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Milioto C, Carcolé M, Giblin A, Coneys R, Attrebi O, Ahmed M, Harris SS, Lee BI, Yang M, Ellingford RA, Nirujogi RS, Biggs D, Salomonsson S, Zanovello M, de Oliveira P, Katona E, Glaria I, Mikheenko A, Geary B, Udine E, Vaizoglu D, Anoar S, Jotangiya K, Crowley G, Smeeth DM, Adams ML, Niccoli T, Rademakers R, van Blitterswijk M, Devoy A, Hong S, Partridge L, Coyne AN, Fratta P, Alessi DR, Davies B, Busche MA, Greensmith L, Fisher EMC, Isaacs AM. PolyGR and polyPR knock-in mice reveal a conserved neuroprotective extracellular matrix signature in C9orf72 ALS/FTD neurons. Nat Neurosci 2024; 27:643-655. [PMID: 38424324 PMCID: PMC11001582 DOI: 10.1038/s41593-024-01589-4] [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: 02/08/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Dipeptide repeat proteins are a major pathogenic feature of C9orf72 amyotrophic lateral sclerosis (C9ALS)/frontotemporal dementia (FTD) pathology, but their physiological impact has yet to be fully determined. Here we generated C9orf72 dipeptide repeat knock-in mouse models characterized by expression of 400 codon-optimized polyGR or polyPR repeats, and heterozygous C9orf72 reduction. (GR)400 and (PR)400 knock-in mice recapitulate key features of C9ALS/FTD, including cortical neuronal hyperexcitability, age-dependent spinal motor neuron loss and progressive motor dysfunction. Quantitative proteomics revealed an increase in extracellular matrix (ECM) proteins in (GR)400 and (PR)400 spinal cord, with the collagen COL6A1 the most increased protein. TGF-β1 was one of the top predicted regulators of this ECM signature and polyGR expression in human induced pluripotent stem cell neurons was sufficient to induce TGF-β1 followed by COL6A1. Knockdown of TGF-β1 or COL6A1 orthologues in polyGR model Drosophila exacerbated neurodegeneration, while expression of TGF-β1 or COL6A1 in induced pluripotent stem cell-derived motor neurons of patients with C9ALS/FTD protected against glutamate-induced cell death. Altogether, our findings reveal a neuroprotective and conserved ECM signature in C9ALS/FTD.
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Affiliation(s)
- Carmelo Milioto
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Mireia Carcolé
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Ashling Giblin
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UCL Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Rachel Coneys
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Olivia Attrebi
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Mhoriam Ahmed
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Samuel S Harris
- UK Dementia Research Institute, University College London, London, UK
| | - Byung Il Lee
- UK Dementia Research Institute, University College London, London, UK
| | - Mengke Yang
- UK Dementia Research Institute, University College London, London, UK
| | | | - Raja S Nirujogi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Daniel Biggs
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sally Salomonsson
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Matteo Zanovello
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Paula de Oliveira
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Eszter Katona
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Idoia Glaria
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Research Support Service, Institute of Agrobiotechnology, CSIC-Government of Navarra, Mutilva, Spain
| | - Alla Mikheenko
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Bethany Geary
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Evan Udine
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Deniz Vaizoglu
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Sharifah Anoar
- UCL Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Khrisha Jotangiya
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Gerard Crowley
- UK Dementia Research Institute, University College London, London, UK
| | - Demelza M Smeeth
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Mirjam L Adams
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Teresa Niccoli
- UCL Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Rosa Rademakers
- VIB Center for Molecular Neurology, University of Antwerp, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Anny Devoy
- UK Dementia Research Institute, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Soyon Hong
- UK Dementia Research Institute, University College London, London, UK
| | - Linda Partridge
- UCL Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Alyssa N Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, London, UK
| | - Dario R Alessi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ben Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Francis Crick Institute, London, UK
| | - Marc Aurel Busche
- UK Dementia Research Institute, University College London, London, UK
| | - Linda Greensmith
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, London, UK
| | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
- UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, London, UK.
| | - Adrian M Isaacs
- UK Dementia Research Institute, University College London, London, UK.
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.
- UCL Queen Square Motor Neuron Disease Centre, UCL Queen Square Institute of Neurology, London, UK.
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2
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Seddighi S, Qi YA, Brown AL, Wilkins OG, Bereda C, Belair C, Zhang YJ, Prudencio M, Keuss MJ, Khandeshi A, Pickles S, Kargbo-Hill SE, Hawrot J, Ramos DM, Yuan H, Roberts J, Sacramento EK, Shah SI, Nalls MA, Colón-Mercado JM, Reyes JF, Ryan VH, Nelson MP, Cook CN, Li Z, Screven L, Kwan JY, Mehta PR, Zanovello M, Hallegger M, Shantaraman A, Ping L, Koike Y, Oskarsson B, Staff NP, Duong DM, Ahmed A, Secrier M, Ule J, Jacobson S, Reich DS, Rohrer JD, Malaspina A, Dickson DW, Glass JD, Ori A, Seyfried NT, Maragkakis M, Petrucelli L, Fratta P, Ward ME. Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD. Sci Transl Med 2024; 16:eadg7162. [PMID: 38277467 DOI: 10.1126/scitranslmed.adg7162] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 01/17/2023] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Functional loss of TDP-43, an RNA binding protein genetically and pathologically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), leads to the inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote the degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. Here, we show that mRNA transcripts harboring cryptic exons generated de novo proteins in TDP-43-depleted human iPSC-derived neurons in vitro, and de novo peptides were found in cerebrospinal fluid (CSF) samples from patients with ALS or FTD. Using coordinated transcriptomic and proteomic studies of TDP-43-depleted human iPSC-derived neurons, we identified 65 peptides that mapped to 12 cryptic exons. Cryptic exons identified in TDP-43-depleted human iPSC-derived neurons were predictive of cryptic exons expressed in postmortem brain tissue from patients with TDP-43 proteinopathy. These cryptic exons produced transcript variants that generated de novo proteins. We found that the inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Last, we showed that 18 de novo peptides across 13 genes were present in CSF samples from patients with ALS/FTD spectrum disorders. The demonstration of cryptic exon translation suggests new mechanisms for ALS/FTD pathophysiology downstream of TDP-43 dysfunction and may provide a potential strategy to assay TDP-43 function in patient CSF.
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Affiliation(s)
- Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Oscar G Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- Francis Crick Institute, London, UK
| | - Colleen Bereda
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Matthew J Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Aditya Khandeshi
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Sarah Pickles
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Sarah E Kargbo-Hill
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - James Hawrot
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Hebao Yuan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jessica Roberts
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Erika Kelmer Sacramento
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Syed I Shah
- Data Tecnica International, Washington, DC, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Jennifer M Colón-Mercado
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Joel F Reyes
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Veronica H Ryan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Matthew P Nelson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Casey N Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Ziyi Li
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Laurel Screven
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Justin Y Kwan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Puja R Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Martina Hallegger
- Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
| | | | - Lingyan Ping
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Yuka Koike
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Björn Oskarsson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Nathan P Staff
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Aisha Ahmed
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, UCL, London, UK
| | - Jernej Ule
- Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
| | - Steven Jacobson
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel S Reich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan D Rohrer
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Andrea Malaspina
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Jonathan D Glass
- Department of Neurology, Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, USA
| | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- Francis Crick Institute, London, UK
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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3
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Bryce-Smith S, Brown AL, Mehta PR, Mattedi F, Mikheenko A, Barattucci S, Zanovello M, Dattilo D, Yome M, Hill SE, Qi YA, Wilkins OG, Sun K, Ryadnov E, Wan Y, Vargas JNS, Birsa N, Raj T, Humphrey J, Keuss M, Ward M, Secrier M, Fratta P. TDP-43 loss induces extensive cryptic polyadenylation in ALS/FTD. bioRxiv 2024:2024.01.22.576625. [PMID: 38313254 PMCID: PMC10836071 DOI: 10.1101/2024.01.22.576625] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 is the hallmark of ALS, occurring in over 97% of cases. A key consequence of TDP-43 nuclear loss is the de-repression of cryptic exons. Whilst TDP-43 regulated cryptic splicing is increasingly well catalogued, cryptic alternative polyadenylation (APA) events, which define the 3' end of last exons, have been largely overlooked, especially when not associated with novel upstream splice junctions. We developed a novel bioinformatic approach to reliably identify distinct APA event types: alternative last exons (ALE), 3'UTR extensions (3'Ext) and intronic polyadenylation (IPA) events. We identified novel neuronal cryptic APA sites induced by TDP-43 loss of function by systematically applying our pipeline to a compendium of publicly available and in house datasets. We find that TDP-43 binding sites and target motifs are enriched at these cryptic events and that TDP-43 can have both repressive and enhancing action on APA. Importantly, all categories of cryptic APA can also be identified in ALS and FTD post mortem brain regions with TDP-43 proteinopathy underlining their potential disease relevance. RNA-seq and Ribo-seq analyses indicate that distinct cryptic APA categories have different downstream effects on transcript and translation. Intriguingly, cryptic 3'Exts occur in multiple transcription factors, such as ELK1, SIX3, and TLX1, and lead to an increase in wild-type protein levels and function. Finally, we show that an increase in RNA stability leading to a higher cytoplasmic localisation underlies these observations. In summary, we demonstrate that TDP-43 nuclear depletion induces a novel category of cryptic RNA processing events and we expand the palette of TDP-43 loss consequences by showing this can also lead to an increase in normal protein translation.
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Affiliation(s)
- Sam Bryce-Smith
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Puja R. Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Francesca Mattedi
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Alla Mikheenko
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Simone Barattucci
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Dario Dattilo
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matthew Yome
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Sarah E. Hill
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Yue A. Qi
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Oscar G. Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
| | - Kai Sun
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Eugeni Ryadnov
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Yixuan Wan
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | | | - Jose Norberto S. Vargas
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Nicol Birsa
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Michael Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
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4
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Wilkins OG, Chien MZ, Wlaschin JJ, Pisliakova M, Thompson D, Digby H, Simkin RL, Diaz JA, Mehta PR, Keuss MJ, Zanovello M, Brown AL, Harley P, Darbey A, Karda R, Fisher EM, Cunningham TJ, Le Pichon CE, Ule J, Fratta P. Creation of de novo cryptic splicing for ALS/FTD precision medicine. bioRxiv 2023:2023.11.15.565967. [PMID: 38014203 PMCID: PMC10680699 DOI: 10.1101/2023.11.15.565967] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
A system enabling the expression of therapeutic proteins specifically in diseased cells would be transformative, providing greatly increased safety and the possibility of pre-emptive treatment. Here we describe "TDP-REG", a precision medicine approach primarily for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), which exploits the cryptic splicing events that occur in cells with TDP-43 loss-of-function (TDP-LOF) in order to drive expression specifically in diseased cells. In addition to modifying existing cryptic exons for this purpose, we develop a deep-learning-powered algorithm for generating customisable cryptic splicing events, which can be embedded within virtually any coding sequence. By placing part of a coding sequence within a novel cryptic exon, we tightly couple protein expression to TDP-LOF. Protein expression is activated by TDP-LOF in vitro and in vivo, including TDP-LOF induced by cytoplasmic TDP-43 aggregation. In addition to generating a variety of fluorescent and luminescent reporters, we use this system to perform TDP-LOF-dependent genomic prime editing to ablate the UNC13A cryptic donor splice site. Furthermore, we design a panel of tightly gated, autoregulating vectors encoding a TDP-43/Raver1 fusion protein, which rescue key pathological cryptic splicing events. In summary, we combine deep-learning and rational design to create sophisticated splicing sensors, resulting in a platform that provides far safer therapeutics for neurodegeneration, potentially even enabling preemptive treatment of at-risk individuals.
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Affiliation(s)
- Oscar G. Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Max Z.Y.J. Chien
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Josette J. Wlaschin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892, USA
| | - Maria Pisliakova
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - David Thompson
- Mammalian Genetics Unit, MRC Harwell Institute; Oxfordshire, OX11 0RD, UK
| | - Holly Digby
- The Francis Crick Institute; London, NW1 1AT, UK
- UK Dementia Research Institute at King’s College London, Maurice Wohl Clinical Neuroscience Institute; London, SE5 9RX, UK
| | - Rebecca L. Simkin
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Juan Antinao Diaz
- EGA-Institute for Women’s Health, University College London; London, WC1E 6HX, UK
| | - Puja R. Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Matthew J. Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Peter Harley
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Annalucia Darbey
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Rajvinder Karda
- EGA-Institute for Women’s Health, University College London; London, WC1E 6HX, UK
| | - Elizabeth M.C. Fisher
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Tom J. Cunningham
- Mammalian Genetics Unit, MRC Harwell Institute; Oxfordshire, OX11 0RD, UK
| | - Claire E. Le Pichon
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892, USA
| | - Jernej Ule
- The Francis Crick Institute; London, NW1 1AT, UK
- UK Dementia Research Institute at King’s College London, Maurice Wohl Clinical Neuroscience Institute; London, SE5 9RX, UK
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
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5
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Ibañez K, Jadhav B, Facchini S, Garg P, Zanovello M, Martin-Trujillo A, Gies SJ, Deforie VG, Gagliardi D, Hensman D, Moutsianas L, Shoai M, Caulfield MJ, Cortese A, Escott-Price V, Hardy J, Houlden H, Sharp AJ, Tucci A. POPULATION FREQUENCY OF REPEAT EXPANSIONS INDICATES INCREASED DISEASE PREVALENCE ESTIMATES ACROSS DIFFERENT POPULATIONS. medRxiv 2023:2023.07.03.23292162. [PMID: 37461547 PMCID: PMC10350132 DOI: 10.1101/2023.07.03.23292162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Repeat expansion disorders (REDs) are a devastating group of predominantly neurological diseases. Together they are common, affecting 1 in 3,000 people worldwide with population-specific differences. However, prevalence estimates of REDs are hampered by heterogeneous clinical presentation, variable geographic distributions, and technological limitations leading to under-ascertainment. Here, leveraging whole genome sequencing data from 82,176 individuals from different populations we found an overall carrier frequency of REDs of 1 in 340 individuals. Modelling disease prevalence using genetic data, age at onset and survival, we show that REDs are up to 3-fold more prevalent than currently reported figures. While some REDs are population-specific, e.g. Huntington's disease type 2, most REDs are represented in all broad genetic ancestries, including Africans and Asians, challenging the notion that some REDs are found only in European populations. These results have worldwide implications for local and global health communities in the diagnosis and management of REDs both at local and global levels.
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Affiliation(s)
- Kristina Ibañez
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Bharati Jadhav
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Stefano Facchini
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, UK
- IRCCS Mondino Foundation, Pavia, Italy
| | - Paras Garg
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Matteo Zanovello
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, UK
| | - Alejandro Martin-Trujillo
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Scott J Gies
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | | | - Delia Gagliardi
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, UK
| | - Davina Hensman
- St George’s, University of London, London, SW17 0RE, UK
- Department of Neurodegenerative Disorders, Institute of Neurology, UCL, London, UK
| | | | - Maryam Shoai
- Department of Neurodegenerative Disorders, Institute of Neurology, UCL, London, UK
| | | | | | - Mark J Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Andrea Cortese
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, UK
| | - Valentina Escott-Price
- Department of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, UK
- Dementia Research Institute, Cardiff University, UK
| | - John Hardy
- Department of Neurodegenerative Disorders, Institute of Neurology, UCL, London, UK
| | - Henry Houlden
- Department of Neurodegenerative Disorders, Institute of Neurology, UCL, London, UK
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, UK
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Arianna Tucci
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
- Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, UK
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6
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Zanovello M, Ibáñez K, Brown AL, Sivakumar P, Bombaci A, Santos L, van Vugt JJFA, Narzisi G, Karra R, Scholz SW, Ding J, Gibbs JR, Chiò A, Dalgard C, Weisburd B, Hanna MG, Greensmith L, Phatnani H, Veldink JH, Traynor BJ, Polke J, Houlden H, Fratta P, Tucci A. Unexpected frequency of the pathogenic AR CAG repeat expansion in the general population. Brain 2023; 146:2723-2729. [PMID: 36797998 PMCID: PMC10316764 DOI: 10.1093/brain/awad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/24/2022] [Accepted: 01/15/2023] [Indexed: 02/18/2023] Open
Abstract
CAG repeat expansions in exon 1 of the AR gene on the X chromosome cause spinal and bulbar muscular atrophy, a male-specific progressive neuromuscular disorder associated with a variety of extra-neurological symptoms. The disease has a reported male prevalence of approximately 1:30 000 or less, but the AR repeat expansion frequency is unknown. We established a pipeline, which combines the use of the ExpansionHunter tool and visual validation, to detect AR CAG expansion on whole-genome sequencing data, benchmarked it to fragment PCR sizing, and applied it to 74 277 unrelated individuals from four large cohorts. Our pipeline showed sensitivity of 100% [95% confidence interval (CI) 90.8-100%], specificity of 99% (95% CI 94.2-99.7%), and a positive predictive value of 97.4% (95% CI 84.4-99.6%). We found the mutation frequency to be 1:3182 (95% CI 1:2309-1:4386, n = 117 734) X chromosomes-10 times more frequent than the reported disease prevalence. Modelling using the novel mutation frequency led to estimate disease prevalence of 1:6887 males, more than four times more frequent than the reported disease prevalence. This discrepancy is possibly due to underdiagnosis of this neuromuscular condition, reduced penetrance, and/or pleomorphic clinical manifestations.
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Affiliation(s)
- Matteo Zanovello
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Kristina Ibáñez
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Anna-Leigh Brown
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Prasanth Sivakumar
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Alessandro Bombaci
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
- ‘Rita Levi Montalcini’ Department of Neuroscience, University of Turin, Turin 10126, Italy
| | - Liana Santos
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Joke J F A van Vugt
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht 3508, The Netherlands
| | - Giuseppe Narzisi
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Ramita Karra
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Neurology, Brain Sciences Institute, Baltimore, MD 21287, USA
| | - Sonja W Scholz
- Department of Neurology, Brain Sciences Institute, Baltimore, MD 21287, USA
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinhui Ding
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adriano Chiò
- ‘Rita Levi Montalcini’ Department of Neuroscience, University of Turin, Turin 10126, Italy
| | - Clifton Dalgard
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MT 02142, USA
| | - Michael G Hanna
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Linda Greensmith
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Jan H Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht 3508, The Netherlands
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Neurology, Brain Sciences Institute, Baltimore, MD 21287, USA
| | - James Polke
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Pietro Fratta
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Arianna Tucci
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
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7
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Rauch S, Regli IB, Martínez Salazar B, Seraglio PM, Zanovello M, Schüpfer G, Bock M. On-the-Job Safety During Enlarging an Intensive Care Unit for the COVID-19 Pandemic: Team-Based Approach with Low Infection Rate of the Staff. Turk J Anaesthesiol Reanim 2022; 50:S42-S49. [PMID: 35775797 PMCID: PMC9632642 DOI: 10.5152/tjar.2021.21116] [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] [Indexed: 11/22/2022] Open
Abstract
Objective: Healthcare workers had a 7.4-fold risk of severe coronavirus disease-19 than non-essential employees in the United Kingdom during the first phase of the pandemic. In this study, we describe interdisciplinary measures for increasing on-the-job safety used during the first phase of the pandemic in an Italian hospital. Methods: We converted an intensive care/intermediate care unit into a fully equipped 16-bed intensive care unit with adjustments for infection control and on-the-job safety within 4 days. We compared our actions with a recently published concept on team management in the pandemic and described the implementation of each issue. It was our principal goal in this completely unknown emergency to guarantee safety for both staff and patients. We defined independent pathways for staff, patients, material, and waste. Clear procedures were defined for protecting the employees and for creating a working environment that minimizes mistakes despite challenging conditions. Results: From March 7 to April 29, we treated 34 mechanically ventilated patients in our intensive care unit with a mean bed occupancy rate of 62%. The team worked in the upgraded intensive care unit with an increased perception of safety. After cessation of the first wave of the pandemic, we tested the department’s entire staff for antibodies against severe acute respiratory syndrome coronavirus 2. Totally 2 of 122 (1.6%) team members developed anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin-G antibodies during the intensive care unit’s running time. Conclusion: The successful implementation of theoretical concepts on team management into clinical practice was crucial for staff safety and on-the-job safety during the pandemic.
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Affiliation(s)
- Simon Rauch
- Department of Anaesthesia and Intensive Care, “F. Tappeiner” Hospital, Merano, Italy
- Institute of Mountain Emergency Medicine, Eurac Research, Bolzano, Italy
| | - Ivo Beat Regli
- Department of Anaesthesia and Intensive Care, “F. Tappeiner” Hospital, Merano, Italy
- Institute of Mountain Emergency Medicine, Eurac Research, Bolzano, Italy
| | | | - Paolo Mario Seraglio
- Department of Anaesthesia and Intensive Care, “F. Tappeiner” Hospital, Merano, Italy
| | | | - Guido Schüpfer
- Department of Anaesthesia, Cantonal Hospital, Lucerne, Switzerland
| | - Matthias Bock
- Department of Anaesthesia and Intensive Care, “F. Tappeiner” Hospital, Merano, Italy
- Department of Anaesthesia, Perioperative Medicine and Intensive Care, Paracelsus Medical University, Salzburg, Austria
- Corresponding author: Matthias Bock, e-mail:
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8
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Brown AL, Wilkins OG, Keuss MJ, Hill SE, Zanovello M, Lee WC, Bampton A, Lee FCY, Masino L, Qi YA, Bryce-Smith S, Gatt A, Hallegger M, Fagegaltier D, Phatnani H, Newcombe J, Gustavsson EK, Seddighi S, Reyes JF, Coon SL, Ramos D, Schiavo G, Fisher EMC, Raj T, Secrier M, Lashley T, Ule J, Buratti E, Humphrey J, Ward ME, Fratta P. TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A. Nature 2022; 603:131-137. [PMID: 35197628 PMCID: PMC8891020 DOI: 10.1038/s41586-022-04436-3] [Citation(s) in RCA: 154] [Impact Index Per Article: 77.0] [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: 04/02/2021] [Accepted: 01/18/2022] [Indexed: 12/12/2022]
Abstract
Variants of UNC13A, a critical gene for synapse function, increase the risk of amyotrophic lateral sclerosis and frontotemporal dementia1-3, two related neurodegenerative diseases defined by mislocalization of the RNA-binding protein TDP-434,5. 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.
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Affiliation(s)
- Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Oscar G Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
| | - Matthew J Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Sarah E Hill
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Weaverly Colleen Lee
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Alexander Bampton
- Queen Square Brain Bank, UCL Queen Square Institute of Neurology, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Flora C Y Lee
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
| | | | - Yue A Qi
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Sam Bryce-Smith
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Ariana Gatt
- Queen Square Brain Bank, UCL Queen Square Institute of Neurology, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Martina Hallegger
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
| | - Delphine Fagegaltier
- Center for Genomics of Neurodegenerative Disease, New York Genome Center (NYGC), New York, NY, USA
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center (NYGC), New York, NY, USA
| | - Jia Newcombe
- NeuroResource, Department of Neuroinflammation, UCL Queen Square Institute of Neurology, London, UK
| | - Emil K Gustavsson
- Queen Square Brain Bank, UCL Queen Square Institute of Neurology, University College London, London, UK
- Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, UK
| | - Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joel F Reyes
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Steven L Coon
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Daniel Ramos
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Giampietro Schiavo
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- UK Dementia Research Institute, University College London, London, UK
| | - Elizabeth M C Fisher
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Towfique Raj
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- 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
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank, UCL Queen Square Institute of Neurology, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Jernej Ule
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Emanuele Buratti
- Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Jack Humphrey
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- 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
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK.
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9
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Zanovello M, Sorarù G, Campi C, Anglani M, Spimpolo A, Berti S, Bussè C, Mozzetta S, Cagnin A, Cecchin D. Brainstem glucose hypermetabolism in ALS/FTD and shorten survival: a 18F-FDG PET/MR study. J Nucl Med 2021; 63:777-784. [PMID: 34503963 DOI: 10.2967/jnumed.121.262232] [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] [Received: 03/03/2021] [Revised: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
Introduction: A few 18F-FDG (FDG) PET-CT studies revealed the presence of brain hypermetabolism in the brainstem and cervical spinal cord of patients within the Amyotrophic Lateral Sclerosis - Frontotemporal Dementia (ALS/FTD) spectrum. We aim to investigate this finding through a hybrid PET-MR system, allowing a more precise spatial pattern of metabolic changes in the brainstem and cervical spinal cord. Methods: Twenty-eight patients with a diagnosis of ALS or behavioural variant FTD plus motoneuron disease and 13 healthy subjects underwent 18F-FDG PET-MR study. Mean normalized FDG uptake values in the midbrain/pons, medulla oblongata, and cervical spinal cord defined on individual's MR scans were compared between groups. Furthermore, the associations between regional FDG uptake values and clinical and demographic characteristics, including gene mutation, type of onset (bulbar, spinal, dementia), and clinical characteristics were investigated. Results: A significant (P < 0.005) increment in glucose metabolism in the midbrain/pons and medulla oblongata was found in ALS/FTD patients in comparison to controls, independent from the type of disease onset. No relevant associations between clinical and metabolic features were reported, although medulla oblongata hypermetabolism was associated with shortened survival (P < 0.001). Conclusion: Increased glucose metabolism in the brainstem might be due to the local activation of astrocytes. FDG PET/MR could be a valuable tool to assess glial changes in the ALS/FTD spectrum and could serve as a prognostic biomarker. Large prospective initiatives would likely shed more light on the promising application of PET/MR in this setting.
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Affiliation(s)
- Matteo Zanovello
- Neurology Unit, Department of Neurosciences (DNS), University of Padua, Italy, Italy
| | - Gianni Sorarù
- Neurology Unit, Department of Neurosciences (DNS), University of Padova, Italy
| | - Cristina Campi
- Mathematics, Department of Mathematics, University of Genova, Genova, Italy
| | - Mariagiulia Anglani
- Neuroradiology Unit, Department of Neurology, University-Hospital of Padova, Italy
| | - Alessandro Spimpolo
- Nuclear Medicine Unit, Department of Medicine (DIMED), University-Hospital of Padova, Italy, Italy
| | - Sara Berti
- Nuclear Medicine Unit, Department of Medicine (DIMED), University-Hospital of Padova, Italy, Italy
| | - Cinzia Bussè
- Neurology Unit, Department of Neurosciences (DNS), University of Padova, Italy
| | - Stefano Mozzetta
- Neurology Unit, Department of Neurosciences (DNS), University of Padova, Italy
| | - Annachiara Cagnin
- Neurology Unit, Department of Neurosciences (DNS), University of Padova, Italy
| | - Diego Cecchin
- Nuclear Medicine Unit, Department of Medicine (DIMED), University-Hospital of Padova, Italy, Italy
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