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      TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A

      research-article
      1 , 1 , 2 , 1 , 3 , 1 , 1 , 4 , 5 , 1 , 2 , 2 , 6 , 1 , 4 , 5 , 1 , 2 , 7 , 7 , NYGC ALS Consortium, 8 , 4 , 9 , 3 , 10 , 3 , 11 , 3 , 6 , 1 , 12 , 1 , 13 , 14 , 15 , 16 , 17 , 4 , 5 , 1 , 2 , 18 , 19 , 13 , 14 , 15 , 16 , 3 , , 1 ,
      Nature
      Nature Publishing Group UK
      Amyotrophic lateral sclerosis, Neurodegeneration

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          Abstract

          Variants of UNC13A, a critical gene for synapse function, increase the risk of amyotrophic lateral sclerosis and frontotemporal dementia 13 , two related neurodegenerative diseases defined by mislocalization of the RNA-binding protein TDP-43 4, 5 . Here we show that TDP-43 depletion induces robust inclusion of a cryptic exon in UNC13A, resulting in nonsense-mediated decay and loss of UNC13A protein. Two common intronic UNC13A polymorphisms strongly associated with amyotrophic lateral sclerosis and frontotemporal dementia risk overlap with TDP-43 binding sites. These polymorphisms potentiate cryptic exon inclusion, both in cultured cells and in brains and spinal cords from patients with these conditions. Our findings, which demonstrate a genetic link between loss of nuclear TDP-43 function and disease, reveal the mechanism by which UNC13A variants exacerbate the effects of decreased TDP-43 function. They further provide a promising therapeutic target for TDP-43 proteinopathies.

          Abstract

          Risk variants for ALS and FTD in the synaptic gene UNC13A increase the expression of an UNC13A cryptic exon in neurons with TDP-43 depletion.

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          Most cited references66

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

            The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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              The Sequence Alignment/Map format and SAMtools

              Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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                Author and article information

                Contributors
                wardme@nih.gov
                p.fratta@ucl.ac.uk
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                23 February 2022
                23 February 2022
                2022
                : 603
                : 7899
                : 131-137
                Affiliations
                [1 ]GRID grid.83440.3b, ISNI 0000000121901201, UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, , UCL Queen Square Institute of Neurology, UCL, ; London, UK
                [2 ]GRID grid.451388.3, ISNI 0000 0004 1795 1830, The Francis Crick Institute, ; London, UK
                [3 ]GRID grid.416870.c, ISNI 0000 0001 2177 357X, National Institute of Neurological Disorders and Stroke, NIH, ; Bethesda, MD USA
                [4 ]GRID grid.83440.3b, ISNI 0000000121901201, Queen Square Brain Bank, UCL Queen Square Institute of Neurology, , University College London, ; London, UK
                [5 ]GRID grid.83440.3b, ISNI 0000000121901201, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, , University College London, ; London, UK
                [6 ]GRID grid.94365.3d, ISNI 0000 0001 2297 5165, Center for Alzheimer’s and Related Dementias, , National Institutes of Health, ; Bethesda, MD USA
                [7 ]GRID grid.429884.b, ISNI 0000 0004 1791 0895, Center for Genomics of Neurodegenerative Disease, , New York Genome Center (NYGC), ; New York, NY USA
                [8 ]GRID grid.83440.3b, ISNI 0000000121901201, NeuroResource, Department of Neuroinflammation, , UCL Queen Square Institute of Neurology, ; London, UK
                [9 ]GRID grid.83440.3b, ISNI 0000000121901201, Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, , University College London, ; London, UK
                [10 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Medical Scientist Training Program, , Johns Hopkins University School of Medicine, ; Baltimore, MD USA
                [11 ]GRID grid.420089.7, ISNI 0000 0000 9635 8082, Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, ; Bethesda, MD USA
                [12 ]GRID grid.83440.3b, ISNI 0000000121901201, UK Dementia Research Institute, , University College London, ; London, UK
                [13 ]GRID grid.59734.3c, ISNI 0000 0001 0670 2351, Nash Family Department of Neuroscience and Friedman Brain Institute, , Icahn School of Medicine at Mount Sinai, ; New York, NY USA
                [14 ]GRID grid.59734.3c, ISNI 0000 0001 0670 2351, Ronald M. Loeb Center for Alzheimer’s Disease, , Icahn School of Medicine at Mount Sinai, ; New York, NY USA
                [15 ]GRID grid.59734.3c, ISNI 0000 0001 0670 2351, Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, , Icahn School of Medicine at Mount Sinai, ; New York, NY USA
                [16 ]GRID grid.59734.3c, ISNI 0000 0001 0670 2351, Estelle and Daniel Maggin Department of Neurology, , Icahn School of Medicine at Mount Sinai, ; New York, NY USA
                [17 ]GRID grid.83440.3b, ISNI 0000000121901201, Department of Genetics, Evolution and Environment, UCL Genetics Institute, , University College London, ; London, UK
                [18 ]GRID grid.454324.0, ISNI 0000 0001 0661 0844, Department of Molecular Biology and Nanobiotechnology, , National Institute of Chemistry, ; Ljubljana, Slovenia
                [19 ]GRID grid.425196.d, ISNI 0000 0004 1759 4810, Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), ; Trieste, Italy
                [20 ]GRID grid.264727.2, ISNI 0000 0001 2248 3398, Department of Neurology, , Lewis Katz School of Medicine, Temple University, ; Philadelphia, PA USA
                [21 ]GRID grid.19006.3e, ISNI 0000 0000 9632 6718, Cedars-Sinai Department of Biomedical Sciences, Board of Governors Regenerative Medicine Institute and Brain Program, Cedars-Sinai Medical Center, , University of California, ; Los Angeles, CA USA
                [22 ]GRID grid.19006.3e, ISNI 0000 0000 9632 6718, Department of Medicine, , University of California, ; Los Angeles, CA USA
                [23 ]GRID grid.29857.31, ISNI 0000 0001 2097 4281, Department of Biochemistry and Molecular Biology, Penn State Institute for Personalized Medicine, , The Pennsylvania State University, ; Hershey, PA USA
                [24 ]GRID grid.29857.31, ISNI 0000 0001 2097 4281, Department of Neurology, , The Pennsylvania State University, ; Hershey, PA USA
                [25 ]GRID grid.239864.2, ISNI 0000 0000 8523 7701, Department of Neurology, , Henry Ford Health System, ; Detroit, MI USA
                [26 ]GRID grid.25879.31, ISNI 0000 0004 1936 8972, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, , University of Pennsylvania, ; Philadelphia, PA USA
                [27 ]GRID grid.21729.3f, ISNI 0000000419368729, Department of Neurology, Center for Motor Neuron Biology and Disease, Institute for Genomic Medicine, , Columbia University, ; New York, NY USA
                [28 ]GRID grid.116068.8, ISNI 0000 0001 2341 2786, Department of Biological Engineering, , Massachusetts Institute of Technology, ; Cambridge, MA USA
                [29 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Department of Neurology, , Johns Hopkins School of Medicine, ; Baltimore, MD USA
                [30 ]GRID grid.5650.6, ISNI 0000000404654431, Department of Neurogenetics, , Academic Medical Centre, ; Amsterdam, The Netherlands
                [31 ]GRID grid.10419.3d, ISNI 0000000089452978, Leiden University Medical Center, ; Leiden, The Netherlands
                [32 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Department of Medicine, , Lung Biology Center, University of California, ; San Francisco, CA USA
                [33 ]GRID grid.38142.3c, ISNI 000000041936754X, ALS Multidisciplinary Clinic, Neuromuscular Division, Department of Neurology, , Harvard Medical School, ; Boston, MA USA
                [34 ]GRID grid.32224.35, ISNI 0000 0004 0386 9924, Neurological Clinical Research Institute, Massachusetts General Hospital, ; Boston, MA USA
                [35 ]GRID grid.4868.2, ISNI 0000 0001 2171 1133, Centre for Neuroscience and Trauma, Blizard Institute, Barts, , Queen Mary University of London, ; London, UK
                [36 ]GRID grid.4868.2, ISNI 0000 0001 2171 1133, The London School of Medicine and Dentistry, , Queen Mary University of London, ; London, UK
                [37 ]GRID grid.439462.e, ISNI 0000 0004 0399 6800, Department of Neurology, , Basildon University Hospital, ; Basildon, UK
                [38 ]GRID grid.249880.f, ISNI 0000 0004 0374 0039, The Jackson Laboratory, ; Bar Harbor, ME USA
                [39 ]GRID grid.266093.8, ISNI 0000 0001 0668 7243, Department of Psychiatry and Human Behavior, Department of Biological Chemistry, School of Medicine, , University of California, ; Irvine, CA USA
                [40 ]GRID grid.266093.8, ISNI 0000 0001 0668 7243, Department of Neurobiology and Behavior, School of Biological Sciences, , University of California, ; Irvine, CA USA
                [41 ]GRID grid.249878.8, ISNI 0000 0004 0572 7110, Taube/Koret Center for Neurodegenerative Disease Research, Roddenberry Center for Stem Cell Biology and Medicine, , Gladstone Institute, ; San Francisco, CA USA
                [42 ]GRID grid.410558.d, ISNI 0000 0001 0035 6670, Department of Neurology and Sensory Organs, , University of Thessaly, ; Thessaly, Greece
                [43 ]GRID grid.4367.6, ISNI 0000 0001 2355 7002, Department of Neurology, , Washington University in St Louis, ; St Louis, MO USA
                [44 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, Centre for Clinical Brain Sciences, , Anne Rowling Regenerative Neurology Clinic, Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, ; Edinburgh, UK
                [45 ]GRID grid.13992.30, ISNI 0000 0004 0604 7563, Department of Molecular Genetics, , Weizmann Institute of Science, ; Rehovot, Israel
                [46 ]GRID grid.59734.3c, ISNI 0000 0001 0670 2351, Department of Neurology, , Icahn School of Medicine at Mount Sinai, ; New York, NY USA
                [47 ]GRID grid.264727.2, ISNI 0000 0001 2248 3398, Center for Neurodegenerative Disorders, Department of Neurology, , the Lewis Katz School of Medicine, Temple University, ; Philadelphia, PA USA
                [48 ]GRID grid.225279.9, ISNI 0000 0004 0387 3667, Cold Spring Harbor Laboratory, ; Cold Spring Harbor, NY USA
                [49 ]GRID grid.38142.3c, ISNI 000000041936754X, Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, ; Boston, MA USA
                [50 ]GRID grid.36425.36, ISNI 0000 0001 2216 9681, Department of Anesthesiology, , Stony Brook University, ; Stony Brook, NY USA
                [51 ]GRID grid.416870.c, ISNI 0000 0001 2177 357X, Section of Infections of the Nervous System, , National Institute of Neurological Disorders and Stroke, NIH, ; Bethesda, MD USA
                [52 ]GRID grid.427785.b, ISNI 0000 0001 0664 3531, Department of Neurology, Barrow Neurological Institute, St Joseph’s Hospital, ; Phoenix, AZ USA
                [53 ]GRID grid.240866.e, ISNI 0000 0001 2110 9177, Medical Center, Department of Neurobiology, Barrow Neurological Institute, , St Joseph’s Hospital and Medical Center, ; Phoenix, AZ USA
                [54 ]GRID grid.21729.3f, ISNI 0000000419368729, Department of Neurology, Division of Neuromuscular Medicine, , Columbia University, ; New York, NY USA
                [55 ]GRID grid.7177.6, ISNI 0000000084992262, Department of Neuropathology, Academic Medical Center, , University of Amsterdam, ; Amsterdam, The Netherlands
                [56 ]GRID grid.29857.31, ISNI 0000 0001 2097 4281, Department of Biology and Veterinary and Biomedical Sciences, , The Pennsylvania State University, ; University Park, PA USA
                [57 ]GRID grid.25879.31, ISNI 0000 0004 1936 8972, New York Stem Cell Foundation, Department of Bioengineering, School of Engineering and Applied Sciences, , University of Pennsylvania, ; Philadelphia, PA USA
                [58 ]GRID grid.59734.3c, ISNI 0000 0001 0670 2351, Department of Pathology, Fishberg Department of Neuroscience, , Icahn School of Medicine at Mount Sinai, ; New York, NY USA
                [59 ]GRID grid.38142.3c, ISNI 000000041936754X, Department of Neurology, , Harvard Medical School, Neurological Clinical Research Institute, Massachusetts General Hospital, ; Boston, MA USA
                [60 ]GRID grid.239915.5, ISNI 0000 0001 2285 8823, Department of Neurology, , Hospital for Special Surgery, ; New York, NY USA
                [61 ]GRID grid.413734.6, ISNI 0000 0000 8499 1112, Weill Cornell Medical Center, ; New York, NY USA
                [62 ]GRID grid.416113.0, ISNI 0000 0000 9759 4781, Medical Genetics, , Atlantic Health System, Morristown Medical Center, ; Morristown, NJ USA
                [63 ]GRID grid.417328.b, ISNI 0000 0000 8945 8587, Overlook Medical Center, ; Summit, NJ USA
                [64 ]GRID grid.417975.9, ISNI 0000 0004 0620 8857, Center of Clinical Research, Experimental Surgery and Translational Research, , Biomedical Research Foundation of the Academy of Athens (BRFAA), ; Athens, Greece
                [65 ]GRID grid.5216.0, ISNI 0000 0001 2155 0800, 1st Department of Neurology, Eginition Hospital, , Medical School, National and Kapodistrian University of Athens, ; Athens, Greece
                [66 ]GRID grid.9619.7, ISNI 0000 0004 1937 0538, Neuromuscular/EMG service and ALS/Motor Neuron Disease Clinic, , Hebrew University-Hadassah Medical Center, ; Jerusalem, Israel
                [67 ]Board of Governors Regenerative Medicine Institute, Los Angeles, CA USA
                [68 ]GRID grid.50956.3f, ISNI 0000 0001 2152 9905, Department of Neurology, , Cedars-Sinai Medical Center, ; Los Angeles, CA USA
                [69 ]GRID grid.416228.b, ISNI 0000 0004 0451 8771, Harvard Medical School, Department of Physical Medicine and Rehabilitation, , Spaulding Rehabilitation Hospital, ; Boston, MA USA
                [70 ]GRID grid.239552.a, ISNI 0000 0001 0680 8770, Center for Cellular and Molecular Therapeutics, , Children’s Hospital of Philadelphia, ; Philadelphia, PA USA
                [71 ]GRID grid.25879.31, ISNI 0000 0004 1936 8972, Department of Genetics, Perelman School of Medicine, , University of Pennsylvania, ; Philadelphia, PA USA
                [72 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, Centre for Clinical Brain Sciences, , University of Edinburgh, ; Edinburgh, UK
                [73 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, Euan MacDonald Centre for Motor Neurone Disease Research, , University of Edinburgh, ; Edinburgh, UK
                [74 ]GRID grid.59734.3c, ISNI 0000 0001 0670 2351, Department of Genetics and Genomic Sciences, , Icahn Institute of Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, ; New York, NY USA
                [75 ]GRID grid.411667.3, ISNI 0000 0001 2186 0438, Department of Neuropathology, Georgetown Brain Bank, , Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, ; Washington, DC USA
                [76 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Neuroradiology Section, Department of Radiology and Biomedical Imaging, , University of California, San Francisco, ; San Francisco, CA USA
                [77 ]GRID grid.12136.37, ISNI 0000 0004 1937 0546, Neuromuscular Diseases Unit, Department of Neurology, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, , Tel-Aviv University, ; Tel-Aviv, Israel
                [78 ]GRID grid.266100.3, ISNI 0000 0001 2107 4242, Department of Neuroscience, , University of California San Diego, ; La Jolla, CA USA
                [79 ]GRID grid.25879.31, ISNI 0000 0004 1936 8972, Department of Neurology, , University of Pennsylvania Perelman School of Medicine, ; Philadelphia, PA USA
                [80 ]GRID grid.239585.0, ISNI 0000 0001 2285 2675, Department of Neurology, , Columbia University Medical Center, ; New York, NY USA
                [81 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Department of Pharmaceutical Chemistry, , University of California San Francisco, ; San Francisco, CA USA
                [82 ]GRID grid.9619.7, ISNI 0000 0004 1937 0538, Hadassah Hebrew University, ; Jerusalem, Israel
                [83 ]GRID grid.427785.b, ISNI 0000 0001 0664 3531, Department of Translational Neuroscience, , Barrow Neurological Institute, ; Phoenix, AZ USA
                [84 ]GRID grid.250942.8, ISNI 0000 0004 0507 3225, The Translational Genomics Research Institute (TGen), ; Phoenix, AZ USA
                [85 ]GRID grid.66859.34, ISNI 0000 0004 0546 1623, Broad Institute, ; Cambridge, MA USA
                [86 ]GRID grid.32224.35, ISNI 0000 0004 0386 9924, Massachusetts General Hospital, ; Boston, MA USA
                [87 ]GRID grid.416477.7, ISNI 0000 0001 2168 3646, Institute of Molecular Medicine, Feinstein Institutes for Medical Research, , Northwell Health, ; Manhasset, NY USA
                [88 ]GRID grid.37172.30, ISNI 0000 0001 2292 0500, Korea Advanced Institute of Science and Technology (KAIST), ; Daejeon, South Korea
                [89 ]GRID grid.482226.8, ISNI 0000 0004 0437 5686, Perron Institute for Neurological and Translational Science, ; Nedlands, Western Australia Australia
                [90 ]GRID grid.419681.3, ISNI 0000 0001 2164 9667, Integrative Immunobiology Section, National Institute of Allergy and Infectious Disease, NIH, ; Bethesda, MD USA
                Author information
                http://orcid.org/0000-0002-8499-7455
                http://orcid.org/0000-0001-9609-7975
                http://orcid.org/0000-0002-4319-8745
                http://orcid.org/0000-0002-9355-5704
                http://orcid.org/0000-0003-2758-1741
                http://orcid.org/0000-0002-2452-4277
                http://orcid.org/0000-0002-1356-9074
                http://orcid.org/0000-0002-8762-8188
                Article
                4436
                10.1038/s41586-022-04436-3
                8891020
                35197628
                338f061f-4ae7-4383-ab92-2bea76fdd367
                © The Author(s) 2022

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 2 April 2021
                : 18 January 2022
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                © The Author(s), under exclusive licence to Springer Nature Limited 2022

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                amyotrophic lateral sclerosis,neurodegeneration
                Uncategorized
                amyotrophic lateral sclerosis, neurodegeneration

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