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iacobucci"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"disease":["Aortic Valve Stenosis"],"software":[""],"submitter_keywords":["Extracellular matrix remodeling  proteomics","Calcific aortic valve disease","Collagen post-translational modifications","Aortic valve stenosis"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD073246"],"tissue":["Heart"],"sample_protocol":["The valves were crushed in liquid nitrogen to obtain a fine powder. A minimum of approximately 30 mg of powder was weighed for each sample. Subsequently, 20 µl of a decalcification solution (0.5 M EDTA pH=8 and protease inhibitors) was added and the samples were left overnight at 4°C, to chelate Ca2+ cations present in the tissue. To obtain the protein extracts, cell lysis was performed using a lysis buffer (5% sodium dodecyl sulphate, 50mM ammonium bicarbonate) and crushing for 10 minutes at low temperature with a pestle. Then, the sample was sonicated and centrifuged at 13,000rpm for 30 minutes at 20°C. The supernatants, containing the protein extract, have been collected and each protein lysate was quantified with BCA assay (Thermo Fisher Scientific, Waltham, MA, USA), following the manufacturer instructions. Proteins were digested using a shotgun proteomics approach onto micro S-Trap columns (Protifi), as previously reported  . For Data-Dependent Acquisition (DDA) was used a linear gradient of eluent B (0.2% formic acid in 95% acetonitrile) in A (0.2% formic acid and 2% acetonitrile in LC-MS grade water) from 2% to 90% in 73 minutes with the following set up: 1) scan spectrum spanned from 300 to 1800 m/z, 2) top 20 ions in each scan were selected for the fragmentation, 3) 45s for the dynamic exclusion window."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["To determine the levels of prolines hydroxylation and Asn/Gln deamidation, samples were analyzed in Data-Dependent Acquisition DDA and processed with MaxQuant using a database containing only collagen-related protein family, and by selecting hydroxyproline modificationand N/Q deamidation as variable modification in two independent run. The parameters selected for protein identification were minimum 4 peptides, at least 2 unique and 1% FDR was applied. Statistically significant hydroxyproline peptides were evaluated using Perseus software version 1.6.15.0, applying a statistical filter based on Student’s t-test (5% FDR). To assess the significance of modification variation between severe and control data plotted in Figure 6, two-way ANOVA with Bonferroni multiple comparisons test were performed. To investigate the presence of dysregulated semitryptic peptides, samples, analyzed in DDA mode, were processed with Proteome Discoverer  using a human extracellular matrix protein database downloaded by MatrixDB and converted to a FASTA   file with Uniprot UniProt ID mapping tool. The parameters selected for protein identification were minimum 3 peptides, at least 1 unique and a false discovery rate (FDR) of 0.01 was applied. Protein and peptide groups were analyzed with Perseus software to highlight statistically varying peptides, applying a statistical Student’s t-test (FDR= <0.05)."],"omics_type":["Proteomics"],"labhead":["Maria Monti"],"instrument_platform":[""],"labhead_affiliation":["University of Naples Federico II and CEINGE Biotecnoloige Avanzate \"Franco Salvatore\""],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["iacobucci@ceinge.unina.it"],"publication":["42104263 Iacobucci I, Monaco V, Lobianco AL, Cipolletta B, Birolo L, Conte M, Myasoedova VA, Valerio V, Poggio P, Parisi V, Monti M. Proteomic and degradomic signatures of extracellular matrix remodeling in calcific aortic valve stenosis. Mol Med. 2026 10.1186/s10020-026-01499-0"],"submitter_affiliation":["Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy \nCEINGE Advanced Biotechnologies, University of Naples Federico II, Naples 80145, Italy"],"submitter_country":["Italy"],"pubmed_abstract":["<h4>Background</h4>Aortic stenosis is a progressive fibro-inflammatory valvular disorder with major clinical burden and no disease-modifying pharmacological therapy. Defining molecular circuits associated with thrombo-inflammatory activation to extracellular matrix remodeling may enable future therapeutic targeting and biomarker development.<h4>Methods</h4>Human aortic valves explanted from patients with severe aortic stenosis and non-stenotic surgical controls (aortic regurgitation) were profiled using a multi-layer mass spectrometry strategy. Global protein changes were quantified by label-free proteomics (data-independent acquisition). Extracellular matrix proteolysis was interrogated using an extracellular matrix-focused semi-tryptic peptide workflow. Collagen qualitative remodeling was assessed by mapping hydroxyproline enrichment. Differential abundance was evaluated using multiple-testing correction (false discovery rate). Selected candidates were validated by targeted multiple reaction monitoring, and elastin integrity was assessed histologically.<h4>Results</h4>We identified 594 significantly modulated proteins in severe aortic stenosis, with predominant upregulation of complement/coagulation and extracellular matrix-related pathways. Targeted Multiple Reaction Monitoring confirmed key thrombo-inflammatory and matrix-associated candidates. Semi-tryptic profiling revealed a focused extracellular matrix degradomic signature dominated by small leucine-rich proteoglycans (decorin, lumican, PRELP), fibrillin-1, and collagen VI, consistent with preferential proteolytic targeting of structural matrix scaffolds. Histology showed marked elastin fragmentation in stenotic leaflets. Collagen post-translational modification analysis revealed increased hydroxyproline- bearing peptides across selected collagen chains despite minimal changes in total collagen abundance, indicating qualitative remodeling beyond protein accumulation.<h4>Conclusions</h4>An integrated proteomic-degradomic-post-translational modification framework reveals concomitant thrombo-inflammatory activation to matrix breakdown and qualitative collagen remodeling in severe aortic stenosis, highlighting molecular circuits that may inform future biomarker development and therapeutic target discovery."],"pubmed_title":["Proteomic and degradomic signatures of extracellular matrix remodeling in calcific aortic valve stenosis."],"pubmed_authors":["Iacobucci Ilaria I, Monaco Vittoria V, Lobianco Alessia Lubrano AL, Cipolletta Brunella B, Birolo Leila L, Conte Maddalena M, Myasoedova Veronika A VA, Valerio Vincenza V, Poggio Paolo P, Parisi Valentina V, Monti Maria M"],"additional_accession":[]},"is_claimable":false,"name":"Proteomic and degradomic signatures of extracellular matrix remodeling in calcific aortic valve","description":"Calcific aortic valve disease (CAVD) is the most common valvular heart disease in older adults, but no medical therapy is currently able to halt or reverse its progression, partly because the molecular mechanisms of valve remodeling remain incompletely understood. Here, we aimed to dissect the extracellular matrix (ECM)-centered mechanisms altered in CAVD by integrating untargeted and targeted proteomics, degradomics, collagen post-translational modification (PTM) mapping, and histology in human aortic valves. We analyzed valvular tissue from patients with severe aortic stenosis (n = 10) and non-stenotic controls (n = 9) using data-independent acquisition (DIA) LC–MS/MS, followed by Gene Ontology enrichment, semi-tryptic peptide profiling, hydroxyproline-focused PTM analysis, Multiple Reaction Monitoring (MRM) validation, and elastin staining. DIA proteomics quantified 1,971 proteins and identified 462 significantly modulated in severe CAVD, revealing a landscape dominated by complement activation, coagulation and fibrinolysis, humoral immune response, and extensive ECM organization and wound-healing programs, alongside down-regulation of biosynthetic and metabolic pathways. A degradomic-like analysis of 1,564 semi-tryptic peptides, filtered to exclude proteins with overall abundance changes, yielded 11 preferential ECM substrates, forming a highly interconnected network enriched in small leucine-rich proteoglycans (decorin, lumican, PRELP), microfibrillar components (fibrillin-1), and collagen VI, with fibrinogen and complement C1s bridging toward the thrombo-inflammatory milieu. Collagen-specific PTM mapping demonstrated a marked increase in hydroxyproline-containing peptides in several fibrillar and non-fibrillar collagen chains, despite largely unchanged or even reduced total collagen abundance, indicating qualitative remodeling with enhanced collagen maturation and potential ECM stiffening rather than simple protein accumulation. Histological assessment using Verhoeff–Van Gieson staining confirmed prominent elastin rarefaction and fragmentation with collagen-rich replacement in stenotic cusps. MRM validation of a focused panel of coagulation, complement, and ECM-related proteins (including F2, F9, F10, C3, KNG1, FGG, KLKB1, ACAN, EMILIN1, and HTRA1) corroborated their up-regulation in diseased valves. Together, these multi-layer data support a model in which CAVD is driven by an ECM-centered, thrombo-inflammatory remodeling process characterized by selective proteolysis of key structural matrix components, collagen PTM dysregulation, and loss of elastin integrity. This integrated “structural–degradomic–PTM” signature may provide a basis for developing tissue and circulating biomarkers of disease activity and for identifying novel targets to modulate matrix remodeling in calcific aortic valve disease.","dates":{"publication":"2026-05-29","submission":"2026-01-19"},"accession":"PXD073246","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:6703","NEWT:3555","NEWT:71647","NEWT:2","NEWT:157546","NEWT:474186","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:1496","NEWT:544496","NEWT:2102","NEWT:2042546","NEWT:259447","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:180454","NEWT:5722","NEWT:1247","NEWT:6938","NEWT:1129","NEWT:376741","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:281395","NEWT:10360","NEWT:1211601","NEWT:876138","NEWT:47664","NEWT:317548","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:272563","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:82688","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:5821","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:28903","NEWT:3880","NEWT:272559","NEWT:28909","NEWT:515849","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:143361","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4442","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NEWT:2164133","NCBITaxon:183674","NEWT:224308","NEWT:167387","NEWT:84645","NEWT:44586","NEWT:626528","NEWT:3347","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:211586","NEWT:747078","NEWT:1282","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:294381","NEWT:197","NEWT:1390363","NEWT:77133","NEWT:288705","NEWT:29176","NEWT:145481","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:556182","NEWT:1270","NEWT:374990","NEWT:1392","NEWT:498217","NEWT:156471","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:156476","NEWT:286","NEWT:391619","NEWT:360104","NEWT:246196","NEWT:287","NEWT:246197","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:161934","NEWT:1148","NEWT:580240","NEWT:5508","NEWT:294128","NEWT:5507","NEWT:11676","NEWT:55571","NEWT:35500","NEWT:1140","NEWT:100226","NEWT:4530","NEWT:1143","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:1336795","NEWT:172","NEWT:644042","NEWT:296543","NEWT:316435","NEWT:42157","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:1034304","NEWT:105023","NEWT:866628","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:9378","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NEWT:8175","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:47946","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:1077286","NEWT:243277","NEWT:990119","NEWT:2850","NEWT:408172","NEWT:227321","NEWT:408170","NEWT:493760","NEWT:106590","NEWT:260710","NEWT:257313","NEWT:3827","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:930945","NEWT:106592","NEWT:536231","NEWT:46704","NEWT:1436733","NEWT:460519","NEWT:1187947","NEWT:572307","NEWT:1432138","NEWT:269796","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:1194599","NEWT:272844","NEWT:54571","NEWT:9598","NEWT:8030","NEWT:9483","NEWT:1513458","NCBITaxon:40559","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:759272","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:109757","NEWT:943146","NEWT:2711","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:508771","NEWT:1883446","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:89920","NEWT:29158","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:180923","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:118499","NEWT:169963","NEWT:32644","NEWT:527796","NEWT:225117","NEWT:746128","NEWT:499175","NEWT:109779","NEWT:43665","NEWT:1266464","NEWT:1715989","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:375451","NEWT:352472","NEWT:357","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:1328426","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NCBITaxon:138","NEWT:40483","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:38293","NEWT:1428","NEWT:327159","NEWT:178876","NEWT:1660","NEWT:327160","NEWT:573","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:1055524","NEWT:42528","NEWT:190802","NEWT:977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