636d1ba2167bfb62bd81e2cb7e0c6c1e 309040.pdf 6332e6cbe41a72831702117c0cc28ba1f79d3f4a 309040.pdf 5c2685712a71d522cd2a75508e55b86e31de18aceecda5020bd6681c752e0b68 309040.pdf Title: Decoding the muscle transcriptome of patients with late-onset Pompe disease reveals markers of disease progression Subject: DOI: 10.1093/brain/awae249; Brain, 147, 12, 2024-07-24.; Abstract: 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.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 Keywords: glycogen storage disease; mitochondria abnormality; metabolism Author: Alexandra Monceau Creator: Servigistics Arbortext Advanced Print Publisher 11.1.4546/W-x64 Producer: PDFlib+PDI 9.0.7p3 (C++/Win64) CreationDate: Tue Dec 3 01:50:16 2024 CET ModDate: Tue Dec 3 10:36:28 2024 CET Custom Metadata: yes Metadata Stream: yes Tagged: yes UserProperties: no Suspects: no Form: AcroForm JavaScript: no Pages: 14 Encrypted: no Page size: 612.283 x 790.866 pts Page rot: 0 File size: 1671331 bytes Optimized: no PDF version: 1.6 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- MNRNHH+CaeciliaLTStd-Bold Type 1C Custom yes yes yes 1152 0 NIYTCC+CaeciliaLTStd-Roman Type 1C Custom yes yes yes 1157 0 OLOBKR+CaeciliaLTStd-Heavy Type 1C Custom yes yes yes 64 0 EMCHTF+CaeciliaLTStd-Italic Type 1C Custom yes yes yes 69 0 YICAXU+TimesNewRomanPSMT CID TrueType Identity-H yes yes yes 88 0 PMCFLH+STIXGeneral-Regular Type 1C Custom yes yes yes 93 0 UHFNUS+CaeciliaLTStd-BoldItalic Type 1C Custom yes yes yes 34 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2025-03-14 02:45:20 CET RepresentationInformation: 309040.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2025-03-13 13:48:26 CET Size: 1671331 Format: PDF Version: 1.6 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf Profile: Tagged PDF PDFMetadata: Objects: 1246 FreeObjects: 3 IncrementalUpdates: 3 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: false CenterWindow: false DisplayDocTitle: true NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: OneColumn PageMode: UseOutlines Language: en Outlines: Item: Title: Introduction Destination: secawae249-s1 Item: Title: Materials and methods Destination: secawae249-s2 Children: Item: Title: Muscle samples Destination: secawae249-s2.1 Item: Title: Purification of nuclei from human muscle biopsies Destination: secawae249-s2.2 Item: Title: Single-nucleus RNA sequencing Destination: secawae249-s2.3 Item: Title: Bioinformatic analysis of single nuclei Destination: secawae249-s2.4 Item: Title: Enriched signalling pathway analysis Destination: secawae249-s2.5 Item: Title: Metabolic and autophagy pathway score Destination: secawae249-s2.6 Item: Title: NanoString GeoMX digital spatial profiler Destination: secawae249-s2.7 Item: Title: Differential gene expression analysis of GeoMX data Destination: secawae249-s2.8 Item: Title: Statistical analysis Destination: secawae249-s2.9 Item: Title: Results Destination: secawae249-s3 Children: Item: Title: Patients and samples Destination: secawae249-s3.1 Item: Title: Cell populations identified in the skeletal muscle samples Destination: secawae249-s3.2 Item: Title: Differences in cell populations between control and Pompe disease samples Destination: secawae249-s3.3 Item: Title: Muscle samples from Pompe disease patients do not show prominent signs of regeneration Destination: secawae249-s3.4 Item: Title: Gene expression profile of myofibres reveals differences between Pompe disease and controls Destination: secawae249-s3.5 Item: Title: Pompe muscle fibres exhibit altered gene expression in metabolic pathways Destination: secawae249-s3.6 Item: Title: Pompe disease muscle fibres display dysregulated autophagy Destination: secawae249-s3.7 Item: Title: Spatial transcriptomics suggest a sequence of biological events Destination: secawae249-s3.8 Item: Title: Characterization of myofibre gene expression profile reveals changes between Pompe and Pompe + ERT Destination: secawae249-s3.9 Item: Title: Discussion Destination: secawae249-s4 Item: Title: Conclusion Destination: secawae249-s5 Item: Title: Data availability Destination: secawae249-s6 Item: Title: Acknowledgements Destination: acknow Item: Title: Funding Destination: secawae249-s7 Item: Title: Competing interests Destination: secawae249-s8 Item: Title: Supplementary material Destination: secawae249-s9 Item: Title: References Destination: reflist Info: Title: Decoding the muscle transcriptome of patients with late-onset Pompe disease reveals markers of disease progression Author: Alexandra Monceau Subject: DOI: 10.1093/brain/awae249; Brain, 147, 12, 2024-07-24.; Abstract: 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.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 Keywords: glycogen storage disease; mitochondria abnormality; metabolism Creator: Servigistics Arbortext Advanced Print Publisher 11.1.4546/W-x64 Producer: PDFlib+PDI 9.0.7p3 (C++/Win64) CreationDate: Tue Dec 03 02:20:16 CET 2024 ModDate: Tue Dec 03 11:06:28 CET 2024 ID: 0x235210d104ec20e1c89362cac714eca4, 0x228ca18d8de4684587887729d0612b70 Filters: FilterPipeline: FlateDecode FilterPipeline: DCTDecode Images: Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 2236 ImageHeight: 254 BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 1100 ImageHeight: 1411 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 1000 ImageHeight: 1410 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 1000 ImageHeight: 1060 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 1000 ImageHeight: 1353 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 1333 ImageHeight: 983 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 1100 ImageHeight: 1264 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Fonts: Type0: Font: BaseFont: YICAXU+TimesNewRomanPSMT Encoding: Identity-H ToUnicode: true Type1: Font: BaseFont: MNRNHH+CaeciliaLTStd-Bold FontSubset: true FirstChar: 1 LastChar: 71 FontDescriptor: FontName: MNRNHH+CaeciliaLTStd-Bold Flags: Nonsymbolic, ForceBold FontBBox: -166, -273, 1141, 938 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: OLOBKR+CaeciliaLTStd-Heavy FontSubset: true FirstChar: 1 LastChar: 31 FontDescriptor: FontName: OLOBKR+CaeciliaLTStd-Heavy Flags: Nonsymbolic, ForceBold FontBBox: -170, -277, 1146, 970 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: UHFNUS+CaeciliaLTStd-BoldItalic FontSubset: true FirstChar: 1 LastChar: 1 FontDescriptor: FontName: UHFNUS+CaeciliaLTStd-BoldItalic Flags: Nonsymbolic, Italic, ForceBold FontBBox: -169, -273, 1082, 932 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: NIYTCC+CaeciliaLTStd-Roman FontSubset: true FirstChar: 1 LastChar: 95 FontDescriptor: FontName: NIYTCC+CaeciliaLTStd-Roman Flags: Nonsymbolic FontBBox: -167, -270, 1136, 926 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: EMCHTF+CaeciliaLTStd-Italic FontSubset: true FirstChar: 1 LastChar: 60 FontDescriptor: FontName: EMCHTF+CaeciliaLTStd-Italic Flags: Nonsymbolic, Italic FontBBox: -166, -270, 1053, 915 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: PMCFLH+STIXGeneral-Regular FontSubset: true FirstChar: 1 LastChar: 10 FontDescriptor: FontName: PMCFLH+STIXGeneral-Regular Flags: Nonsymbolic FontBBox: -995, -455, 2000, 1055 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true CIDFontType2: Font: BaseFont: YICAXU+TimesNewRomanPSMT CIDSystemInfo: Registry: Adobe Registry: Identity Supplement: 0 FontDescriptor: FontName: YICAXU+TimesNewRomanPSMT Flags: Nonsymbolic FontBBox: -568, -307, 2046, 1040 FontFile2: true XMP: uuid:2d377ea8-5a34-4dbc-8395-8244e06cb7b8 uuid:D86F6F7A-068C-B416-4B1C-EFD9C6B7AE21 True glycogen storage disease; mitochondria abnormality; metabolism PDFlib+PDI 9.0.7p3 (C++/Win64) application/pdf 10.1093/brain/awae249 en Oxford University Press Decoding the muscle transcriptome of patients with late-onset Pompe disease reveals markers of disease progression Alexandra Monceau Rasya Gokul Nath Xavier Suárez-Calvet Olimpia Musumeci Antonio Toscano Biruta Kierdaszuk Anna Kostera-Pruszczyk Cristina Domínguez-González Aurelio Hernández-Lain Carmen Paradas Eloy Rivas George Papadimas Constantinos Papadopoulos Margarita Chrysanthou-Piterou Eduard Gallardo Montse Olivé James Lilleker Mark E. Roberts Domenica Marchese Giulia Lunazzi Holger Heyn Esther Fernández-Simón Elisa Villalobos James Clark Panos Katsikis Catherine Collins Priyanka Mehra Zoe Laidler Amy Vincent Giorgio Tasca Chiara Marini-Bettolo Michela Guglieri Volker Straub Nina Raben Jordi Díaz-Manera DOI: 10.1093/brain/awae249; Brain, 147, 12, 2024-07-24.; Abstract: 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.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 © The Author(s) 2024. Published by Oxford University Press on behalf of the Guarantors of Brain. glycogen storage disease mitochondria abnormality metabolism Journal Brain © The Author(s) 2024. 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