Phosphoproteomics and morphology of stored human red blood cells treated by protein tyrosine phosphatases inhibitor.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37910801", "kind": "science-record", "revision": 3, "content_hash": "sha256:e3068e1753591b0f832a83cd2677216902aac093d80534f0edd6929dfc2dd0b4", "created_at": "2026-11-01T19:02:48Z", "updated_at": "2026-11-01T21:31:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Phosphoproteomics and morphology of stored human red blood cells treated by protein tyrosine phosphatases inhibitor.", "doi": "10.1182/bloodadvances.2023009964", "pmid": "37910801", "authors": ["Manon Bardyn", "David Crettaz", "Benjamin Rappaz", "Romain Hamelin", "Florence Armand", "Jean-Daniel Tissot", "Gerardo Turcatti", "Michel Prudent"], "journal": "Blood advances", "year": 2024, "abstract": "ABSTRACT: The process of protein phosphorylation is involved in numerous cell functions. In particular, phosphotyrosine (pY) has been reported to play a role in red blood cell (RBC) functions, including the cytoskeleton organization. During their storage before transfusion, RBCs suffer from storage lesions that affect their energy metabolism and morphology. This study investigated the relationship between pY and the storage lesions. To do so, RBCs were treated (in the absence of calcium) with a protein tyrosine phosphatase inhibitor (orthovanadate [OV]) to stimulate phosphorylation and with 3 selective kinase inhibitors (KIs). Erythrocyte membrane proteins were studied by western blot analyses and phosphoproteomics (data are available via ProteomeXchange with identifier PXD039914) and cell morphology by digital holographic microscopy. The increase of pY triggered by OV treatment (inducing a global downregulation of pS and pT) disappeared during the storage. Phosphoproteomic analysis identified 609 phosphoproteins containing 1752 phosphosites, of which 41 pY were upregulated and 2 downregulated by OV. After these phosphorylation processes, the shape of RBCs shifted from discocytes to spherocytes, and the addition of KIs partially inhibited this transition. The KIs modulated either pY or pS and pT via diverse mechanisms related to cell shape, thereby affecting RBC morphology. The capacity of RBCs to maintain their function is central in transfusion medicine, and the presented results contribute to a better understanding of RBC biology.", "claims": [{"id": "claim-method", "statement": "A t test analysis was performed using Perseus 1.6.0.7,45 and graphs were generated with homemade programs (R environment).46 Class 1 phosphosites with intensities in monophosphopeptides (multiplicity = 1), with at least 12 valid values in at least 1 group (OV or Control), were kept for the analysis (3 valid values in at least 1 group for KIs). The significantly differentially quantified phosphosites were defined according to a permutation-based multiple-testing analysis (250 permutations; false discovery rate (FDR) = 0.05; S0 = 1; and S0 = 0.1 for the KIs).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37910801", "locator": "sections[7] \"Phosphoproteomics\" paragraph 2", "quote": "A t test analysis was performed using Perseus 1.6.0.7,45 and graphs were generated with homemade programs (R environment).46 Class 1 phosphosites with intensities in monophosphopeptides (multiplicity = 1), with at least 12 valid values in at least 1 group (OV or Control), were kept for the analysis (3 valid values in at least 1 group for KIs). The significantly differentially quantified phosphosites were defined according to a permutation-based multiple-testing analysis (250 permutations; false discovery rate (FDR) = 0.05; S0 = 1; and S0 = 0.1 for the KIs)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Additional data are available upon reasonable request from the corresponding author, Michel Prudent (Michel.Prudent@itransfusion.ch).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37910801", "locator": "sections[23] \"Footnotes\" paragraph 2", "quote": "Additional data are available upon reasonable request from the corresponding author, Michel Prudent (Michel.Prudent@itransfusion.ch)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Phosphoproteomic analysis identified 609 phosphoproteins containing 1752 phosphosites, of which 41 pY were upregulated and 2 downregulated by OV.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37910801", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Phosphoproteomic analysis identified 609 phosphoproteins containing 1752 phosphosites, of which 41 pY were upregulated and 2 downregulated by OV."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Phosphoproteomic analysis identified 609 phosphoproteins containing 1752 phosphosites, of which 41 pY were upregulated and 2 downregulated by OV.", "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:37910801"], "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:PXD039914"], "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:PXD039914"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37910801", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1182/bloodadvances.2023009964", "sha256": "sha256:9461462bc4b0cde8bbbb69f2609e06eafa0d558107eb8285286613a72e1cbc84", "bytes": 50696, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1182/bloodadvances.2023009964", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10784683", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD039914", "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=PXD039914", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD039914", "version": null, "note": "Additional data are available upon reasonable request from the corresponding author, Michel Prudent (Michel.Prudent@itransfusion.ch).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Additional data are available upon reasonable request from the corresponding author, Michel Prudent (Michel.Prudent@itransfusion.ch).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Phosphoproteomics and Morphology of Red Blood Cells treated by Protein-Tyrosine-Phosphatases Inhibitor", "resolution_checked_at": "2026-11-01T19:09:50Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD039914 not downloaded", "asset:data:geo:PXD039914 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "t test analysis and permutation-based multiple-testing analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A t test analysis was performed using Perseus 1.6.0.7,45 and graphs were generated with homemade programs (R environment).46 Class 1 phosphosites with intensities in monophosphopeptides (multiplicity = 1), with at least 12 valid values in at least 1 group (OV or Control), were kept for the analysis (3 valid values in at least 1 group for KIs). 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