{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/checksum.txt"],"Mzml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/Vesicles.mzML","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/Lysate.mzML"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/TDP-43-Q331K-Cherry2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evTDP-43-Q331K3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evTDP-43-Q331K-Cherry2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evWT1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/WT-Myc1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evWT-Myc3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/WT-Cherry2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evWT-Myc2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/TDP-43-Q331K2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evTDP-43-Q331K-Cherry1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evWT2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/TDP-43-Q331K-Cherry1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/TDP-43-Q331K-Cherry3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evTDP-43-Q331K-Myc3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/WT2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evWT-Cherry1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/TDP-43-Q331K1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/WT-Cherry1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/WT3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evWT3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/TDP-43-Q331K-Myc.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/TDP-43-Q331K-Myc2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evWT-Cherry2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/WT1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/WT-Myc3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evTDP-43-Q331K-Myc2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evTDP-43-Q331K2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evTDP-43-Q331K-Cherry3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/TDP-43-Q331K-Myc3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/WT-Cherry3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/TDP-43-Q331K3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/WT-Myc2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evWT-Cherry3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evTDP-43-Q331K1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evTDP-43-Q331K-Myc1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/evWT-Myc1.raw"],"Mzid":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/Vesicles.mzid","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD064120/Lysate.mzid"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["manuela.basso@unitn.it"],"submitter":["Romina Belli"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":[""],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD064120"],"tissue":["Primary Cerebral Cortical Neuron�"],"sample_protocol":["For proteomic analysis, extracellular vesicles (EVs) were isolated from 72 mL of conditioned media collected from primary astrocytes cultured from C57BL/6 mouse pups (P0–P2), either wild-type or transgenic for the human TDP-43Q331K mutation, with at least three biological replicates per condition. EVs were isolated as previously described, with the only modification being the omission of the 10,000 g centrifugation step to allow simultaneous isolation of both large and small vesicles. Primary astrocytes were resuspended in lysis buffer (2% SDS, 50 mM HEPES, 500 units/mL Benzonase) and incubated for 30 minutes at 4°C. Samples were then boiled for 5 minutes and clarified by centrifugation at 14,000 g for 15 minutes. EVs derived from astrocytes were lysed in RIPA buffer for 30 minutes at 4°C. Samples were then adjusted to a final concentration of 1% SDS and 100 mM ammonium bicarbonate (NH₄HCO₃), and sonicated at 4°C for 10 minutes using a Q700 Sonicator (30 s on/30 s off, amplitude 35). Total protein content in cell and EV lysates was quantified using a BCA assay. Cell lysates (30 μg) and EV lysates (10 μg) were reduced and alkylated by adding 10 mM DTT and 22.5 mM iodoacetamide (IAA), and incubating for 30 minutes at 37°C. Excess IAA was quenched with an additional 10 mM DTT. Protein digestion was performed using a 1:1 ratio of magnetic carboxylate-modified beads (GE Healthcare), as previously described. Briefly, washed beads were added to the samples at a ratio of 10 µg of beads per 1 µg of protein. Acetonitrile (ACN) was added to a final concentration of 70% (v/v), and samples were incubated at room temperature for 18 minutes. Supernatants were removed, and the beads were washed twice with 70% ethanol and once with ACN (200 µL each). Beads were then resuspended in 45 μL of 50 mM NH₄HCO₃ and 5 mM CaCl₂, supplemented with 1 µg of trypsin. Following overnight digestion at 37°C, peptides were collected using a magnetic rack. EV samples underwent an additional detergent removal step using HiPPR resin (Thermo Scientific) to improve cleanup of SDS and lipids. Peptides were transferred to fresh tubes, acidified with 1% trifluoroacetic acid, desalted using C18 stage tips, lyophilized, and resuspended in 0.1% formic acid for LC-MS/MS analysis.  For the LCMS analysis, peptides were separated on an Easy-nLC 1200 HPLC system (Thermo Scientific). A 28 cm reversed-phase column (inner diameter 75 µm packed in-house with ReproSil-Pur C18-AQ material: 3µm particle size, Dr. Maisch, GmbH), heated at 40°C, was used for separating the peptides, with a two-component mobile phase system of 0.1% formic acid in water (buffer A) and 0.1% formic acid in 80% acetonitrile (buffer B). The peptides were then eluted using a gradient from 5% to 25% over 52 minutes, followed by 25% to 40% over 8 minutes, and 40% to 98% over 10 minutes at a flow rate of 200 nL/min. The peptides were analyzed on an Orbitrap Fusion Tribrid mass spectrometer (Thermo Fisher Scientific) in data-dependent mode, with the full scans performed at a resolving power of 120.000 FWHM (mass range: 350–1100 m/z, AGC target value: 1x10e6 ions, maximum injection time: 50 ms). Each full scan was followed by a set of (HCD) MS/MS scans within a 3 sec cycle time, with a collision energy of 30%. Fragment data were acquired in the ion trap mass analyzer (AGC target: 5e4 ions, maximum injection time: 150 ms). The Ion transfer tube temperature was set at 275°C. Dynamic exclusion was enabled and set to 40 sec, with a mass tolerance of 5 ppm."],"repository":["Pride"],"modification":[""],"quantification_method":["Not available"],"data_protocol":["All proteomic data were searched against the in-silico digested UniProt Mus musculus database (downloaded in April 2021) with major known contaminants and reversed versions of each sequence. Proteome Discoverer v.2.2.0 (Thermo Scientific) and MASCOT search engine (v.2.6.2, MatrixScience) were used to identify proteins (precursor mass tolerance: 10 ppm, product mass tolerance: 0.6 Da). Trypsin/P was chosen as the enzyme with 5 missed cleavages. Static modification of carbamidomethyl (C) and variable modification of oxidation (M) and N-terminal protein acetylation were incorporated in the search. FDR was set to < 0.01 for both peptides and proteins. Contaminants were filtered out.  Peptide intensities were log2 transformed, normalized (median normalization), and summarized into proteins (median sweeping) with functions in the DEqMS Bioconductor package 147. Imputation of the missing intensities was executed by the functions scImpute and tImpute from PhosR package 148. Differential analysis was performed with the DEqMS package, proteins with absolute log 2 FC ≥ 0.75 and P-value ≤ 0.05 were considered significant. To perform proteomics data functional enrichment analysis, we took advantage of the gseGO function from the clusterProfiler package 149. The GSEA plots were created with the R package enrichplot (https://yulab-smu.top/biomedical-knowledge-mining-book/)."],"omics_type":["Proteomics"],"labhead":["Manuela Basso"],"instrument_platform":[""],"labhead_affiliation":["Laboratory of neurobiology and pathology, Department of Cellular, Computational and Integrative Biology (DeCIBIO), University of Trento, Italy"],"submission_type":["COMPLETE"],"species":["Mus Musculus (mouse)"],"publication":["41004427 Fioretti PV, Barbieri A, Migazzi A, Bressan D, Grassano M, Donini L, Roccuzzo M, Torrieri MC, Conci F, Ferracci E, Invernizzi S, Bowden KM, Bacchetti F, Cappelli S, Peroni D, Belli R, Pancher M, Mugoni V, Scarduelli G, Gianesello M, Pasetto L, Canarutto G, Carra S, Soldano A, Bisio A, Robbiati S, Valentini C, Nardella C, Piazza S, D'Agostino VG, Quattrone A, Sleiman S, Whitfield JR, Soucek L, Vignoli B, Viero G, Tiberi L, Zippo A, Demichelis F, Bonetto V, Milanese M, Buratti E, Verde F, Ticozzi N, Calvo A, Ratti A, Shaw PJ, Terenzio M, Chiacchiera F, Pennuto M, Basso M. MYC-driven gliosis impairs neuron-glia communication in amyotrophic lateral sclerosis. Brain. 2026 149(5):1604-1622 10.1093/brain/awaf360"],"submitter_mail":["romina.belli@unitn.it"],"submitter_affiliation":["University of Trento"],"submitter_country":["Italy"],"doi":["10.6019/PXD064120"],"pubmed_abstract":["Chronic activation of glial cells leads to the dysfunction and degeneration of motor and cortical neurons in amyotrophic lateral sclerosis and frontotemporal dementia with an unknown mechanism. To shed light on the molecular pathogenetic processes underlying the exordium and contribution of gliosis to disease onset and progression, we used cells, mice and patient-derived cells modelling TDP-43, SOD1 and C9ORF72-linked and sporadic ALS. Our data reveal a sequential disease progression, starting with enhanced glial reactivity and proliferation, and transitioning into inflammation with upregulation of pro-inflammatory genes. Using mouse genetics, we show that expression of mutant TDP-43 in astrocytes is necessary to cause gliosis and behavioural abnormalities. Mechanistically, we show that glial MYC gain-of-function drives neurodegeneration by promoting the release of astrocyte-derived extracellular vesicles that nonetheless fail to provide trophic support to surrounding neurons. Our research reveals a novel functional role for MYC in glia-to-neuron miscommunication in ALS."],"pubmed_title":["MYC-driven gliosis impairs neuron-glia communication in amyotrophic lateral sclerosis."],"pubmed_authors":["Fioretti Paolo V PV, Barbieri Anna A, Migazzi Alice A, Bressan Davide D, Grassano Maurizio M, Donini Luisa L, Roccuzzo Michela M, Torrieri Maria Claudia MC, Conci Francesca F, Ferracci Elisa E, Invernizzi Sabrina S, Bowden Katie M KM, Bacchetti Francesca F, Cappelli Sara S, Peroni Daniele D, Belli Romina R, Pancher Michael M, Mugoni Vera V, Scarduelli Giorgina G, Gianesello Matteo M, Pasetto Laura L, Canarutto Giulia G, Carra Serena S, Soldano Alessia A, Bisio Alessandra A, Robbiati Sergio S, Valentini Chiara C, Nardella Caterina C, Piazza Silvano S, D'Agostino Vito G VG, Quattrone Alessandro A, Sleiman Sama S, Whitfield Jonathan R JR, Soucek Laura L, Vignoli Beatrice B, Viero Gabriella G, Tiberi Luca L, Zippo Alessio A, Demichelis Francesca F, Bonetto Valentina V, Milanese Marco M, Buratti Emanuele E, Verde Federico F, Ticozzi Nicola N, Calvo Andrea A, Ratti Antonia A, Shaw Pamela J PJ, Terenzio Marco M, Chiacchiera Fulvio F, Pennuto Maria M, Basso Manuela M"],"additional_accession":[]},"is_claimable":false,"name":"Astrogliosis and miscommunication in ALS","description":"Chronic activation of glial cells leads to the dysfunction and degeneration of motor and cortical neurons in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) with an unknown mechanism. To shed light on the molecular pathogenetic processes underlying the exordium and contribution of gliosis to disease onset and progression, we used cells, mice, and patient-derived cells modeling TDP-43, SOD1, and C9orf72-linked and sporadic ALS. We identify an initial phase of the disease marked by increased astrocyte proliferation, followed by a typical activation stage with elevated expression of pro-inflammatory genes. Using mouse genetics, we show that expression of mutant TDP-43 in astrocytes is necessary to cause gliosis and behavioral abnormalities. Mechanistically, we show that c-Myc gain-of-function drives astrocyte proliferation by promoting the release of EVs that nonetheless fail to provide trophic support to surrounding neurons. Our research reveals a novel functional role for c-Myc in astrocytes in the miscommunication from glia to neurons in ALS.","dates":{"publication":"2026-06-29","submission":"2025-05-20"},"accession":"PXD064120","cross_references":{"TAXONOMY":["NEWT:68239","NEWT:108018","NEWT:377960","NEWT:1131","NEWT:190486","NEWT:2042546","NEWT:148942","NEWT:295546","NEWT:258594","NEWT:1126","NEWT:1129","NEWT:89187","NEWT:309807","NEWT:89184","NEWT:309800","NEWT:1323429","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:592321","NEWT:1073882","NEWT:6819","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:10034","NEWT:661410","NEWT:488003","NEWT:224326","NEWT:376619","NEWT:3765","NEWT:3767","NEWT:433727","NEWT:135622","NEWT:672127","NEWT:656061","NEWT:37965","NEWT:656064","NEWT:3760","NEWT:36630","NEWT:381198","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:44250","NEWT:317447","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:1562698","NEWT:12637","NEWT:2164133","NEWT:2767846","NEWT:1343074","NEWT:314344","NEWT:108061","NEWT:224308","NEWT:49928","NEWT:160621","NEWT:110368","NEWT:1916073","NEWT:1310161","NEWT:1230383","NEWT:77133","NEWT:1310165","NEWT:114727","NEWT:5516","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:1310173","NEWT:37919","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:419481","NEWT:5507","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:1143","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:709964","NEWT:3712","NEWT:3711","NEWT:3714","NEWT:65121","NEWT:3715","NEWT:2065263","NEWT:1549675","NEWT:177437","NEWT:9014","NEWT:10891","NEWT:226126","NEWT:1616117","NEWT:34865","NEWT:28174","NEWT:550537","NEWT:284812","NEWT:3701","NEWT:3702","NEWT:1245466","NEWT:3704","NEWT:1246791","NEWT:9005","NEWT:34871","NEWT:9006","NEWT:33548","NEWT:1883426","NEWT:657321","NEWT:10886","NEWT:3708","NEWT:536231","NEWT:219813","NEWT:215451","NEWT:460519","NEWT:272844","NEWT:1348799","NEWT:55784","NEWT:485","NEWT:2709072","NEWT:2499525","NEWT:142786","NEWT:2853422","NEWT:487","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:216778","NEWT:376686","NEWT:237610","EFO:0001352","NEWT:219809","NEWT:219808","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:141469","NEWT:272831","NEWT:987059","NEWT:491","NEWT:460523","NEWT:85694","NEWT:85692","NEWT:911045","NEWT:3750","NEWT:291146","NEWT:29466","NEWT:233271","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:278161","NEWT:415978","NEWT:410289","NEWT:191701","NEWT:9054","NEWT:472","NEWT:29459","NEWT:1380096","NEWT:28128","NEWT:470","NEWT:41122","NEWT:1328300","NEWT:748693","NCBITaxon:50557","NEWT:3735","NEWT:29491","NEWT:911022","NEWT:446","NEWT:153481","NEWT:445","NEWT:2003758","NEWT:63366","NEWT:63367","NEWT:29488","NEWT:215402","NEWT:3726","NEWT:30455","NEWT:28141","NEWT:9030","NEWT:9031","NEWT:3728","NEWT:108931","NEWT:219799","NEWT:219798","NEWT:548","NEWT:150475","NEWT:256737","NEWT:51350","NEWT:8694","NEWT:8692","NEWT:542","NEWT:394503","NEWT:13076","NEWT:219785","NEWT:451515","NEWT:8673","NEWT:550","NEWT:10804","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:42410","NEWT:1225786","NEWT:771870","NEWT:8665","NEWT:51338","NEWT:9995","NEWT:28112","NEWT:49012","NEWT:28110","NEWT:10832","NEWT:311339","NEWT:507601","NEWT:520","NEWT:64657","NEWT:186441","NEWT:2585209","NEWT:643680","NEWT:214092","NEWT:40697","NEWT:13095","NEWT:162425","NEWT:242124","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:595495","NEWT:80833","NEWT:479096","NEWT:28108","NEWT:28104","NEWT:1114957","NEWT:568703","NEWT:568708","NEWT:52641","NEWT:353152","NEWT:353153","NEWT:227377","NEWT:1774284","NEWT:27689","NEWT:207769","NEWT:40674","NEWT:51329","NCBITaxon:1763","NEWT:443906","NEWT:13037","NEWT:519","NEWT:7394","NEWT:6063","NEWT:404330","NEWT:1328388","NEWT:13064","NEWT:300641","NEWT:39655","NEWT:38323","NEWT:206411","NEWT:80869","NEWT:214053","NEWT:80863","NEWT:665890","NEWT:52639","NEWT:52638","NEWT:8697","NEWT:861109","NEWT:8695","NEWT:1196866","NEWT:6039","NEWT:510516","NEWT:1045775","NEWT:1123869","NCBITaxon:1335626","NEWT:7370","NEWT:83906","NEWT:99488","NEWT:1134506","NEWT:255470","NEWT:762903","NEWT:27697","NEWT:86185","NEWT:9935","NEWT:266940","NEWT:287889","NEWT:1028307","NEWT:52603","NEWT:92867","NEWT:92866","NEWT:1344414","NEWT:202950","NEWT:741158","NEWT:1293091","NEWT:202956","NEWT:315750","NEWT:632957","NEWT:9925","NCBITaxon:9606","NEWT:1436183","NEWT:1479235","NEWT:4232","NEWT:9922","NEWT:416348","NEWT:105812","NEWT:11298","NEWT:4233","NEWT:4236","NEWT:398031","NEWT:196627","NEWT:523840","NEWT:1076878","NEWT:200308","NEWT:200302","NEWT:9913","NEWT:9915","NEWT:105841","NEWT:1170227","NEWT:2666255","NEWT:999810","NEWT:28995","NEWT:1392998","NEWT:1150621","NEWT:1085791","NEWT:745531","NEWT:226900","NEWT:231490","NEWT:590651","NEWT:449239","NEWT:244704","NEWT:9909","NEWT:9902","NEWT:430615","NEWT:563041","NEWT:36599","NEWT:41949","NEWT:9900","NEWT:326423","NEWT:326424","NEWT:13013","NEWT:749906","NEWT: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