token_classification/10-1002_emmm-201202176.xml

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<article doi="10.1002/emmm.201202176" abstract="A recently proposed therapeutic approach for lysosomal storage disorders (LSDs) relies upon the ability of transcription factor EB (TFEB) to stimulate autophagy and induce lysosomal exocytosis leading to cellular clearance. This approach is particularly attractive in glycogen storage disease type II [a severe metabolic myopathy, Pompe disease (PD)] as the currently available therapy, replacement of the missing enzyme acid alpha-glucosidase, fails to reverse skeletal muscle pathology. PD, a paradigm for LSDs, is characterized by both lysosomal abnormality and dysfunctional autophagy. Here, we show that TFEB is a viable therapeutic target in PD: overexpression of TFEB in a new muscle cell culture system and in mouse models of the disease reduced glycogen load and lysosomal size, improved autophagosome processing, and alleviated excessive accumulation of autophagic vacuoles. Unexpectedly, the exocytosed vesicles were labelled with lysosomal and autophagosomal membrane markers, suggesting that TFEB induces exocytosis of autophagolysosomes. Furthermore, the effects of TFEB were almost abrogated in the setting of genetically suppressed autophagy, supporting the role of autophagy in TFEB-mediated cellular clearance."><fig id="5287"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5287"/><sd-panel panel_id="16105"><p>A. <sd-tag id="sdTag1" source="sdapi" category="assay" entity_type="" role="" text="Confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Confocal microscopy</sd-tag> image of PD <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="cell_type" role="component" text="myotubes" ext_ids="CL:0002372" norm_text="" ext_dbs="CL" in_caption="True" ext_names="myotube" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">myotubes</sd-tag> (cl. <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="cell_type" role="component" text="3LE8" ext_ids="CL:0002372" norm_text="" ext_dbs="CL" in_caption="True" ext_names="myotube" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">3LE8</sd-tag>) infected for 72 h with <sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="organism" role="component" text="adenovirus" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">adenovirus</sd-tag> containing <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag> (PD + <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="organism" role="component" text="Ad" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Ad</sd-tag>-<sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag> 72 h) shows a dramatic reduction in the number of large <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag>-positive <sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (red) compared to that in untreated (PD) or <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="organism" role="component" text="adenovirus" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">adenovirus</sd-tag> (PD + <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="organism" role="component" text="Ad" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Ad</sd-tag>-null)-treated PD <sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="cell_type" role="component" text="myotubes" ext_ids="CL:0002372" norm_text="" ext_dbs="CL" in_caption="True" ext_names="myotube" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">myotubes</sd-tag>. WT <sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="cell_type" role="component" text="myotubes" ext_ids="CL:0002372" norm_text="" ext_dbs="CL" in_caption="True" ext_names="myotube" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">myotubes</sd-tag> are shown on the left panel. <sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Nuclei" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Nuclei</sd-tag> are stained with <sd-tag id="sdTag9" source="sdapi" category="assay" entity_type="" role="" text="Hoechst" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Hoechst</sd-tag> (blue). <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TFEB" ext_ids="Q9R210" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">TFEB</sd-tag> was detected with anti-<sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag> antibody (green).</p><p>B. Distribution of <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomal" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomal</sd-tag> size differs significantly in <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="organism" role="component" text="Ad" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Ad</sd-tag>-null and <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="organism" role="component" text="Ad" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Ad</sd-tag>-<sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag> PD <sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="cell_type" role="component" text="myotubes" ext_ids="CL:0002372" norm_text="" ext_dbs="CL" in_caption="True" ext_names="myotube" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">myotubes</sd-tag> (p = 6.32 × 10<sup>−8</sup>; Kolmogorov-Smirnov test). <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Lysosomal" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Lysosomal</sd-tag> size is expressed as number of pixels representing <sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomal" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomal</sd-tag> area (<sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag>-positive structures). The median <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomal" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomal</sd-tag> size of <sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="organism" role="component" text="Ad" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Ad</sd-tag>-<sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag> infected <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="cell_type" role="component" text="myotubes" ext_ids="CL:0002372" norm_text="" ext_dbs="CL" in_caption="True" ext_names="myotube" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">myotubes</sd-tag> (m = 367.13 pixels, n = 703, range 208-2659) was significantly lower than that of <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="organism" role="component" text="Ad" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Ad</sd-tag>-null infected <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="cell_type" role="component" text="myotubes" ext_ids="CL:0002372" norm_text="" ext_dbs="CL" in_caption="True" ext_names="myotube" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">myotubes</sd-tag> (m = 491.16 pixels, n = 1395, range 200-2857; p = 6.5 × 10<sup>−12</sup>; Wilcoxon rank sum test).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16105"/></sd-panel><sd-panel panel_id="16095"><p>C. <sd-tag id="sdTag37" source="sdapi" category="assay" entity_type="" role="" text="Confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Confocal microscopy</sd-tag> image of PD <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="cell_type" role="component" text="myotubes" ext_ids="CL:0002372" norm_text="" ext_dbs="CL" in_caption="True" ext_names="myotube" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">myotubes</sd-tag> infected for 24 h with <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="organism" role="component" text="Ad" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Ad</sd-tag>-<sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag> shows relocation of <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> to the <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="plasma membrane" ext_ids="GO:0005886" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="plasma membrane" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">plasma membrane</sd-tag> (top). Images showing <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> staining (red) on <sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="plasma membrane" ext_ids="GO:0005886" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="plasma membrane" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">plasma membrane</sd-tag> in a PD <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="cell_type" role="component" text="myotube" ext_ids="CL:0002372" norm_text="" ext_dbs="CL" in_caption="True" ext_names="myotube" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">myotube</sd-tag> infected with <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="organism" role="component" text="Ad" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Ad</sd-tag>-<sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag> (bottom; arrows) but not in a non-infected cell (middle). Non-permeabilized cells were incubated with anti-<sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> antibody at 4°C for 40 min, followed by fixation and staining with secondary antibody.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16095"/></sd-panel><sd-panel panel_id="16096"><p>D. <sd-tag id="sdTag55" source="sdapi" category="assay" entity_type="" role="" text="Confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Confocal microscopy</sd-tag> images of live non-infected PD <sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="cell_type" role="component" text="myotubes" ext_ids="CL:0002372" norm_text="" ext_dbs="CL" in_caption="True" ext_names="myotube" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">myotubes</sd-tag> (left) or PD <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="cell_type" role="component" text="myotubes" ext_ids="CL:0002372" norm_text="" ext_dbs="CL" in_caption="True" ext_names="myotube" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">myotubes</sd-tag> infected for 72 h with <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="organism" role="component" text="Ad" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Ad</sd-tag>-<sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag> (right) show a dramatic reduction in the amount of accumulated <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="glycogen" ext_ids="CHEBI:5466" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">glycogen</sd-tag> in <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated cells. The cells were incubated with the fluorescent <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="glucose" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">glucose</sd-tag> (<sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="2-NBDG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">2-NBDG</sd-tag>; green), extensively washed, and analysed by <sd-tag id="sdTag52" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Bar: 10 µm for all panels.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16096"/></sd-panel></fig><fig id="5288"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5288"/><sd-panel panel_id="16097"><p><sd-tag id="sdTag77" source="sdapi" category="assay" entity_type="" role="" text="Confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Confocal microscopy</sd-tag> of live unstained <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> from a <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>:WT <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="organism" role="component" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag> (WT) and from untreated (<sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag>−/−) or ERT-treated (<sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag>−/−; +ERT) <sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>:<sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag>−/− <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>. Images show typical centrally located autophagic build-up with multiple clusters of <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-positive <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag>. Structures like these are never seen in WT <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscle" ext_ids="UBERON:0002385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscle</sd-tag>. Autophagic build-up is present virtually in all <sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> derived from <sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="EDL" ext_ids="UBERON:0001386" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="extensor digitorum longus" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">EDL</sd-tag> or <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="tissue" role="component" text="gastrocnemius" ext_ids="UBERON:0001388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="gastrocnemius" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">gastrocnemius</sd-tag><sd-pretag id="sdPretag14474357635830" parent-tag-id="312">muscles</sd-pretag> (not shown), but only in 60-70% of <sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="FDB" ext_ids="UBERON:0014380" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="flexor digitorum brevis muscle" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">FDB</sd-tag><sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag>. Labelled recombinant human <sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GAA" ext_ids="2548" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag> (red) was administered i.v. into 3-4 month-old <sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>:<sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag>−/− <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> (n = 5) at a dose of 100 mg/kg twice with a 24 h interval. <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="organism" role="component" text="Mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Mice</sd-tag> were sacrificed the next day, and live <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> (shown for <sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="EDL" ext_ids="UBERON:0001386" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="extensor digitorum longus" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">EDL</sd-tag><sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscle" ext_ids="UBERON:0002385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscle</sd-tag>) were analysed by <sd-tag id="sdTag88" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. The labelled recombinant <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GAA" ext_ids="P10253" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GAA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GAA</sd-tag> was detected almost exclusively in the <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic vesicles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic vesicles</sd-tag>. At least 500 <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> were analysed for each condition. Bar: 10 µm.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16097"/></sd-panel></fig><fig id="5289"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5289"/><sd-panel panel_id="16098"><p>A. <sd-tag id="sdTag96" source="sdapi" category="assay" entity_type="" role="" text="Immunostaining" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunostaining</sd-tag> of non-infected cells (day 13 in differentiation medium) and cells infected with a mutant form of <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag> (TFEBmt) with <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> (red) and <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag> (green). <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="organism" role="component" text="Ad" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Ad</sd-tag>-<sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>mt was added to the <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="cell_type" role="component" text="myotubes" ext_ids="CL:0002372" norm_text="" ext_dbs="CL" in_caption="True" ext_names="myotube" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">myotubes</sd-tag> for 72 h on day 10 in differentiation medium. <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="organism" role="component" text="Ad" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Ad</sd-tag>-<sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>mt-infected cells show massive accumulation of <sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TFEB" ext_ids="Q9R210" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">TFEB</sd-tag> in the <sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="nuclei" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nuclei</sd-tag> and significant reduction in <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomal" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomal</sd-tag> size, similar to that seen with <sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16098"/></sd-panel><sd-panel panel_id="16099"><p>B. <sd-tag id="sdTag114" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> of cell lysates confirms the presence of <sd-tag id="sdTag115" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TFEB" ext_ids="Q9R210" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">TFEB</sd-tag> in the <sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="nuclear" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nuclear</sd-tag> fraction; the different intensities of the two bands corresponding to <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> protein in untreated and <sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>mt-treated samples may reflect the differences in the glycosylation pattern.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16099"/></sd-panel><sd-panel panel_id="16100"><p>C. <sd-tag id="sdTag131" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> of protein lysates from untreated, <sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="organism" role="component" text="Ad" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Ad</sd-tag>-null, <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>, and <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>mt-treated <sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="cell_type" role="component" text="myotubes" ext_ids="CL:0002372" norm_text="" ext_dbs="CL" in_caption="True" ext_names="myotube" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">myotubes</sd-tag> with anti-<sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="protein" role="assayed" text="caspase-3" ext_ids="P70677" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Casp3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">caspase-3</sd-tag> antibody. No activated (cleaved) products are detected in any condition. <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="α-Tubulin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">α-Tubulin</sd-tag> was used as a loading control.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16100"/></sd-panel><sd-panel panel_id="16101"><p>D. <sd-tag id="sdTag137" source="sdapi" category="assay" entity_type="" role="" text="TUNEL" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TUNEL</sd-tag> assay shows the presence of some apoptotic cells in <sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="organism" role="component" text="Ad" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Ad</sd-tag>-<sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-infected cultures, but not in control cultures infected with <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="organism" role="component" text="adenovirus" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">adenovirus</sd-tag> alone (n = 3). Bar: 10 µm for all panels.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16101"/></sd-panel></fig><fig id="5290"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5290"/><sd-panel panel_id="16102"><p>A. <sd-tag id="sdTag147" source="sdapi" category="assay" entity_type="" role="" text="Confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Confocal microscopy</sd-tag> images of live <sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="cell_type" role="component" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> derived from 3 to 4 month-old <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>:WT (top left), untreated <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>:<sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag>−/− (bottom left) or <sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>:<sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag>−/− (right) <sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>. All <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="cell_type" role="component" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> were transfected with <sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>-<sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> to visualize <sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (red). The effects of <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TFEB" ext_ids="Q9R210" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">TFEB</sd-tag> are clearly visible - overall reduction in <sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomal" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomal</sd-tag> size, appearance of normal size <sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (similar to those in the WT), and <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomal" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomal</sd-tag> docking to the <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="plasma membrane" ext_ids="GO:0005886" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="plasma membrane" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">plasma membrane</sd-tag> (inset). Bar: 10 µm.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16102"/></sd-panel><sd-panel panel_id="16106"><p>B. <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="tissue" role="component" text="FDB" ext_ids="UBERON:0014380" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="flexor digitorum brevis muscle" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">FDB</sd-tag><sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscle" ext_ids="UBERON:0002385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscle</sd-tag> of a <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="gene" role="component" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag>−/− <sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="organism" role="component" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag> was transfected with both <sd-tag id="sdTag197" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag> and <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>-<sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> (<sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="gene" role="component" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag>−/− + <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag203" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>). Images were taken before (left) and after 4 h (right) of <sd-tag id="sdTag204" source="sdapi" category="assay" entity_type="" role="" text="time-lapse microscopy" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">time-lapse microscopy</sd-tag>. <sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Lysosomal" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Lysosomal</sd-tag> clearance is visible in the <sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-transfected <sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fibre" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibre</sd-tag> at both time points. <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Lysosomes</sd-tag> appear to "exit" the <sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fibre" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibre</sd-tag> (inset and arrow) at the 4 h time point when <sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag> is activated as evidenced by its <sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="nuclear" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nuclear</sd-tag> translocation (green <sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="nuclei" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nuclei</sd-tag>). Bar: 10 µm.</p><p>C. The mean maximum velocity of <sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (top) and the number of large (&gt;3.5 µm) <sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (bottom) in untreated and <sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TFEB" ext_ids="Q9R210" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">TFEB</sd-tag>-treated PD <sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> (note: all data for <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>- and <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated <sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> are pooled). <sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Lysosomal" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Lysosomal</sd-tag> velocities were calculated from <sd-tag id="sdTag232" source="sdapi" category="assay" entity_type="" role="" text="time-lapse images" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">time-lapse images</sd-tag> using ImageJ software with the manual tracking plug-in. For each condition the trajectories of multiple <sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> were followed (n = 26 untreated; n = 43 <sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated) and the three highest velocity measurements per <sd-tag id="sdTag233" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosome" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosome</sd-tag> were recorded. In <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated <sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag>, the maximum velocity of <sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> was significantly increased (p = 2.07 × 10<sup>−17</sup>) and the number of large <sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> was significantly decreased (p = 1.0 × 10<sup>−3</sup>). Ten untreated and 24 <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated <sd-tag id="sdTag229" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> were analysed for the size calculations. * indicates statistically significant differences (p ≤ 0.001; Student's t-test). Error bars represent 95% confidence intervals.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16106"/></sd-panel></fig><fig id="5291"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5291"/><sd-panel panel_id="16087"><p><sd-tag id="sdTag243" source="sdapi" category="assay" entity_type="" role="" text="Confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Confocal microscopy</sd-tag> images of live <sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="cell_type" role="component" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> from <sd-tag id="sdTag245" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>:<sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="gene" role="component" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag>−/− <sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>.</p><p>Muscle was transfected with <sd-tag id="sdTag249" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>-<sd-tag id="sdTag235" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> only. The image (a single frame from the time-lapse series presented in Movie 5) shows <sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (red), <sd-tag id="sdTag250" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-positive <sd-tag id="sdTag237" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> (green) and a number of <sd-tag id="sdTag238" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autolysosomes" ext_ids="GO:0044754" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autolysosomes</sd-tag> (yellow).</p><p>Muscle was transfected with <sd-tag id="sdTag251" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>-<sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag> and <sd-tag id="sdTag253" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>-<sd-tag id="sdTag261" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag>. Massive formation of <sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autolysosomes" ext_ids="GO:0044754" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autolysosomes</sd-tag> is indicated by yellow structures; the three lower panels provide a snapshot of the process of exocytosis. The structures at the <sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="subcellular" role="component" text="plasma membrane" ext_ids="GO:0005886" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="plasma membrane" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">plasma membrane</sd-tag> are labelled with both <sd-tag id="sdTag257" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and <sd-tag id="sdTag239" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag>, indicating that they represent <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="amphisomes" ext_ids="GO:0044753" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="amphisome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">amphisomes</sd-tag> (a product of fusion between <sd-tag id="sdTag258" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic vesicles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic <sd-pretag id="sdPretag14476115986620" parent-tag-id="333">vesicles</sd-pretag></sd-tag> and <sd-tag id="sdTag241" source="sdapi" category="entity" entity_type="subcellular" role="component" text="late endosomes" ext_ids="GO:0005770" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="late endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">late endosomes</sd-tag>) or <sd-tag id="sdTag259" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autolysosomes" ext_ids="GO:0044754" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autolysosomes</sd-tag> (a product of fusion between <sd-tag id="sdTag260" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic vesicles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic <sd-pretag id="sdPretag14476115546660" parent-tag-id="333">vesicles</sd-pretag></sd-tag> and <sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag>). Bar: 10 µm for all panels.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16087"/></sd-panel></fig><fig id="5292"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5292"/><sd-panel panel_id="16088"><p><sd-tag id="sdTag269" source="sdapi" category="assay" entity_type="" role="" text="Confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Confocal microscopy</sd-tag> images of live <sd-tag id="sdTag270" source="sdapi" category="entity" entity_type="cell_type" role="component" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> from <sd-tag id="sdTag271" source="sdapi" category="entity" entity_type="tissue" role="intervention" text="muscle" ext_ids="UBERON:0002385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscle</sd-tag>-specific autophagy-deficient <sd-tag id="sdTag272" source="sdapi" category="entity" entity_type="gene" role="component" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag>−/− <sd-tag id="sdTag273" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> (<sd-tag id="sdTag262" source="sdapi" category="entity" entity_type="gene" role="component" text="Atg7" ext_ids="74244" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg7" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg7</sd-tag>:<sd-tag id="sdTag274" source="sdapi" category="entity" entity_type="gene" role="component" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag> DKO).</p><p>Muscle was transfected with <sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>-<sd-tag id="sdTag276" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> only.</p><p>Muscle was transfected with <sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag> and <sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>-<sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> (<sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="gene" role="component" text="Atg7" ext_ids="74244" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg7" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg7</sd-tag>:<sd-tag id="sdTag282" source="sdapi" category="entity" entity_type="gene" role="component" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag> DKO +<sd-tag id="sdTag283" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag284" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>). The <sd-tag id="sdTag285" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-transfected <sd-tag id="sdTag286" source="sdapi" category="entity" entity_type="cell_type" role="component" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> show realignment of the <sd-tag id="sdTag287" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> and membrane detachment (most striking in top and bottom panels) similar to those in <sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-transfected <sd-tag id="sdTag289" source="sdapi" category="entity" entity_type="cell_type" role="component" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> from PD <sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> (see Fig 4B inset). <sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Lysosomes</sd-tag> can be seen in the space between the fibre and <sd-tag id="sdTag291" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="plasma membrane" ext_ids="GO:0005886" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="plasma membrane" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">plasma membrane</sd-tag> (arrows). Bar: 10 µm for all panels.</p><p>The mean maximum velocity of <sd-tag id="sdTag292" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (top) and the number of large (&gt;3.5 µm) <sd-tag id="sdTag267" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (bottom) in untreated and <sd-tag id="sdTag293" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated autophagy-deficient <sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="gene" role="component" text="Atg7" ext_ids="74244" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg7" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg7</sd-tag>:<sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="gene" role="component" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag> DKO <sd-tag id="sdTag296" source="sdapi" category="entity" entity_type="cell_type" role="component" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag>. The increase in maximum velocity (41%) is significant (p = 2.729 × 10<sup>−18</sup>; n = 57 <sd-tag id="sdTag297" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> for untreated; n = 52 <sd-tag id="sdTag298" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> for <sd-tag id="sdTag299" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated), but there is only a slight trend toward smaller <sd-tag id="sdTag300" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomal" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomal</sd-tag> size (p = 7.0 × 10<sup>−2</sup>; n = 10 <sd-tag id="sdTag301" source="sdapi" category="entity" entity_type="cell_type" role="component" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> for untreated; n = 21 <sd-tag id="sdTag302" source="sdapi" category="entity" entity_type="cell_type" role="component" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> for <sd-tag id="sdTag303" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated). The corresponding values from <sd-tag id="sdTag304" source="sdapi" category="entity" entity_type="gene" role="component" text="GAA" ext_ids="14387" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gaa" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAA</sd-tag>−/− <sd-tag id="sdTag305" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> are presented for comparison (for <sd-tag id="sdTag306" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated condition: n = 19 <sd-tag id="sdTag307" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> for velocity measurements, and n = 10 <sd-tag id="sdTag308" source="sdapi" category="entity" entity_type="cell_type" role="component" text="fibres" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibres</sd-tag> for the <sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomal" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomal</sd-tag> size measurements). * indicates statistically significant differences (p ≤ 1.0 × 10<sup>−5</sup> for the top panel and p ≤ 0.01 for the lower panel; Student's t-test).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16088"/></sd-panel></fig><fig id="5293"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5293"/><sd-panel panel_id="16089"><p>A. <sd-tag id="sdTag313" source="sdapi" category="assay" entity_type="" role="" text="Glycogen assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Glycogen assay</sd-tag> in <sd-tag id="sdTag315" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-injected <sd-tag id="sdTag311" source="sdapi" category="entity" entity_type="tissue" role="component" text="gastrocnemii" ext_ids="UBERON:0001388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="gastrocnemius" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">gastrocnemii</sd-tag> and in the contralateral <sd-tag id="sdTag312" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag>. In <sd-tag id="sdTag316" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-injected <sd-tag id="sdTag317" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag><sd-tag id="sdTag314" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="glycogen" ext_ids="CHEBI:5466" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">glycogen</sd-tag> levels were significantly decreased compared to those in untreated <sd-tag id="sdTag318" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag>. * indicates statistically significant differences (p = 1.0 × 10<sup>−4</sup>; n = 6; Student's t-test).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16089"/></sd-panel><sd-panel panel_id="16090"><p>B. <sd-tag id="sdTag323" source="sdapi" category="assay" entity_type="" role="" text="PAS staining" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">PAS staining</sd-tag> of <sd-tag id="sdTag326" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated <sd-tag id="sdTag327" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscle" ext_ids="UBERON:0002385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscle</sd-tag> shows a reduction of <sd-tag id="sdTag324" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomal" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomal</sd-tag><sd-tag id="sdTag325" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="glycogen" ext_ids="CHEBI:5466" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">glycogen</sd-tag> stores (puncta) compared to those in untreated <sd-tag id="sdTag328" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscle" ext_ids="UBERON:0002385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscle</sd-tag>. Original magnification: 20×.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16090"/></sd-panel><sd-panel panel_id="16091"><p>C. <sd-tag id="sdTag341" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> staining of <sd-tag id="sdTag335" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-injected <sd-tag id="sdTag336" source="sdapi" category="entity" entity_type="tissue" role="component" text="gastrocnemii" ext_ids="UBERON:0001388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="gastrocnemius" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">gastrocnemii</sd-tag> and of the contralateral untreated <sd-tag id="sdTag337" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag>. In <sd-tag id="sdTag338" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated <sd-tag id="sdTag339" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag>, the size of <sd-tag id="sdTag340" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag>-positive <sd-tag id="sdTag333" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag> was reduced. Bar: 2 µm.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16091"/></sd-panel></fig><fig id="5294"><title></title><label>Figure 8</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5294"/><sd-panel panel_id="16092"><p>A. <sd-tag id="sdTag346" source="sdapi" category="assay" entity_type="" role="" text="EM" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">EM</sd-tag> images of <sd-tag id="sdTag355" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscle" ext_ids="UBERON:0002385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscle</sd-tag> injected with either <sd-tag id="sdTag347" source="sdapi" category="entity" entity_type="organism" role="component" text="AAV" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">AAV</sd-tag>-<sd-tag id="sdTag348" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> (untreated) or <sd-tag id="sdTag357" source="sdapi" category="entity" entity_type="organism" role="component" text="AAV" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="unidentified adenovirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">AAV</sd-tag>-<sd-tag id="sdTag358" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag> (<sd-tag id="sdTag359" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated). Asterisks indicate <sd-tag id="sdTag349" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="glycogen" ext_ids="CHEBI:5466" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">glycogen</sd-tag>-containing <sd-tag id="sdTag360" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag>. Bar: 1.5 µm (upper panels) and 0.45 µm (lower panels). Higher magnification images (lower panels) show that <sd-tag id="sdTag370" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="glycogen" ext_ids="CHEBI:5466" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">glycogen</sd-tag> particles are less densely packed in <sd-tag id="sdTag361" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TFEB" ext_ids="21425" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Tfeb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TFEB</sd-tag>-treated <sd-tag id="sdTag362" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscle" ext_ids="UBERON:0002385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscle</sd-tag>. Black arrows indicate <sd-tag id="sdTag350" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosome" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosome</sd-tag> profiles; the white empty arrow shows remnants of <sd-tag id="sdTag351" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> engulfed by the <sd-tag id="sdTag352" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosome" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosome</sd-tag>.</p><p>B. Graphical presentations of <sd-tag id="sdTag353" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomal" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomal</sd-tag> length (average ± SE; n = 100 <sd-tag id="sdTag354" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag>; p = 6.31 × 10<sup>−5</sup>), the number of <sd-tag id="sdTag363" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> per 5 µm<sup>2</sup> area of <sd-tag id="sdTag364" source="sdapi" category="entity" entity_type="cell_type" role="component" text="muscle fibre" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">muscle fibre</sd-tag> section (average ± SE; n = 50 fields; p = 4.80 × 10<sup>−3</sup>), and the number of <sd-tag id="sdTag365" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> flanking <sd-tag id="sdTag366" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="glycogen" ext_ids="CHEBI:5466" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">glycogen</sd-tag>-containing <sd-tag id="sdTag367" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (average ± SE; n = 100 <sd-tag id="sdTag368" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag>; p = 4.39 × 10<sup>−5</sup> &lt; 0.001). Student's t-test was used for each comparison.</p><p>C. Graphical presentations of mitochondrial size (average ± SE; n = 100) and the number of <sd-tag id="sdTag369" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> per 5 µm<sup>2</sup> area of <sd-tag id="sdTag356" source="sdapi" category="entity" entity_type="cell_type" role="component" text="muscle fibre" ext_ids="CL:0008002" norm_text="" ext_dbs="CL" in_caption="True" ext_names="skeletal muscle fiber" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">muscle fibre</sd-tag> section (average ± SE; n = 50 fields). The differences were not significant by Student's t-test (p = 3.65 × 10<sup>−1</sup> and 4.27 × 10<sup>−1</sup>, respectively).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16092"/></sd-panel></fig></article>