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Thumbadoo KM, Dieriks BV, Murray HC, Swanson MEV, Yoo JH, Mehrabi NF, Turner C, Dragunow M, Faull RLM, Curtis MA, Siddique T, Shaw CE, Newell KL, Henden L, Williams KL, Nicholson GA, Scotter EL. Hippocampal aggregation signatures of pathogenic UBQLN2 in amyotrophic lateral sclerosis and frontotemporal dementia. Brain 2024:awae140. [PMID: 38703371 DOI: 10.1093/brain/awae140] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 03/03/2024] [Accepted: 03/07/2024] [Indexed: 05/06/2024] Open
Abstract
Pathogenic variants in the UBQLN2 gene cause X-linked dominant amyotrophic lateral sclerosis and/or frontotemporal dementia characterised by ubiquilin 2 aggregates in neurons of the motor cortex, hippocampus, and spinal cord. However, ubiquilin 2 neuropathology is also seen in sporadic and familial amyotrophic lateral sclerosis and/or frontotemporal dementia cases not caused by UBQLN2 pathogenic variants, particularly C9orf72-linked cases. This makes the mechanistic role of mutant ubiquilin 2 protein and the value of ubiquilin 2 pathology for predicting genotype unclear. Here we examine a cohort of 44 genotypically diverse amyotrophic lateral sclerosis cases with or without frontotemporal dementia, including eight cases with UBQLN2 variants (resulting in p.S222G, p.P497H, p.P506S, p.T487I (two cases), and p.P497L (three cases)). Using multiplexed (5-label) fluorescent immunohistochemistry, we mapped the co-localisation of ubiquilin 2 with phosphorylated TDP-43, dipeptide repeat aggregates, and p62, in the hippocampus of controls (n = 6), or amyotrophic lateral sclerosis with or without frontotemporal dementia in sporadic (n = 20), unknown familial (n = 3), SOD1-linked (n = 1), FUS-linked (n = 1), C9orf72-linked (n = 5), and UBQLN2-linked (n = 8) cases. We differentiate between i) ubiquilin 2 aggregation together with phosphorylated TDP-43 or dipeptide repeat proteins, and ii) ubiquilin 2 self-aggregation promoted by UBQLN2 pathogenic variants that cause amyotrophic lateral sclerosis/and frontotemporal dementia. Overall, we describe a hippocampal protein aggregation signature that fully distinguishes mutant from wildtype ubiquilin 2 in amyotrophic lateral sclerosis with or without frontotemporal dementia, whereby mutant ubiquilin 2 is more prone than wildtype to aggregate independently of driving factors. This neuropathological signature can be used to assess the pathogenicity of UBQLN2 gene variants and to understand the mechanisms of UBQLN2-linked disease.
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Affiliation(s)
- Kyrah M Thumbadoo
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Centre for Brain Research, University of Auckland, Auckland 1010, New Zealand
| | - Birger V Dieriks
- Centre for Brain Research, University of Auckland, Auckland 1010, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland 1010, New Zealand
| | - Helen C Murray
- Centre for Brain Research, University of Auckland, Auckland 1010, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland 1010, New Zealand
| | - Molly E V Swanson
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland 1010, New Zealand
| | - Ji Hun Yoo
- Centre for Brain Research, University of Auckland, Auckland 1010, New Zealand
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland 1010, New Zealand
| | - Nasim F Mehrabi
- Centre for Brain Research, University of Auckland, Auckland 1010, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland 1010, New Zealand
| | - Clinton Turner
- Centre for Brain Research, University of Auckland, Auckland 1010, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland 1010, New Zealand
- Department of Anatomical Pathology, LabPlus, Auckland City Hospital, Auckland 1010, New Zealand
| | - Michael Dragunow
- Centre for Brain Research, University of Auckland, Auckland 1010, New Zealand
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland 1010, New Zealand
| | - Richard L M Faull
- Centre for Brain Research, University of Auckland, Auckland 1010, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland 1010, New Zealand
| | - Maurice A Curtis
- Centre for Brain Research, University of Auckland, Auckland 1010, New Zealand
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland 1010, New Zealand
| | - Teepu Siddique
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Christopher E Shaw
- Centre for Brain Research, University of Auckland, Auckland 1010, New Zealand
- UK Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Lyndal Henden
- Macquarie University Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Kelly L Williams
- Macquarie University Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Garth A Nicholson
- Macquarie University Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Northcott Neuroscience Laboratory, Australian and New Zealand Army Corps (ANZAC) Research Institute, Concord, New South Wales 2139, Australia
- Faculty of Medicine, University of Sydney, Sydney, New South Wales 2050, Australia
- Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia
| | - Emma L Scotter
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Centre for Brain Research, University of Auckland, Auckland 1010, New Zealand
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2
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Grima N, Liu S, Southwood D, Henden L, Smith A, Lee A, Rowe DB, D'Silva S, Blair IP, Williams KL. RNA sequencing of peripheral blood in amyotrophic lateral sclerosis reveals distinct molecular subtypes: Considerations for biomarker discovery. Neuropathol Appl Neurobiol 2023; 49:e12943. [PMID: 37818590 PMCID: PMC10946588 DOI: 10.1111/nan.12943] [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: 06/08/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/12/2023]
Abstract
AIM Amyotrophic lateral sclerosis (ALS) is a heterogeneous neurodegenerative disease with limited therapeutic options. A key factor limiting the development of effective therapeutics is the lack of disease biomarkers. We sought to assess whether biomarkers for diagnosis, prognosis or cohort stratification could be identified by RNA sequencing (RNA-seq) of ALS patient peripheral blood. METHODS Whole blood RNA-seq data were generated for 96 Australian sporadic ALS (sALS) cases and 48 healthy controls (NCBI GEO accession GSE234297). Differences in sALS-control gene expression, transcript usage and predicted leukocyte proportions were assessed, with pathway analysis used to predict the activity state of biological processes. Weighted Gene Co-expression Network Analysis (WGCNA) and machine learning algorithms were applied to search for diagnostic and prognostic gene expression patterns. Unsupervised clustering analysis was employed to determine whether sALS patient subgroups could be detected. RESULTS Two hundred and forty-five differentially expressed genes were identified in sALS patients relative to controls, with enrichment of immune, metabolic and stress-related pathways. sALS patients also demonstrated switches in transcript usage across a small set of genes. We established a classification model that distinguished sALS patients from controls with an accuracy of 78% (sensitivity: 79%, specificity: 75%) using the expression of 20 genes. Clustering analysis identified four patient subgroups with gene expression signatures and immune cell proportions reflective of distinct peripheral effects. CONCLUSIONS Our findings suggest that peripheral blood RNA-seq can identify diagnostic biomarkers and distinguish molecular subtypes of sALS patients however, its prognostic value requires further investigation.
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Affiliation(s)
- Natalie Grima
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Sidong Liu
- Centre for Health InformaticsFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Dean Southwood
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Lyndal Henden
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Andrew Smith
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Albert Lee
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Dominic B. Rowe
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Susan D'Silva
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Ian P. Blair
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Kelly L. Williams
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
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3
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Ragagnin AMG, Sundaramoorthy V, Farzana F, Gautam S, Saravanabavan S, Takalloo Z, Mehta P, Do-Ha D, Parakh S, Shadfar S, Hunter J, Vidal M, Jagaraj CJ, Brocardo M, Konopka A, Yang S, Rayner SL, Williams KL, Blair IP, Chung RS, Lee A, Ooi L, Atkin JD. ALS/FTD-associated mutation in cyclin F inhibits ER-Golgi trafficking, inducing ER stress, ERAD and Golgi fragmentation. Sci Rep 2023; 13:20467. [PMID: 37993492 PMCID: PMC10665471 DOI: 10.1038/s41598-023-46802-9] [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: 04/03/2023] [Accepted: 11/05/2023] [Indexed: 11/24/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a severely debilitating neurodegenerative condition that is part of the same disease spectrum as frontotemporal dementia (FTD). Mutations in the CCNF gene, encoding cyclin F, are present in both sporadic and familial ALS and FTD. However, the pathophysiological mechanisms underlying neurodegeneration remain unclear. Proper functioning of the endoplasmic reticulum (ER) and Golgi apparatus compartments is essential for normal physiological activities and to maintain cellular viability. Here, we demonstrate that ALS/FTD-associated variant cyclin FS621G inhibits secretory protein transport from the ER to Golgi apparatus, by a mechanism involving dysregulation of COPII vesicles at ER exit sites. Consistent with this finding, cyclin FS621G also induces fragmentation of the Golgi apparatus and activates ER stress, ER-associated degradation, and apoptosis. Induction of Golgi fragmentation and ER stress were confirmed with a second ALS/FTD variant cyclin FS195R, and in cortical primary neurons. Hence, this study provides novel insights into pathogenic mechanisms associated with ALS/FTD-variant cyclin F, involving perturbations to both secretory protein trafficking and ER-Golgi homeostasis.
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Affiliation(s)
- Audrey M G Ragagnin
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Vinod Sundaramoorthy
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Fabiha Farzana
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shashi Gautam
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Sayanthooran Saravanabavan
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Zeinab Takalloo
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Prachi Mehta
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Dzung Do-Ha
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Sonam Parakh
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Sina Shadfar
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Julie Hunter
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Marta Vidal
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Cyril J Jagaraj
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mariana Brocardo
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Anna Konopka
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shu Yang
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Stephanie L Rayner
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Kelly L Williams
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ian P Blair
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Roger S Chung
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Albert Lee
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Lezanne Ooi
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Julie D Atkin
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia.
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4
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Davidson JM, Wu SSL, Rayner SL, Cheng F, Duncan K, Russo C, Newbery M, Ding K, Scherer NM, Balez R, García-Redondo A, Rábano A, Rosa-Fernandes L, Ooi L, Williams KL, Morsch M, Blair IP, Di Ieva A, Yang S, Chung RS, Lee A. The E3 Ubiquitin Ligase SCF Cyclin F Promotes Sequestosome-1/p62 Insolubility and Foci Formation and is Dysregulated in ALS and FTD Pathogenesis. Mol Neurobiol 2023; 60:5034-5054. [PMID: 37243816 PMCID: PMC10415446 DOI: 10.1007/s12035-023-03355-2] [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: 08/07/2022] [Accepted: 04/15/2023] [Indexed: 05/29/2023]
Abstract
Amyotrophic lateral sclerosis (ALS)- and frontotemporal dementia (FTD)-linked mutations in CCNF have been shown to cause dysregulation to protein homeostasis. CCNF encodes for cyclin F, which is part of the cyclin F-E3 ligase complex SCFcyclinF known to ubiquitylate substrates for proteasomal degradation. In this study, we identified a function of cyclin F to regulate substrate solubility and show how cyclin F mechanistically underlies ALS and FTD disease pathogenesis. We demonstrated that ALS and FTD-associated protein sequestosome-1/p62 (p62) was a canonical substrate of cyclin F which was ubiquitylated by the SCFcyclinF complex. We found that SCFcyclin F ubiquitylated p62 at lysine(K)281, and that K281 regulated the propensity of p62 to aggregate. Further, cyclin F expression promoted the aggregation of p62 into the insoluble fraction, which corresponded to an increased number of p62 foci. Notably, ALS and FTD-linked mutant cyclin F p.S621G aberrantly ubiquitylated p62, dysregulated p62 solubility in neuronal-like cells, patient-derived fibroblasts and induced pluripotent stem cells and dysregulated p62 foci formation. Consistently, motor neurons from patient spinal cord tissue exhibited increased p62 ubiquitylation. We suggest that the p.S621G mutation impairs the functions of cyclin F to promote p62 foci formation and shift p62 into the insoluble fraction, which may be associated to aberrant mutant cyclin F-mediated ubiquitylation of p62. Given that p62 dysregulation is common across the ALS and FTD spectrum, our study provides insights into p62 regulation and demonstrates that ALS and FTD-linked cyclin F mutant p.S621G can drive p62 pathogenesis associated with ALS and FTD.
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Affiliation(s)
- Jennilee M Davidson
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia.
| | - Sharlynn S L Wu
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Stephanie L Rayner
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Flora Cheng
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Kimberley Duncan
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Carlo Russo
- Computational NeuroSurgery (CNS) Lab, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Michelle Newbery
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW, 2522, Australia
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Kunjie Ding
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Natalie M Scherer
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Rachelle Balez
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW, 2522, Australia
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Alberto García-Redondo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER U-723), Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, SERMAS, Madrid, Spain
| | - Alberto Rábano
- Neuropathology Department and CIEN Tissue Bank, Alzheimer's Centre Reina Sofia-CIEN Foundation, 28031, Madrid, Spain
| | - Livia Rosa-Fernandes
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW, 2522, Australia
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Marco Morsch
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Antonio Di Ieva
- Computational NeuroSurgery (CNS) Lab, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Shu Yang
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Roger S Chung
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Albert Lee
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Level 1, 75 Talavera Road, Sydney, NSW, 2109, Australia
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5
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Henden L, Fearnley LG, Grima N, McCann EP, Dobson-Stone C, Fitzpatrick L, Friend K, Hobson L, Chan Moi Fat S, Rowe DB, D'Silva S, Kwok JB, Halliday GM, Kiernan MC, Mazumder S, Timmins HC, Zoing M, Pamphlett R, Adams L, Bahlo M, Blair IP, Williams KL. Short tandem repeat expansions in sporadic amyotrophic lateral sclerosis and frontotemporal dementia. Sci Adv 2023; 9:eade2044. [PMID: 37146135 PMCID: PMC10162670 DOI: 10.1126/sciadv.ade2044] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Pathogenic short tandem repeat (STR) expansions cause over 20 neurodegenerative diseases. To determine the contribution of STRs in sporadic amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), we used ExpansionHunter, REviewer, and polymerase chain reaction validation to assess 21 neurodegenerative disease-associated STRs in whole-genome sequencing data from 608 patients with sporadic ALS, 68 patients with sporadic FTD, and 4703 matched controls. We also propose a data-derived outlier detection method for defining allele thresholds in rare STRs. Excluding C9orf72 repeat expansions, 17.6% of clinically diagnosed ALS and FTD cases had at least one expanded STR allele reported to be pathogenic or intermediate for another neurodegenerative disease. We identified and validated 162 disease-relevant STR expansions in C9orf72 (ALS/FTD), ATXN1 [spinal cerebellar ataxia type 1 (SCA1)], ATXN2 (SCA2), ATXN8 (SCA8), TBP (SCA17), HTT (Huntington's disease), DMPK [myotonic dystrophy type 1 (DM1)], CNBP (DM2), and FMR1 (fragile-X disorders). Our findings suggest clinical and pathological pleiotropy of neurodegenerative disease genes and highlight their importance in ALS and FTD.
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Affiliation(s)
- Lyndal Henden
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Liam G Fearnley
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Natalie Grima
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Emily P McCann
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Carol Dobson-Stone
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Lauren Fitzpatrick
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Kathryn Friend
- SA Pathology, Women's and Children's Hospital, North Adelaide, SA 5006, Australia
| | - Lynne Hobson
- SA Pathology, Women's and Children's Hospital, North Adelaide, SA 5006, Australia
| | - Sandrine Chan Moi Fat
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Dominic B Rowe
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Department of Clinical Medicine, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Susan D'Silva
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Department of Clinical Medicine, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - John B Kwok
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Glenda M Halliday
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Matthew C Kiernan
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- Department of Neurology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Srestha Mazumder
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Hannah C Timmins
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Margaret Zoing
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
| | - Roger Pamphlett
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- Discipline of Pathology, The University of Sydney, Sydney, NSW 2050, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Lorel Adams
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Ian P Blair
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Kelly L Williams
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
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6
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McCann EP, Grima N, Fifita JA, Chan Moi Fat S, Lehnert K, Henden L, Blair IP, Williams KL. Characterising the Genetic Landscape of Amyotrophic Lateral Sclerosis: A Catalogue and Assessment of Over 1,000 Published Genetic Variants. J Neuromuscul Dis 2023; 10:1127-1141. [PMID: 37638449 PMCID: PMC10657717 DOI: 10.3233/jnd-230148] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with genetic and phenotypic heterogeneity. Pathogenic genetic variants remain the only validated cause of disease, the majority of which were discovered in familial ALS patients. While causal gene variants are a lesser contributor to sporadic ALS, an increasing number of risk alleles (low penetrance genetic variants associated with a small increase in disease risk) and variants of uncertain significance have been reported. OBJECTIVE To examine the pathogenic potential of genetic variation in ALS, we sought to characterise variant- and gene-level attributes of previously reported ALS-implicated variants. METHODS A list of 1,087 genetic variants reported in ALS to March 2021 was compiled through comprehensive literature review. Individual variants were annotated using in silico tools and databases across variant features including pathogenicity scores, localisation to protein domains, evolutionary conservation, and minor allele frequencies. Gene level attributes of genic tolerance, gene expression in ALS-relevant tissues and gene ontology terms were assessed for 33 ALS genes. Statistical analysis was performed for each characteristic, and we compared the most penetrant variants found in familial cases with risk alleles exclusive to sporadic cases, to explore genetic variant features that associate with disease penetrance. RESULTS We provide spreadsheet (hg19 and GRCh38) and variant call format (GRCh38) resources for all 1,087 reported ALS-implicated variants, including detailed summaries for each attribute. We demonstrate that the characteristics of variants found exclusively in sporadic ALS cases are less severe than those observed in familial ALS. CONCLUSIONS We provide a comprehensive, literature-derived catalogue of genetic variation in ALS thus far and reveal crucial attributes that contribute to ALS pathogenicity. Our variant- and gene-level observations highlight the complexity of genetic variation in ALS, and we discuss important implications and considerations for novel variant interpretation.
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Affiliation(s)
- Emily P. McCann
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Natalie Grima
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jennifer A. Fifita
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Sandrine Chan Moi Fat
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Klaus Lehnert
- School of Biological Sciences, Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Lyndal Henden
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ian P. Blair
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Kelly L. Williams
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
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7
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Opie-Martin S, Iacoangeli A, Topp SD, Abel O, Mayl K, Mehta PR, Shatunov A, Fogh I, Bowles H, Limbachiya N, Spargo TP, Al-Khleifat A, Williams KL, Jockel-Balsarotti J, Bali T, Self W, Henden L, Nicholson GA, Ticozzi N, McKenna-Yasek D, Tang L, Shaw PJ, Chio A, Ludolph A, Weishaupt JH, Landers JE, Glass JD, Mora JS, Robberecht W, Damme PV, McLaughlin R, Hardiman O, van den Berg L, Veldink JH, Corcia P, Stevic Z, Siddique N, Silani V, Blair IP, Fan DS, Esselin F, de la Cruz E, Camu W, Basak NA, Siddique T, Miller T, Brown RH, Al-Chalabi A, Shaw CE. The SOD1-mediated ALS phenotype shows a decoupling between age of symptom onset and disease duration. Nat Commun 2022; 13:6901. [PMID: 36371497 PMCID: PMC9653399 DOI: 10.1038/s41467-022-34620-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
Superoxide dismutase (SOD1) gene variants may cause amyotrophic lateral sclerosis, some of which are associated with a distinct phenotype. Most studies assess limited variants or sample sizes. In this international, retrospective observational study, we compare phenotypic and demographic characteristics between people with SOD1-ALS and people with ALS and no recorded SOD1 variant. We investigate which variants are associated with age at symptom onset and time from onset to death or censoring using Cox proportional-hazards regression. The SOD1-ALS dataset reports age of onset for 1122 and disease duration for 883 people; the comparator population includes 10,214 and 9010 people respectively. Eight variants are associated with younger age of onset and distinct survival trajectories; a further eight associated with younger onset only and one with distinct survival only. Here we show that onset and survival are decoupled in SOD1-ALS. Future research should characterise rarer variants and molecular mechanisms causing the observed variability.
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Affiliation(s)
- Sarah Opie-Martin
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry Psychology & Neuroscience, King's College London, SE5 8AF, London, UK
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London, London, UK
| | - Simon D Topp
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Olubunmi Abel
- Homerton University Hospital, Homerton Row, London, E9 6SR, UK
| | - Keith Mayl
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Puja R Mehta
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Blue Block 1.09, Sherrington Building, Crown St, Liverpool, L693BX, UK
- Institute of Medicine, North-Eastern Federal University, 58 Belinsky str, Yakutsk, 677000, Russia
| | - Isabella Fogh
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Harry Bowles
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Naomi Limbachiya
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Thomas P Spargo
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Ahmad Al-Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Kelly L Williams
- Macquarie University Centre for MND Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | | | - Taha Bali
- Department of Neurology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Wade Self
- Department of Neurology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Lyndal Henden
- Macquarie University Centre for MND Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Garth A Nicholson
- Macquarie University Centre for MND Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Concord Clinical School, ANZAC Research Institute, Concord Repatriation Hospital, Sydney, NSW, 2139, Australia
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20095, Cusano Milanino, MiIan, Italy
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, Center for Neurotechnology and Brain Therapeutics, Università degli Studi di Milano, Milan, Italy
| | - Diane McKenna-Yasek
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 02125, USA
| | - Lu Tang
- Department of Neurology, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, PR China
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, S10 2HQ, UK
| | - Adriano Chio
- Rita Levi Montalcini' Department of Neuroscience, University of Turin, Turin, Italy
- Neurology 1, AOU Città della Salute e della Scienza of Torino, Turin, 10124, Torino, Italy
| | - Albert Ludolph
- Department of Neurology, Ulm University, Oberer Eselsberg 45, 89081, Ulm, Germany
- German Center for Neurodegenerative Diseases, DZNE, Ulm, Germany
| | - Jochen H Weishaupt
- Department of Neurology, University of Ulm, Oberer Eselsberg 45, 89081, Ulm, Germany
- Division of Neurodegenerative Disorders, Department of Neurology, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 02125, USA
| | - Jonathan D Glass
- Department Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jesus S Mora
- ALS Unit, Department of Neurology, Hospital San Rafael, 28016, Madrid, Spain
| | - Wim Robberecht
- Neurology Department, Univeristy Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Philip Van Damme
- Neurology Department, Univeristy Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
- Neuroscience Department, KU Leuven and Center for Brain & Disease Research VIB Leuven, Leuven, Belgium
| | - Russell McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Leonard van den Berg
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Jan H Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Phillippe Corcia
- Centre de Référence pour la SLA et les Autres Maladies du Motoneurone (FILSLAN), 2 Avenue Martin Luther King, 87042, Limoges Cedex, France
- Centre de Compétences Neuropathies Amyloïdes Familiales et Autres Neuropathies Périphériques Rares (NNERF), Poitiers, France
| | - Zorica Stevic
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Studentski trg 1, Belgrade, Serbia
| | - Nailah Siddique
- Neuromuscular Disorders Program, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60208, USA
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20095, Cusano Milanino, MiIan, Italy
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, Center for Neurotechnology and Brain Therapeutics, Università degli Studi di Milano, Milan, Italy
| | - Ian P Blair
- Macquarie University Centre for MND Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Dong-Sheng Fan
- Department of Neurology, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, PR China
| | - Florence Esselin
- Reference Center for ALS and Other Rare Motoneuron Disorders, University Hospital Gui de Chauliac, 34295, Montpellier, France
| | - Elisa de la Cruz
- Reference Center for ALS and Other Rare Motoneuron Disorders, University Hospital Gui de Chauliac, 34295, Montpellier, France
| | - William Camu
- Reference Center for ALS and Other Rare Motoneuron Disorders, University Hospital Gui de Chauliac, 34295, Montpellier, France
| | - Nazli A Basak
- Koç University, School of Medicine Translational Medicine Research Center KUTTAM-NDAL, 34450, Sarıyer, Istanbul, Turkey
| | - Teepu Siddique
- Neuromuscular Disorders Program, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60208, USA
| | - Timothy Miller
- Department of Neurology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 02125, USA
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Christopher E Shaw
- UK Dementia Research Institute Centre at King's College London, School of Neuroscience, King's College London, Strand, London, WC2R 2LS, UK.
- Centre for Brain Research, University of Auckland, 85 Park Road, Grafton, Auckland, 1023, New Zealand.
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8
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Freydenzon A, Nabais MF, Lin T, Williams KL, Wallace L, Henders AK, Blair IP, Wray NR, Pamphlett R, McRae AF. Association between DNA methylation variability and self-reported exposure to heavy metals. Sci Rep 2022; 12:10582. [PMID: 35732753 PMCID: PMC9217962 DOI: 10.1038/s41598-022-13892-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
Individuals encounter varying environmental exposures throughout their lifetimes. Some exposures such as smoking are readily observed and have high personal recall; others are more indirect or sporadic and might only be inferred from long occupational histories or lifestyles. We evaluated the utility of using lifetime-long self-reported exposures for identifying differential methylation in an amyotrophic lateral sclerosis cases-control cohort of 855 individuals. Individuals submitted paper-based surveys on exposure and occupational histories as well as whole blood samples. Genome-wide DNA methylation levels were quantified using the Illumina Infinium Human Methylation450 array. We analyzed 15 environmental exposures using the OSCA software linear and MOA models, where we regressed exposures individually by methylation adjusted for batch effects and disease status as well as predicted scores for age, sex, cell count, and smoking status. We also regressed on the first principal components on clustered environmental exposures to detect DNA methylation changes associated with a more generalised definition of environmental exposure. Five DNA methylation probes across three environmental exposures (cadmium, mercury and metalwork) were significantly associated using the MOA models and seven through the linear models, with one additionally across a principal component representing chemical exposures. Methylome-wide significance for four of these markers was driven by extreme hyper/hypo-methylation in small numbers of individuals. The results indicate the potential for using self-reported exposure histories in detecting DNA methylation changes in response to the environment, but also highlight the confounded nature of environmental exposure in cohort studies.
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Affiliation(s)
- Anna Freydenzon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Marta F Nabais
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,University of Exeter Medical School, Exeter, EX2 5DW, Devon, UK
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Macquarie University, Exeter, NSW, 2109, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Macquarie University, Exeter, NSW, 2109, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Roger Pamphlett
- Brain and Mind Centre, The University of Sydney, Sydney, NSW, 2050, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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9
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Grima N, Henden L, Fearnley LG, Rowe DB, D'Silva S, Pamphlett R, Adams L, Kiernan MC, Mazumder S, Timmins HC, Zoing M, Bahlo M, Blair IP, Williams KL. NEK1 and STMN2 short tandem repeat lengths are not associated with Australian amyotrophic lateral sclerosis risk. Neurobiol Aging 2022; 116:92-95. [DOI: 10.1016/j.neurobiolaging.2022.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 10/18/2022]
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10
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Hop PJ, Zwamborn RA, Hannon E, Shireby GL, Nabais MF, Walker EM, van Rheenen W, van Vugt JJ, Dekker AM, Westeneng HJ, Tazelaar GH, van Eijk KR, Moisse M, Baird D, Khleifat AA, Iacoangeli A, Ticozzi N, Ratti A, Cooper-Knock J, Morrison KE, Shaw PJ, Basak AN, Chiò A, Calvo A, Moglia C, Canosa A, Brunetti M, Grassano M, Gotkine M, Lerner Y, Zabari M, Vourc’h P, Corcia P, Couratier P, Pardina JSM, Salas T, Dion P, Ross JP, Henderson RD, Mathers S, McCombe PA, Needham M, Nicholson G, Rowe DB, Pamphlett R, Mather KA, Sachdev PS, Furlong S, Garton FC, Henders AK, Lin T, Ngo ST, Steyn FJ, Wallace L, Williams KL, Neto MM, Cauchi RJ, Blair IP, Kiernan MC, Drory V, Povedano M, de Carvalho M, Pinto S, Weber M, Rouleau GA, Silani V, Landers JE, Shaw CE, Andersen PM, McRae AF, van Es MA, Pasterkamp RJ, Wray NR, McLaughlin RL, Hardiman O, Kenna KP, Tsai E, Runz H, Al-Chalabi A, van den Berg LH, Van Damme P, Mill J, Veldink JH. Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS. Sci Transl Med 2022; 14:eabj0264. [PMID: 35196023 PMCID: PMC10040186 DOI: 10.1126/scitranslmed.abj0264] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an estimated heritability between 40 and 50%. DNA methylation patterns can serve as proxies of (past) exposures and disease progression, as well as providing a potential mechanism that mediates genetic or environmental risk. Here, we present a blood-based epigenome-wide association study meta-analysis in 9706 samples passing stringent quality control (6763 patients, 2943 controls). We identified a total of 45 differentially methylated positions (DMPs) annotated to 42 genes, which are enriched for pathways and traits related to metabolism, cholesterol biosynthesis, and immunity. We then tested 39 DNA methylation-based proxies of putative ALS risk factors and found that high-density lipoprotein cholesterol, body mass index, white blood cell proportions, and alcohol intake were independently associated with ALS. Integration of these results with our latest genome-wide association study showed that cholesterol biosynthesis was potentially causally related to ALS. Last, DNA methylation at several DMPs and blood cell proportion estimates derived from DNA methylation data were associated with survival rate in patients, suggesting that they might represent indicators of underlying disease processes potentially amenable to therapeutic interventions.
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Affiliation(s)
- Paul J. Hop
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Ramona A.J. Zwamborn
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Gemma L. Shireby
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Marta F. Nabais
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Emma M. Walker
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Wouter van Rheenen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Joke J.F.A. van Vugt
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Annelot M. Dekker
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Henk-Jan Westeneng
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Gijs H.P. Tazelaar
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Kristel R. van Eijk
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Matthieu Moisse
- KU Leuven–University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven 3000, Belgium
- VIB, Center for Brain and Disease Research, Leuven 3000, Belgium
- University Hospitals Leuven, Department of Neurology, Leuven 3000, Belgium
| | - Denis Baird
- Translational Biology, Biogen, Boston, MA 02142, USA
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol BS8 2BN, UK
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- National Institute for Health Research Biomedical Research Centre and Dementia Unit, South London and Maudsley NHS Foundation Trust and King’s College London, London SE5 8AZ, UK
| | - Nicola Ticozzi
- Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan 20149, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan 20122, Italy
| | - Antonia Ratti
- Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan 20149, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milano 20145, Italy
| | - Jonathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Karen E. Morrison
- School of Medicine, Dentistry, and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - A. Nazli Basak
- Koc University, School of Medicine, Translational Medicine Research Center, NDAL, Istanbul, 34450, Turkey
| | - Adriano Chiò
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, SC Neurologia 1U, Turin 10126, Italy
| | - Andrea Calvo
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, SC Neurologia 1U, Turin 10126, Italy
| | - Cristina Moglia
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, SC Neurologia 1U, Turin 10126, Italy
| | - Antonio Canosa
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, SC Neurologia 1U, Turin 10126, Italy
| | - Maura Brunetti
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
| | - Maurizio Grassano
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
| | - Marc Gotkine
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center, Jerusalem 91120, Israel
| | - Yossef Lerner
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center, Jerusalem 91120, Israel
| | - Michal Zabari
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center, Jerusalem 91120, Israel
| | - Patrick Vourc’h
- Service de Biochimie et Biologie moléculaire, CHU de Tours, Tours 37044, France
- UMR 1253, Université de Tours, Inserm, Tours 37044, France
| | - Philippe Corcia
- UMR 1253, Université de Tours, Inserm, Tours 37044, France
- Centre de référence sur la SLA, CHU de Tours, Tours 37044, France
| | - Philippe Couratier
- Centre de référence sur la SLA, CHRU de Limoges, Limoges 87042, France
- UMR 1094, Université de Limoges, Inserm, Limoges 87025, France
| | | | - Teresa Salas
- Department of Neurology, Hospital La Paz-Carlos III, Madrid 28046, Spain
| | - Patrick Dion
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC H3A 2B4, Canada
| | - Jay P. Ross
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Robert D. Henderson
- Department of Neurology, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
| | - Susan Mathers
- Calvary Health Care Bethlehem, Parkdale, VIC 3195, Australia
| | - Pamela A. McCombe
- Centre for Clinical Research, University of Queensland, Brisbane, QLD 4019, Australia
| | - Merrilee Needham
- Fiona Stanley Hospital, Perth, WA 6150, Australia
- Notre Dame University, Fremantle, WA 6160, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - Garth Nicholson
- ANZAC Research Institute, Concord Repatriation General Hospital, Sydney, NSW 2139, Australia
| | - Dominic B. Rowe
- Centre for Motor Neuron Disease Research, Macquarie University, NSW 2109, Australia
| | - Roger Pamphlett
- Discipline of Pathology and Department of Neuropathology, Brain and Mind Centre, University of Sydney, Sydney, NSW 2050, Australia
| | - Karen A. Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2031, Australia
- Neuroscience Research Australia Institute, Randwick, NSW 2031, Australia
| | - Perminder S. Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2031, Australia
- Neuropsychiatric Institute, Prince of Wales Hospital, UNSW, Randwick, NSW 2031, Australia
| | - Sarah Furlong
- Centre for Motor Neuron Disease Research, Macquarie University, NSW 2109, Australia
| | - Fleur C. Garton
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Anjali K. Henders
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Tian Lin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Shyuan T. Ngo
- Centre for Clinical Research, University of Queensland, Brisbane, QLD 4019, Australia
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Frederik J. Steyn
- Centre for Clinical Research, University of Queensland, Brisbane, QLD 4019, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Kelly L. Williams
- Centre for Motor Neuron Disease Research, Macquarie University, NSW 2109, Australia
| | | | | | | | - Ruben J. Cauchi
- Center for Molecular Medicine and Biobanking and Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, 2023 Msida, Malta
| | - Ian P. Blair
- Centre for Motor Neuron Disease Research, Macquarie University, NSW 2109, Australia
| | - Matthew C. Kiernan
- Brain and Mind Centre, University of Sydney, Sydney, NSW, 2050, Australia
- Department of Neurology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Vivian Drory
- Department of Neurology, Tel-Aviv Sourasky Medical Centre, Tel-Aviv 64239, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Monica Povedano
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, L’Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Mamede de Carvalho
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon 1649-028, Portugal
| | - Susana Pinto
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon 1649-028, Portugal
| | - Markus Weber
- Neuromuscular Diseases Unit/ALS Clinic, Kantonsspital St. Gallen, 9007 St. Gallen, Switzerland
| | - Guy A. Rouleau
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC H3A 2B4, Canada
| | - Vincenzo Silani
- Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan 20149, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan 20122, Italy
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Christopher E. Shaw
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Peter M. Andersen
- Department of Clinical Science, Umeå University, Umeå SE-901 85, Sweden
| | - Allan F. McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Michael A. van Es
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - R. Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, 3584 CX, Netherlands
| | - Naomi R. Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Russell L. McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Kevin P. Kenna
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, 3584 CX, Netherlands
| | - Ellen Tsai
- Translational Biology, Biogen, Boston, MA 02142, USA
| | - Heiko Runz
- Translational Biology, Biogen, Boston, MA 02142, USA
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- King’s College Hospital, Denmark Hill, London SE5 9RS, UK
| | - Leonard H. van den Berg
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Philip Van Damme
- KU Leuven–University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven 3000, Belgium
- VIB, Center for Brain and Disease Research, Leuven 3000, Belgium
- University Hospitals Leuven, Department of Neurology, Leuven 3000, Belgium
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Jan H. Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
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11
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Grima N, Henden L, Watson O, Blair IP, Williams KL. Simultaneous Isolation of High-Quality RNA and DNA From Postmortem Human Central Nervous System Tissues for Omics Studies. J Neuropathol Exp Neurol 2021; 81:135-145. [PMID: 34939123 DOI: 10.1093/jnen/nlab129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Multi-omics approaches are increasingly being adopted to understand the complex networks underlying disease. The coisolation of high-quality nucleotides from affected tissues is paramount for the parallel analysis of transcriptomic, genomic, and epigenomic data sets. Although nucleotides extracted from postmortem central nervous system (CNS) tissue are widely used in the study of neurodegenerative disease, assessment of methods for the simultaneous isolation of DNA and RNA is limited. Herein, we describe a strategy for the isolation of high-quality DNA and RNA from postmortem human tissue from 7 CNS regions. Motor cortex, frontal cortex, hippocampus, occipital cortex, anterior cingulate cortex, cerebellum, and spinal cord tissues were obtained from 22 individuals diagnosed with motor neuron disease (MND) and 13 neurologically normal controls (n = 245 tissues). We demonstrated that the Qiagen AllPrep DNA/RNA kit consistently isolated DNA and RNA of high yield and quality from all 6 brain regions. Importantly, phenol-chloroform-based extraction was required to isolate high-yield RNA from spinal cord. RNA sequencing using RNA extracted from 6 CNS regions (n = 60) generated high-quality transcriptomes. Hierarchical clustering of data from motor cortex, using an MND susceptibility gene panel and marker genes of disease-associated microglia, demonstrated that MND-specific gene expression signatures could be detected in the transcriptome data.
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Affiliation(s)
- Natalie Grima
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
| | - Lyndal Henden
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
| | - Owen Watson
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
| | - Ian P Blair
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
| | - Kelly L Williams
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
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12
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van Rheenen W, van der Spek RAA, Bakker MK, van Vugt JJFA, Hop PJ, Zwamborn RAJ, de Klein N, Westra HJ, Bakker OB, Deelen P, Shireby G, Hannon E, Moisse M, Baird D, Restuadi R, Dolzhenko E, Dekker AM, Gawor K, Westeneng HJ, Tazelaar GHP, van Eijk KR, Kooyman M, Byrne RP, Doherty M, Heverin M, Al Khleifat A, Iacoangeli A, Shatunov A, Ticozzi N, Cooper-Knock J, Smith BN, Gromicho M, Chandran S, Pal S, Morrison KE, Shaw PJ, Hardy J, Orrell RW, Sendtner M, Meyer T, Başak N, van der Kooi AJ, Ratti A, Fogh I, Gellera C, Lauria G, Corti S, Cereda C, Sproviero D, D'Alfonso S, Sorarù G, Siciliano G, Filosto M, Padovani A, Chiò A, Calvo A, Moglia C, Brunetti M, Canosa A, Grassano M, Beghi E, Pupillo E, Logroscino G, Nefussy B, Osmanovic A, Nordin A, Lerner Y, Zabari M, Gotkine M, Baloh RH, Bell S, Vourc'h P, Corcia P, Couratier P, Millecamps S, Meininger V, Salachas F, Mora Pardina JS, Assialioui A, Rojas-García R, Dion PA, Ross JP, Ludolph AC, Weishaupt JH, Brenner D, Freischmidt A, Bensimon G, Brice A, Durr A, Payan CAM, Saker-Delye S, Wood NW, Topp S, Rademakers R, Tittmann L, Lieb W, Franke A, Ripke S, Braun A, Kraft J, Whiteman DC, Olsen CM, Uitterlinden AG, Hofman A, Rietschel M, Cichon S, Nöthen MM, Amouyel P, Traynor BJ, Singleton AB, Mitne Neto M, Cauchi RJ, Ophoff RA, Wiedau-Pazos M, Lomen-Hoerth C, van Deerlin VM, Grosskreutz J, Roediger A, Gaur N, Jörk A, Barthel T, Theele E, Ilse B, Stubendorff B, Witte OW, Steinbach R, Hübner CA, Graff C, Brylev L, Fominykh V, Demeshonok V, Ataulina A, Rogelj B, Koritnik B, Zidar J, Ravnik-Glavač M, Glavač D, Stević Z, Drory V, Povedano M, Blair IP, Kiernan MC, Benyamin B, Henderson RD, Furlong S, Mathers S, McCombe PA, Needham M, Ngo ST, Nicholson GA, Pamphlett R, Rowe DB, Steyn FJ, Williams KL, Mather KA, Sachdev PS, Henders AK, Wallace L, de Carvalho M, Pinto S, Petri S, Weber M, Rouleau GA, Silani V, Curtis CJ, Breen G, Glass JD, Brown RH, Landers JE, Shaw CE, Andersen PM, Groen EJN, van Es MA, Pasterkamp RJ, Fan D, Garton FC, McRae AF, Davey Smith G, Gaunt TR, Eberle MA, Mill J, McLaughlin RL, Hardiman O, Kenna KP, Wray NR, Tsai E, Runz H, Franke L, Al-Chalabi A, Van Damme P, van den Berg LH, Veldink JH. Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology. Nat Genet 2021; 53:1636-1648. [PMID: 34873335 PMCID: PMC8648564 DOI: 10.1038/s41588-021-00973-1] [Citation(s) in RCA: 170] [Impact Index Per Article: 56.7] [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: 03/12/2021] [Accepted: 10/18/2021] [Indexed: 02/01/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a lifetime risk of one in 350 people and an unmet need for disease-modifying therapies. We conducted a cross-ancestry genome-wide association study (GWAS) including 29,612 patients with ALS and 122,656 controls, which identified 15 risk loci. When combined with 8,953 individuals with whole-genome sequencing (6,538 patients, 2,415 controls) and a large cortex-derived expression quantitative trait locus (eQTL) dataset (MetaBrain), analyses revealed locus-specific genetic architectures in which we prioritized genes either through rare variants, short tandem repeats or regulatory effects. ALS-associated risk loci were shared with multiple traits within the neurodegenerative spectrum but with distinct enrichment patterns across brain regions and cell types. Of the environmental and lifestyle risk factors obtained from the literature, Mendelian randomization analyses indicated a causal role for high cholesterol levels. The combination of all ALS-associated signals reveals a role for perturbations in vesicle-mediated transport and autophagy and provides evidence for cell-autonomous disease initiation in glutamatergic neurons.
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Affiliation(s)
- Wouter van Rheenen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| | - Rick A A van der Spek
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Mark K Bakker
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Joke J F A van Vugt
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Paul J Hop
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ramona A J Zwamborn
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Niek de Klein
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Olivier B Bakker
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Patrick Deelen
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Gemma Shireby
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Matthieu Moisse
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Denis Baird
- Translational Biology, Biogen, Boston, MA, USA
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, UK
| | - Restuadi Restuadi
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | | | - Annelot M Dekker
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Klara Gawor
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Henk-Jan Westeneng
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Gijs H P Tazelaar
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Kristel R van Eijk
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Maarten Kooyman
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ross P Byrne
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Mark Doherty
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Mark Heverin
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- National Institute for Health Research Biomedical Research Centre and Dementia Unit, South London and Maudsley NHS Foundation Trust and King's College London, London, UK
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Nicola Ticozzi
- Department of Neurology, Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Bradley N Smith
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Marta Gromicho
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Siddharthan Chandran
- Euan MacDonald Centre for Motor Neurone Disease Research, Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
| | - Suvankar Pal
- Euan MacDonald Centre for Motor Neurone Disease Research, Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
| | - Karen E Morrison
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - John Hardy
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Richard W Orrell
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Thomas Meyer
- Charité University Hospital, Humboldt University, Berlin, Germany
| | - Nazli Başak
- Koç University, School of Medicine, KUTTAM-NDAL, Istanbul, Turkey
| | | | - Antonia Ratti
- Department of Neurology, Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Isabella Fogh
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Cinzia Gellera
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Giuseppe Lauria
- 3rd Neurology Unit, Motor Neuron Diseases Center, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', MIlan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Stefania Corti
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
- Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Daisy Sproviero
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Sandra D'Alfonso
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Gianni Sorarù
- Department of Neurosciences, University of Padova, Padova, Italy
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Massimiliano Filosto
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Alessandro Padovani
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Adriano Chiò
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Neurologia 1, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Andrea Calvo
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Neurologia 1, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Cristina Moglia
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Neurologia 1, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Maura Brunetti
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
| | - Antonio Canosa
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Neurologia 1, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Maurizio Grassano
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
| | - Ettore Beghi
- Laboratory of Neurological Diseases, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Elisabetta Pupillo
- Laboratory of Neurological Diseases, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giancarlo Logroscino
- Department of Clinical Research in Neurology, University of Bari at 'Pia Fondazione Card G. Panico' Hospital, Bari, Italy
| | - Beatrice Nefussy
- Neuromuscular Diseases Unit, Department of Neurology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Alma Osmanovic
- Department of Neurology, Hannover Medical School, Hannover, Germany
- Essener Zentrum für Seltene Erkrankungen (EZSE), University Hospital Essen, Essen, Germany
| | - Angelica Nordin
- Department of Clinical Sciences, Neurosciences, Umeå University, Umeå, Sweden
| | - Yossef Lerner
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Neurology, the Agnes Ginges Center for Human Neurogenetics, Hadassah Medical Center, Jerusalem, Israel
| | - Michal Zabari
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Neurology, the Agnes Ginges Center for Human Neurogenetics, Hadassah Medical Center, Jerusalem, Israel
| | - Marc Gotkine
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Neurology, the Agnes Ginges Center for Human Neurogenetics, Hadassah Medical Center, Jerusalem, Israel
| | - Robert H Baloh
- Center for Neural Science and Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Neurology, Neuromuscular Division, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shaughn Bell
- Center for Neural Science and Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Neurology, Neuromuscular Division, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Patrick Vourc'h
- Service de Biochimie et Biologie Moléculaire, CHU de Tours, Tours, France
- UMR 1253, Université de Tours, Inserm, Tours, France
| | - Philippe Corcia
- UMR 1253, Université de Tours, Inserm, Tours, France
- Centre de référence sur la SLA, CHU de Tours, Tours, France
| | - Philippe Couratier
- Centre de référence sur la SLA, CHRU de Limoges, Limoges, France
- UMR 1094, Université de Limoges, Inserm, Limoges, France
| | - Stéphanie Millecamps
- ICM, Institut du Cerveau, Inserm, CNRS, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | | | - François Salachas
- ICM, Institut du Cerveau, Inserm, CNRS, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
- Département de Neurologie, Centre de référence SLA Ile de France, Hôpital de la Pitié-Salpêtrière, AP-HP, Paris, France
| | | | - Abdelilah Assialioui
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ricardo Rojas-García
- MND Clinic, Neurology Department, Hospital de la Santa Creu i Sant Pau de Barcelona, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Patrick A Dion
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Jay P Ross
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Jochen H Weishaupt
- Division of Neurodegeneration, Department of Neurology, University Medicine Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - David Brenner
- Division of Neurodegeneration, Department of Neurology, University Medicine Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Axel Freischmidt
- Department of Neurology, Ulm University, Ulm, Germany
- German Center for Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
| | - Gilbert Bensimon
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpêtrière, UPMC Pharmacologie, AP-HP, Paris, France
- Pharmacologie Sorbonne Université, Paris, France
- Institut du Cerveau, Paris Brain Institute ICM, Paris, France
- Laboratoire de Biostatistique, Epidémiologie Clinique, Santé Publique Innovation et Méthodologie (BESPIM), CHU-Nîmes, Nîmes, France
| | - Alexis Brice
- Sorbonne Université, Paris Brain Institute, APHP, INSERM, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Alexandra Durr
- Sorbonne Université, Paris Brain Institute, APHP, INSERM, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Christine A M Payan
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpêtrière, UPMC Pharmacologie, AP-HP, Paris, France
| | | | - Nicholas W Wood
- Department of Clinical and Movement Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Simon Topp
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, FL, USA
| | - Lukas Tittmann
- Popgen Biobank and Institute of Epidemiology, Christian Albrechts-University Kiel, Kiel, Germany
| | - Wolfgang Lieb
- Popgen Biobank and Institute of Epidemiology, Christian Albrechts-University Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Alice Braun
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Julia Kraft
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - David C Whiteman
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Catherine M Olsen
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Andre G Uitterlinden
- Department of Internal Medicine, Genetics Laboratory, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marcella Rietschel
- Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
- Central Institute of Mental Health, Mannheim, Germany
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life and Brain Center, Bonn, Germany
- Division of Medical Genetics, University Hospital Basel and Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Neuroscience and Medicine INM-1, Research Center Juelich, Juelich, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life and Brain Center, Bonn, Germany
| | - Philippe Amouyel
- INSERM UMR1167-RID-AGE LabEx DISTALZ-Risk Factors and Molecular Determinants of Aging-Related Diseases, University of Lille, Centre Hospitalier of the University of Lille, Institut Pasteur de Lille, Lille, France
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
| | | | - Ruben J Cauchi
- Centre for Molecular Medicine and Biobanking and Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Roel A Ophoff
- University Medical Center Utrecht, Department of Psychiatry, Rudolf Magnus Institute of Neuroscience, Utrecht, the Netherlands
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Martina Wiedau-Pazos
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | - Vivianna M van Deerlin
- Center for Neurodegenerative Disease Research, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Julian Grosskreutz
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
- Precision Neurology Unit, Department of Neurology, University Hospital Schleswig-Holstein, University of Luebeck, Luebeck, Germany
| | | | - Nayana Gaur
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Alexander Jörk
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Tabea Barthel
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Erik Theele
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Benjamin Ilse
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | | | - Otto W Witte
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Robert Steinbach
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | | | - Caroline Graff
- Department of Geriatric Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Lev Brylev
- Department of Neurology, Bujanov Moscow Clinical Hospital, Moscow, Russia
- Moscow Research and Clinical Center for Neuropsychiatry of the Healthcare Department, Moscow, Russia
- Department of Functional Biochemistry of the Nervous System, Institute of Higher Nervous Activity and Neurophysiology Russian Academy of Sciences, Moscow, Russia
| | - Vera Fominykh
- Department of Neurology, Bujanov Moscow Clinical Hospital, Moscow, Russia
- Department of Functional Biochemistry of the Nervous System, Institute of Higher Nervous Activity and Neurophysiology Russian Academy of Sciences, Moscow, Russia
| | - Vera Demeshonok
- ALS-Care Center, 'GAOORDI', Medical Clinic of the St. Petersburg, St. Petersburg, Russia
| | - Anastasia Ataulina
- Department of Neurology, Bujanov Moscow Clinical Hospital, Moscow, Russia
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
- Biomedical Research Institute BRIS, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Koritnik
- Ljubljana ALS Centre, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Janez Zidar
- Ljubljana ALS Centre, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Metka Ravnik-Glavač
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Zorica Stević
- Clinic of Neurology, Clinical Center of Serbia, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vivian Drory
- Neuromuscular Diseases Unit, Department of Neurology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Monica Povedano
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Matthew C Kiernan
- Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Beben Benyamin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Australian Centre for Precision Health and Allied Health and Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Robert D Henderson
- Centre for Clinical Research, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Sarah Furlong
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Susan Mathers
- Calvary Health Care Bethlehem, Parkdale, Victoria, Australia
| | - Pamela A McCombe
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Merrilee Needham
- Fiona Stanley Hospital, Perth, Western Australia, Australia
- Notre Dame University, Fremantle, Western Australia, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia
| | - Shyuan T Ngo
- Centre for Clinical Research, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Garth A Nicholson
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Roger Pamphlett
- Discipline of Pathology and Department of Neuropathology, Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Dominic B Rowe
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Frederik J Steyn
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- The School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
- Neuroscience Research Australia Institute, Randwick, New South Wales, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
- Neuropsychiatric Institute, the Prince of Wales Hospital, UNSW, Randwick, New South Wales, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Mamede de Carvalho
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Susana Pinto
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Susanne Petri
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Markus Weber
- Neuromuscular Diseases Unit/ALS Clinic, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Guy A Rouleau
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Vincenzo Silani
- Department of Neurology, Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Charles J Curtis
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) & Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
| | - Gerome Breen
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) & Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
| | - Jonathan D Glass
- Department Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christopher E Shaw
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Peter M Andersen
- Department of Clinical Sciences, Neurosciences, Umeå University, Umeå, Sweden
| | - Ewout J N Groen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Michael A van Es
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Dongsheng Fan
- Department of Neurology, Third Hospital, Peking University, Beijing, China
| | - Fleur C Garton
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, Bristol, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, Bristol, UK
| | | | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Russell L McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Kevin P Kenna
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Ellen Tsai
- Translational Biology, Biogen, Boston, MA, USA
| | - Heiko Runz
- Translational Biology, Biogen, Boston, MA, USA
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- King's College Hospital, London, UK
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Leonard H van den Berg
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jan H Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
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13
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Hogan AL, Grima N, Fifita JA, McCann EP, Heng B, Fat SCM, Wu S, Maharjan R, Cain AK, Henden L, Rayner S, Tarr I, Zhang KY, Zhao Q, Zhang ZH, Wright A, Lee A, Morsch M, Yang S, Williams KL, Blair IP. Splicing factor proline and glutamine rich intron retention, reduced expression and aggregate formation are pathological features of amyotrophic lateral sclerosis. Neuropathol Appl Neurobiol 2021; 47:990-1003. [PMID: 34288034 DOI: 10.1111/nan.12749] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/12/2021] [Indexed: 12/13/2022]
Abstract
AIM Splicing factor proline and glutamine rich (SFPQ) is an RNA-DNA binding protein that is dysregulated in Alzheimer's disease and frontotemporal dementia. Dysregulation of SFPQ, specifically increased intron retention and nuclear depletion, has been linked to several genetic subtypes of amyotrophic lateral sclerosis (ALS), suggesting that SFPQ pathology may be a common feature of this heterogeneous disease. Our study aimed to investigate this hypothesis by providing the first comprehensive assessment of SFPQ pathology in large ALS case-control cohorts. METHODS We examined SFPQ at the RNA, protein and DNA levels. SFPQ RNA expression and intron retention were examined using RNA-sequencing and quantitative PCR. SFPQ protein expression was assessed by immunoblotting and immunofluorescent staining. At the DNA level, SFPQ was examined for genetic variation novel to ALS patients. RESULTS At the RNA level, retention of SFPQ intron nine was significantly increased in ALS patients' motor cortex. In addition, SFPQ RNA expression was significantly reduced in the central nervous system, but not blood, of patients. At the protein level, neither nuclear depletion nor reduced expression of SFPQ was found to be a consistent feature of spinal motor neurons. However, SFPQ-positive ubiquitinated protein aggregates were observed in patients' spinal motor neurons. At the DNA level, our genetic screen identified two novel and two rare SFPQ sequence variants not previously reported in the literature. CONCLUSIONS Our findings confirm dysregulation of SFPQ as a pathological feature of the central nervous system of ALS patients and indicate that investigation of the functional consequences of this pathology will provide insight into ALS biology.
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Affiliation(s)
- Alison L Hogan
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Natalie Grima
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jennifer A Fifita
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Emily P McCann
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Benjamin Heng
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Sandrine Chan Moi Fat
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Sharlynn Wu
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ram Maharjan
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Lyndal Henden
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Stephanie Rayner
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ingrid Tarr
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Katharine Y Zhang
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Qiongyi Zhao
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Zong-Hong Zhang
- School of Medicine, IMPACT, Bioinformatics Core Research Facility, Deakin University, Geelong, Victoria, Australia
| | - Amanda Wright
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Albert Lee
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Marco Morsch
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Shu Yang
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
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14
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Fifita JA, Chan Moi Fat S, McCann EP, Williams KL, Twine NA, Bauer DC, Rowe DB, Pamphlett R, Kiernan MC, Tan VX, Blair IP, Guillemin GJ. Genetic Analysis of Tryptophan Metabolism Genes in Sporadic Amyotrophic Lateral Sclerosis. Front Immunol 2021; 12:701550. [PMID: 34194442 PMCID: PMC8236844 DOI: 10.3389/fimmu.2021.701550] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 04/28/2021] [Accepted: 05/31/2021] [Indexed: 01/17/2023] Open
Abstract
The essential amino acid tryptophan (TRP) is the initiating metabolite of the kynurenine pathway (KP), which can be upregulated by inflammatory conditions in cells. Neuroinflammation-triggered activation of the KP and excessive production of the KP metabolite quinolinic acid are common features of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). In addition to its role in the KP, genes involved in TRP metabolism, including its incorporation into proteins, and synthesis of the neurotransmitter serotonin, have also been genetically and functionally linked to these diseases. ALS is a late onset neurodegenerative disease that is classified as familial or sporadic, depending on the presence or absence of a family history of the disease. Heritability estimates support a genetic basis for all ALS, including the sporadic form of the disease. However, the genetic basis of sporadic ALS (SALS) is complex, with the presence of multiple gene variants acting to increase disease susceptibility and is further complicated by interaction with potential environmental factors. We aimed to determine the genetic contribution of 18 genes involved in TRP metabolism, including protein synthesis, serotonin synthesis and the KP, by interrogating whole-genome sequencing data from 614 Australian sporadic ALS cases. Five genes in the KP (AFMID, CCBL1, GOT2, KYNU, HAAO) were found to have either novel protein-altering variants, and/or a burden of rare protein-altering variants in SALS cases compared to controls. Four genes involved in TRP metabolism for protein synthesis (WARS) and serotonin synthesis (TPH1, TPH2, MAOA) were also found to carry novel variants and/or gene burden. These variants may represent ALS risk factors that act to alter the KP and lead to neuroinflammation. These findings provide further evidence for the role of TRP metabolism, the KP and neuroinflammation in ALS disease pathobiology.
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Affiliation(s)
- Jennifer A. Fifita
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sandrine Chan Moi Fat
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Emily P. McCann
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Kelly L. Williams
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Natalie A. Twine
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organization, Health & Biosecurity Flagship, Sydney, NSW, Australia
| | - Denis C. Bauer
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organization, Health & Biosecurity Flagship, Sydney, NSW, Australia
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Applied BioSciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Dominic B. Rowe
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Roger Pamphlett
- Discipline of Pathology, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
| | - Matthew C. Kiernan
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
- Institute of Clinical Neurosciences, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Vanessa X. Tan
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian P. Blair
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Gilles J. Guillemin
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
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15
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Restuadi R, Garton FC, Benyamin B, Lin T, Williams KL, Vinkhuyzen A, van Rheenen W, Zhu Z, Laing NG, Mather KA, Sachdev PS, Ngo ST, Steyn FJ, Wallace L, Henders AK, Visscher PM, Needham M, Mathers S, Nicholson G, Rowe DB, Henderson RD, McCombe PA, Pamphlett R, Blair IP, Wray NR, McRae AF. Polygenic risk score analysis for amyotrophic lateral sclerosis leveraging cognitive performance, educational attainment and schizophrenia. Eur J Hum Genet 2021; 30:532-539. [PMID: 33907316 PMCID: PMC9090723 DOI: 10.1038/s41431-021-00885-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 03/24/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is recognised to be a complex neurodegenerative disease involving both genetic and non-genetic risk factors. The underlying causes and risk factors for the majority of cases remain unknown; however, ever-larger genetic data studies and methodologies promise an enhanced understanding. Recent analyses using published summary statistics from the largest ALS genome-wide association study (GWAS) (20,806 ALS cases and 59,804 healthy controls) identified that schizophrenia (SCZ), cognitive performance (CP) and educational attainment (EA) related traits were genetically correlated with ALS. To provide additional evidence for these correlations, we built single and multi-trait genetic predictors using GWAS summary statistics for ALS and these traits, (SCZ, CP, EA) in an independent Australian cohort (846 ALS cases and 665 healthy controls). We compared methods for generating the risk predictors and found that the combination of traits improved the prediction (Nagelkerke-R2) of the case-control logistic regression. The combination of ALS, SCZ, CP, and EA, using the SBayesR predictor method gave the highest prediction (Nagelkerke-R2) of 0.027 (P value = 4.6 × 10-8), with the odds-ratio for estimated disease risk between the highest and lowest deciles of individuals being 3.15 (95% CI 1.96-5.05). These results support the genetic correlation between ALS, SCZ, CP and EA providing a better understanding of the complexity of ALS.
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Affiliation(s)
- Restuadi Restuadi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Fleur C Garton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Beben Benyamin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Australian Centre for Precision Health, University of South Australia Cancer Research Institute, School of Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Kelly L Williams
- Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Anna Vinkhuyzen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | | | - Zhihong Zhu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nigel G Laing
- Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia.,Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia.,Neuroscience Research Australia Institute, Randwick, NSW, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia.,Neuropsychiatric Institute, The Prince of Wales Hospital, UNSW, Randwick, NSW, Australia
| | - Shyuan T Ngo
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.,The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Frederik J Steyn
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.,School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Merrilee Needham
- Fiona Stanley Hospital, Perth, WA, Australia.,Notre Dame University, Fremantle, WA, Australia.,Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
| | - Susan Mathers
- Calvary Health Care Bethlehem, Parkdale, VIC, Australia
| | - Garth Nicholson
- Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.,ANZAC Research Institute, Concord Repatriation General Hospital, Sydney, NSW, Australia
| | - Dominic B Rowe
- Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Robert D Henderson
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.,The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Pamela A McCombe
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.,Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Roger Pamphlett
- Discipline of Pathology and Department of Neuropathology, Brain and Mind Centre, The University of Sydney, Sydney, NSW, Australia
| | - Ian P Blair
- Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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16
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Nabais MF, Laws SM, Lin T, Vallerga CL, Armstrong NJ, Blair IP, Kwok JB, Mather KA, Mellick GD, Sachdev PS, Wallace L, Henders AK, Zwamborn RAJ, Hop PJ, Lunnon K, Pishva E, Roubroeks JAY, Soininen H, Tsolaki M, Mecocci P, Lovestone S, Kłoszewska I, Vellas B, Furlong S, Garton FC, Henderson RD, Mathers S, McCombe PA, Needham M, Ngo ST, Nicholson G, Pamphlett R, Rowe DB, Steyn FJ, Williams KL, Anderson TJ, Bentley SR, Dalrymple-Alford J, Fowder J, Gratten J, Halliday G, Hickie IB, Kennedy M, Lewis SJG, Montgomery GW, Pearson J, Pitcher TL, Silburn P, Zhang F, Visscher PM, Yang J, Stevenson AJ, Hillary RF, Marioni RE, Harris SE, Deary IJ, Jones AR, Shatunov A, Iacoangeli A, van Rheenen W, van den Berg LH, Shaw PJ, Shaw CE, Morrison KE, Al-Chalabi A, Veldink JH, Hannon E, Mill J, Wray NR, McRae AF. Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders. Genome Biol 2021; 22:90. [PMID: 33771206 PMCID: PMC8004462 DOI: 10.1186/s13059-021-02275-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [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: 07/13/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND People with neurodegenerative disorders show diverse clinical syndromes, genetic heterogeneity, and distinct brain pathological changes, but studies report overlap between these features. DNA methylation (DNAm) provides a way to explore this overlap and heterogeneity as it is determined by the combined effects of genetic variation and the environment. In this study, we aim to identify shared blood DNAm differences between controls and people with Alzheimer's disease, amyotrophic lateral sclerosis, and Parkinson's disease. RESULTS We use a mixed-linear model method (MOMENT) that accounts for the effect of (un)known confounders, to test for the association of each DNAm site with each disorder. While only three probes are found to be genome-wide significant in each MOMENT association analysis of amyotrophic lateral sclerosis and Parkinson's disease (and none with Alzheimer's disease), a fixed-effects meta-analysis of the three disorders results in 12 genome-wide significant differentially methylated positions. Predicted immune cell-type proportions are disrupted across all neurodegenerative disorders. Protein inflammatory markers are correlated with profile sum-scores derived from disease-associated immune cell-type proportions in a healthy aging cohort. In contrast, they are not correlated with MOMENT DNAm-derived profile sum-scores, calculated using effect sizes of the 12 differentially methylated positions as weights. CONCLUSIONS We identify shared differentially methylated positions in whole blood between neurodegenerative disorders that point to shared pathogenic mechanisms. These shared differentially methylated positions may reflect causes or consequences of disease, but they are unlikely to reflect cell-type proportion differences.
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Grants
- U24 AG021886 NIA NIH HHS
- U01 AG016976 NIA NIH HHS
- Department of Health
- U01 AG024904 NIA NIH HHS
- 108890/Z/15/Z Wellcome Trust
- 503480 Medical Research Council
- TURNER/OCT15/972-797 Motor Neurone Disease Association
- U01 AG032984 NIA NIH HHS
- R01 HL105756 NHLBI NIH HHS
- 082604/2/07/Z Wellcome Trust
- R01 AG033193 NIA NIH HHS
- National Health and Medical Research Council
- Motor Neurone Disease Research Institute of Australia Ice Bucket Challenge
- Medical Research Council (UK)
- Economic and Social Research Council
- National Institute for Health Research (NIHR)
- the European Community’s Health Seventh Framework Programme
- Horizon 2020 Programme
- MND Association and the Wellcome Trust.
- European Research Council (ERC)
- EU Joint Programme – Neurodegenerative Disease Research ()
- EU Joint Programme - Neurodegenerative Disease Research (JPND)
- Australian Research Council
- Mater Foundation
- ForeFront - NHMRC
- Australian National Health and Medical Research Council
- University of Otago Research Grant, together with financial support from the Jim and Mary Carney Charitable Trust
- Commonwealth Scientific Industrial and research Organization (CSIRO), Edith Cowan University (ECU), Mental Health Research institute (MHRI), National Ageing Research Institute (NARI), Austin Health, CogState Ltd
- National Health and Medical Research Council and the Dementia Collaborative Research Centres program (DCRC2), as well as funding from the Science and Industry Endowment Fund (SIEF) and the Cooperative Research Centre (CRC) for Mental Health – funded throug
- EU Joint Programme - Neurodegenerative Disease Research (JPND), co-funded through the Australian National Health and Medical Research (NHMRC) Council, Motor Neurone Disease Research Institute of Australia Ice Bucket Challenge,
- EU Joint Programme - Neurodegenerative Disease Research (JPND), United Kingdom Medical Research Council, Economic and Social Research Council, Motor Neuro Disease Association (GB), National Institute for Health Research (NIHR) Biomedical Research Centre at
- EU Joint Programme - Neurodegenerative Disease Research (JPND), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program, PPP Allowance made available by Health~Holland, Top Sector Life Sciences & Health, Unit
- National Health and Medical Research Council, Australian Research Council, Mater Foundation,
- Australian National Health and Medical Research Council (
- University of Otago Research Grant, Jim and Mary Carney Charitable Trust
- Commonwealth Scientific Industrial and research Organization (CSIRO), Edith Cowan University (ECU), Mental Health Research institute (MHRI), National Ageing Research Institute (NARI), Austin Health, CogState Ltd., National Health and Medical Research Counc
- EFPIA companies and SMEs as part of InnoMed (Innovative Medicines in Europe), an Integrated Project funded by the European Union of the Sixth Framework program
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Affiliation(s)
- Marta F Nabais
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Simon M Laws
- School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA, 6027, Australia
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Costanza L Vallerga
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Department of Internal Medicine, Erasmus MC, University Medical Center, 3015GD, Rotterdam, The Netherlands
| | | | - Ian P Blair
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, School of Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - John B Kwok
- Brain and Mind Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2031, Australia
- Neuroscience Research Australia Institute, Randwick, NSW, 2031, Australia
| | - George D Mellick
- Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2031, Australia
- Neuropsychiatric Institute, The Prince of Wales Hospital, UNSW, Randwick, NSW, 2031, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ramona A J Zwamborn
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Paul J Hop
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Katie Lunnon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Ehsan Pishva
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Janou A Y Roubroeks
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Hilkka Soininen
- Institute of Clinical Medicine, Neurology, University of Eastern Finland, Kuopio, Finland
| | - Magda Tsolaki
- 1st Department of Neurology, Memory and Dementia Unit, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Patrizia Mecocci
- Department of Medicine, Institute of Gerontology and Geriatrics, University of Perugia, Perugia, Italy
| | - Simon Lovestone
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, UK
| | | | - Bruno Vellas
- INSERM U 558, University of Toulouse, Toulouse, France
| | - Sarah Furlong
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Fleur C Garton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Robert D Henderson
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Susan Mathers
- Calvary Health Care Bethlehem, Parkdale, VIC, 3195, Australia
| | - Pamela A McCombe
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Merrilee Needham
- Fiona Stanley Hospital, Perth, WA, 6150, Australia
- Notre Dame University, Fremantle, WA, 6160, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, 6150, Australia
| | - Shyuan T Ngo
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Garth Nicholson
- ANZAC Research Institute, Concord Repatriation General Hospital, Sydney, NSW, 2139, Australia
| | - Roger Pamphlett
- Discipline of Pathology and Department of Neuropathology, Brain and Mind Centre, The University of Sydney, Sydney, NSW, 2050, Australia
| | - Dominic B Rowe
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Frederik J Steyn
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Tim J Anderson
- New Zealand Brain Research Institute, Christchurch, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Steven R Bentley
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - John Dalrymple-Alford
- New Zealand Brain Research Institute, Christchurch, New Zealand
- School of Psychology, Speech and Hearing, University of Canterbury, Christchurch, New Zealand
| | - Javed Fowder
- Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, Australia
| | - Jacob Gratten
- Mater Research, Translational Research Institute, Brisbane, Australia
- Mater Research Institute, The University of Queensland, Brisbane, Australia
| | - Glenda Halliday
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Ian B Hickie
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Martin Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simon J G Lewis
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - John Pearson
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Toni L Pitcher
- New Zealand Brain Research Institute, Christchurch, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Peter Silburn
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Futao Zhang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts group, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Ian J Deary
- Department of Psychology, Lothian Birth Cohorts group, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Wouter van Rheenen
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | | | - Cristopher E Shaw
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | | | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
- King's College Hospital, London, SE5 9RS, UK
| | - Jan H Veldink
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Eilis Hannon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Jonathan Mill
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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17
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Iacoangeli A, Lin T, Al Khleifat A, Jones AR, Opie-Martin S, Coleman JRI, Shatunov A, Sproviero W, Williams KL, Garton F, Restuadi R, Henders AK, Mather KA, Needham M, Mathers S, Nicholson GA, Rowe DB, Henderson R, McCombe PA, Pamphlett R, Blair IP, Schultz D, Sachdev PS, Newhouse SJ, Proitsi P, Fogh I, Ngo ST, Dobson RJB, Wray NR, Steyn FJ, Al-Chalabi A. Genome-wide Meta-analysis Finds the ACSL5-ZDHHC6 Locus Is Associated with ALS and Links Weight Loss to the Disease Genetics. Cell Rep 2020; 33:108323. [PMID: 33113361 PMCID: PMC7610013 DOI: 10.1016/j.celrep.2020.108323] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 07/28/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
We meta-analyze amyotrophic lateral sclerosis (ALS) genome-wide association study (GWAS) data of European and Chinese populations (84,694 individuals). We find an additional significant association between rs58854276 spanning ACSL5-ZDHHC6 with ALS (p = 8.3 × 10−9), with replication in an independent Australian cohort (1,502 individuals; p = 0.037). Moreover, B4GALNT1, G2E3-SCFD1, and TRIP11-ATXN3 are identified using a gene-based analysis. ACSL5 has been associated with rapid weight loss, as has another ALS-associated gene, GPX3. Weight loss is frequent in ALS patients and is associated with shorter survival. We investigate the effect of the ACSL5 and GPX3 single-nucleotide polymorphisms (SNPs), using longitudinal body composition and weight data of 77 patients and 77 controls. In patients’ fat-free mass, although not significant, we observe an effect in the expected direction (rs58854276: −2.1 ± 1.3 kg/A allele, p = 0.053; rs3828599: −1.0 ± 1.3 kg/A allele, p = 0.22). No effect was observed in controls. Our findings support the increasing interest in lipid metabolism in ALS and link the disease genetics to weight loss in patients. Cross-ethnic meta-analysis finds an association between the ACSL5-ZDHHC6 locus and ALS The ACSL5-ZDHHC6 association is replicated in an independent Australian cohort ACSL5-ZDHHC6 lead SNP is in ACSL5 and is an eQTL of ZDHHC6 in brain tissues ACSL5 SNPs might have an effect on fat-free mass in ALS patients
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Affiliation(s)
- Alfredo Iacoangeli
- Department of Biostatistics and Health Informatics, King's College London, London, UK; Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK; National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK.
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Brisbane QLD 4072, Australia
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK
| | - Ashley R Jones
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK
| | - Sarah Opie-Martin
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK
| | - Jonathan R I Coleman
- National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK; Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK
| | - William Sproviero
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Macquarie University, Sidney NSW 2109, Australia
| | - Fleur Garton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Brisbane QLD 4072, Australia
| | - Restuadi Restuadi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Brisbane QLD 4072, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Brisbane QLD 4072, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW Medicine, University of New South Wales, Sydney NSW, Australia; Neuroscience Research Australia, Randwick NSW, Australia
| | - Merilee Needham
- Fiona Stanley Hospital, 11 Robin Warren Drive, Murdoch Perth WA 6150, Australia; Notre Dame University, 32 Mouat Street, Fremantle WA 6160, Australia; Murdoch University, 90 South Street, Murdoch WA 6150, Australia
| | - Susan Mathers
- Calvary Health Care Bethlehem, Parkdale VIC 3195, Australia
| | - Garth A Nicholson
- ANZAC Research Institute, Concord Repatriation General Hospital, Sydney NSW 2139, Australia
| | - Dominic B Rowe
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Robert Henderson
- Centre for Clinical Research, The University of Queensland, Brisbane QLD, Australia; Queensland Brain Institute, The University of Queensland, Brisbane QLD, Australia
| | - Pamela A McCombe
- Centre for Clinical Research, The University of Queensland, Brisbane QLD, Australia; Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane QLD, Australia
| | - Roger Pamphlett
- Brain and Mind Centre, The University of Sydney, Sydney NSW, Australia
| | - Ian P Blair
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - David Schultz
- Flinders Medical Centre, Bedford Park SA 5042, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW Medicine, University of New South Wales, Sydney NSW, Australia; Neuropsychiatric Institute, Prince of Wales Hospital, Sydney NSW Australia
| | - Stephen J Newhouse
- Department of Biostatistics and Health Informatics, King's College London, London, UK; National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK; Institute of Health Informatics, University College London, London, UK
| | - Petroula Proitsi
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK
| | - Isabella Fogh
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Shyuan T Ngo
- Centre for Clinical Research, The University of Queensland, Brisbane QLD, Australia; Queensland Brain Institute, The University of Queensland, Brisbane QLD, Australia; Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane QLD, Australia; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane QLD, Australia
| | - Richard J B Dobson
- Department of Biostatistics and Health Informatics, King's College London, London, UK; National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK; Institute of Health Informatics, University College London, London, UK
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Brisbane QLD 4072, Australia; Queensland Brain Institute, The University of Queensland, Brisbane QLD, Australia
| | - Frederik J Steyn
- Centre for Clinical Research, The University of Queensland, Brisbane QLD, Australia; Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane QLD, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane QLD, Australia
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK; King's College Hospital, Bessemer Road, London SE5 9RS, UK
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18
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McCann EP, Henden L, Fifita JA, Zhang KY, Grima N, Bauer DC, Chan Moi Fat S, Twine NA, Pamphlett R, Kiernan MC, Rowe DB, Williams KL, Blair IP. Evidence for polygenic and oligogenic basis of Australian sporadic amyotrophic lateral sclerosis. J Med Genet 2020; 58:jmedgenet-2020-106866. [PMID: 32409511 DOI: 10.1136/jmedgenet-2020-106866] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/02/2020] [Accepted: 03/22/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with phenotypic and genetic heterogeneity. Approximately 10% of cases are familial, while remaining cases are classified as sporadic. To date, >30 genes and several hundred genetic variants have been implicated in ALS. METHODS Seven hundred and fifty-seven sporadic ALS cases were recruited from Australian neurology clinics. Detailed clinical data and whole genome sequencing (WGS) data were available from 567 and 616 cases, respectively, of which 426 cases had both datasets available. As part of a comprehensive genetic analysis, 853 genetic variants previously reported as ALS-linked mutations or disease-associated alleles were interrogated in sporadic ALS WGS data. Statistical analyses were performed to identify correlation between clinical variables, and between phenotype and the number of ALS-implicated variants carried by an individual. Relatedness between individuals carrying identical variants was assessed using identity-by-descent analysis. RESULTS Forty-three ALS-implicated variants from 18 genes, including C9orf72, ATXN2, TARDBP, SOD1, SQSTM1 and SETX, were identified in Australian sporadic ALS cases. One-third of cases carried at least one variant and 6.82% carried two or more variants, implicating a potential oligogenic or polygenic basis of ALS. Relatedness was detected between two sporadic ALS cases carrying a SOD1 p.I114T mutation, and among three cases carrying a SQSTM1 p.K238E mutation. Oligogenic/polygenic sporadic ALS cases showed earlier age of onset than those with no reported variant. CONCLUSION We confirm phenotypic associations among ALS cases, and highlight the contribution of genetic variation to all forms of ALS.
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Affiliation(s)
- Emily P McCann
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Lyndal Henden
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jennifer A Fifita
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Katharine Y Zhang
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Natalie Grima
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Denis C Bauer
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation, Sydney, New South Wales, Australia
| | - Sandrine Chan Moi Fat
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Natalie A Twine
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation, Sydney, New South Wales, Australia
| | - Roger Pamphlett
- Discipline of Pathology and Department of Neuropathology, The University of Sydney, Sydney, New South Wales, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, New South Wales, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Matthew C Kiernan
- Brain and Mind Centre, The University of Sydney, Sydney, New South Wales, Australia
- Institute of Clinical Neurosciences, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Dominic B Rowe
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
- Department of Clinical Medicine, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Kelly L Williams
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ian P Blair
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
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19
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Dobson-Stone C, Hallupp M, Shahheydari H, Ragagnin AMG, Chatterton Z, Carew-Jones F, Shepherd CE, Stefen H, Paric E, Fath T, Thompson EM, Blumbergs P, Short CL, Field CD, Panegyres PK, Hecker J, Nicholson G, Shaw AD, Fullerton JM, Luty AA, Schofield PR, Brooks WS, Rajan N, Bennett MF, Bahlo M, Shankaracharya, Landers JE, Piguet O, Hodges JR, Halliday GM, Topp SD, Smith BN, Shaw CE, McCann E, Fifita JA, Williams KL, Atkin JD, Blair IP, Kwok JB. CYLD is a causative gene for frontotemporal dementia - amyotrophic lateral sclerosis. Brain 2020; 143:783-799. [PMID: 32185393 PMCID: PMC7089666 DOI: 10.1093/brain/awaa039] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [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: 08/01/2019] [Revised: 12/01/2019] [Accepted: 12/17/2019] [Indexed: 02/03/2023] Open
Abstract
Frontotemporal dementia and amyotrophic lateral sclerosis are clinically and pathologically overlapping disorders with shared genetic causes. We previously identified a disease locus on chromosome 16p12.1-q12.2 with genome-wide significant linkage in a large European Australian family with autosomal dominant inheritance of frontotemporal dementia and amyotrophic lateral sclerosis and no mutation in known amyotrophic lateral sclerosis or dementia genes. Here we demonstrate the segregation of a novel missense variant in CYLD (c.2155A>G, p.M719V) within the linkage region as the genetic cause of disease in this family. Immunohistochemical analysis of brain tissue from two CYLD p.M719V mutation carriers showed widespread glial CYLD immunoreactivity. Primary mouse neurons transfected with CYLDM719V exhibited increased cytoplasmic localization of TDP-43 and shortened axons. CYLD encodes a lysine 63 deubiquitinase and CYLD cutaneous syndrome, a skin tumour disorder, is caused by mutations that lead to reduced deubiquitinase activity. In contrast with CYLD cutaneous syndrome-causative mutations, CYLDM719V exhibited significantly increased lysine 63 deubiquitinase activity relative to the wild-type enzyme (paired Wilcoxon signed-rank test P = 0.005). Overexpression of CYLDM719V in HEK293 cells led to more potent inhibition of the cell signalling molecule NF-κB and impairment of autophagosome fusion to lysosomes, a key process in autophagy. Although CYLD mutations appear to be rare, CYLD's interaction with at least three other proteins encoded by frontotemporal dementia and/or amyotrophic lateral sclerosis genes (TBK1, OPTN and SQSTM1) suggests that it may play a central role in the pathogenesis of these disorders. Mutations in several frontotemporal dementia and amyotrophic lateral sclerosis genes, including TBK1, OPTN and SQSTM1, result in a loss of autophagy function. We show here that increased CYLD activity also reduces autophagy function, highlighting the importance of autophagy regulation in the pathogenesis of frontotemporal dementia and amyotrophic lateral sclerosis.
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Affiliation(s)
- Carol Dobson-Stone
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Marianne Hallupp
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
| | - Hamideh Shahheydari
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Audrey M G Ragagnin
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Zac Chatterton
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Francine Carew-Jones
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Claire E Shepherd
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Holly Stefen
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Esmeralda Paric
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Thomas Fath
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Elizabeth M Thompson
- SA Clinical Genetics Service, Women’s and Children’s Hospital, North Adelaide 5006, SA, Australia
- Adelaide Medical School, Faculty of Health Sciences, University of Adelaide, Adelaide SA 5005, Australia
| | - Peter Blumbergs
- Institute of Medical and Veterinary Science, Adelaide, SA 5000, Australia
| | - Cathy L Short
- Department of Neurology, The Queen Elizabeth Hospital, Woodville, SA 5011, Australia
| | - Colin D Field
- Adelaide Dementia Driving Clinic, Adelaide, SA 5041, Australia
| | - Peter K Panegyres
- Neurodegenerative Disorders Research Pty Ltd, West Perth, WA 6005, Australia
| | - Jane Hecker
- Department of General Medicine, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Garth Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW 2137, Australia
- Sydney Medical School, University of Sydney, Camperdown, NSW 2050, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, NSW 2137, Australia
| | - Alex D Shaw
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Janice M Fullerton
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Agnes A Luty
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Peter R Schofield
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - William S Brooks
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Neil Rajan
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Mark F Bennett
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Shankaracharya
- University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - John E Landers
- University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Olivier Piguet
- The University of Sydney, Brain and Mind Centre and School of Psychology, Camperdown, NSW 2006, Australia
- ARC Centre of Excellence in Cognition and its Disorders, Sydney, NSW, Australia
| | - John R Hodges
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- ARC Centre of Excellence in Cognition and its Disorders, Sydney, NSW, Australia
| | - Glenda M Halliday
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Simon D Topp
- UK Dementia Research Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London SE5 9RX, UK
| | - Bradley N Smith
- UK Dementia Research Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London SE5 9RX, UK
| | - Christopher E Shaw
- UK Dementia Research Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London SE5 9RX, UK
| | - Emily McCann
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Jennifer A Fifita
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Julie D Atkin
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC 3083, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - John B Kwok
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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20
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Nabais MF, Lin T, Benyamin B, Williams KL, Garton FC, Vinkhuyzen AAE, Zhang F, Vallerga CL, Restuadi R, Freydenzon A, Zwamborn RAJ, Hop PJ, Robinson MR, Gratten J, Visscher PM, Hannon E, Mill J, Brown MA, Laing NG, Mather KA, Sachdev PS, Ngo ST, Steyn FJ, Wallace L, Henders AK, Needham M, Veldink JH, Mathers S, Nicholson G, Rowe DB, Henderson RD, McCombe PA, Pamphlett R, Yang J, Blair IP, McRae AF, Wray NR. Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. NPJ Genom Med 2020; 5:10. [PMID: 32140259 PMCID: PMC7046630 DOI: 10.1038/s41525-020-0118-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/18/2019] [Indexed: 12/11/2022] Open
Abstract
We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor.
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Affiliation(s)
- Marta F Nabais
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia.,2University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, Devon EX2 5DW UK
| | - Tian Lin
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Beben Benyamin
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia.,3Australian Centre for Precision Health, University of South Australia Cancer Research Institute, School of Health Sciences, University of South Australia, Adelaide, SA 5001 Australia
| | - Kelly L Williams
- 4Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW 2109 Australia
| | - Fleur C Garton
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Anna A E Vinkhuyzen
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Futao Zhang
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Costanza L Vallerga
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Restuadi Restuadi
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Anna Freydenzon
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Ramona A J Zwamborn
- 5Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG Netherlands
| | - Paul J Hop
- 5Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG Netherlands
| | - Matthew R Robinson
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Jacob Gratten
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia.,6Mater Research Institute, The University of Queensland, Brisbane, QLD 4101 Australia
| | - Peter M Visscher
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia.,7Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Eilis Hannon
- 2University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, Devon EX2 5DW UK
| | - Jonathan Mill
- 2University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, Devon EX2 5DW UK.,8Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF UK
| | - Matthew A Brown
- 9Australian Translational Genomics Centre, Queensland University of Technology, Brisbane, QLD 4102 Australia
| | - Nigel G Laing
- 10The Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA 6009 Australia.,11Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009 Australia
| | - Karen A Mather
- 12Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2031 Australia.,13Neuroscience Research Australia Institute, Randwick, NSW 2031 Australia
| | - Perminder S Sachdev
- 12Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2031 Australia.,14Neuropsychiatric Institute, The Prince of Wales Hospital, University of New South Wales, Randwick, NSW 2031 Australia
| | - Shyuan T Ngo
- 7Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072 Australia.,15The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072 Australia.,16Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4019 Australia
| | - Frederik J Steyn
- 15The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072 Australia.,16Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4019 Australia
| | - Leanne Wallace
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Anjali K Henders
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Merrilee Needham
- 17Fiona Stanley Hospital, Perth, WA 6150 Australia.,18The University of Notre Dame Australia, Fremantle, WA 6160 Australia.,19Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150 Australia
| | - Jan H Veldink
- 5Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG Netherlands
| | - Susan Mathers
- 20Calvary Health Care Bethlehem, Parkdale, VIC 3195 Australia
| | - Garth Nicholson
- 21ANZAC Research Institute, Concord Repatriation General Hospital, Sydney, NSW 2139 Australia
| | - Dominic B Rowe
- 4Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW 2109 Australia
| | - Robert D Henderson
- 7Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072 Australia.,16Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4019 Australia.,22Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD 4029 Australia
| | - Pamela A McCombe
- 16Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4019 Australia.,22Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD 4029 Australia
| | - Roger Pamphlett
- 23Discipline of Pathology and Department of Neuropathology, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050 Australia
| | - Jian Yang
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia.,7Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Ian P Blair
- 4Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW 2109 Australia
| | - Allan F McRae
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia.,7Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Naomi R Wray
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia.,7Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072 Australia
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21
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Crook A, Hogden A, Mumford V, Blair IP, Williams KL, Rowe DB. CMS-01 Genetic testing for familial amyotrophic lateral sclerosis (ALS): insights and challenges. Amyotroph Lateral Scler Frontotemporal Degener 2019; 20:327-347. [PMID: 31702461 DOI: 10.1080/21678421.2019.1647002] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Background: Pathogenic variants in ALS genes are known to be present in up to 70% of familial and 10% of apparently sporadic ALS cases, and can be associated with risks for ALS only, or risks for other neurodegenerative diseases (eg. frontotemporal dementia). While there are no changes to medical management for patients confirmed as pathogenic variant carriers, genetic testing may be important for future drug trials. Confirmation of a pathogenic variant also provides relatives with the opportunity to consider predictive and/or reproductive genetic testing. Genetic counselling is an important aspect of testing decision-making as it enables individuals to make informed decisions about genetic testing while minimising adverse psychological, ethical and legal outcomes. Few studies have explored how individuals decide whether to pursue testing, nor the needs and experiences of familial ALS families.Objective: To identify factors that influence patient and family member decision-making about genetic testing for ALS genes, assess the impact of familial disease on the patient and their family, and identify information and support needs.Methods: In-depth, semi-structured interviews with individuals from Australian ALS families with known pathogenic gene variants explored experiences of familial ALS, and factors that influenced genetic testing decision-making. Interviews were analysed using an inductive approach.Results: Thirty-four individuals from 24 families were interviewed and included patients (n = 4), spouses (n = 4), and asymptomatic at-risk relatives (n = 26). Life stage, experience of disease, costs, research opportunities, and attitudes to familial ALS and/or reproductive options influenced decision-making. Some patients and relatives experienced difficulty gaining accurate information from their health professionals about the costs and implications of genetic counselling or testing, resulting in a reluctance to proceed.Discussion and conclusion: This study provides new insight into the Australian experience of genetic testing and counselling for familial ALS. It highlights the need to work together with other health professionals to ensure the complexities of genetic testing decision-making, and referral pathways are better understood.
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Affiliation(s)
- Ashley Crook
- Department of Clinical Medicine.,Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Science, Faculty of Medicine and Health Sciences; Macquarie University, Sydney, Australia.,Graduate School of Health, University of Technology Sydney, Ultimo, Australia
| | - Anne Hogden
- Australian Institute of Health Innovation, Macquarie University, Sydney, Australia.,Australian Institute of Health Service Management, University of Tasmania, Sydney, Australia
| | - Virginia Mumford
- Australian Institute of Health Innovation, Macquarie University, Sydney, Australia
| | - Ian P Blair
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Science, Faculty of Medicine and Health Sciences; Macquarie University, Sydney, Australia
| | - Kelly L Williams
- Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Science, Faculty of Medicine and Health Sciences; Macquarie University, Sydney, Australia
| | - Dominic B Rowe
- Department of Clinical Medicine.,Macquarie University Centre for Motor Neuron Disease Research, Department of Biomedical Science, Faculty of Medicine and Health Sciences; Macquarie University, Sydney, Australia
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22
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Tarr IS, McCann EP, Benyamin B, Peters TJ, Twine NA, Zhang KY, Zhao Q, Zhang ZH, Rowe DB, Nicholson GA, Bauer D, Clark SJ, Blair IP, Williams KL. Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression. Sci Rep 2019; 9:8254. [PMID: 31164693 PMCID: PMC6547746 DOI: 10.1038/s41598-019-44765-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/23/2019] [Indexed: 12/02/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterised by the loss of upper and lower motor neurons. ALS exhibits high phenotypic variability including age and site of onset, and disease duration. To uncover epigenetic and transcriptomic factors that may modify an ALS phenotype, we used a cohort of Australian monozygotic twins (n = 3 pairs) and triplets (n = 1 set) that are discordant for ALS and represent sporadic ALS and the two most common types of familial ALS, linked to C9orf72 and SOD1. Illumina Infinium HumanMethylation450K BeadChip, EpiTYPER and RNA-Seq analyses in these ALS-discordant twins/triplets and control twins (n = 2 pairs), implicated genes with consistent longitudinal differential DNA methylation and/or gene expression. Two identified genes, RAD9B and C8orf46, showed significant differential methylation in an extended cohort of >1000 ALS cases and controls. Combined longitudinal methylation-transcription analysis within a single twin set implicated CCNF, DPP6, RAMP3, and CCS, which have been previously associated with ALS. Longitudinal transcriptome data showed an 8-fold enrichment of immune function genes and under-representation of transcription and protein modification genes in ALS. Examination of these changes in a large Australian sporadic ALS cohort suggest a broader role in ALS. Furthermore, we observe that increased methylation age is a signature of ALS in older patients.
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Affiliation(s)
- Ingrid S Tarr
- Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Emily P McCann
- Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Beben Benyamin
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, School of Health Sciences, University of South Australia, Adelaide, Australia.,South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Timothy J Peters
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Natalie A Twine
- Health and Biosecurity Business Unit, Commonwealth Scientific and Industrial Research Organisation, Sydney, New South Wales, Australia
| | - Katharine Y Zhang
- Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Qiongyi Zhao
- Queensland Brain Institute, University of Queensland, Queensland, Australia
| | - Zong-Hong Zhang
- Queensland Brain Institute, University of Queensland, Queensland, Australia
| | - Dominic B Rowe
- Department of Clinical Medicine, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Garth A Nicholson
- ANZAC Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Molecular Medicine Laboratory, Concord Hospital, Sydney, New South Wales, Australia
| | - Denis Bauer
- Health and Biosecurity Business Unit, Commonwealth Scientific and Industrial Research Organisation, Sydney, New South Wales, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,St Vincent's Clinical School, UNSW Sydney, New South Wales, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia.
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23
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Turner SP, Pompea ST, Williams KL, Kraemer DA, Sholle ET, Chen C, Cole CL, Kaushal R, Campion TR. Implementation of Informatics to Support the NIH All of Us Research Program in a Healthcare Provider Organization. AMIA Jt Summits Transl Sci Proc 2019; 2019:602-609. [PMID: 31259015 PMCID: PMC6568061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The NIH All of Us Research Program, a national effort to collect biospecimens and health data for over one million participants from across the United States, requires participating healthcare provider organizations (HPOs) to use informatics tools maintained by the NIH to manage participant consent, biospecimen processing, physical measurements, and other workflows. HPOs also maintain distinct workflows for handling overlapping tasks within their individual aegis, which do not necessarily achieve seamless interoperability with NIH-maintained cloud-based systems. At our HPO, we implemented informatics to address gaps in enrollment workflows and hardware, clinical workflow integration, patient engagement, laboratory support, and study team reporting. In this case report we detail our approach to inform efforts at other institutions for the NIH All of Us Research Program and other studies.
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Affiliation(s)
- Scott P Turner
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY
| | - Sean T Pompea
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY
| | - Kelly L Williams
- Department of Healthcare Policy & Research, Weill Cornell Medicine, New York, NY
| | - David A Kraemer
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY
| | - Evan T Sholle
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY
| | - Cindy Chen
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY
| | - Curtis L Cole
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Rainu Kaushal
- Department of Healthcare Policy & Research, Weill Cornell Medicine, New York, NY
| | - Thomas R Campion
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY
- Department of Healthcare Policy & Research, Weill Cornell Medicine, New York, NY
- Department of Pediatrics, Weill Cornell Medicine, New York, NY
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24
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Hogan AL, Don EK, Rayner SL, Lee A, Laird AS, Watchon M, Winnick C, Tarr IS, Morsch M, Fifita JA, Gwee SSL, Formella I, Hortle E, Yuan KC, Molloy MP, Williams KL, Nicholson GA, Chung RS, Blair IP, Cole NJ. Expression of ALS/FTD-linked mutant CCNF in zebrafish leads to increased cell death in the spinal cord and an aberrant motor phenotype. Hum Mol Genet 2019; 28:698. [PMID: 30371781 DOI: 10.1093/hmg/ddy362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alison L Hogan
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Emily K Don
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Stephanie L Rayner
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Albert Lee
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Angela S Laird
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Maxinne Watchon
- Northcott Neuroscience Laboratory, ANZAC Research Institute; Molecular Medicine Laboratory, Concord Hospital; Sydney Medical School University of Sydney, NSW, Sydney, Australia
| | - Claire Winnick
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Ingrid S Tarr
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Marco Morsch
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Jennifer A Fifita
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Serene S L Gwee
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Isabel Formella
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Elinor Hortle
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Kristy C Yuan
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Mark P Molloy
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Kelly L Williams
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Garth A Nicholson
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia.,Northcott Neuroscience Laboratory, ANZAC Research Institute; Molecular Medicine Laboratory, Concord Hospital; Sydney Medical School University of Sydney, NSW, Sydney, Australia
| | - Roger S Chung
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Ian P Blair
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Nicholas J Cole
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, North Ryde, NSW, Australia
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25
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Lee A, Rayner SL, De Luca A, Gwee SSL, Morsch M, Sundaramoorthy V, Shahheydari H, Ragagnin A, Shi B, Yang S, Williams KL, Don EK, Walker AK, Zhang KY, Yerbury JJ, Cole NJ, Atkin JD, Blair IP, Molloy MP, Chung RS. Casein kinase II phosphorylation of cyclin F at serine 621 regulates the Lys48-ubiquitylation E3 ligase activity of the SCF (cyclin F) complex. Open Biol 2018; 7:rsob.170058. [PMID: 29021214 PMCID: PMC5666078 DOI: 10.1098/rsob.170058] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 09/15/2017] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder that is characterized by progressive weakness, paralysis and muscle loss often resulting in patient death within 3–5 years of diagnosis. Recently, we identified disease-linked mutations in the CCNF gene, which encodes the cyclin F protein, in cohorts of patients with familial and sporadic ALS and frontotemporal dementia (FTD) (Williams KL et al. 2016 Nat. Commun.7, 11253. (doi:10.1038/ncomms11253)). Cyclin F is a part of a Skp1-Cul-F-box (SCF) E3 ubiquitin-protein ligase complex and is responsible for ubiquitylating proteins for degradation by the proteasome. In this study, we investigated the phosphorylation status of cyclin F and the effect of the serine to glycine substitution at site 621 (S621G) on E3 ligase activity. This specific mutation (S621G) was found in a multi-generational Australian family with ALS/FTD. We identified seven phosphorylation sites on cyclin F, of which five are newly reported including Ser621. These phosphorylation sites were mostly identified within the PEST (proline, glutamic acid, serine and threonine) sequence located at the C-terminus of cyclin F. Additionally, we determined that casein kinase II (CK2) can phosphorylate Ser621 and thereby regulate the E3 ligase activity of the SCF(cyclin F) complex. Furthermore, the S621G mutation in cyclin F prevents phosphorylation by CK2 and confers elevated Lys48-ubiquitylation activity, a hallmark of ALS/FTD pathology. These findings highlight the importance of phosphorylation in regulating the activity of the SCF(cyclin F) E3 ligase complex that can affect downstream processes and may lead to defective motor neuron development, neuron degeneration and ultimately ALS and FTD.
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Affiliation(s)
- Albert Lee
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia .,Australian Proteome Analysis Facility, Research Park Drive, Macquarie University, North Ryde, NSW 2109, Australia
| | - Stephanie L Rayner
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia.,Faculty of Science and Engineering, Department of Chemistry and Biomolecular Sciences, Research Park Drive, Macquarie University, North Ryde, NSW 2109, Australia
| | - Alana De Luca
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Serene S L Gwee
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Marco Morsch
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Vinod Sundaramoorthy
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Hamideh Shahheydari
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Audrey Ragagnin
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Bingyang Shi
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Shu Yang
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Kelly L Williams
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Emily K Don
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Adam K Walker
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Katharine Y Zhang
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, School of Biological Sciences, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Nicholas J Cole
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Julie D Atkin
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Victoria, Australia
| | - Ian P Blair
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Mark P Molloy
- Australian Proteome Analysis Facility, Research Park Drive, Macquarie University, North Ryde, NSW 2109, Australia.,Faculty of Science and Engineering, Department of Chemistry and Biomolecular Sciences, Research Park Drive, Macquarie University, North Ryde, NSW 2109, Australia
| | - Roger S Chung
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW 2109, Australia
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26
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Nicolas A, Kenna KP, Renton AE, Ticozzi N, Faghri F, Chia R, Dominov JA, Kenna BJ, Nalls MA, Keagle P, Rivera AM, van Rheenen W, Murphy NA, van Vugt JJFA, Geiger JT, Van der Spek RA, Pliner HA, Shankaracharya, Smith BN, Marangi G, Topp SD, Abramzon Y, Gkazi AS, Eicher JD, Kenna A, Mora G, Calvo A, Mazzini L, Riva N, Mandrioli J, Caponnetto C, Battistini S, Volanti P, La Bella V, Conforti FL, Borghero G, Messina S, Simone IL, Trojsi F, Salvi F, Logullo FO, D'Alfonso S, Corrado L, Capasso M, Ferrucci L, Moreno CDAM, Kamalakaran S, Goldstein DB, Gitler AD, Harris T, Myers RM, Phatnani H, Musunuri RL, Evani US, Abhyankar A, Zody MC, Kaye J, Finkbeiner S, Wyman SK, LeNail A, Lima L, Fraenkel E, Svendsen CN, Thompson LM, Van Eyk JE, Berry JD, Miller TM, Kolb SJ, Cudkowicz M, Baxi E, Benatar M, Taylor JP, Rampersaud E, Wu G, Wuu J, Lauria G, Verde F, Fogh I, Tiloca C, Comi GP, Sorarù G, Cereda C, Corcia P, Laaksovirta H, Myllykangas L, Jansson L, Valori M, Ealing J, Hamdalla H, Rollinson S, Pickering-Brown S, Orrell RW, Sidle KC, Malaspina A, Hardy J, Singleton AB, Johnson JO, Arepalli S, Sapp PC, McKenna-Yasek D, Polak M, Asress S, Al-Sarraj S, King A, Troakes C, Vance C, de Belleroche J, Baas F, Ten Asbroek ALMA, Muñoz-Blanco JL, Hernandez DG, Ding J, Gibbs JR, Scholz SW, Floeter MK, Campbell RH, Landi F, Bowser R, Pulst SM, Ravits JM, MacGowan DJL, Kirby J, Pioro EP, Pamphlett R, Broach J, Gerhard G, Dunckley TL, Brady CB, Kowall NW, Troncoso JC, Le Ber I, Mouzat K, Lumbroso S, Heiman-Patterson TD, Kamel F, Van Den Bosch L, Baloh RH, Strom TM, Meitinger T, Shatunov A, Van Eijk KR, de Carvalho M, Kooyman M, Middelkoop B, Moisse M, McLaughlin RL, Van Es MA, Weber M, Boylan KB, Van Blitterswijk M, Rademakers R, Morrison KE, Basak AN, Mora JS, Drory VE, Shaw PJ, Turner MR, Talbot K, Hardiman O, Williams KL, Fifita JA, Nicholson GA, Blair IP, Rouleau GA, Esteban-Pérez J, García-Redondo A, Al-Chalabi A, Rogaeva E, Zinman L, Ostrow LW, Maragakis NJ, Rothstein JD, Simmons Z, Cooper-Knock J, Brice A, Goutman SA, Feldman EL, Gibson SB, Taroni F, Ratti A, Gellera C, Van Damme P, Robberecht W, Fratta P, Sabatelli M, Lunetta C, Ludolph AC, Andersen PM, Weishaupt JH, Camu W, Trojanowski JQ, Van Deerlin VM, Brown RH, van den Berg LH, Veldink JH, Harms MB, Glass JD, Stone DJ, Tienari P, Silani V, Chiò A, Shaw CE, Traynor BJ, Landers JE. Genome-wide Analyses Identify KIF5A as a Novel ALS Gene. Neuron 2018; 97:1267-1288. [PMID: 29566793 PMCID: PMC5867896 DOI: 10.1016/j.neuron.2018.02.027] [Citation(s) in RCA: 420] [Impact Index Per Article: 70.0] [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: 12/21/2017] [Revised: 01/21/2018] [Accepted: 02/26/2018] [Indexed: 12/11/2022]
Abstract
To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.
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Affiliation(s)
- Aude Nicolas
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - Kevin P Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Alan E Renton
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy; Department of Pathophysiology and Transplantation, "Dino Ferrari" Center - Università degli Studi di Milano, Milan 20122, Italy
| | - Faraz Faghri
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA; Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ruth Chia
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - Janice A Dominov
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Brendan J Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Mike A Nalls
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA; Data Tecnica International, Glen Echo, MD, USA
| | - Pamela Keagle
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Alberto M Rivera
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - Wouter van Rheenen
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Natalie A Murphy
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - Joke J F A van Vugt
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Joshua T Geiger
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Rick A Van der Spek
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hannah A Pliner
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - Shankaracharya
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Bradley N Smith
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London SE5 9RS, UK
| | - Giuseppe Marangi
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA; Institute of Genomic Medicine, Catholic University, Roma, Italy
| | - Simon D Topp
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London SE5 9RS, UK
| | - Yevgeniya Abramzon
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA; Sobell Department of Motor Neuroscience and Movement Disorders, University College London, Institute of Neurology, London, UK
| | - Athina Soragia Gkazi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London SE5 9RS, UK
| | - John D Eicher
- Genetics and Pharmacogenomics, MRL, Merck & Co., Inc., Boston, MA 02115, USA
| | - Aoife Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gabriele Mora
- ALS Center, Salvatore Maugeri Foundation, IRCCS, Mistretta, Messina, Italy
| | - Andrea Calvo
- "Rita Levi Montalcini" Department of Neuroscience, University of Turin, Turin, Italy
| | | | - Nilo Riva
- Department of Neurology, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Jessica Mandrioli
- Department of Neuroscience, St. Agostino Estense Hospital, Azienda Ospedaliero Universitaria di Modena, Modena, Italy
| | - Claudia Caponnetto
- Department of Neurosciences, Ophthalmology, Genetics, Rehabilitation, Maternal and Child Health, Ospedale Policlinico San Martino, Genoa, Italy
| | - Stefania Battistini
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Paolo Volanti
- ALS Center, Salvatore Maugeri Foundation, IRCCS, Mistretta, Messina, Italy
| | | | - Francesca L Conforti
- Institute of Neurological Sciences, National Research Council, Mangone, Cosenza, Italy
| | - Giuseppe Borghero
- Department of Neurology, Azienda Universitario Ospedaliera di Cagliari and University of Cagliari, Cagliari, Italy
| | - Sonia Messina
- Department of Clinical and Experimental Medicine, University of Messina and Nemo Sud Clinical Center for Neuromuscular Diseases, Aurora Foundation, Messina, Italy
| | - Isabella L Simone
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari, Bari, Italy
| | - Francesca Trojsi
- Department of Medical, Surgical, Neurological, Metabolic and Aging Sciences, University of Campania "Luigi Vanvitelli," Naples, Italy
| | - Fabrizio Salvi
- "Il Bene" Center for Immunological and Rare Neurological Diseases at Bellaria Hospital, IRCCS, Istituto delle Scienze Neurologiche, Bologna, Italy
| | | | - Sandra D'Alfonso
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Lucia Corrado
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | | | - Luigi Ferrucci
- Longitudinal Studies Section, Clinical Research Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | | | | | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tim Harris
- Bioverativ, 225 2nd Avenue, Waltham, MA 02145, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Diseases (CGND), New York Genome Center, New York, NY, USA
| | | | | | | | - Michael C Zody
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Julia Kaye
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Steven Finkbeiner
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA; Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Stacia K Wyman
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Alex LeNail
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Leandro Lima
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Clive N Svendsen
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Leslie M Thompson
- Department of Neurobiology and Behavior, Institute of Memory Impairment and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA; Department of Psychiatry and Human Behavior, Institute of Memory Impairment and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - Jennifer E Van Eyk
- The Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - James D Berry
- Harvard Medical School, Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, USA; Neurological Clinical Research Institute (NCRI), Massachusetts General Hospital, Boston, MA, USA
| | - Timothy M Miller
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephen J Kolb
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Merit Cudkowicz
- Harvard Medical School, Department of Neurology, Massachusetts General Hospital (MGH), Boston, MA, USA; Neurological Clinical Research Institute (NCRI), Massachusetts General Hospital, Boston, MA, USA
| | - Emily Baxi
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Michael Benatar
- Department of Neurology, University of Miami, Miami, FL 33136, USA
| | - J Paul Taylor
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Evadnie Rampersaud
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Joanne Wuu
- Department of Neurology, University of Miami, Miami, FL 33136, USA
| | - Giuseppe Lauria
- 3rd Neurology Unit, Motor Neuron Diseases Center, Fondazione IRCCS Istituto Neurologico "Carlo Besta," and Department of Biomedical and Clinical Sciences "Luigi Sacco," University of Milan, Milan, Italy
| | - Federico Verde
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Isabella Fogh
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy; Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London SE5 9RS, UK
| | - Cinzia Tiloca
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Giacomo P Comi
- Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Gianni Sorarù
- Department of Neurosciences, University of Padova, Padova, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Hannu Laaksovirta
- Department of Neurology, Helsinki University Hospital and Molecular Neurology Programme, Biomedicum, University of Helsinki, Helsinki FIN-02900, Finland
| | - Liisa Myllykangas
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Lilja Jansson
- Department of Neurology, Helsinki University Hospital and Molecular Neurology Programme, Biomedicum, University of Helsinki, Helsinki FIN-02900, Finland
| | - Miko Valori
- Department of Neurology, Helsinki University Hospital and Molecular Neurology Programme, Biomedicum, University of Helsinki, Helsinki FIN-02900, Finland
| | - John Ealing
- Greater Manchester Neurosciences Centre, Salford Royal NHS Foundation Trust, Salford M6 8HD, UK
| | - Hisham Hamdalla
- Greater Manchester Neurosciences Centre, Salford Royal NHS Foundation Trust, Salford M6 8HD, UK
| | - Sara Rollinson
- Faculty of Human and Medical Sciences, University of Manchester, Manchester M13 9PT, UK
| | | | - Richard W Orrell
- Department of Clinical Neuroscience, Institute of Neurology, University College London, London NW3 2PG, UK
| | - Katie C Sidle
- Department of Molecular Neuroscience and Reta Lila Weston Laboratories, Institute of Neurology, University College London, Queen Square House, London WC1N 3BG, UK
| | - Andrea Malaspina
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, NorthEast London and Essex Regional Motor Neuron Disease Care Centre, London E1 2AT, UK
| | - John Hardy
- Department of Molecular Neuroscience and Reta Lila Weston Laboratories, Institute of Neurology, University College London, Queen Square House, London WC1N 3BG, UK
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - Janel O Johnson
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - Sampath Arepalli
- Genomics Technology Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - Peter C Sapp
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Diane McKenna-Yasek
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Meraida Polak
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Seneshaw Asress
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Safa Al-Sarraj
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London SE5 9RS, UK
| | - Andrew King
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London SE5 9RS, UK
| | - Claire Troakes
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London SE5 9RS, UK
| | - Caroline Vance
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London SE5 9RS, UK
| | | | - Frank Baas
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - José Luis Muñoz-Blanco
- ALS-Neuromuscular Unit, Hospital General Universitario Gregorio Marañón, IISGM, Madrid, Spain
| | - Dena G Hernandez
- Genomics Technology Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - J Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Mary Kay Floeter
- Motor Neuron Disorders Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Roy H Campbell
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Francesco Landi
- Center for Geriatric Medicine, Department of Geriatrics, Neurosciences and Orthopedics, Catholic University of Sacred Heart, Rome 00168, Italy
| | - Robert Bowser
- Division of Neurology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Stefan M Pulst
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - John M Ravits
- Department of Neuroscience, University of California, San Diego, La Jolla, CA, USA
| | - Daniel J L MacGowan
- Mount Sinai Beth Israel Hospital, Mount Sinai School of Medicine, New York, NY, USA
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Erik P Pioro
- Department of Neurology, Neuromuscular Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Roger Pamphlett
- Discipline of Pathology, Brain and Mind Centre, The University of Sydney, 94 Mallett Street, Camperdown, NSW 2050, Australia
| | - James Broach
- Department of Biochemistry, Penn State College of Medicine, Hershey, PA, USA
| | - Glenn Gerhard
- Department of Pathology, Penn State College of Medicine, Hershey, PA, USA
| | - Travis L Dunckley
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Christopher B Brady
- Research and Development Service, Veterans Affairs Boston Healthcare System, Boston, MA, USA; Department of Neurology, Program in Behavioral Neuroscience, Boston University School of Medicine, Boston, MA, USA
| | - Neil W Kowall
- Neurology Service, VA Boston Healthcare System and Boston University Alzheimer's Disease Center, Boston, MA 02130, USA
| | - Juan C Troncoso
- Departments of Pathology and Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Isabelle Le Ber
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, Institut du Cerveau et la Moelle (ICM), Assistance Publique Hôpitaux de Paris (AP-HP) - Hôpital Pitié-Salpêtrière, Paris, France
| | - Kevin Mouzat
- INM, University Montpellier, Montpellier, France; Department of Biochemistry, CHU Nîmes, Nîmes, France
| | - Serge Lumbroso
- INM, University Montpellier, Montpellier, France; Department of Biochemistry, CHU Nîmes, Nîmes, France
| | - Terry D Heiman-Patterson
- Department of Neurology, Drexel University College of Medicine, Philadelphia, PA, USA; Department of Neurology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Freya Kamel
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, NC 27709, USA
| | - Ludo Van Den Bosch
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium; VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Robert H Baloh
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tim M Strom
- Institute of Human Genetics, Technische Universität München, Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London SE5 9RS, UK
| | - Kristel R Van Eijk
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mamede de Carvalho
- Institute of Physiology, Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, Lisbon, Portugal; Department of Neurosciences, Hospital de Santa Maria-CHLN, Lisbon, Portugal
| | | | - Bas Middelkoop
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Matthieu Moisse
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium; VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Russell L McLaughlin
- Population Genetics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Republic of Ireland
| | - Michael A Van Es
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Markus Weber
- Neuromuscular Diseases Center/ALS Clinic, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Kevin B Boylan
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - A Nazli Basak
- Suna and Inan Kırac Foundation, Neurodegeneration Research Laboratory, Bogazici University, Istanbul, Turkey
| | - Jesús S Mora
- ALS Unit/Neurology, Hospital San Rafael, Madrid, Spain
| | - Vivian E Drory
- Department of Neurology, Tel-Aviv Sourasky Medical Centre, Tel-Aviv, Israel
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Republic of Ireland
| | - Kelly L Williams
- Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Jennifer A Fifita
- Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Garth A Nicholson
- Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia; ANZAC Research Institute, Concord Hospital, University of Sydney, Sydney, NSW 2139, Australia
| | - Ian P Blair
- Centre for MND Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Jesús Esteban-Pérez
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, SERMAS, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER U-723), Madrid, Spain
| | - Alberto García-Redondo
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, SERMAS, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER U-723), Madrid, Spain
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London SE5 9RS, UK
| | - Ekaterina Rogaeva
- Tanz Centre for Research of Neurodegenerative Diseases, Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Lorne Zinman
- Division of Neurology, Department of Internal Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Lyle W Ostrow
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21287, USA
| | | | | | - Zachary Simmons
- Department of Neurology, Penn State Hershey Medical Center, Hershey, PA, USA
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Alexis Brice
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, Institut du Cerveau et la Moelle (ICM), Assistance Publique Hôpitaux de Paris (AP-HP) - Hôpital Pitié-Salpêtrière, Paris, France
| | | | - Eva L Feldman
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Summer B Gibson
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Franco Taroni
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico "Carlo Besta," Milan 20133, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy; Department of Pathophysiology and Transplantation, "Dino Ferrari" Center - Università degli Studi di Milano, Milan 20122, Italy
| | - Cinzia Gellera
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico "Carlo Besta," Milan 20133, Italy
| | - Philip Van Damme
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium; VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium; University Hospitals Leuven, Department of Neurology, Leuven, Belgium
| | - Wim Robberecht
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium; VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium; University Hospitals Leuven, Department of Neurology, Leuven, Belgium
| | - Pietro Fratta
- Sobell Department of Motor Neuroscience and Movement Disorders, University College London, Institute of Neurology, London, UK
| | - Mario Sabatelli
- Centro Clinico NeMO, Institute of Neurology, Catholic University, Largo F. Vito 1, 00168 Rome, Italy
| | - Christian Lunetta
- NEuroMuscular Omnicenter (NEMO), Serena Onlus Foundation, Milan, Italy
| | - Albert C Ludolph
- Neurology Department, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Peter M Andersen
- Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå SE-90185, Sweden
| | - Jochen H Weishaupt
- Neurology Department, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - William Camu
- ALS Center, CHU Gui de Chauliac, University of Montpellier, Montpellier, France
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vivianna M Van Deerlin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Matthew B Harms
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Jonathan D Glass
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David J Stone
- Genetics and Pharmacogenomics, MRL, Merck & Co., Inc., West Point, PA 19486, USA
| | - Pentti Tienari
- Department of Neurology, Helsinki University Hospital and Molecular Neurology Programme, Biomedicum, University of Helsinki, Helsinki FIN-02900, Finland
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy; Department of Pathophysiology and Transplantation, "Dino Ferrari" Center - Università degli Studi di Milano, Milan 20122, Italy
| | - Adriano Chiò
- "Rita Levi Montalcini" Department of Neuroscience, University of Turin, Turin, Italy; Neuroscience Institute of Torino, Turin 10124, Italy
| | - Christopher E Shaw
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London SE5 9RS, UK
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD 20892, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD 21287, USA.
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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Farg MA, Soo KY, Walker AK, Pham H, Orian J, Horne MK, Warraich ST, Williams KL, Blair IP, Atkin JD. Note in reference to “Mutant FUS induces endoplasmic reticulum stress in amyotrophic lateral sclerosis and interacts with protein disulfide-isomerase” [Neurobiol. Aging 33(12) (2012) 2855-2868]. Neurobiol Aging 2017. [DOI: 10.1016/j.neurobiolaging.2017.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Fifita JA, Zhang KY, Galper J, Williams KL, McCann EP, Hogan AL, Saunders N, Bauer D, Tarr IS, Pamphlett R, Nicholson GA, Rowe D, Yang S, Blair IP. Genetic and Pathological Assessment of hnRNPA1, hnRNPA2/B1, and hnRNPA3 in Familial and Sporadic Amyotrophic Lateral Sclerosis. NEURODEGENER DIS 2017; 17:304-312. [DOI: 10.1159/000481258] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/29/2017] [Indexed: 12/27/2022] Open
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Lee A, Rayner SL, Gwee SSL, De Luca A, Shahheydari H, Sundaramoorthy V, Ragagnin A, Morsch M, Radford R, Galper J, Freckleton S, Shi B, Walker AK, Don EK, Cole NJ, Yang S, Williams KL, Yerbury JJ, Blair IP, Atkin JD, Molloy MP, Chung RS. Pathogenic mutation in the ALS/FTD gene, CCNF, causes elevated Lys48-linked ubiquitylation and defective autophagy. Cell Mol Life Sci 2017; 75:335-354. [DOI: 10.1007/s00018-017-2632-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/29/2017] [Accepted: 08/23/2017] [Indexed: 12/13/2022]
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Sundaramoorthy V, Walker AK, Tan V, Fifita JA, Mccann EP, Williams KL, Blair IP, Guillemin GJ, Farg MA, Atkin JD. Defects in optineurin- and myosin VI-mediated cellular trafficking in amyotrophic lateral sclerosis. Hum Mol Genet 2017; 26:3452. [PMID: 28854706 DOI: 10.1093/hmg/ddx268] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Vinod Sundaramoorthy
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, NSW 2109, Australia.,Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Adam K Walker
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Vanessa Tan
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, NSW 2109, Australia
| | - Jennifer A Fifita
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, NSW 2109, Australia
| | - Emily P Mccann
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, NSW 2109, Australia
| | - Kelly L Williams
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, NSW 2109, Australia
| | - Ian P Blair
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, NSW 2109, Australia
| | - Gilles J Guillemin
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, NSW 2109, Australia
| | - Manal A Farg
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - Julie D Atkin
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, NSW 2109, Australia.,Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
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Kichkin E, Visvanathan A, Lovicu FJ, Shu DY, Das SJ, Reddel SW, McCann EP, Zhang KY, Williams KL, Blair IP, Phillips WD. Postnatal Development of Spasticity Following Transgene Insertion in the Mouse βIV Spectrin Gene (SPTBN4). J Neuromuscul Dis 2017; 4:159-164. [PMID: 28582869 DOI: 10.3233/jnd-160197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND The L25 mouse line was generated by random genomic insertion of a lens-specific transgene. Inbreeding of L25 hemizygotes revealed an unanticipated spastic phenotype in the hind limbs. OBJECTIVE The goals were to characterize the motor phenotype in the L25 mice and to map the transgene insert site within the mouse genome. METHODS Six pairs of L25+/- mice were repeatedly mated. Beginning at weaning, all progeny were inspected for body weight and motor signs twice weekly until they displayed predefined ethical criteria for termination. The transgene insert site was determined by whole genome sequencing. Western blotting was used to compare the expression levels of beta-IV spectrin protein in the brain. RESULTS Matings of hemizygous L25+/- × L25+/- mice yielded 20% (29/148) affected weanlings, identified by an abnormal retraction of the hind limbs when lifted by the tail, and a fine tremor. Affected mice were less mobile and grew more slowly than wild-type littermates. All affected mice required termination due to >15% loss of body weight (50% survival age 92 days). At the endpoint, mice showed varying degrees of spastic paresis or spastic paralysis localised to the hind limbs. Motor endplates remained fully innervated. Genome sequencing confirmed that the transgene was inserted in the locus of βIV spectrin of L25 mice. Western blotting indicated that this random insertion had greatly reduced the expression of βIV spectrin protein in the affected L25 mice. CONCLUSIONS The results confirm the importance of βIV spectrin for maintaining central motor pathway control of the hind limbs, and provide a developmental time course for the phenotype.
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Affiliation(s)
- Eva Kichkin
- Physiology and Bosch Institute, University of Sydney, Sydney, Australia
| | | | - Frank J Lovicu
- Anatomy and Histology and Bosch Institute, University of Sydney, Sydney, Australia
| | - Daisy Y Shu
- Anatomy and Histology and Bosch Institute, University of Sydney, Sydney, Australia
| | - Shannon J Das
- Anatomy and Histology and Bosch Institute, University of Sydney, Sydney, Australia
| | - Stephen W Reddel
- Department of Molecular Medicine, Concord Hospital, Sydney, Australia
| | - Emily P McCann
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - Katharine Y Zhang
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - Kelly L Williams
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - Ian P Blair
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
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Thomas-Jinu S, Gordon PM, Fielding T, Taylor R, Smith BN, Snowden V, Blanc E, Vance C, Topp S, Wong CH, Bielen H, Williams KL, McCann EP, Nicholson GA, Pan-Vazquez A, Fox AH, Bond CS, Talbot WS, Blair IP, Shaw CE, Houart C. Non-nuclear Pool of Splicing Factor SFPQ Regulates Axonal Transcripts Required for Normal Motor Development. Neuron 2017; 94:931. [PMID: 28521142 PMCID: PMC5441113 DOI: 10.1016/j.neuron.2017.04.036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hogan AL, Don EK, Rayner SL, Lee A, Laird AS, Watchon M, Winnick C, Tarr IS, Morsch M, Fifita JA, Gwee SSL, Formella I, Hortle E, Yuan KC, Molloy MP, Williams KL, Nicholson GA, Chung RS, Blair IP, Cole NJ. Expression of ALS/FTD-linked mutant CCNF in zebrafish leads to increased cell death in the spinal cord and an aberrant motor phenotype. Hum Mol Genet 2017; 26:2616-2626. [DOI: 10.1093/hmg/ddx136] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/29/2017] [Indexed: 01/28/2023] Open
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Thomas-Jinu S, Gordon PM, Fielding T, Taylor R, Smith BN, Snowden V, Blanc E, Vance C, Topp S, Wong CH, Bielen H, Williams KL, McCann EP, Nicholson GA, Pan-Vazquez A, Fox AH, Bond CS, Talbot WS, Blair IP, Shaw CE, Houart C. Non-nuclear Pool of Splicing Factor SFPQ Regulates Axonal Transcripts Required for Normal Motor Development. Neuron 2017; 94:322-336.e5. [PMID: 28392072 PMCID: PMC5405110 DOI: 10.1016/j.neuron.2017.03.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/02/2017] [Accepted: 03/17/2017] [Indexed: 12/12/2022]
Abstract
Recent progress revealed the complexity of RNA processing and its association to human disorders. Here, we unveil a new facet of this complexity. Complete loss of function of the ubiquitous splicing factor SFPQ affects zebrafish motoneuron differentiation cell autonomously. In addition to its nuclear localization, the protein unexpectedly localizes to motor axons. The cytosolic version of SFPQ abolishes motor axonal defects, rescuing key transcripts, and restores motility in the paralyzed sfpq null mutants, indicating a non-nuclear processing role in motor axons. Novel variants affecting the conserved coiled-coil domain, so far exclusively found in fALS exomes, specifically affect the ability of SFPQ to localize in axons. They broadly rescue morphology and motility in the zebrafish mutant, but alter motor axon morphology, demonstrating functional requirement for axonal SFPQ. Altogether, we uncover the axonal function of the splicing factor SFPQ in motor development and highlight the importance of the coiled-coil domain in this process. Video Abstract
SFPQ splicing factor is present in motor axons Non-nuclear SFPQ is able to drive axon maturation and connectivity Loss of axonal SFPQ affects axonal morphology Coiled-coil domain of the protein is important for non-nuclear localization
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Affiliation(s)
- Swapna Thomas-Jinu
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Patricia M Gordon
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Triona Fielding
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Richard Taylor
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Bradley N Smith
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Victoria Snowden
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Eric Blanc
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Caroline Vance
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Simon Topp
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Chun-Hao Wong
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Holger Bielen
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Kelly L Williams
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Emily P McCann
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Garth A Nicholson
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia; ANZAC Research Institute, University of Sydney, Concord Hospital, Sydney, NSW 2139, Australia
| | - Alejandro Pan-Vazquez
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Archa H Fox
- School of Anatomy, Physiology, and Human Biology, University of Western Australia, Crawley, WA 6009, Australia; Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, University of Western Australia, Crawley, WA 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia
| | - William S Talbot
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian P Blair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Corinne Houart
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK.
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McCann EP, Williams KL, Fifita JA, Tarr IS, O'Connor J, Rowe DB, Nicholson GA, Blair IP. The genotype-phenotype landscape of familial amyotrophic lateral sclerosis in Australia. Clin Genet 2017; 92:259-266. [PMID: 28105640 DOI: 10.1111/cge.12973] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/12/2017] [Accepted: 01/14/2017] [Indexed: 12/19/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a clinically and genetically heterogeneous fatal neurodegenerative disease. Around 10% of ALS cases are hereditary. ALS gene discoveries have provided most of our understanding of disease pathogenesis. We aimed to describe the genetic landscape of ALS in Australia by assessing 1013 Australian ALS patients for known ALS mutations by direct sequencing, whole exome sequencing or repeat primed polymerase chain reaction. Age of disease onset and disease duration were used for genotype-phenotype correlations. We report 60.8% of Australian ALS families in this cohort harbour a known ALS mutation. Hexanucleotide repeat expansions in C9orf72 accounted for 40.6% of families and 2.9% of sporadic patients. We also report ALS families with mutations in SOD1 (13.7%), FUS (2.4%), TARDBP (1.9%), UBQLN2 (.9%), OPTN (.5%), TBK1 (.5%) and CCNF (.5%). We present genotype-phenotype correlations between these genes as well as between gene mutations. Notably, C9orf72 hexanucleotide repeat expansion positive patients experienced significantly later disease onset than ALS mutation patients. Among SOD1 families, p.I114T positive patients had significantly later onset and longer survival. Our report highlights a unique spectrum of ALS gene frequencies among patients from the Australian population, and further, provides correlations between specific ALS mutations with disease onset and/or duration.
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Affiliation(s)
- E P McCann
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, Australia
| | - K L Williams
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, Australia
| | - J A Fifita
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, Australia
| | - I S Tarr
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, Australia
| | - J O'Connor
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, Australia
| | - D B Rowe
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, Australia
| | - G A Nicholson
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, Australia
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, Australia
| | - I P Blair
- Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, Australia
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36
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Kenna KP, van Doormaal PTC, Dekker AM, Ticozzi N, Kenna BJ, Diekstra FP, van Rheenen W, van Eijk KR, Jones AR, Keagle P, Shatunov A, Sproviero W, Smith BN, van Es MA, Topp SD, Kenna A, Miller JW, Fallini C, Tiloca C, McLaughlin RL, Vance C, Troakes C, Colombrita C, Mora G, Calvo A, Verde F, Al-Sarraj S, King A, Calini D, de Belleroche J, Baas F, van der Kooi AJ, de Visser M, Ten Asbroek ALMA, Sapp PC, McKenna-Yasek D, Polak M, Asress S, Muñoz-Blanco JL, Strom TM, Meitinger T, Morrison KE, Lauria G, Williams KL, Leigh PN, Nicholson GA, Blair IP, Leblond CS, Dion PA, Rouleau GA, Pall H, Shaw PJ, Turner MR, Talbot K, Taroni F, Boylan KB, Van Blitterswijk M, Rademakers R, Esteban-Pérez J, García-Redondo A, Van Damme P, Robberecht W, Chio A, Gellera C, Drepper C, Sendtner M, Ratti A, Glass JD, Mora JS, Basak NA, Hardiman O, Ludolph AC, Andersen PM, Weishaupt JH, Brown RH, Al-Chalabi A, Silani V, Shaw CE, van den Berg LH, Veldink JH, Landers JE. NEK1 variants confer susceptibility to amyotrophic lateral sclerosis. Nat Genet 2016; 48:1037-42. [PMID: 27455347 PMCID: PMC5560030 DOI: 10.1038/ng.3626] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/24/2016] [Indexed: 12/11/2022]
Abstract
To identify genetic factors contributing to amyotrophic lateral sclerosis (ALS), we conducted whole-exome analyses of 1,022 index familial ALS (FALS) cases and 7,315 controls. In a new screening strategy, we performed gene-burden analyses trained with established ALS genes and identified a significant association between loss-of-function (LOF) NEK1 variants and FALS risk. Independently, autozygosity mapping for an isolated community in the Netherlands identified a NEK1 p.Arg261His variant as a candidate risk factor. Replication analyses of sporadic ALS (SALS) cases and independent control cohorts confirmed significant disease association for both p.Arg261His (10,589 samples analyzed) and NEK1 LOF variants (3,362 samples analyzed). In total, we observed NEK1 risk variants in nearly 3% of ALS cases. NEK1 has been linked to several cellular functions, including cilia formation, DNA-damage response, microtubule stability, neuronal morphology and axonal polarity. Our results provide new and important insights into ALS etiopathogenesis and genetic etiology.
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Affiliation(s)
- Kevin P Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Perry T C van Doormaal
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Annelot M Dekker
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Nicola Ticozzi
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Brendan J Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Frank P Diekstra
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Wouter van Rheenen
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Kristel R van Eijk
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Ashley R Jones
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Pamela Keagle
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - William Sproviero
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Bradley N Smith
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Michael A van Es
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Simon D Topp
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Aoife Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jack W Miller
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Claudia Fallini
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Cinzia Tiloca
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Doctoral School in Molecular Medicine, Department of Sciences and Biomedical Technologies, Università degli Studi di Milano, Milan, Italy
| | - Russell L McLaughlin
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Caroline Vance
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Claire Troakes
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Claudia Colombrita
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Gabriele Mora
- Salvatore Maugeri Foundation, IRCSS, Scientific Institute of Milano, Milan, Italy
| | - Andrea Calvo
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
| | - Federico Verde
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Safa Al-Sarraj
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Andrew King
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Daniela Calini
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | | | - Frank Baas
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Anneke J van der Kooi
- Department of Neurogenetics and Neurology, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Marianne de Visser
- Department of Neurogenetics and Neurology, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Anneloor L M A Ten Asbroek
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter C Sapp
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Diane McKenna-Yasek
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Meraida Polak
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - Seneshaw Asress
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - José Luis Muñoz-Blanco
- Unidad de ELA, Instituto de Investigación Hospital Gregorio Marañón de Madrid, Madrid, Spain
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | | | - Giuseppe Lauria
- 3rd Neurology Unit, Motor Neuron Diseases Center, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Kelly L Williams
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - P Nigel Leigh
- Trafford Centre for Medical Research, Brighton and Sussex Medical School, Falmer, UK
| | - Garth A Nicholson
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
- ANZAC Research Institute, Concord Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Ian P Blair
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Claire S Leblond
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Patrick A Dion
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Hardev Pall
- Institute of Clinical Studies, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
- Department of Neurology, Queen Elizabeth Hospital Birmingham, Edgbaston, Birmingham, UK
| | - Pamela J Shaw
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Franco Taroni
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Kevin B Boylan
- Department of Neurology, Mayo Clinic Florida, Jacksonville, Florida, USA
| | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Jesús Esteban-Pérez
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) U-723, Madrid, Spain
| | - Alberto García-Redondo
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) U-723, Madrid, Spain
| | - Phillip Van Damme
- Laboratory of Neurobiology, Department of Neurosciences, KU Leuven and Vesalius Research Centre, VIB, Leuven, Belgium
- Department of Neurology, University Hospitals, Leuven, Belgium
| | - Wim Robberecht
- Laboratory of Neurobiology, Department of Neurosciences, KU Leuven and Vesalius Research Centre, VIB, Leuven, Belgium
- Department of Neurology, University Hospitals, Leuven, Belgium
| | - Adriano Chio
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
| | - Cinzia Gellera
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Carsten Drepper
- Institute of Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
- Department of Child and Adolescent Psychiatry, University Hospital of Würzburg, Würzburg, Germany
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Antonia Ratti
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Jonathan D Glass
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - Jesús S Mora
- ALS Unit/Neurology, Hospital San Rafael, Madrid, Spain
| | - Nazli A Basak
- NDAL, Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | | | - Peter M Andersen
- Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden
| | | | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Vincenzo Silani
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Christopher E Shaw
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Leonard H van den Berg
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Jan H Veldink
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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37
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Fifita JA, Williams KL, Sundaramoorthy V, Mccann EP, Nicholson GA, Atkin JD, Blair IP. A novel amyotrophic lateral sclerosis mutation in OPTN induces ER stress and Golgi fragmentation in vitro. Amyotroph Lateral Scler Frontotemporal Degener 2016; 18:126-133. [DOI: 10.1080/21678421.2016.1218517] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jennifer A. Fifita
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia,
| | - Kelly L. Williams
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia,
| | - Vinod Sundaramoorthy
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia,
| | - Emily P. Mccann
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia,
| | - Garth A. Nicholson
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia,
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales, Australia,
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia,
- Molecular Medicine Laboratory, Concord Hospital, Concord, New South Wales, Australia, and
| | - Julie D. Atkin
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia,
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Victoria, Australia
| | - Ian P. Blair
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia,
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38
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Williams KL, Topp S, Yang S, Smith B, Fifita JA, Warraich ST, Zhang KY, Farrawell N, Vance C, Hu X, Chesi A, Leblond CS, Lee A, Rayner SL, Sundaramoorthy V, Dobson-Stone C, Molloy MP, van Blitterswijk M, Dickson DW, Petersen RC, Graff-Radford NR, Boeve BF, Murray ME, Pottier C, Don E, Winnick C, McCann EP, Hogan A, Daoud H, Levert A, Dion PA, Mitsui J, Ishiura H, Takahashi Y, Goto J, Kost J, Gellera C, Gkazi AS, Miller J, Stockton J, Brooks WS, Boundy K, Polak M, Muñoz-Blanco JL, Esteban-Pérez J, Rábano A, Hardiman O, Morrison KE, Ticozzi N, Silani V, de Belleroche J, Glass JD, Kwok JBJ, Guillemin GJ, Chung RS, Tsuji S, Brown RH, García-Redondo A, Rademakers R, Landers JE, Gitler AD, Rouleau GA, Cole NJ, Yerbury JJ, Atkin JD, Shaw CE, Nicholson GA, Blair IP. CCNF mutations in amyotrophic lateral sclerosis and frontotemporal dementia. Nat Commun 2016; 7:11253. [PMID: 27080313 PMCID: PMC4835537 DOI: 10.1038/ncomms11253] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 03/07/2016] [Indexed: 01/06/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are overlapping, fatal neurodegenerative disorders in which the molecular and pathogenic basis remains poorly understood. Ubiquitinated protein aggregates, of which TDP-43 is a major component, are a characteristic pathological feature of most ALS and FTD patients. Here we use genome-wide linkage analysis in a large ALS/FTD kindred to identify a novel disease locus on chromosome 16p13.3. Whole-exome sequencing identified a CCNF missense mutation at this locus. Interrogation of international cohorts identified additional novel CCNF variants in familial and sporadic ALS and FTD. Enrichment of rare protein-altering CCNF variants was evident in a large sporadic ALS replication cohort. CCNF encodes cyclin F, a component of an E3 ubiquitin-protein ligase complex (SCF(Cyclin F)). Expression of mutant CCNF in neuronal cells caused abnormal ubiquitination and accumulation of ubiquitinated proteins, including TDP-43 and a SCF(Cyclin F) substrate. This implicates common mechanisms, linked to protein homeostasis, underlying neuronal degeneration.
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Affiliation(s)
- Kelly L. Williams
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales 2139, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Simon Topp
- Medical Research Council Centre for Neurodegeneration Research, Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Shu Yang
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales 2139, Australia
| | - Bradley Smith
- Medical Research Council Centre for Neurodegeneration Research, Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Jennifer A. Fifita
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales 2139, Australia
| | - Sadaf T. Warraich
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Katharine Y. Zhang
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Natalie Farrawell
- Illawarra Health and Medical Research Institute, School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Caroline Vance
- Medical Research Council Centre for Neurodegeneration Research, Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Xun Hu
- Medical Research Council Centre for Neurodegeneration Research, Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Alessandra Chesi
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Claire S. Leblond
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Québec, Canada H3A 2B4
- Pathology and Cellular Biology Department, Montreal University, Montreal, QC H3T 1J4 Québec, Canada
| | - Albert Lee
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Stephanie L. Rayner
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Vinod Sundaramoorthy
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Department of Biochemistry, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Carol Dobson-Stone
- Neuroscience Research Australia, Randwick, Sydney, New South Wales 2031, Australia
- School of Medical Sciences, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia
| | - Mark P. Molloy
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, New South Wales 2109, Australia
| | | | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida 32224, USA
| | - Ronald C. Petersen
- Department of Neurology, Mayo Clinic Rochester, Rochester, Minneapolis 55905, USA
| | | | - Bradley F. Boeve
- Department of Neurology, Mayo Clinic Rochester, Rochester, Minneapolis 55905, USA
| | - Melissa E. Murray
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida 32224, USA
| | - Cyril Pottier
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida 32224, USA
| | - Emily Don
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Claire Winnick
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Emily P. McCann
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Alison Hogan
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Hussein Daoud
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Québec, Canada H3A 2B4
- Pathology and Cellular Biology Department, Montreal University, Montreal, QC H3T 1J4 Québec, Canada
| | - Annie Levert
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Québec, Canada H3A 2B4
- Pathology and Cellular Biology Department, Montreal University, Montreal, QC H3T 1J4 Québec, Canada
| | - Patrick A. Dion
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Québec, Canada H3A 2B4
- Pathology and Cellular Biology Department, Montreal University, Montreal, QC H3T 1J4 Québec, Canada
| | - Jun Mitsui
- Medical Genome Center, The University of Tokyo Hospital, The University of Tokyo, Tokyo 113-8655, Japan
| | - Hiroyuki Ishiura
- Medical Genome Center, The University of Tokyo Hospital, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yuji Takahashi
- Medical Genome Center, The University of Tokyo Hospital, The University of Tokyo, Tokyo 113-8655, Japan
| | - Jun Goto
- Medical Genome Center, The University of Tokyo Hospital, The University of Tokyo, Tokyo 113-8655, Japan
| | - Jason Kost
- Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Cinzia Gellera
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico ‘Carlo Besta', 20133 Milan, Italy
| | - Athina Soragia Gkazi
- Medical Research Council Centre for Neurodegeneration Research, Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Jack Miller
- Medical Research Council Centre for Neurodegeneration Research, Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Joanne Stockton
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - William S. Brooks
- Neuroscience Research Australia, Randwick, Sydney, New South Wales 2031, Australia
| | - Karyn Boundy
- The Queen Elizabeth Hospital, Woodville South, South Australia 5011, Australia
| | - Meraida Polak
- Department of Neurology, Emory University, Atlanta, Georgia 30322, USA
| | - José Luis Muñoz-Blanco
- Unidad de ELA, Instituto de Investigación Hospital Gregorio Marañón de Madrid, Sermas 28007, Spain
| | - Jesús Esteban-Pérez
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, Sermas 28041, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER U-723), Madrid 28029, Spain
| | - Alberto Rábano
- Banco de Tejidos, Centro Alzheimer—Fundación Reina Sofia, Fundación CIEN, Madrid 28071, Spain
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Karen E. Morrison
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TH, UK
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy
- Department of Pathophysiology and Transplantation, ‘Dino Ferrari' Center—Università degli Studi di Milano, 20122 Milan, Italy
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy
- Department of Pathophysiology and Transplantation, ‘Dino Ferrari' Center—Università degli Studi di Milano, 20122 Milan, Italy
| | - Jacqueline de Belleroche
- Neurogenetics Group, Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Jonathan D. Glass
- Department of Neurology, Emory University, Atlanta, Georgia 30322, USA
| | - John B. J. Kwok
- Neuroscience Research Australia, Randwick, Sydney, New South Wales 2031, Australia
- School of Medical Sciences, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia
| | - Gilles J. Guillemin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Roger S. Chung
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Shoji Tsuji
- Medical Genome Center, The University of Tokyo Hospital, The University of Tokyo, Tokyo 113-8655, Japan
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Robert H. Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Alberto García-Redondo
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, Sermas 28041, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER U-723), Madrid 28029, Spain
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida 32224, USA
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Guy A. Rouleau
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Québec, Canada H3A 2B4
- Pathology and Cellular Biology Department, Montreal University, Montreal, QC H3T 1J4 Québec, Canada
| | - Nicholas J. Cole
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Justin J. Yerbury
- Illawarra Health and Medical Research Institute, School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Julie D. Atkin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Department of Biochemistry, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Christopher E. Shaw
- Medical Research Council Centre for Neurodegeneration Research, Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Garth A. Nicholson
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales 2139, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
- Molecular Medicine Laboratory, Concord Hospital, New South Wales 2139, Australia
| | - Ian P. Blair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales 2139, Australia
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Williams KL, McCann EP, Fifita JA, Zhang K, Duncan EL, Leo PJ, Marshall M, Rowe DB, Nicholson GA, Blair IP. Novel TBK1 truncating mutation in a familial amyotrophic lateral sclerosis patient of Chinese origin. Neurobiol Aging 2015; 36:3334.e1-3334.e5. [PMID: 26350399 DOI: 10.1016/j.neurobiolaging.2015.08.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/11/2015] [Accepted: 08/11/2015] [Indexed: 12/21/2022]
Abstract
Missense and frameshift mutations in TRAF family member-associated NF-kappa-B activator (TANK)-binding kinase 1 (TBK1) have been reported in European sporadic and familial amyotrophic lateral sclerosis (ALS) cohorts. To assess the role of TBK1 in ALS patient cohorts of wider ancestry, we have analyzed whole-exome sequence data from an Australian cohort of familial ALS (FALS) patients and controls. We identified a novel TBK1 deletion (c.1197delC) in a FALS patient of Chinese origin. This frameshift mutation (p.L399fs) likely results in a truncated protein that lacks functional domains required for adapter protein binding, as well as protein activation and structural integrity. No novel or reported TBK1 mutations were identified in FALS patients of European ancestry. This is the first report of a TBK1 mutation in an ALS patient of Asian origin and indicates that sequence variations in TBK1 are a rare cause of FALS in Australia.
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Affiliation(s)
- Kelly L Williams
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Emily P McCann
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jennifer A Fifita
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Katharine Zhang
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Emma L Duncan
- Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Paul J Leo
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Mhairi Marshall
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Dominic B Rowe
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Garth A Nicholson
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia; University of Sydney, ANZAC Research Institute, Concord Hospital, Sydney, New South Wales, Australia
| | - Ian P Blair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia.
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Sundaramoorthy V, Walker AK, Tan V, Fifita JA, Mccann EP, Williams KL, Blair IP, Guillemin GJ, Farg MA, Atkin JD. Defects in optineurin- and myosin VI-mediated cellular trafficking in amyotrophic lateral sclerosis. Hum Mol Genet 2015; 24:3830-46. [DOI: 10.1093/hmg/ddv126] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/07/2015] [Indexed: 12/12/2022] Open
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Fifita JA, Williams KL, McCann EP, O'Brien A, Bauer DC, Nicholson GA, Blair IP. Mutation analysis of MATR3 in Australian familial amyotrophic lateral sclerosis. Neurobiol Aging 2014; 36:1602.e1-2. [PMID: 25523636 DOI: 10.1016/j.neurobiolaging.2014.11.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 11/15/2014] [Indexed: 11/17/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that arises from the progressive degeneration of the motor neurons. Recently, mutations in the matrin 3 (MATR3) gene were described in both ALS and autosomal dominant distal myopathy with vocal cord and pharyngeal weakness. We sought to determine the prevalence of MATR3 mutations in Australian familial ALS (n = 106) using whole exome sequencing. No mutations were identified, indicating that MATR3 mutations are not a common cause of ALS in Australian familial cases with predominately European ancestry.
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Affiliation(s)
- Jennifer A Fifita
- Australian School of Advanced Medicine, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Kelly L Williams
- Australian School of Advanced Medicine, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Emily P McCann
- Australian School of Advanced Medicine, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Aidan O'Brien
- Digital Productivity, Commonwealth Scientific and Industrial Research Organization, Sydney, New South Wales, Australia
| | - Denis C Bauer
- Digital Productivity, Commonwealth Scientific and Industrial Research Organization, Sydney, New South Wales, Australia
| | - Garth A Nicholson
- Australian School of Advanced Medicine, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, New South Wales, Australia; Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales, Australia; Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia; Molecular Medicine Laboratory, Concord Hospital, Concord, New South Wales, Australia
| | - Ian P Blair
- Australian School of Advanced Medicine, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, New South Wales, Australia.
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Smith BN, Ticozzi N, Fallini C, Gkazi AS, Topp S, Kenna KP, Scotter EL, Kost J, Keagle P, Miller JW, Calini D, Vance C, Danielson EW, Troakes C, Tiloca C, Al-Sarraj S, Lewis EA, King A, Colombrita C, Pensato V, Castellotti B, de Belleroche J, Baas F, ten Asbroek ALMA, Sapp PC, McKenna-Yasek D, McLaughlin RL, Polak M, Asress S, Esteban-Pérez J, Muñoz-Blanco JL, Simpson M, van Rheenen W, Diekstra FP, Lauria G, Duga S, Corti S, Cereda C, Corrado L, Sorarù G, Morrison KE, Williams KL, Nicholson GA, Blair IP, Dion PA, Leblond CS, Rouleau GA, Hardiman O, Veldink JH, van den Berg LH, Al-Chalabi A, Pall H, Shaw PJ, Turner MR, Talbot K, Taroni F, García-Redondo A, Wu Z, Glass JD, Gellera C, Ratti A, Brown RH, Silani V, Shaw CE, Landers JE. Exome-wide rare variant analysis identifies TUBA4A mutations associated with familial ALS. Neuron 2014; 84:324-31. [PMID: 25374358 DOI: 10.1016/j.neuron.2014.09.027] [Citation(s) in RCA: 264] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2014] [Indexed: 12/11/2022]
Abstract
Exome sequencing is an effective strategy for identifying human disease genes. However, this methodology is difficult in late-onset diseases where limited availability of DNA from informative family members prohibits comprehensive segregation analysis. To overcome this limitation, we performed an exome-wide rare variant burden analysis of 363 index cases with familial ALS (FALS). The results revealed an excess of patient variants within TUBA4A, the gene encoding the Tubulin, Alpha 4A protein. Analysis of a further 272 FALS cases and 5,510 internal controls confirmed the overrepresentation as statistically significant and replicable. Functional analyses revealed that TUBA4A mutants destabilize the microtubule network, diminishing its repolymerization capability. These results further emphasize the role of cytoskeletal defects in ALS and demonstrate the power of gene-based rare variant analyses in situations where causal genes cannot be identified through traditional segregation analysis.
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Affiliation(s)
- Bradley N Smith
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy; Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, 20122 Milan, Italy
| | - Claudia Fallini
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Athina Soragia Gkazi
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Simon Topp
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Kevin P Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Emma L Scotter
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Jason Kost
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Pamela Keagle
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jack W Miller
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Daniela Calini
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy; Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, 20122 Milan, Italy
| | - Caroline Vance
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Eric W Danielson
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Claire Troakes
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Cinzia Tiloca
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy
| | - Safa Al-Sarraj
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Elizabeth A Lewis
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Andrew King
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - Claudia Colombrita
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy; Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, 20122 Milan, Italy
| | - Viviana Pensato
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Barbara Castellotti
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Jacqueline de Belleroche
- Neurogenetics Group, Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, Burlington Danes Building, Du Cane Road, London, W12 0NN, UK
| | - Frank Baas
- Department of Genome analysis and Neurogenetics, Academic Medical Centre, Amsterdam, The Netherlands
| | | | - Peter C Sapp
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Diane McKenna-Yasek
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Russell L McLaughlin
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Meraida Polak
- Department of Neurology, Emory University, Atlanta, GA 30322, USA
| | - Seneshaw Asress
- Department of Neurology, Emory University, Atlanta, GA 30322, USA
| | - Jesús Esteban-Pérez
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, SERMAS, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER U-723), 28041 Madrid, Spain
| | - José Luis Muñoz-Blanco
- Unidad de ELA, Instituto de Investigación Hospital Gregorio Marañón de Madrid, SERMAS, 28007 Madrid, Spain
| | - Michael Simpson
- Department of Genetics and Molecular Medicine, King's College London, Tower Wing, Guy's Hospital, London, SE1 7EH, UK
| | | | - Wouter van Rheenen
- Department of Neurology, Brain Center Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, 3508 GA Utrecht, the Netherlands
| | - Frank P Diekstra
- Department of Neurology, Brain Center Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, 3508 GA Utrecht, the Netherlands
| | - Giuseppe Lauria
- 3rd Neurology Unit, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Stefano Duga
- Department of Medical Biotechnology and Translational Medicine - Università degli Studi di Milano, 20133 Milan, Italy
| | - Stefania Corti
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, 20122 Milan, Italy; Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Cristina Cereda
- Experimental Neurobiology Laboratory, IRCCS 'C. Mondino' National Neurological Institute, 27100 Pavia, Italy
| | - Lucia Corrado
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), "A. Avogadro" University, 28100 Novara, Italy
| | - Gianni Sorarù
- Department of Neurosciences, University of Padova, 35122 Padova, Italy
| | - Karen E Morrison
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2WB, UK
| | - Kelly L Williams
- Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Garth A Nicholson
- Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia; Northcott Neuroscience Laboratory, University of Sydney, ANZAC Research Institute, Sydney, NSW 2139, Australia
| | - Ian P Blair
- Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Patrick A Dion
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, 3801 Montreal, QC H3A 2B4, Canada
| | - Claire S Leblond
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, 3801 Montreal, QC H3A 2B4, Canada
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, 3801 Montreal, QC H3A 2B4, Canada
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, 3508 GA Utrecht, the Netherlands
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, 3508 GA Utrecht, the Netherlands
| | - Ammar Al-Chalabi
- Department of Clinical Neuroscience, Medical Research Council Centre for Neurodegeneration Research, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, WC2R 2LS, UK
| | - Hardev Pall
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, S10 2HQ, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Franco Taroni
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Alberto García-Redondo
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, SERMAS, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER U-723), 28041 Madrid, Spain
| | - Zheyang Wu
- Department of Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Jonathan D Glass
- Department of Neurology, Emory University, Atlanta, GA 30322, USA
| | - Cinzia Gellera
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy; Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, 20122 Milan, Italy
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy; Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center - Università degli Studi di Milano, 20122 Milan, Italy
| | - Christopher E Shaw
- Centre for Neurodegeneration Research, King's College London, Department of Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, London, SE5 8AF, UK
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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Kaminsky LA, Ozemek C, Williams KL, Byun W. Precision of total and regional body fat estimates from dual-energy X-ray absorptiometer measurements. J Nutr Health Aging 2014; 18:591-4. [PMID: 24950149 DOI: 10.1007/s12603-014-0012-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
OBJECTIVES To evaluate the precision of both total %fat and all the regional %fat measures acquired from both the Lunar Prodigy and Lunar iDXA software. DESIGN Cross-sectional study. SETTING University-based research laboratory. PARTICIPANTS The sample consisted of 300 individual test records from men and women who had volunteered to participate in dual-energy x-ray absorptiometer (DXA) technician precision training studies. Subjects ranged in age from 20-84 years and in body mass index from 15.7-52.0 kg.m-2. MEASUREMENTS A total of 27 different technicians performed three total body scan measurements on 10-15 different subjects. The Lunar Prodigy and Lunar iDXA were used for 253 and 47 precision training evaluations, respectively. The regions of interest (ROI) were automatically determined by the enCORE software (autoROI) for total body, android, gynoid, trunk, legs, and arms regions and the region %fat data were used for analyses. RESULTS The CV for total body %fat was 1.9% and 0.9% for the Prodigy and iDXA, respectively. CV's for %fat measures at regional sites ranged from 1.2-4.4% for the Prodigy measures and 0.9-2.4% for the iDXA measures. The ICC for both devices ranged from 0.990 to 0.999. CONCLUSION Monitoring the status of body composition changes with age is gaining more clinical acceptance. Thus, it is important that practitioners use measures that are both precise and accurate. The findings from the current study add support that DXA measurements can be used with a high level of confidence for serial testing of patients.
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Affiliation(s)
- L A Kaminsky
- Leonard A. Kaminsky, Ball State University, Human Performance Laboratory, Clinical Exercise Physiology Program, Muncie, IN 47304, USA,
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Abstract
The mating reaction (macrocyst formation) and vegetative compatibility (which is believed to be associated with only the mating type locus in D. discoideum) of asexual, bisexual and homothallic strains of Dictyostelium discoideum were examined. Three asexual strains were vegetatively compatible with a matA tester strain and vegetatively incompatible with a mata tester strain, so we propose that these asexual strains are in fact strains of matA mating type with defective mating capacity. Two bisexual and two homothallic strains were vegetatively incompatible with both matA and mata tester strains, indicating that they either express both mating alleles or that they have a third mating type allele. On the basis of observations on the relative mating capacity with matA and mata tester strains, we propose that bisexual strains are closely related to homothallic strains and are not strains carrying a third mating type allele. Hence we suggest that D. discoideum has a one locus, two allele mating system. The homothallic strains AC4 and ZA3A may express both established mating type alleles (matA and mata). They are, however, normal haploid strains with seven chromosomes. The hypothesis that the homothallic P. pallidum strain PP28S is a diploid, was rejected.
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Affiliation(s)
- G E Robson
- Genetics Department, Research School of Biological Sciences, Australian National University, P.O. Box 475, 2601, Canberra City, A.C.T., Australia
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Abstract
OBJECTIVE Expansions of a hexanucleotide repeat in C9ORF72 are a common cause of familial amyotrophic lateral sclerosis (ALS) and a small proportion of sporadic ALS cases. We sought to examine clinical and neurophysiological features of familial and sporadic ALS with C9ORF72 expansions. METHODS C9ORF72 was screened for expansions in familial and sporadic ALS. Clinical features of expansion positive cases are described. Cortical excitability studies used novel threshold tracking transcranal magnetic stimulation techniques with motor evoked responses recorded over the abductor pollicis brevis. RESULTS AND CONCLUSIONS Analysis of large clinical cohorts identified C9ORF72 expansions in 38.5% (72/187) of ALS families and 3.5% (21/606) of sporadic ALS cases. Two expansion positive families were known to carry reported ANG mutations, possibly implicating an oligogenic model of ALS. 6% of familial ALS cases with C9ORF72 expansions were also diagnosed with dementia. The penetrance of ALS was 50% at age 58 years in male subjects and 63 years in female subjects. 100% penetrance of ALS was observed in male subjects by 86 years, while 6% of female subjects remained asymptomatic at age 82 years. Gender specific differences in age of onset were evident, with male subjects significantly more likely to develop ALS at a younger age. Importantly, features of cortical hyperexcitability were apparent in C9ORF72-linked familial ALS as demonstrated by significant reduction in short interval intracortical inhibition and cortical silent period duration along with an increase in intracortical facilitation and motor evoked potential amplitude, indicating that cortical hyperexcitability is an intrinsic process in C9ORF72-linked ALS.
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Affiliation(s)
- Kelly L Williams
- Australian School of Advanced Medicine, Macquarie University, Sydney, New South Wales, Australia
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Chesi A, Staahl BT, Jovicic A, Couthouis J, Fasolino M, Raphael AR, Yamazaki T, Elias L, Polak M, Kelly C, Williams KL, Fifita JA, Maragakis NJ, Nicholson GA, King OD, Reed R, Crabtree GR, Blair IP, Glass JD, Gitler AD. Exome sequencing to identify de novo mutations in sporadic ALS trios. Nat Neurosci 2013; 16:851-5. [PMID: 23708140 PMCID: PMC3709464 DOI: 10.1038/nn.3412] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/01/2013] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease whose causes are still poorly understood. To identify additional genetic risk factors, we assessed the role of de novo mutations in ALS by sequencing the exomes of 47 ALS patients and both of their unaffected parents (n = 141 exomes). We found that amino acid-altering de novo mutations were enriched in genes encoding chromatin regulators, including the neuronal chromatin remodeling complex (nBAF) component SS18L1 (also known as CREST). CREST mutations inhibited activity-dependent neurite outgrowth in primary neurons, and CREST associated with the ALS protein FUS. These findings expand our understanding of the ALS genetic landscape and provide a resource for future studies into the pathogenic mechanisms contributing to sporadic ALS.
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Affiliation(s)
- Alessandra Chesi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Brett T. Staahl
- Howard Hughes Medical Institute and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Ana Jovicic
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Julien Couthouis
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Maria Fasolino
- Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
| | - Alya R. Raphael
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Tomohiro Yamazaki
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Laura Elias
- Howard Hughes Medical Institute and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Meraida Polak
- Department of Neurology, Emory University, Atlanta, GA 30322
| | - Crystal Kelly
- Department of Neurology, Emory University, Atlanta, GA 30322
| | - Kelly L. Williams
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, 2139, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
- Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Jennifer A. Fifita
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, 2139, Australia
- Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Nicholas J. Maragakis
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Garth A. Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, 2139, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Oliver D. King
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Gerald R. Crabtree
- Howard Hughes Medical Institute and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Ian P. Blair
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, 2139, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
- Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | | | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
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Williams KL, Solski JA, Nicholson GA, Blair IP. Mutation analysis of VCP in familial and sporadic amyotrophic lateral sclerosis. Neurobiol Aging 2012; 33:1488.e15-6. [DOI: 10.1016/j.neurobiolaging.2011.11.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 11/20/2011] [Accepted: 11/20/2011] [Indexed: 10/14/2022]
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Williams KL, Warraich ST, Yang S, Solski JA, Fernando R, Rouleau GA, Nicholson GA, Blair IP. UBQLN2/ubiquilin 2 mutation and pathology in familial amyotrophic lateral sclerosis. Neurobiol Aging 2012; 33:2527.e3-10. [PMID: 22717235 DOI: 10.1016/j.neurobiolaging.2012.05.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/18/2012] [Accepted: 05/20/2012] [Indexed: 01/12/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) shows clinical and pathological overlap with frontotemporal dementia that includes the presence of hallmark ubiquitinated inclusions in affected neurons. Mutations in UBQLN2, which encodes ubiquilin 2, were recently identified in X-linked juvenile and adult-onset ALS and ALS/dementia. As part of an established exome sequencing program to identify disease genes in familial ALS, we identified a novel missense UBQLN2 mutation (c.1460C>T, p.T487I) in 2 apparently unrelated multigenerational ALS families with no evidence of frontotemporal dementia. This mutation segregated with the disease and was absent in 820 healthy controls and all public single nucleotide polymorphism databases. The UBQLN2 p.T487I mutation substitutes a highly conserved residue and is located immediately upstream of a PXX region where all previous mutations have been identified. Immunostaining of spinal cord from a patient with UBQLN2 p.T487I mutation showed colocalization of ubiquilin 2 with ubiquitin in all neuronal inclusions examined and frequent colocalization with TAR DNA-binding protein 43 (TDP-43) and fused in sarcoma protein (FUS). To examine ubiquilin 2 pathology in broader ALS, we showed that ubiquilin 2 pathology also extends to ALS with a FUS mutation. These data further support the importance of ubiquilin 2 in the pathogenesis of ALS.
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Affiliation(s)
- Kelly L Williams
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales, Australia
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Frankel NS, Vander Zanden HB, Reich KJ, Williams KL, Bjorndal KA. Mother−offspring stable isotope discrimination in loggerhead sea turtles Caretta caretta. ENDANGER SPECIES RES 2012. [DOI: 10.3354/esr00412] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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50
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Farg MA, Soo KY, Walker AK, Pham H, Orian J, Horne MK, Warraich ST, Williams KL, Blair IP, Atkin JD. Mutant FUS induces endoplasmic reticulum stress in amyotrophic lateral sclerosis and interacts with protein disulfide-isomerase. Neurobiol Aging 2012; 33:2855-68. [PMID: 22459602 DOI: 10.1016/j.neurobiolaging.2012.02.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 01/04/2012] [Accepted: 02/10/2012] [Indexed: 12/13/2022]
Abstract
Mutations in the gene encoding fused in sarcoma (FUS) are linked to amyotrophic lateral sclerosis (ALS), but the mechanisms by which these mutants trigger neurodegeneration remain unknown. Endoplasmic reticulum (ER) stress is increasingly recognized as an important and early pathway to motor neuron death in ALS. FUS is normally located in the nucleus but in ALS, FUS redistributes to the cytoplasm and forms inclusions. In this study, we investigated whether FUS induces ER stress in a motor neuron like cell line (NSC-34). We demonstrate that ER stress is triggered in cells expressing mutant FUS, and this is closely associated with redistribution of mutant FUS to the cytoplasm. Mutant FUS also colocalized with protein disulfide-isomerase (PDI), an important ER chaperone, in NSC-34 cells and PDI was colocalized with FUS inclusions in human ALS lumbar spinal cords, in both sporadic ALS and mutant FUS-linked familial ALS tissues. These findings implicate ER stress in the pathophysiology of FUS, and provide evidence for common pathogenic pathways in ALS linked to the ER.
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Affiliation(s)
- Manal A Farg
- Department of Biochemistry, La Trobe University, Bundoora, Victoria, Australia
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