Proteomic Analysis in Valvular Cardiomyopathy: Aortic Regurgitation vs. Aortic Stenosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36980219", "kind": "science-record", "revision": 2, "content_hash": "sha256:af4013ddd2181a48af444a45e739882d1cfb91300bdf8313b7443988524c4dfe", "created_at": "2026-11-01T19:01:38Z", "updated_at": "2026-11-01T21:30:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic Analysis in Valvular Cardiomyopathy: Aortic Regurgitation vs. Aortic Stenosis.", "doi": "10.3390/cells12060878", "pmid": "36980219", "authors": ["Theresa Holst", "Johannes Petersen", "Sabine Ameling", "Lisa Müller", "Torsten Christ", "Naomi Gedeon", "Thomas Eschenhagen", "Hermann Reichenspurner", "Elke Hammer", "Evaldas Girdauskas"], "journal": "Cells", "year": 2023, "abstract": "Left ventricular (LV) reverse remodeling after aortic valve (AV) surgery is less predictable in chronic aortic regurgitation (AR) than in aortic stenosis (AS). We aimed to disclose specific LV myocardial protein signatures possibly contributing to differential disease progression. Global protein profiling of LV myocardial samples excised from the subaortic interventricular septum in patients with isolated AR or AS undergoing AV surgery was performed using liquid chromatography-electrospray ionization-tandem mass spectrometry. Based on label-free quantitation protein intensities, a logistic regression model was calculated and adjusted for age, sex and protein concentration. Web-based functional enrichment analyses of phenotype-associated proteins were performed utilizing g:Profiler and STRING. Data are available via ProteomeXchange with identifier PXD039662. Lysates from 38 patients, including 25 AR and 13 AS samples, were analyzed. AR patients presented with significantly larger LV diameters and volumes (end-diastolic diameter: 61 (12) vs. 48 (13) mm, p < 0.001; end-diastolic volume: 180.0 (74.6) vs. 92.3 (78.4), p = 0.001). A total of 171 proteins were associated with patient phenotype: 117 were positively associated with AR and the enrichment of intracellular compartment proteins (i.e., assigned to carbohydrate and nucleotide metabolism, protein biosynthesis and the proteasome) was detected. Additionally, 54 were positively associated with AS and the enrichment of extracellular compartment proteins (i.e., assigned to the immune and hematopoietic system) was observed. In summary, functional enrichment analysis revealed specific AR- and AS-associated signatures of LV myocardial proteins.", "claims": [{"id": "claim-method", "statement": "Consideration of age, sex and protein concentration as covariates led to a stepwise reduction in data variance. Hence, the logistic regression model was adjusted accordingly and used to identify proteins showing associations with patient classification (as defined by Odds ratio (OR, i.e., the chance to be assigned to the AR or AS group when protein intensity is high) and p < 0.075).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36980219", "locator": "sections[2] \"2. Materials and Methods\" paragraph 6", "quote": "Consideration of age, sex and protein concentration as covariates led to a stepwise reduction in data variance. Hence, the logistic regression model was adjusted accordingly and used to identify proteins showing associations with patient classification (as defined by Odds ratio (OR, i.e., the chance to be assigned to the AR or AS group when protein intensity is high) and p < 0.075)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD039662.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36980219", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD039662."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 171 LV myocardial proteins were associated with the AR or AS patient phenotype.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36980219", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 171 proteins were associated with patient phenotype: 117 were positively associated with AR and the enrichment of intracellular compartment proteins (i.e., assigned to carbohydrate and nucleotide metabolism, protein biosynthesis and the proteasome) was detected. Additionally, 54 were positively associated with AS and the enrichment of extracellular compartment proteins (i.e., assigned to the immune and hematopoietic system) was observed."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 171 LV myocardial proteins were associated with the AR or AS patient phenotype.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:36980219"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD039662"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD039662"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36980219", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/cells12060878", "sha256": "sha256:f17eec09870c7baab3f7fcdc947d6e281459266b77afa27bda6258b618a4dad9", "bytes": 30003, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/cells12060878", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10047037", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD039662", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD039662", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD039662", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD039662.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD039662.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Protein profiling of left ventricular tissue of patients with aortic valve disease", "resolution_checked_at": "2026-11-01T18:46:41Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD039662 not downloaded", "asset:data:geo:PXD039662 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Consideration of age, sex and protein concentration as covariates led to a stepwise reduction in data variance. 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