanov R, Zou Y, Da'as SI, Maroofian R, Donkervoort S, Dominik N, Lauffer M, Ferla MP, Orioli A, Giess A, Tucci A, Beetz C, Sedghi M, Ansari B, Barresi R, Basiri K, Cortese A, Elgar G, Fernandez-Garcia MA, Yip J, Foley AR, Gutowski N, Jungbluth H, Lassche S, Lavin T, Marcelis C, Marks P, Marini-Bettolo C, Medne L, Moslemi AR, Sarkozy A, Reilly MM, Muntoni F, Millan F, Muraresku CC, Need AC, Nemeth AH, Neuhaus SB, Norwood F, O'Donnell M, O'Driscoll M, Rankin J, Yum SW, Zolkipli-Cunningham Z, Brusius I, Wunderlich G, Karakaya M, Wirth B, Fakhro KA, Tajsharghi H, Bönnemann CG, Taylor JC, Houlden H. An ancestral 10-bp repeat expansion in VWA1 causes recessive hereditary motor neuropathy. Brain 2021; 144:584-600. [PMID: 33559681 PMCID: PMC8263055 DOI: 10.1093/brain/awaa420] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/16/2020] [Accepted: 10/15/2020] [Indexed: 01/26/2023] Open
Abstract
The extracellular matrix comprises a network of macromolecules such as collagens, proteoglycans and glycoproteins. VWA1 (von Willebrand factor A domain containing 1) encodes a component of the extracellular matrix that interacts with perlecan/collagen VI, appears to be involved in stabilizing extracellular matrix structures, and demonstrates high expression levels in tibial nerve. Vwa1-deficient mice manifest with abnormal peripheral nerve structure/function; however, VWA1 variants have not previously been associated with human disease. By interrogating the genome sequences of 74 180 individuals from the 100K Genomes Project in combination with international gene-matching efforts and targeted sequencing, we identified 17 individuals from 15 families with an autosomal-recessive, non-length dependent, hereditary motor neuropathy and rare biallelic variants in VWA1. A single disease-associated allele p.(G25Rfs*74), a 10-bp repeat expansion, was observed in 14/15 families and was homozygous in 10/15. Given an allele frequency in European populations approaching 1/1000, the seven unrelated homozygote individuals ascertained from the 100K Genomes Project represents a substantial enrichment above expected. Haplotype analysis identified a shared 220 kb region suggesting that this founder mutation arose >7000 years ago. A wide age-range of patients (6-83 years) helped delineate the clinical phenotype over time. The commonest disease presentation in the cohort was an early-onset (mean 2.0 ± 1.4 years) non-length-dependent axonal hereditary motor neuropathy, confirmed on electrophysiology, which will have to be differentiated from other predominantly or pure motor neuropathies and neuronopathies. Because of slow disease progression, ambulation was largely preserved. Neurophysiology, muscle histopathology, and muscle MRI findings typically revealed clear neurogenic changes with single isolated cases displaying additional myopathic process. We speculate that a few findings of myopathic changes might be secondary to chronic denervation rather than indicating an additional myopathic disease process. Duplex reverse transcription polymerase chain reaction and immunoblotting using patient fibroblasts revealed that the founder allele results in partial nonsense mediated decay and an absence of detectable protein. CRISPR and morpholino vwa1 modelling in zebrafish demonstrated reductions in motor neuron axonal growth, synaptic formation in the skeletal muscles and locomotive behaviour. In summary, we estimate that biallelic variants in VWA1 may be responsible for up to 1% of unexplained hereditary motor neuropathy cases in Europeans. The detailed clinical characterization provided here will facilitate targeted testing on suitable patient cohorts. This novel disease gene may have previously evaded detection because of high GC content, consequential low coverage and computational difficulties associated with robustly detecting repeat-expansions. Reviewing previously unsolved exomes using lower QC filters may generate further diagnoses.
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Affiliation(s)
- Alistair T Pagnamenta
- NIHR Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Yaqun Zou
- Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, National Institutes of Health, Bethesda, MD, USA
| | - Sahar I Da'as
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, National Institutes of Health, Bethesda, MD, USA
| | - Natalia Dominik
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Marlen Lauffer
- Institute of Human Genetics, Center for Molecular Medicine Cologne (CMMC), Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Matteo P Ferla
- NIHR Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Andrea Orioli
- William Harvey Research Institute, Queen Mary University of London, London, UK
- Genomics England, London, UK
| | - Adam Giess
- William Harvey Research Institute, Queen Mary University of London, London, UK
- Genomics England, London, UK
| | - Arianna Tucci
- William Harvey Research Institute, Queen Mary University of London, London, UK
- Genomics England, London, UK
| | | | - Maryam Sedghi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Behnaz Ansari
- Department of Neurology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rita Barresi
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Keivan Basiri
- Department of Neurology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Andrea Cortese
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Greg Elgar
- William Harvey Research Institute, Queen Mary University of London, London, UK
- Genomics England, London, UK
| | - Miguel A Fernandez-Garcia
- Department of Paediatric Neurology - Neuromuscular Service, Evelina Children's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Janice Yip
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, National Institutes of Health, Bethesda, MD, USA
| | - Nicholas Gutowski
- Department of Neurology, Royal Devon and Exeter NHS Trust, Exeter, UK
| | - Heinz Jungbluth
- Department of Paediatric Neurology - Neuromuscular Service, Evelina Children's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
- Randall Division of Cell and Molecular Biophysics Muscle Signalling Section, King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Saskia Lassche
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Tim Lavin
- Department of Neurology, Salford Royal NHS Foundation Trust, Manchester, UK
| | - Carlo Marcelis
- Department of Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Peter Marks
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - Chiara Marini-Bettolo
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Livija Medne
- Divisions of Neurology and Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ali-Reza Moslemi
- Department of Pathology, University of Gothenburg, Sahlgrenska University Hospital, Sweden
| | - Anna Sarkozy
- The Dubowitz Neuromuscular Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, and Great Ormond Street Hospital Trust, London, UK
| | - Mary M Reilly
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Francesco Muntoni
- The Dubowitz Neuromuscular Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, and Great Ormond Street Hospital Trust, London, UK
| | | | - Colleen C Muraresku
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, PA, USA
| | - Anna C Need
- William Harvey Research Institute, Queen Mary University of London, London, UK
- Genomics England, London, UK
| | - Andrea H Nemeth
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Sarah B Neuhaus
- Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, National Institutes of Health, Bethesda, MD, USA
| | - Fiona Norwood
- Department of Neurology, King's College Hospital, London, UK
| | - Marie O'Donnell
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - Mary O'Driscoll
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - Julia Rankin
- Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Trust, Exeter, UK
| | - Sabrina W Yum
- Division of Pediatric Neurology, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Zarazuela Zolkipli-Cunningham
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA, USA
| | - Isabell Brusius
- Institute of Human Genetics, Center for Molecular Medicine Cologne (CMMC), Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Gilbert Wunderlich
- Department of Neurology, Center for Rare Diseases Cologne, University Hospital Cologne, Cologne, Germany
| | - Mert Karakaya
- Institute of Human Genetics, Center for Molecular Medicine Cologne (CMMC), Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne (CMMC), Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, Doha, Qatar
| | - Homa Tajsharghi
- School of Health Science, Division Biomedicine and Translational Medicine, University of Skovde, Sweden
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, National Institutes of Health, Bethesda, MD, USA
| | - Jenny C Taylor
- NIHR Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
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3
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Beecroft SJ, Cortese A, Sullivan R, Yau WY, Dyer Z, Wu TY, Mulroy E, Pelosi L, Rodrigues M, Taylor R, Mossman S, Leadbetter R, Cleland J, Anderson T, Ravenscroft G, Laing NG, Houlden H, Reilly MM, Roxburgh RH. A Māori specific RFC1 pathogenic repeat configuration in CANVAS, likely due to a founder allele. Brain 2020; 143:2673-2680. [PMID: 32851396 PMCID: PMC7526724 DOI: 10.1093/brain/awaa203] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/12/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
Cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS) is a recently recognized neurodegenerative disease with onset in mid- to late adulthood. The genetic basis for a large proportion of Caucasian patients was recently shown to be the biallelic expansion of a pentanucleotide (AAGGG)n repeat in RFC1. Here, we describe the first instance of CANVAS genetic testing in New Zealand Māori and Cook Island Māori individuals. We show a novel, possibly population-specific CANVAS configuration (AAAGG)10-25(AAGGG)exp, which was the cause of CANVAS in all patients. There were no apparent phenotypic differences compared with European CANVAS patients. Presence of a common disease haplotype among this cohort suggests this novel repeat expansion configuration is a founder effect in this population, which may indicate that CANVAS will be especially prevalent in this group. Haplotype dating estimated the most recent common ancestor at ∼1430 ce. We also show the same core haplotype as previously described, supporting a single origin of the CANVAS mutation.
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Affiliation(s)
- Sarah J Beecroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Andrea Cortese
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
- Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Roisin Sullivan
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Wai Yan Yau
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Zoe Dyer
- Neurology Department, Auckland City Hospital, Auckland, New Zealand
| | - Teddy Y Wu
- Department of Neurology, Christchurch Hospital, Christchurch, New Zealand
| | - Eoin Mulroy
- Neurology Department, Auckland City Hospital, Auckland, New Zealand
| | - Luciana Pelosi
- Neurology Department, Auckland City Hospital, Auckland, New Zealand
| | - Miriam Rodrigues
- Neurology Department, Auckland City Hospital, Auckland, New Zealand
| | - Rachael Taylor
- Centre for Brain Research Neurogenetics Research Clinic, University of Auckland, Auckland, New Zealand
| | - Stuart Mossman
- Neurology Department, Wellington Hospital, Wellington, New Zealand
| | - Ruth Leadbetter
- Neurology Department, Wellington Hospital, Wellington, New Zealand
| | - James Cleland
- Neurology Department, Tauranga Hospital, Tauranga, New Zealand
| | - Tim Anderson
- Department of Neurology, Christchurch Hospital, Christchurch, New Zealand
| | - Gianina Ravenscroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Nigel G Laing
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Mary M Reilly
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Richard H Roxburgh
- Neurology Department, Auckland City Hospital, Auckland, New Zealand
- Centre for Brain Research Neurogenetics Research Clinic, University of Auckland, Auckland, New Zealand
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