Candidate Interaction Partners of Calpain-5 Suggest Clues to Its Involvement in Neovascular Inflammatory Vitreoretinopathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41597217", "kind": "science-record", "revision": 2, "content_hash": "sha256:df1381ec6e09f5d8e41a4505f89bad149ec078580ef125c6c08f90ab14e09474", "created_at": "2026-11-01T20:31:33Z", "updated_at": "2026-11-01T21:36:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Candidate Interaction Partners of Calpain-5 Suggest Clues to Its Involvement in Neovascular Inflammatory Vitreoretinopathy.", "doi": "10.3390/cells15020142", "pmid": "41597217", "authors": ["Jozsef Gal", "Vimala Bondada", "Rachel Crasta", "Dorothy E Croall", "Calvin P Vary", "James W Geddes"], "journal": "Cells", "year": 2026, "abstract": "Although calpain-5/CAPN5 is widely expressed in mammals, little is known regarding its functions. Pathogenic mutations of CAPN5 are causal for a devastating autoimmune eye disease, neovascular inflammatory vitreoretinopathy (NIV). To provide insight into both the physiological and pathological roles of CAPN5, it is essential to identify candidate interaction partners and possible substrates. Human SH-SY5Y neuroblastoma cells, transfected with full-length catalytically dead (Cys81Ala) CAPN5-3×FLAG, were used for anti-FLAG co-immunoprecipitation (co-IP) and quantitative proteomics using Sequential Window Acquisition of all THeoretical mass spectra (SWATH-MS). Fifty-one proteins were enriched at least four-fold, p < 0.01, relative to cells transfected with an empty FLAG vector. A high proportion (24/51) of candidate CAPN5 interaction partners are associated with protein quality control, including components of the chaperonin, chaperone, and ubiquitin-proteasome systems. Additional candidate interactors include tubulins, kinases, phosphatases, G proteins, and mitochondrial proteins. CAPN5 interactions for 14 of the candidate proteins were confirmed by co-IP and immunoblotting. Of these 14 proteins, 11 exhibited in vitro calcium-induced proteolysis following co-IP with WT CAPN5-3×FLAG. Impaired calcium-induced proteolysis of co-IP proteins was observed for the pathogenic CAPN5 variants R243L and R289W. Further studies are needed to validate the association of candidate CAPN5 interactors with proteins and complexes suggested by the SWATH-MS and co-IP results, and the possible role of CAPN5 within such complexes. The possible involvement of CAPN5 in protein quality control is relevant to NIV, as defects in protein quality control have been implicated in inherited retinal disorders. Proteomic data are available via ProteomeXchange with identifier PXD068008.", "claims": [{"id": "claim-method", "statement": "Based on these data, lists of proteins and their corresponding relative levels with appropriate statistics were generated by our software workflow that included the SCIEX programs ProteinPilot (data-dependent peptide ion libraries), PeakView, version 2.2 (linking data-independent SWATH MS/MS analysis and ion library data, quantification of peaks, determination of the false discovery rate, quality control analytics, via the SWATH microapp, version 2.0.1), and MarkerView, version 1.3 (principle component analysis [42], p-values, t-test comparisons).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41597217", "locator": "sections[9] \"2.5. SWATH-MS Analysis\" paragraph 2", "quote": "Based on these data, lists of proteins and their corresponding relative levels with appropriate statistics were generated by our software workflow that included the SCIEX programs ProteinPilot (data-dependent peptide ion libraries), PeakView, version 2.2 (linking data-independent SWATH MS/MS analysis and ion library data, quantification of peaks, determination of the false discovery rate, quality control analytics, via the SWATH microapp, version 2.0.1), and MarkerView, version 1.3 (principle component analysis [42], p-values, t-test comparisons)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data is contained within the article or Supplementary Materials. Further data will be made available on request from the authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41597217", "locator": "sections[22] \"Data Availability Statement\" paragraph 2", "quote": "Data is contained within the article or Supplementary Materials. Further data will be made available on request from the authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "SWATH-MS analysis identified 51 significantly enriched candidate CAPN5 interaction partners, and confirmatory experiments validated 14 interactions, with 11 of those proteins undergoing calcium-induced proteolysis.", "kind": "quantitative", "target": {"value": 0.01, "unit": "p-value", "tolerance": null, "source": "Following anti-FLAG immunoprecipitation of lysates of SH-SY5Y cells stably transfected with C81A CAPN5-3×FLAG, SWATH-MS analysis identified 1088 co-immunoprecipitated proteins, of which 51 exhibited greater than four-fold enrichment relative to 3×FLAG vector immunoprecipitated controls and were statistically significant at p < 0.01."}, "evidence": [{"asset": "source:pmid:41597217", "locator": "sections[13] \"3. Results\" paragraph 2", "quote": "Following anti-FLAG immunoprecipitation of lysates of SH-SY5Y cells stably transfected with C81A CAPN5-3×FLAG, SWATH-MS analysis identified 1088 co-immunoprecipitated proteins, of which 51 exhibited greater than four-fold enrichment relative to 3×FLAG vector immunoprecipitated controls and were statistically significant at p < 0.01."}, {"asset": "source:pmid:41597217", "locator": "sections[0] \"Abstract\" paragraph 6", "quote": "CAPN5 interactions for 14 of the candidate proteins were confirmed by co-IP and immunoblotting. Of these 14 proteins, 11 exhibited in vitro calcium-induced proteolysis following co-IP with WT CAPN5-3×FLAG."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "SWATH-MS analysis identified 51 significantly enriched candidate CAPN5 interaction partners, and confirmatory experiments validated 14 interactions, with 11 of those proteins undergoing calcium-induced proteolysis.", "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:41597217"], "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:PXD068008"], "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:PXD068008"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41597217", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/cells15020142", "sha256": "sha256:8cb1d4b7015e07fc1fe6e3ccc8cb6d656a48fe9b313a5f129f03400ce86de632", "bytes": 104662, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/cells15020142", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12839053", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD068008", "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=PXD068008", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD068008", "version": null, "note": "Data is contained within the article or Supplementary Materials. Further data will be made available on request from the authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data is contained within the article or Supplementary Materials. Further data will be made available on request from the authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Identification of Candidate Interaction Partners of Human Calpain-5 in Neuroblastoma Cells with SWATH-MS Analysis", "resolution_checked_at": "2026-11-01T20:16:18Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD071887", "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=PXD071887", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD071887", "version": null, "note": "Data is contained within the article or Supplementary Materials. Further data will be made available on request from the authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data is contained within the article or Supplementary Materials. Further data will be made available on request from the authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Capture of candidate calpain5 interacting proteins from lysates of the human neuroblastoma SH-SY5Y cell line with analysis of LC-MSMS data using SWATH", "resolution_checked_at": "2026-11-01T20:16:18Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD068008 not downloaded", "asset:data:geo:PXD068008 licence not read", "asset:data:geo:PXD071887 not downloaded", "asset:data:geo:PXD071887 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Based on these data, lists of proteins and their corresponding relative levels with appropriate statistics were generated by our software workflow that included the SCIEX programs ProteinPilot (data-dependent peptide ion libraries), PeakView, version 2.2 (linking data-independent SWATH MS/MS analysis and ion library data, quantification of peaks, determination of the false discovery rate, quality control analytics, via the SWATH microapp, version 2.0.1), and MarkerView, version 1.3 (principle component analysis [42], p-values, t-test comparisons)."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 0.01, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_named_unmapped"]}, "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 (t-test), 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": ["PXD068008", "PXD071887"], "resolved_accessions": ["PXD068008", "PXD071887"], "statements": ["Data is contained within the article or Supplementary Materials. Further data will be made available on request from the authors."], "basis": "The paper names PXD068008, PXD071887 in ProteomeXchange via PRIDE and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:41597217", "data:geo:PXD068008"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD068008"]}, "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": "2026-11-01T20:11:14Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 31292, "completion_tokens": 2342, "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:41597217", "type": "paper", "label": "pmid:41597217"}, {"id": "source:pmid:41597217", "type": "manuscript", "label": "PMID 41597217 full text"}, {"id": "data:geo:PXD068008", "type": "dataset", "label": "GEO PXD068008"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41597217", "type": "paper", "label": "pmid:41597217"}, {"id": "source:pmid:41597217", "type": "manuscript", "label": "PMID 41597217 full text"}, {"id": "data:geo:PXD068008", "type": "dataset", "label": "GEO PXD068008"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41597217", "type": "extraction", "used": ["source:pmid:41597217"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD068008", "type": "accession_resolution", "used": ["data:geo:PXD068008"], "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:41597217", "parent_hash": "sha256:f27c028b4a2bc5b3e09a24c63d4afefe82fa27db7877caad4099f147cab742d5", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:PXD068008 licence not read", "asset:data:geo:PXD068008 not downloaded", "asset:data:geo:PXD071887 licence not read", "asset:data:geo:PXD071887 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tion partners and possible substrates. Human SH-SY5Y neuroblastoma cells, transfected with full-l", "(ATCC, Manassas, VA, USA, CRL-2266 [34]) was cultured in MEM (Corning, Corning, NY, USA, 10-010-CV) w", "Cell Lines The human neuroblastoma cell line SH-SY5Y (ATCC, Manassas, VA, USA, CRL-2266 [34]) was", "partners of CAPN5; Table S2: The proteome of SH-SY5Y cells; Table S3: AP-MS-SWATH analysis of the"], "order_basis": "paper_text_order:480", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["bstrates. Human SH-SY5Y neuroblastoma cells, transfected with full-length catalytically dead (Cys81Al", "least four-fold, p < 0.01, relative to cells transfected with an empty FLAG vector. A high proportion", "ified cell culture incubator. The cells were transfected with pIRESpuro3-C81A CAPN5-3×FLAG or the pIR"], "order_basis": "paper_text_order:509", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ndidate proteins were confirmed by co-IP and immunoblotting. Of these 14 proteins, 11 exhibited in vitro", "N5_SWATH_uncropped_images.zip: The uncropped immunoblotting images used to prepare Figure 2 and Figures"], "order_basis": "paper_text_order:1255", "id": "assay:3"}]}