Comparative Proteomic Analysis of Aqueous Humor, Anterior Lens Capsules, and Crystalline Lenses in Different Human Cataract Subtypes Versus Healthy Controls.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41283652", "kind": "science-record", "revision": 4, "content_hash": "sha256:7746e8d66945f1e6fdea8450465acae5171d124d07f5f185da6048936a081176", "created_at": "2026-11-01T20:31:19Z", "updated_at": "2026-11-01T22:57:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparative Proteomic Analysis of Aqueous Humor, Anterior Lens Capsules, and Crystalline Lenses in Different Human Cataract Subtypes Versus Healthy Controls.", "doi": "10.3390/proteomes13040062", "pmid": "41283652", "authors": ["Christina Karakosta", "Martina Samiotaki", "Anastasios Bisoukis", "Konstantinos I Bougioukas", "George Panayotou", "Nantieznta Kyriakidou", "Konstantinos Moschou", "Marilita M Moschos"], "journal": "Proteomes", "year": 2025, "abstract": "BACKGROUND: The aim of this study is to investigate the pathophysiology of cataract by analyzing signaling pathways in three sample types obtained from four different lens groups: age-related (ARC), diabetic (DC), post-vitrectomy cataract (PVC) and clear control lenses.\nMETHODS: Three sample types-the aqueous humor, the anterior capsule and the phaco cassette content-were collected during cataract surgery from 39 participants (ARC = 12, DC = 11, PVC = 7 and control = 9). The samples were prepared based on Sp3 protocol. The recognition and quantification of proteins were performed with liquid chromatography online with tandem mass spectrometry using the DIA-NN software. Perseus software (v1.6.15.0) was used for statistical analysis. Data are available via ProteomeXchange with identifiers PXD045547, PXD045554, PXD045557, and PXD069667.\nRESULTS: In total, 1986 proteins were identified in the aqueous humor, 2804 in the anterior capsule, and 3337 in the phaco cassette samples. Proteins involved in actin and microtubule cytoskeleton organization, including ACTN4, were downregulated in all three cataract groups compared to controls. Proteins involved in glycolipid metabolic process, including GAL3ST1, GAL3ST4, and GLA, were upregulated in ARC compared to controls. Proteins involved in the non-canonical Wnt receptor signaling pathway, including FRZB, SFRP1, SFRP2, SFRP5, WNT5A, and WNT7A, were upregulated in ARC compared to DC, PVC, and controls.\nCONCLUSIONS: Comprehensive proteomic profiles were generated using DIA proteomics by comparing ARC, DC, and PVC versus controls. This is the first study to use phaco cassette contents to investigate cataract formation in comparison to controls. Our findings significantly enhance the current understanding of human cataract pathophysiology and provide novel insights into the mechanisms underlying cataract formation.", "claims": [{"id": "claim-method", "statement": "Group comparisons among ARC–controls, DC–controls, and PVC–controls were conducted using two-sample t-tests, and volcano plots were generated with a permutation-based false discovery rate (FDR) threshold of 1% and an S0 parameter of 0.1. To assess differences across all cohorts, one-way ANOVA was applied, and results were visualized as heatmaps using the same FDR and S0 parameters, with hierarchical clustering based on Euclidean distance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41283652", "locator": "sections[8] \"2.6. Statistical Analysis\" paragraph 2", "quote": "Group comparisons among ARC–controls, DC–controls, and PVC–controls were conducted using two-sample t-tests, and volcano plots were generated with a permutation-based false discovery rate (FDR) threshold of 1% and an S0 parameter of 0.1. To assess differences across all cohorts, one-way ANOVA was applied, and results were visualized as heatmaps using the same FDR and S0 parameters, with hierarchical clustering based on Euclidean distance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD045547, PXD045554, PXD045557, PXD069667 [46].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41283652", "locator": "sections[23] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD045547, PXD045554, PXD045557, PXD069667 [46]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 1,986 proteins in aqueous humor, 2,804 in the anterior capsule, and 3,337 in phaco cassette samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41283652", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In total, 1986 proteins were identified in the aqueous humor, 2804 in the anterior capsule, and 3337 in the phaco cassette samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 1,986 proteins in aqueous humor, 2,804 in the anterior capsule, and 3,337 in phaco cassette samples.", "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:41283652"], "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. 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