{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T12:30:05Z","timestamp":1791462605252,"version":"4.3.4"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2024,7,24]],"date-time":"2024-07-24T00:00:00Z","timestamp":1721779200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000691","name":"Academy of Medical Sciences Professorship Scheme","doi-asserted-by":"publisher","award":["APR4\/1007"],"award-info":[{"award-number":["APR4\/1007"]}],"id":[{"id":"10.13039\/501100000691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007155","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/W019086\/1"],"award-info":[{"award-number":["MR\/W019086\/1"]}],"id":[{"id":"10.13039\/501100007155","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021566","name":"Fundaci\u00f3n Isabel Gemio","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100021566","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017547","name":"Spark Therapeutics","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100017547","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Late-onset Pompe disease (LOPD) is a rare genetic disorder caused by the deficiency of acid alpha-glucosidase leading to progressive cellular dysfunction owing to the accumulation of glycogen in the lysosome. The mechanism of relentless muscle damage (a classic manifestation of the disease) has been studied extensively by analysing the whole-muscle tissue; however, little, if anything, is known about transcriptional heterogeneity among nuclei within the multinucleated skeletal muscle cells. This is the first report of application of single-nucleus RNA sequencing to uncover changes in the gene expression profile in muscle biopsies from eight patients with LOPD and four muscle samples from age- and sex-matched healthy controls. We matched these changes with histological findings using GeoMx spatial transcriptomics to compare the transcriptome of control myofibres from healthy individuals with non-vacuolated (histologically unaffected) and vacuolated (histologically affected) myofibres of LODP patients.<\/jats:p>\n                  <jats:p>We observed an increase in the proportion of slow and regenerative muscle fibres and macrophages in LOPD muscles. The expression of the genes involved in glycolysis was reduced, whereas the expression of the genes involved in the metabolism of lipids and amino acids was increased in non-vacuolated fibres, indicating early metabolic abnormalities. Additionally, we detected upregulation of autophagy genes and downregulation of the genes involved in ribosomal and mitochondrial function leading to defective oxidative phosphorylation. Upregulation of genes associated with inflammation, apoptosis and muscle regeneration was observed only in vacuolated fibres. Notably, enzyme replacement therapy (the only available therapy for the disease) showed a tendency to restore dysregulated metabolism, particularly within slow fibres. A combination of single-nucleus RNA sequencing and spatial transcriptomics revealed the landscape of the normal and diseased muscle and highlighted the early abnormalities associated with disease progression. Thus, the application of these two new cutting-edge technologies provided insight into the molecular pathophysiology of muscle damage in LOPD and identified potential avenues for therapeutic intervention.<\/jats:p>","DOI":"10.1093\/brain\/awae249","type":"journal-article","created":{"date-parts":[[2024,7,22]],"date-time":"2024-07-22T17:06:28Z","timestamp":1721667988000},"page":"4213-4226","source":"Crossref","is-referenced-by-count":9,"title":["Decoding the muscle transcriptome of patients with late-onset Pompe disease reveals markers of disease progression"],"prefix":"10.1093","volume":"147","author":[{"given":"Alexandra","family":"Monceau","sequence":"first","affiliation":[{"name":"The John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute, Newcastle Upon Tyne NHS Trust , Newcastle Upon Tyne, NE13BZ ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rasya Gokul","family":"Nath","sequence":"additional","affiliation":[{"name":"The John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute, Newcastle Upon Tyne NHS Trust , Newcastle Upon Tyne, NE13BZ ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xavier","family":"Su\u00e1rez-Calvet","sequence":"additional","affiliation":[{"name":"Institut d\u2019Investigaci\u00f3 Biom\u00e8dica Sant Pau (IIB SANT PAU) , Neuromuscular Disease Unit, 08041 Barcelona ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olimpia","family":"Musumeci","sequence":"additional","affiliation":[{"name":"Unit of Neurology and Neuromuscular Diseases, Department of Clinical and Experimental Medicine, University of Messina , 98122 Messina ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Toscano","sequence":"additional","affiliation":[{"name":"Unit of Neurology and Neuromuscular Diseases, Department of Clinical and Experimental Medicine, University of Messina , 98122 Messina ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Biruta","family":"Kierdaszuk","sequence":"additional","affiliation":[{"name":"Department of Neurology, Medical University of Warsaw , 02-097 Warsaw ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Kostera-Pruszczyk","sequence":"additional","affiliation":[{"name":"Department of Neurology, Medical University of Warsaw , 02-097 Warsaw ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5151-988X","authenticated-orcid":false,"given":"Cristina","family":"Dom\u00ednguez-Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Department of Neurology, Neuromuscular Unit, Instituto de Investigaci\u00f3n imas12, Hospital 12 de Octubre , 28041 Madrid ,","place":["Spain"]},{"name":"Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III , 28029 Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1933-2238","authenticated-orcid":false,"given":"Aurelio","family":"Hern\u00e1ndez-Lain","sequence":"additional","affiliation":[{"name":"Department of Neurology, Neuromuscular Unit, Instituto de Investigaci\u00f3n imas12, Hospital 12 de Octubre , 28041 Madrid ,","place":["Spain"]},{"name":"Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III , 28029 Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6917-2236","authenticated-orcid":false,"given":"Carmen","family":"Paradas","sequence":"additional","affiliation":[{"name":"Neurology Department, Neuromuscular Disorders Unit, Instituto de Biomedicina de Sevilla, Hospital U Virgen del Roc\u00edo, CSIC, Universidad de Sevilla , 41013 Sevilla ,","place":["Spain"]},{"name":"Center for Biomedical Network Research on Neurodegenerative Disorders (CIBERNED), Instituto de Salud Carlos III , 28029 Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eloy","family":"Rivas","sequence":"additional","affiliation":[{"name":"Neurology Department, Neuromuscular Disorders Unit, Instituto de Biomedicina de Sevilla, Hospital U Virgen del Roc\u00edo, CSIC, Universidad de Sevilla , 41013 Sevilla ,","place":["Spain"]},{"name":"Center for Biomedical Network Research on Neurodegenerative Disorders (CIBERNED), Instituto de Salud Carlos III , 28029 Madrid ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Papadimas","sequence":"additional","affiliation":[{"name":"Department of Neurology, Eginition Hospital, Medical School, National and Kapodistrian University of Athens , 157 72 Athens ,","place":["Greece"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Constantinos","family":"Papadopoulos","sequence":"additional","affiliation":[{"name":"Department of Neurology, Eginition Hospital, Medical School, National and Kapodistrian University of Athens , 157 72 Athens ,","place":["Greece"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margarita","family":"Chrysanthou-Piterou","sequence":"additional","affiliation":[{"name":"Department of Neurology, Eginition Hospital, Medical School, National and Kapodistrian University of Athens , 157 72 Athens ,","place":["Greece"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduard","family":"Gallardo","sequence":"additional","affiliation":[{"name":"Institut d\u2019Investigaci\u00f3 Biom\u00e8dica Sant Pau (IIB SANT PAU) , Neuromuscular Disease Unit, 08041 Barcelona ,","place":["Spain"]},{"name":"Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III , 28029 Madrid ,","place":["Spain"]},{"name":"Servei de Neurologia, Unitat malalties neuromusculars, Hospital de la Santa Creu i Sant Pau , 08025 Barcelona ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Montse","family":"Oliv\u00e9","sequence":"additional","affiliation":[{"name":"Institut d\u2019Investigaci\u00f3 Biom\u00e8dica Sant Pau (IIB SANT PAU) , Neuromuscular Disease Unit, 08041 Barcelona ,","place":["Spain"]},{"name":"Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III , 28029 Madrid ,","place":["Spain"]},{"name":"Servei de Neurologia, Unitat malalties neuromusculars, Hospital de la Santa Creu i Sant Pau , 08025 Barcelona ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9230-4137","authenticated-orcid":false,"given":"James","family":"Lilleker","sequence":"additional","affiliation":[{"name":"Division of Musculoskeletal and Dermatological Sciences, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester , Manchester, M13 9PL ,","place":["UK"]},{"name":"Muscle Disease Unit, Manchester Centre for Clinical Neurosciences, Northern Care Alliance NHS Foundation Trust , Salford, M6 8HD ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark E","family":"Roberts","sequence":"additional","affiliation":[{"name":"Muscle Disease Unit, Manchester Centre for Clinical Neurosciences, Northern Care Alliance NHS Foundation Trust , Salford, M6 8HD ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Domenica","family":"Marchese","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), CNAG-CRG, Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF) , 08028 Barcelona ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giulia","family":"Lunazzi","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), CNAG-CRG, Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF) , 08028 Barcelona ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3276-1889","authenticated-orcid":false,"given":"Holger","family":"Heyn","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), CNAG-CRG, Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF) , 08028 Barcelona ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esther","family":"Fern\u00e1ndez-Sim\u00f3n","sequence":"additional","affiliation":[{"name":"The John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute, Newcastle Upon Tyne NHS Trust , Newcastle Upon Tyne, NE13BZ ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisa","family":"Villalobos","sequence":"additional","affiliation":[{"name":"The John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute, Newcastle Upon Tyne NHS Trust , Newcastle Upon Tyne, NE13BZ ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Clark","sequence":"additional","affiliation":[{"name":"The John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute, Newcastle Upon Tyne NHS Trust , Newcastle Upon Tyne, NE13BZ ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Panos","family":"Katsikis","sequence":"additional","affiliation":[{"name":"The John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute, Newcastle Upon Tyne NHS Trust , Newcastle Upon Tyne, NE13BZ ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Collins","sequence":"additional","affiliation":[{"name":"The John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute, Newcastle Upon Tyne NHS Trust , Newcastle Upon Tyne, NE13BZ ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Priyanka","family":"Mehra","sequence":"additional","affiliation":[{"name":"The John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute, Newcastle Upon Tyne NHS Trust , Newcastle Upon Tyne, NE13BZ ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zoe","family":"Laidler","sequence":"additional","affiliation":[{"name":"The John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute, Newcastle Upon Tyne NHS Trust , Newcastle Upon Tyne, NE13BZ ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0360-6644","authenticated-orcid":false,"given":"Amy","family":"Vincent","sequence":"additional","affiliation":[{"name":"The John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute, Newcastle Upon Tyne NHS Trust , Newcastle Upon Tyne, NE13BZ ,","place":["UK"]},{"name":"Wellcome Trust Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University , Newcastle upon Tyne, NE2 3NU ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giorgio","family":"Tasca","sequence":"additional","affiliation":[{"name":"The John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute, Newcastle Upon 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,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,7,24]]},"reference":[{"key":"2024121301175026100_awae249-B1","doi-asserted-by":"crossref","first-page":"1342","DOI":"10.1016\/S0140-6736(08)61555-X","article-title":"Pompe\u2019s disease","volume":"372","author":"van der Ploeg","year":"2008","journal-title":"Lancet."},{"key":"2024121301175026100_awae249-B2","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.3390\/biom10091339","article-title":"Pompe disease: New developments in an old lysosomal storage disorder","volume":"10","author":"Meena","year":"2020","journal-title":"Biomolecules"},{"key":"2024121301175026100_awae249-B3","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1186\/s13023-016-0442-y","article-title":"Childhood Pompe disease: Clinical spectrum and genotype in 31 patients","volume":"11","author":"van Capelle","year":"2016","journal-title":"Orphanet J Rare 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