Characterization of Glycoproteoforms of Integrins α2 and β1 in Megakaryocytes in the Occurrence of JAK2V617F Mutation-Induced Primary Myelofibrosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35182768", "kind": "science-record", "revision": 3, "content_hash": "sha256:670b37efd0b0e1172c4eca5002cb3135ddbf674f3a77c530858b50856a0e8fcb", "created_at": "2026-11-01T17:36:56Z", "updated_at": "2026-11-01T18:58:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Characterization of Glycoproteoforms of Integrins α2 and β1 in Megakaryocytes in the Occurrence of JAK2V617F Mutation-Induced Primary Myelofibrosis.", "doi": "10.1016/j.mcpro.2022.100213", "pmid": "35182768", "authors": ["Maissa M Gaye", "Christina M Ward", "Andrew J Piasecki", "Vanessa L Stahl", "Aikaterini Karagianni", "Catherine E Costello", "Katya Ravid"], "journal": "Molecular & cellular proteomics : MCP", "year": 2022, "abstract": "Primary myelofibrosis (PMF) is a neoplasm prone to leukemic transformation, for which limited treatment is available. Among individuals diagnosed with PMF, the most prevalent mutation is the JAK2V617F somatic point mutation that activates the Janus kinase 2 (JAK2) enzyme. Our earlier reports on hyperactivity of β1 integrin and enhanced adhesion activity of the α2β1 complex in JAK2V617F megakaryocytes (MKs) led us to examine the new hypothesis that this mutation leads to posttranslational modification via changes in glycosylation. Samples were derived from immunoprecipitation of MKs obtained from Vav1-hJAK2V617F and WT mice. Immunoprecipitated fractions were separated by SDS-PAGE and analyzed using LC-MS/MS techniques in a bottom-up glycoproteomics workflow. In the immunoprecipitate, glycopeptiforms corresponding to 11 out of the 12 potential N-glycosylation sites of integrin β1 and to all nine potential glycosylation sites of integrin α2 were observed. Glycopeptiforms were compared across WT and JAK2V617F phenotypes for both integrins. The overall trend observed is that JAK2V617F mutation in PMF MKs leads to changes in β1 glycosylation; in most cases, it results in an increase in the integrated area of glycopeptiforms. We also observed that in mutated MKs, changes in integrin α2 glycosylation were more substantial than those observed for integrin β1 glycosylation, a finding that suggests that altered integrin α2 glycosylation may also affect activation. Additionally, the identification of proteins associated to the cytoskeleton that were co-immunoprecipitated with integrins α2 and β1 demonstrated the potential of the methodology employed in this study to provide some insight, at the peptide level, into the consequences of integrin activation in MKs. The extensive and detailed glycosylation patterns we uncovered provide a basis for future functional studies of each site in control cells as compared to JAK2V617F-mutated cells. Data are available via ProteomeXchange with identifier PXD030550.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (56) via the PRIDE (57) partner repository with the dataset identifier PXD030550 and are reported in compliance with MIRAGE standards (58).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35182768", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (56) via the PRIDE (57) partner repository with the dataset identifier PXD030550 and are reported in compliance with MIRAGE standards (58)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Changes in glycosylation were documented at multiple sites in integrins β1 and α2 isolated from bone marrow of WT and myelofibrotic (JAK2V617F) mouse megakaryocytes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35182768", "locator": "sections[0] \"Abstract\" paragraph 8", "quote": "Changes in glycosylation were documented at multiple sites in integrins β1 and α2 isolated from bone marrow of WT and myelofibrotic (JAK2V617F) mouse megakaryocytes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Changes in glycosylation were documented at multiple sites in integrins β1 and α2 isolated from bone marrow of WT and myelofibrotic (JAK2V617F) mouse megakaryocytes.", "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:35182768"], "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:PXD030550"], "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:PXD030550"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35182768", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.mcpro.2022.100213", "sha256": "sha256:37ec2dcc138bd6cbbfa34a1aaff76c479208989cdd6b80b986399cd1efbc39ba", "bytes": 68714, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.mcpro.2022.100213", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8968581", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD030550", "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=PXD030550", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD030550", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (56) via the PRIDE (57) partner repository with the dataset identifier PXD030550 and are reported in compliance with MIRAGE standards (58).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (56) via the PRIDE (57) partner repository with the dataset identifier PXD030550 and are reported in compliance with MIRAGE standards (58).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Glycoproteoforms of Integrins α2 and β1 in Megakaryocytes in the Occurrence of Primary Myelofibrosis", "resolution_checked_at": "2026-11-01T18:06:51Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD030550 not downloaded", "asset:data:geo:PXD030550 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD030550"], "resolved_accessions": ["PXD030550"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (56) via the PRIDE (57) partner repository with the dataset identifier PXD030550 and are reported in compliance with MIRAGE standards (58)."], "basis": "The paper names PXD030550 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:35182768", "data:geo:PXD030550"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD030550"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:34:46Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 20142, "completion_tokens": 990, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:35182768", "type": "paper", "label": "pmid:35182768"}, {"id": "source:pmid:35182768", "type": "manuscript", "label": "PMID 35182768 full text"}, {"id": "data:geo:PXD030550", "type": "dataset", "label": "GEO PXD030550"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35182768", "type": "paper", "label": "pmid:35182768"}, {"id": "source:pmid:35182768", "type": "manuscript", "label": "PMID 35182768 full text"}, {"id": "data:geo:PXD030550", "type": "dataset", "label": "GEO PXD030550"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35182768", "type": "extraction", "used": ["source:pmid:35182768"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD030550", "type": "accession_resolution", "used": ["data:geo:PXD030550"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:35182768", "parent_hash": "sha256:8f98140385e85e3b04295b64bfac27a4aaaf4af58730a3a41269def48aa0cd9a", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD030550 licence not read", "asset:data:geo:PXD030550 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ere separated by SDS-PAGE and analyzed using LC-MS/MS techniques in a bottom-up glycoproteomics wo", "no technical replicate was acquired for the mass spectrometric data due to the limited amount of these samp", "sm GraphPad software. Sample Preparation for Mass Spectrometry The components in lysates and co-IP fraction", "e gel were combined into one sample prior to mass spectrometric analysis. Gel bands were cut according to th"], "order_basis": "paper_text_order:811", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["analyzed were derived from a Vav1-hJAK2V617F mouse colony (JAK2V167F), and age-, sex-, strain-m", "y small pools of integrins isolated from the mouse MKs. For each phenotype, the sample was sepa", "blished by Alagesan et al. (28). Recombinant mouse integrin α2β1 protein expressed in CHO cells"], "order_basis": "paper_text_order:2256", "id": "assay:2"}]}