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Kadri"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"disease":["Idiopathic Pulmonary Fibrosis"],"software":[""],"submitter_keywords":["Human lung fibroblast"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD063448"],"tissue":["Cell Culture","Fibroblast"],"sample_protocol":["Phosphoproteome sample preparation CytoSoft 6-well dishes (Advanced BioMatrix, Inc. San Diego, CA) with elastic modules 0.2, 0.5, 2, 8, 16 and 32 kPa or normal plastic dishes were coated with 10 µg/ml fibronectin (FN) 1h, RT. 500,000 cells were seeded per well for 120 min and lysed in 1 ml guanidinium chloride (GdmCl) lysis buffer (6 M GdmCl, 100 mM Tris pH 8.5, 10 mM Tris (2-carboxyethyl)phosphine (TCEP), 40 mM 2-chloroacetamide (CAA)).  Collected lysates were heated for 5 min, 95 °C. Lysates were cooled on ice for 15 min, sonicated with Bioruptor (Diagenode Inc., Denville, NJ) at maximum energy for 10 x 30 sec cycles and heated again for 5 min, 95 °C.  Protein lysates were diluted 1:2 with water. Proteins were precipitated o.n. with 4 x volume of ice-cold acetone. Proteins were collected by centrifugation for 10 min at 4,000 g (4°C). Pellets were washed twice with ice-cold 80 % acetone, and air dried for 10 min, RT. Pellets were resuspended in 500 µL 2,2,2-trifluoroethanol (TFE) digestion buffer (10% TFE, 100 mM ammonium bicarbonate) with sonication in Bioruptor at maximum energy for 10 x 30 sec cycle or until a homogenous suspension was formed. Phosphopeptides were enriched according to the protocol as previously described (Humphrey et al, 2015)). Briefly, samples were digested overnight in 500 μl TFE digestion buffer. A first digestion was carried out with Lys-C 1:100 enzyme-to-protein ratio (wt/wt) at 37°C for 1h, 2,000 rpm, 37°C, followed by trypsin digestion o.n., 2,000 rpm, 37°C. 150 μl 3.2 M KCl, 55 μl 150 mM KH2PO4, 800 μl acetonitrile (ACN) and 95 μl trifluoroacetic acid (TFA) were added to the digested peptides. Peptides were mixed for 1 min, 2,000 rpm, RT, cleared by centrifugation and transferred to a clean 2 ml 96-well deep-well plate (DWP, Eppendorf, Hamburg, Germany). TiO2 beads (Titansphere® Phos-TiO Bulk 10 µm, GL Science Inc., Tokyo, Japan, #5010-21315) were subsequently added to peptides at a ratio of 1:10 beads/protein, suspended in 80 % ACN/6% TFA, and incubated  for 5 min, 2,000 rpm, 40 °C. Beads were pelleted by centrifugation for 1 min, 3,500 g, and the supernatant (containing non-phosphopeptides) was aspirated and discarded. Beads were suspended in wash buffer (60% ACN, 1% TFA) and transferred to a clean 2 ml DWP, and washed a further four times with 1 ml of wash buffer. After the final wash, beads were suspended in 100 μl transfer buffer (80 % ACN, 0.5% acetic acid), transferred onto the top of a C8 StageTip, and centrifuged for 3–5 min, 500 g or until no liquid remained on the StageTips. Bound phosphopeptides were eluted 2 times with 30 μl elution buffer (40 % ACN, 15 % NH4OH (25 %, HPLC grade)) each and collected by centrifugation into clean PCR tubes (Eppendorf). Samples were concentrated in a SpeedVac for 15 min, 45 °C and acidified with 10 μl 10 % TFA.  StageTip desalting of peptides and phosphopeptides Peptides were loaded onto styrenedivinylbenzene–reversed phase sulfonated (SDB-RPS; 3M Empore) StageTips in 100 μl SDB-RPS wash buffer (0.2 % TFA), and centrifuged for 3 min at 500 g or until ≤ 5 μl remained. StageTips were washed with a further 100 μl SDB-RPS wash buffer, and phosphopeptides were subsequently eluted with 60 μl SDB-RPS elution buffer (80 % ACN, 5 % NH4OH (25 %, HPLC grade)) into clean tubes by centrifugation for ~5 min at 500 g. Samples were immediately concentrated in a SpeedVac for 30min at 45 °C, or until ~2 μl remained. 7 μl MS loading buffer (2 % ACN, 0.3 % TFA) was added. Single-run MS/MS measurement Peptides were loaded onto a 40cm column with a 75 μM inner diameter, packed in-house with 1.9μM C18 ReproSil particles (Dr. Maisch GmbH). Column temperature was maintained at 50°C using a homemade column oven. An EASY-nLC 1000 system (Thermo Fisher Scientific) was connected to the mass spectrometer with a nanospray ion source, and peptides were separated with a binary buffer system of 0.1% formic acid (buffer A) and 60% ACN plus 0.1% formic (buffer B), at a flow rate of 300nl/min. Peptides were eluted with a gradient of 5–25% buffer B over 85 or 180min followed by 25–50% buffer B over 35 or 60min, resulting in ~2- or 4h gradients respectively. Peptides were analyzed on a Q Exactive benchtop Orbitrap mass spectrometer (Thermo Fisher Scientific), with one full scan (300–1,600 m/z, R = 60,000 at 200 m/z) at a target of 3e6 ions, followed by up to five data-dependent MS/MS scans with higher-energy collisional dissociation (HCD) (target 1e5 ions, max ion fill time 120ms, isolation window 1.6m/z, normalized collision energy (NCE) 25%, underfill ratio 40%), detected in the Orbitrap (R = 15,000 at 200 m/z). Dynamic exclusion (40s or 60s) and apex trigger (4 to 7s) were enabled."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["MS raw files were processed using MaxQuant Version 1.5.3.34. The spectra were searched with the Andromeda search engine using a false discovery rate (FDR) of < 0.01 on the protein level as well as on the peptide and modification level. In general, the default settings of MaxQuant were used but with following changes. Methionine (M), acetylation (protein N-terminus) and phosphorylation (STY) were selected as variable modification. Carbamidomethyl (C) was selected as fixed modification. Furthermore, only peptides with a minimal length of seven amino acids were taken into account. The ‘match between runs’ option was turned on using a matching time window of 0.7 minutes. Peptide and protein identification was done by using the UniProt database from human (April, 2018) which contained 20,138 entries. Each raw file was handled as one experiment. For the rigidity phosphoproteomic dataset replicate 1 of 0.5 kP was removed for the final analysis because of low identification number and outlier clustering within the replicates. Exactly the same was done with the phosphoproteomic spreading data set. Here the following replicates were not considered for the final analysis: replicate 2 of 20 min and replicate 4 of 30 min."],"omics_type":["Proteomics"],"labhead":["Herbert Schiller"],"instrument_platform":[""],"labhead_affiliation":["Research Unit for Precision Regenerative Medicine, Helmholtz Munich, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, Munich, Germany"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["safouane.kadri@helmholtz-muenchen.de"],"publication":["Not available"],"submitter_affiliation":["Helmholtz-Muenchen"],"submitter_country":["Germany"],"additional_accession":[]},"is_claimable":false,"name":"Phosphoproteomics of cellular mechanosensing reveals NFATC4 as a regulator of myofibroblast activity","description":"Feedback connections between tissue stiffness and cellular contractile forces can instruct cell identity and activity via a process referred to as mechanosensing. Specific phosphoproteome changes during mechanosensing are poorly characterized. In this work, we chart the global phosphoproteome dynamics of primary human lung fibroblasts sensing the stiffness of injury relevant fibronectin coated Poly(dimethylsiloxane) substrates. We discovered a key signaling threshold at a Young's modulus of eight kPa stiffness, above which cells activated a large number of pathways including RhoA, CK2A1, PKA, AMPK, AKT1, and Hippo-YAP1/TAZ mediated signaling. Time-resolved phosphoproteomics of cell spreading on stiff substrates revealed the temporal dynamics of these stiffness-sensitive signaling pathways. ECM substrate stiffness above eight kPA induced fibroblast contractility, cytoskeletal rearrangements, ECM secretion, and a fibroblast to myofibroblast transition. Our data indicate that phosphorylation of the transcriptional regulator NFATC4 at S213/S217 enhances myofibroblast activity, which is the key hallmark of fibrotic diseases. NFATC4 knock down cells display reduced stiffness induced collagen secretion, collagen gel contraction, and cell invasion, suggesting NFATC4 as a novel target for antifibrotic therapy.","dates":{"publication":"2026-06-02","submission":"2025-04-29"},"accession":"PXD063448","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:241368","NEWT:2","NEWT:157546","NEWT:190802","NEWT:35554","NEWT:9778","NEWT:150475","NEWT:9417","NEWT:347515","NEWT:1216979","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:5180","NEWT:256737","NEWT:2042546","NEWT:115104","NEWT:1081927","NEWT:67825","NEWT:43179","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:55153","NEWT:1736309","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:415540","NEWT:4081","NEWT:876138","NEWT:554","NEWT:98334","NEWT:426428","NEWT:237561","NEWT:6928","NEWT:10036","NEWT:7574","NEWT:1351","NEWT:7215","NEWT:272563","NEWT:507601","NCBITaxon:79857","NCBITaxon:6157","NEWT:95648","NEWT:3885","NEWT:746360","NEWT:6239","NEWT:1589","NEWT:470150","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:4054","NEWT:3880","NEWT:3641","NEWT:8782","NEWT:1263854","NEWT:1000589","NEWT:1902","NEWT:85962","NEWT:160488","NEWT:28104","NEWT:317447","NEWT:7955","NCBITaxon:2","NEWT:985076","NEWT:7959","NEWT:2261","NEWT:4565","NEWT:1264690","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:216595","NEWT:243230","NEWT:8355","NEWT:1283","NEWT:931281","NEWT:7029","NEWT:1283300","NEWT:6183","NEWT:334747","NEWT:61235","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:436486","NEWT:6287","NEWT:2242","NEWT:300641","NEWT:4784","NEWT:727","NEWT:9796","NEWT:725","NEWT:360106","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10239","NCBITaxon:6191","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:1735272","NEWT:83334","NEWT:185431","NEWT:83332","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:44685","NEWT:2697049","NEWT:1148","NEWT:11676","NEWT:55571","NEWT:100226","NCBITaxon:6073","NEWT:4530","NEWT:4896","NEWT:6279","NEWT:1123869","NEWT:7370","NEWT:75058","NEWT:83906","NEWT:607699","NEWT:6282","NEWT:208964","NEWT:1134506","NEWT:575584","NEWT:1773","NEWT:38783","NEWT:8727","NEWT:1895","NEWT:1182590","NEWT:8726","NEWT:6669","NEWT:10090","NEWT:935293","NEWT:64152","NEWT:749200","NEWT:4120","NEWT:51515","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:990346","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:230741","NEWT:284812","NCBITaxon:10359","NCBITaxon:1313","NEWT:43330","NEWT:242619","NEWT:44544","NEWT:632957","NEWT:373995","NEWT:5689","NEWT:645463","NEWT:544404","NEWT:3702","NEWT:129249","NEWT:9925","NEWT:8839","NEWT:4232","NEWT:990119","NEWT:2758385","NEWT:4113","NEWT:837","NEWT:11298","NEWT:171101","NEWT:196627","NEWT:408172","NEWT:5691","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:627025","NEWT:400772","NEWT:1097677","NEWT:3708","NEWT:128161","NEWT:106592","NEWT:1117957","NEWT:9913","NEWT:1432138","NEWT:10312","NEWT:1424507","NEWT:4100","NEWT:1076","NEWT:6763","NEWT:803","NEWT:8030","NEWT:29722","NEWT:380394","NEWT:1692259","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:180066","NEWT:67767","NEWT:46835","NEWT:135588","NEWT:1843183","NEWT:95486","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:5664","NEWT:2157","NEWT:146479","NEWT:10306","NEWT:1911079","NEWT:8022","NEWT:145943","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:1480154","NEWT:1274414","NEWT:59202","NEWT:9975","NEWT:3197","NEWT:9615","NEWT:10299","NEWT:860688","NEWT:884019","NEWT:169963","NEWT:36329","NEWT:1147787","NEWT:72407","NEWT:9606","NEWT:367830","NEWT:157295","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:915099","NEWT:74940","NEWT:1450511","NEWT:360094","NEWT:470","NEWT:84023","NEWT:9838","NCBITaxon:9615","NEWT:58334","NEWT:1193501","NEWT:3055","NEWT:6326","NEWT:6689","NEWT:2762","NEWT:5476","NEWT:1174673","NEWT:562","NEWT:33952","NEWT:1274432","NEWT:1274426","NEWT:1423","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:1274423","NEWT:3603","NEWT:698936","NEWT:2759","NEWT:3847","NEWT:39946","NEWT:9823","NEWT:9940","NEWT:327160","NEWT:573","NEWT:9031","NEWT:1274420","NEWT:7091"],"ORCID":["0000-0003-1710-9275"]}}