Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis
Amyotrophic lateral sclerosis (ALS) is a complex disease that leads to motor neuron death. Despite heritability estimates of 52%, genome-wide association studies (GWASs) have discovered relatively few loci. We developed a machine learning approach called RefMap, which integrates functional genomics...
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Published in | Neuron (Cambridge, Mass.) Vol. 110; no. 6; pp. 992 - 1008.e11 |
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Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
United States
Elsevier Inc
16.03.2022
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Subjects | |
Online Access | Get full text |
ISSN | 0896-6273 1097-4199 1097-4199 |
DOI | 10.1016/j.neuron.2021.12.019 |
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Abstract | Amyotrophic lateral sclerosis (ALS) is a complex disease that leads to motor neuron death. Despite heritability estimates of 52%, genome-wide association studies (GWASs) have discovered relatively few loci. We developed a machine learning approach called RefMap, which integrates functional genomics with GWAS summary statistics for gene discovery. With transcriptomic and epigenetic profiling of motor neurons derived from induced pluripotent stem cells (iPSCs), RefMap identified 690 ALS-associated genes that represent a 5-fold increase in recovered heritability. Extensive conservation, transcriptome, network, and rare variant analyses demonstrated the functional significance of candidate genes in healthy and diseased motor neurons and brain tissues. Genetic convergence between common and rare variation highlighted KANK1 as a new ALS gene. Reproducing KANK1 patient mutations in human neurons led to neurotoxicity and demonstrated that TDP-43 mislocalization, a hallmark pathology of ALS, is downstream of axonal dysfunction. RefMap can be readily applied to other complex diseases.
•Machine learning method identifies risk genes by integrating GWASs and epigenetic data•Discovered ALS risk genes lead to a 5-fold increase in recovered heritability•Genetic and experimental support for initiation of ALS pathogenesis in the distal axon•Convergent genetic and experimental data establish KANK1 as a new ALS gene
Zhang et al. develop a new machine learning method that integrates epigenetic profiling with GWAS summary statistics for gene discovery. Application to ALS identifies 690 risk genes with 5-fold increase in recovered heritability. Leading candidate KANK1 is reproduced in human neurons leading to TDP-43 mislocalization, a hallmark pathology of ALS. |
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AbstractList | Amyotrophic lateral sclerosis (ALS) is a complex disease that leads to motor neuron death. Despite heritability estimates of 52%, genome-wide association studies (GWASs) have discovered relatively few loci. We developed a machine learning approach called RefMap, which integrates functional genomics with GWAS summary statistics for gene discovery. With transcriptomic and epigenetic profiling of motor neurons derived from induced pluripotent stem cells (iPSCs), RefMap identified 690 ALS-associated genes that represent a 5-fold increase in recovered heritability. Extensive conservation, transcriptome, network, and rare variant analyses demonstrated the functional significance of candidate genes in healthy and diseased motor neurons and brain tissues. Genetic convergence between common and rare variation highlighted KANK1 as a new ALS gene. Reproducing KANK1 patient mutations in human neurons led to neurotoxicity and demonstrated that TDP-43 mislocalization, a hallmark pathology of ALS, is downstream of axonal dysfunction. RefMap can be readily applied to other complex diseases. Amyotrophic lateral sclerosis (ALS) is a complex disease that leads to motor neuron death. Despite heritability estimates of 52%, genome-wide association studies (GWASs) have discovered relatively few loci. We developed a machine learning approach called RefMap, which integrates functional genomics with GWAS summary statistics for gene discovery. With transcriptomic and epigenetic profiling of motor neurons derived from induced pluripotent stem cells (iPSCs), RefMap identified 690 ALS-associated genes that represent a 5-fold increase in recovered heritability. Extensive conservation, transcriptome, network, and rare variant analyses demonstrated the functional significance of candidate genes in healthy and diseased motor neurons and brain tissues. Genetic convergence between common and rare variation highlighted KANK1 as a new ALS gene. Reproducing KANK1 patient mutations in human neurons led to neurotoxicity and demonstrated that TDP-43 mislocalization, a hallmark pathology of ALS, is downstream of axonal dysfunction. RefMap can be readily applied to other complex diseases.Amyotrophic lateral sclerosis (ALS) is a complex disease that leads to motor neuron death. Despite heritability estimates of 52%, genome-wide association studies (GWASs) have discovered relatively few loci. We developed a machine learning approach called RefMap, which integrates functional genomics with GWAS summary statistics for gene discovery. With transcriptomic and epigenetic profiling of motor neurons derived from induced pluripotent stem cells (iPSCs), RefMap identified 690 ALS-associated genes that represent a 5-fold increase in recovered heritability. Extensive conservation, transcriptome, network, and rare variant analyses demonstrated the functional significance of candidate genes in healthy and diseased motor neurons and brain tissues. Genetic convergence between common and rare variation highlighted KANK1 as a new ALS gene. Reproducing KANK1 patient mutations in human neurons led to neurotoxicity and demonstrated that TDP-43 mislocalization, a hallmark pathology of ALS, is downstream of axonal dysfunction. RefMap can be readily applied to other complex diseases. Amyotrophic lateral sclerosis (ALS) is a complex disease that leads to motor neuron death. Despite heritability estimates of 52%, genome-wide association studies (GWASs) have discovered relatively few loci. We developed a machine learning approach called RefMap, which integrates functional genomics with GWAS summary statistics for gene discovery. With transcriptomic and epigenetic profiling of motor neurons derived from induced pluripotent stem cells (iPSCs), RefMap identified 690 ALS-associated genes that represent a 5-fold increase in recovered heritability. Extensive conservation, transcriptome, network, and rare variant analyses demonstrated the functional significance of candidate genes in healthy and diseased motor neurons and brain tissues. Genetic convergence between common and rare variation highlighted KANK1 as a new ALS gene. Reproducing KANK1 patient mutations in human neurons led to neurotoxicity and demonstrated that TDP-43 mislocalization, a hallmark pathology of ALS, is downstream of axonal dysfunction. RefMap can be readily applied to other complex diseases. •Machine learning method identifies risk genes by integrating GWASs and epigenetic data•Discovered ALS risk genes lead to a 5-fold increase in recovered heritability•Genetic and experimental support for initiation of ALS pathogenesis in the distal axon•Convergent genetic and experimental data establish KANK1 as a new ALS gene Zhang et al. develop a new machine learning method that integrates epigenetic profiling with GWAS summary statistics for gene discovery. Application to ALS identifies 690 risk genes with 5-fold increase in recovered heritability. Leading candidate KANK1 is reproduced in human neurons leading to TDP-43 mislocalization, a hallmark pathology of ALS. Amyotrophic lateral sclerosis (ALS) is a complex disease leading to motor neuron death. Despite heritability estimates of 52%, genome-wide association studies (GWAS) have discovered relatively few loci. We developed a machine learning approach called RefMap which integrates functional genomics with GWAS summary statistics for gene discovery. With transcriptomic and epigenetic profiling of motor neurons derived from induced pluripotent stem cells (iPSCs), RefMap identified 690 ALS-associated genes which represents a 5-fold increase in recovered heritability. Extensive conservation, transcriptome, network, and rare variant analyses demonstrated the functional significance of candidate genes in healthy and diseased motor neurons and brain tissues. Genetic convergence between common and rare variation highlighted KANK1 as a new ALS gene. Reproducing KANK1 patient mutations in human neurons led to neurotoxicity and demonstrated that TDP-43 mislocalization, a hallmark pathology of ALS, is downstream of axonal dysfunction. RefMap can be readily applied to other complex diseases. Zhang et al. develop a new machine learning method which integrates epigenetic profiling with GWAS summary statistics for gene discovery. Application to ALS identifies 690 risk genes with 5-fold increase in recovered heritability. Leading candidate KANK1 is reproduced in human neurons leading to TDP-43 mislocalization, a hallmark pathology of ALS. |
Author | Shaw, Pamela J. Veldink, Jan H. Eitan, Chen Kiernan, Matthew Moll, Tobias Povedano, Monica McLaughin, Russell Wray, Naomi R. Snyder, Michael P. Mora Pardina, Jesus S. Livesey, Matthew R. Başak, Nazli A. Shaw, Chris Mitne Neto, Miguel Morrison, Karen E. Shi, Minyi Weber, Markus Landers, John E. Li, Jingjing Blair, Ian Cauchi, Ruben Marshall, Jack N.G. Ferraiuolo, Laura Drory, Vivian Weimer, Annika K. Ticozzi, Nicola de Carvalho, Mamede Ning, Ke Pasniceanu, Iris Robberecht, Wim Corcia, Philippe Nezhad, Helia Ghahremani Cooper-Knock, Johnathan Al-Chalabi, Ammar Gotkine, Marc Franklin, John Wang, Cheng van Damme, Philip Elhaik, Eran Andersen, Peter Dilliott, Allison A. Couratier, Philippe Zhang, Sai Farhan, Sali Hornstein, Eran Glass, Jonathan D. Harvey, Calum van den Berg, Leonard H. Souza, Cleide dos Santos Silani, Vincenzo Kenna, Kevin P. Chio, Adriano Hardiman, Orla |
AuthorAffiliation | 7 Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands 5 Department of Biology, Lund University, Lund 223 62, Sweden 1 Department of Genetics, Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA 2 Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK 9 Lead contact 6 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel 3 The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, the Bakar Computational Health Sciences Institute, the Parker Institute for Cancer Immunotherapy, and the Department of Neurology, School of Medicine, University of California, San Francisco, CA 94143, USA 8 These authors contributed equally 4 Department of Neurology and Neurosurgery, the Montreal Neurological Institute, McGill University, Montreal, QC H3A 1A1, Canada |
AuthorAffiliation_xml | – name: 5 Department of Biology, Lund University, Lund 223 62, Sweden – name: 8 These authors contributed equally – name: 1 Department of Genetics, Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA – name: 6 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel – name: 7 Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands – name: 4 Department of Neurology and Neurosurgery, the Montreal Neurological Institute, McGill University, Montreal, QC H3A 1A1, Canada – name: 9 Lead contact – name: 3 The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, the Bakar Computational Health Sciences Institute, the Parker Institute for Cancer Immunotherapy, and the Department of Neurology, School of Medicine, University of California, San Francisco, CA 94143, USA – name: 2 Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK |
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mpsnyder@stanford.edu organization: Department of Genetics, Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/35045337$$D View this record in MEDLINE/PubMed |
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ContentType | Journal Article |
Contributor | Morrison, Karen E Veldink, Jan H Mora Pardina, Jesus S Kiernan, Matthew Robberecht, Wim Corcia, Philippe Povedano, Monica McLaughin, Russell Al-Chalabi, Ammar Glass, Jonathan D Gotkine, Marc van den Berg, Leonard H Başak, Nazli A Shaw, Chris Mitne Neto, Miguel van Damme, Philip Andersen, Peter Couratier, Philippe Wray, Naomi R Landers, John E Weber, Markus Shaw, Pamela J Blair, Ian Cauchi, Ruben Drory, Vivian Ticozzi, Nicola Silani, Vincenzo Chio, Adriano de Carvalho, Mamede Hardiman, Orla |
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Copyright | 2021 The Author(s) Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved. |
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CorporateAuthor | Project MinE ALS Sequencing Consortium Bioinformatik Department of Biology Biologiska institutionen Forskargrupper vid Biologiska institutionen Lunds universitet Naturvetenskapliga fakulteten Faculty of Science Lund University Research groups at the Department of Biology Bioinformatics |
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Keywords | motor neurons genetics gene discovery iPSC ALS multiomics TDP-43 mislocalization axonal dysfunction machine learning epigenetics |
Language | English |
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Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 AUTHOR CONTRIBUTIONS S.Z., J.C.-K. and M.P.S. conceived and designed the study. S.Z. designed and implemented RefMap. S.Z., J.C.-K., A.K.W., M.S., T.M., J.N.G.M., I.P., M.R.L., C.H., H.G.N., J.F., C.S.S., K.N., S.F., A.A.D., J.V., L.F., P.J.S. and M.P.S. were responsible for data acquisition. S.Z., J.C.-K., A.K.W., M.S., T.M., J.N.G.M., C.H., H.G.N., J.F., C.S.S., K.N., C.W., J.L., S.F., A.A.D., E.E., I.P., M.R.L., C.E., E.H., J.V., L.F., P.J.S. and M.P.S. were responsible for analysis of data. S.Z., J.C.-K., A.K.W., T.M., J.N.G.M., C.H., H.G.N., J.F., C.S.S., K.N., C.W., J.L., S.F., A.A.D., E.E., I.P., M.R.L., C.E., E.H., K.P.K., J.V., L.F., P.J.S. and M.P.S. were responsible for interpretation of data. The Project MinE ALS Sequencing Consortium was involved in data acquisition and analysis. S.Z., J.C.-K. and M.P.S. prepared the manuscript with assistance from all authors. All authors meet the four ICMJE authorship criteria, and were responsible for revising the manuscript, approving the final version for publication, and for accuracy and integrity of the work. |
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Snippet | Amyotrophic lateral sclerosis (ALS) is a complex disease that leads to motor neuron death. Despite heritability estimates of 52%, genome-wide association... Amyotrophic lateral sclerosis (ALS) is a complex disease leading to motor neuron death. Despite heritability estimates of 52%, genome-wide association studies... |
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SubjectTerms | Adaptor Proteins, Signal Transducing - genetics ALS Amyotrophic Lateral Sclerosis - genetics Amyotrophic Lateral Sclerosis - pathology axonal dysfunction Basic Medicine Cell Death - genetics Cytoskeletal Proteins - genetics epigenetics gene discovery genetics Genome-Wide Association Study Humans Induced Pluripotent Stem Cells - pathology iPSC machine learning Medical and Health Sciences Medical Genetics and Genomics (including Gene Therapy) Medicin och hälsovetenskap Medicinsk genetik och genomik (Här ingår: Genterapi) Medicinska och farmaceutiska grundvetenskaper motor neurons Motor Neurons - pathology multiomics TDP-43 mislocalization |
Title | Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis |
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