{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T12:57:48Z","timestamp":1787662668439,"version":"build-2736575974"},"reference-count":46,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T00:00:00Z","timestamp":1763683200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Operational Programme \u201cCompetitiveness, Entrepreneurship and Innovation\u201d","award":["NSRF 2014-2020"],"award-info":[{"award-number":["NSRF 2014-2020"]}]},{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proteomes"],"abstract":"<jats:p>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. Methods: Three sample types\u2014the aqueous humor, the anterior capsule and the phaco cassette content\u2014were 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. Results: 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. Conclusions: 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.<\/jats:p>","DOI":"10.3390\/proteomes13040062","type":"journal-article","created":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T09:50:26Z","timestamp":1763718626000},"page":"62","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Comparative Proteomic Analysis of Aqueous Humor, Anterior Lens Capsules, and Crystalline Lenses in Different Human Cataract Subtypes Versus Healthy Controls"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9349-4043","authenticated-orcid":false,"given":"Christina","family":"Karakosta","sequence":"first","affiliation":[{"name":"School of Medicine, National and Kapodistrian University of Athens, 12462 Athens, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9952-0636","authenticated-orcid":false,"given":"Martina","family":"Samiotaki","sequence":"additional","affiliation":[{"name":"Biomedical Sciences Research Center \u201cAlexander Fleming\u201d, 16672 Vari, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasios","family":"Bisoukis","sequence":"additional","affiliation":[{"name":"Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol BS1 2LX, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6533-1391","authenticated-orcid":false,"given":"Konstantinos I.","family":"Bougioukas","sequence":"additional","affiliation":[{"name":"Department of Hygiene, Social-Preventive Medicine and Medical Statistics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Panayotou","sequence":"additional","affiliation":[{"name":"Biomedical Sciences Research Center \u201cAlexander Fleming\u201d, 16672 Vari, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nantieznta","family":"Kyriakidou","sequence":"additional","affiliation":[{"name":"Day Unit Clinic DIATHLASIS, 54627 Thessaloniki, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konstantinos","family":"Moschou","sequence":"additional","affiliation":[{"name":"Day Unit Clinic DIATHLASIS, 54627 Thessaloniki, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marilita M.","family":"Moschos","sequence":"additional","affiliation":[{"name":"School of Medicine, National and Kapodistrian University of Athens, 12462 Athens, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Mencucci, R., Stefanini, S., Favuzza, E., Cennamo, M., De Vitto, C., and Mossello, E. (2023). Beyond vision: Cataract and health status in old age, a narrative review. Front. Med., 10.","DOI":"10.3389\/fmed.2023.1110383"},{"key":"ref_2","unstructured":"Nizami, A.A., Gurnani, B., and Gulani, A.C. (2024). Cataract. Principles and Practice in Ophthalmic Assisting: A Comprehensive Textbook, StatPearls Publishing."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.jpba.2018.06.049","article-title":"Analysis of pharmaceuticals and small molecules in aqueous humor","volume":"159","author":"Pietrowska","year":"2018","journal-title":"J. Pharm. Biomed. Anal."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Dmuchowska, D.A., Pietrowska, K., Krasnicki, P., Kowalczyk, T., Misiura, M., Grochowski, E.T., Mariak, Z., Kretowski, A., and Ciborowski, M. (2021). Metabolomics Reveals Differences in Aqueous Humor Composition in Patients With and Without Pseudoexfoliation Syndrome. Front. Mol. Biosci., 8.","DOI":"10.3389\/fmolb.2021.682600"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.exer.2008.08.002","article-title":"The Lens Capsule","volume":"88","author":"Danysh","year":"2008","journal-title":"Exp. Eye Res."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1016\/j.matbio.2009.12.004","article-title":"Characterizing molecular diffusion in the lens capsule","volume":"29","author":"Danysh","year":"2009","journal-title":"Matrix Biol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1016\/j.bbagen.2015.08.016","article-title":"The etiology of human age-related cataract. Proteins don\u2019t last forever","volume":"1860","author":"Truscott","year":"2016","journal-title":"Biochim. Biophys. Acta (BBA)-Gen. Subj."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Li, J., Buonfiglio, F., Zeng, Y., Pfeiffer, N., and Gericke, A. (2024). Oxidative Stress in Cataract Formation: Is There a Treatment Approach on the Horizon?. Antioxidants, 13.","DOI":"10.3390\/antiox13101249"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"140","DOI":"10.4239\/wjd.v10.i3.140","article-title":"Cataract in diabetes mellitus","volume":"10","author":"Kiziltoprak","year":"2019","journal-title":"World J. Diabetes"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/j.ajo.2004.09.046","article-title":"Vitrectomy surgery increases oxygen exposure to the lens: A possible mechanism for nuclear cataract formation","volume":"139","author":"Holekamp","year":"2005","journal-title":"Am. J. Ophthalmol."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Beebe, D.C., Holekamp, N.M., Siegfried, C., and Shui, Y.B. (2011). Vitreoretinal influences on lens function and cataract. Philos. Trans. R. Soc. B Biol. Sci., 366.","DOI":"10.1098\/rstb.2010.0228"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1128\/MMBR.66.1.39-63.2002","article-title":"Molecular biologist\u2019s guide to proteomics","volume":"66","author":"Graves","year":"2002","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.ddtec.2021.06.006","article-title":"Data-independent acquisition (DIA): An emerging proteomics technology for analysis of drug-metabolizing enzymes and transporters","volume":"39","author":"Li","year":"2021","journal-title":"Drug Discov. Today Technol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"108679","DOI":"10.1016\/j.exer.2021.108679","article-title":"New insights into the mechanisms of age-related protein-protein crosslinking in the human lens","volume":"209","author":"Schey","year":"2021","journal-title":"Exp. Eye Res."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"100802","DOI":"10.1016\/j.preteyeres.2019.100802","article-title":"Spatiotemporal Changes in the Human Lens Proteome: Critical Insights into Long-lived Proteins","volume":"76","author":"Schey","year":"2020","journal-title":"Prog. Retin. Eye Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/s41594-020-00543-9","article-title":"Imbalances in the eye lens proteome are linked to cataract formation","volume":"28","author":"Schmid","year":"2021","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"3667","DOI":"10.1007\/s12013-024-01455-x","article-title":"Effects of Aging on Intrinsic Protein Disorder in Human Lenses and Zonules","volume":"82","author":"Antonietti","year":"2024","journal-title":"Cell Biochem. Biophys."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Karakosta, C., Samiotaki, M., Bisoukis, A., Bougioukas, K.I., Panayotou, G., Papaconstantinou, D., and Moschos, M.M. (2025). Differential Signaling Pathways Identified in Aqueous Humor, Anterior Capsule, and Crystalline Lens of Age-Related, Diabetic, and Post-Vitrectomy Cataract. Proteomes, 13.","DOI":"10.3390\/proteomes13010007"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1111\/ceo.12206","article-title":"Myopia and the long-term incidence of cataract and cataract surgery: The Blue Mountains Eye Study","volume":"42","author":"Kanthan","year":"2014","journal-title":"Clin. Exp. Ophthalmol."},{"key":"ref_20","unstructured":"(2025, February 03). KEGG PATHWAY Database. Available online: https:\/\/www.genome.jp\/kegg\/pathway.html."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.exer.2008.07.018","article-title":"TGF\u03b2 promotes Wnt expression during cataract development","volume":"88","author":"Chong","year":"2008","journal-title":"Exp. Eye Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.devcel.2009.06.016","article-title":"Wnt\/\u03b2-catenin signaling: Components, mechanisms, and diseases","volume":"17","author":"MacDonald","year":"2009","journal-title":"Dev. Cell"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"7880","DOI":"10.1101\/cshperspect.a007880","article-title":"Frizzled and LRP5\/6 Receptors for Wnt\/\u03b2-Catenin Signaling","volume":"4","author":"MacDonald","year":"2012","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"503637","DOI":"10.1016\/j.mrgentox.2023.503637","article-title":"Low-dose ionizing radiation: Effects on the proliferation and migration of lens epithelial cells via activation of the Wnt\/\u03b2-catenin pathway","volume":"888","author":"Wang","year":"2023","journal-title":"Mutat. Res. Genet. Toxicol. Environ. Mutagen."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Chen, Y., Stump, R.J.W., Lovicu, F.J., and McAvoy, J.W. (2006). A role for Wnt\/Planar Cell Polarity signaling during lens fiber cell differentiation?. Semin. Cell Dev. Biol., 17.","DOI":"10.1016\/j.semcdb.2006.11.005"},{"key":"ref_26","first-page":"2654","article-title":"Wnt Expression in TGF\u00df\u2013induced Cataract Models","volume":"45","author":"Chong","year":"2004","journal-title":"Investig. Ophthalmol. Vis. Sci."},{"key":"ref_27","unstructured":"Glycolipid Composition of Human Cataractous Lenses (2025, October 24). Characterization of Lewisx Glycolipids\u2014PubMed, Available online: https:\/\/pubmed.ncbi.nlm.nih.gov\/7905480\/."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Rao, P.V., and Maddala, R. (2006). The Role of the Lens Actin Cytoskeleton in Fiber Cell Elongation and Differentiation. Semin. Cell Dev. Biol., 17.","DOI":"10.1016\/j.semcdb.2006.10.011"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Karakosta, C., Samiotaki, M., Panayotou, G., Papaconstantinou, D., and Moschos, M.M. (2024). Proteomic Changes of Glycolipid Pathways in Age-Related, Diabetic, and Post-Vitrectomy Cataracts. J. Clin. Med., 13.","DOI":"10.3390\/jcm13237287"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1837","DOI":"10.1172\/JCI38277","article-title":"Functions of the intermediate filament cytoskeleton in the eye lens","volume":"119","author":"Song","year":"2009","journal-title":"J. Clin. Investig."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1086\/302872","article-title":"Autosomal-dominant congenital cataract associated with a deletion mutation in the human beaded filament protein gene BFSP2","volume":"66","author":"Jakobs","year":"2000","journal-title":"Am. J. Hum. Genet."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/S0014-4835(02)00330-5","article-title":"Knockout of the intermediate filament protein CP49 destabilises the lens fibre cell cytoskeleton and decreases lens optical quality, but does not induce cataract","volume":"76","author":"Sandilands","year":"2003","journal-title":"Exp. Eye Res."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Cosar, B., Nefesoglu, M.S., Altinoz, M.A., Akgun, E., Sahin, B., Baykal, A., and Serteser, M. (2025). Lens Proteomics Provide Novel Clues for Cataractogenesis: Original Investigation and a Broad Literature Survey. J. Clin. Med., 14.","DOI":"10.3390\/jcm14134737"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Beyer, E.C., Mathias, R.T., and Berthoud, V.M. (2022). Loss of fiber cell communication may contribute to the development of cataracts of many different etiologies. Front. Physiol., 13.","DOI":"10.3389\/fphys.2022.989524"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcp.1041430308","article-title":"Volume regulation in lens epithelial cells and differentiating lens fiber cells","volume":"143","author":"Beebe","year":"1990","journal-title":"J. Cell Physiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"169","DOI":"10.3109\/02713688208997691","article-title":"Microfilament assembly during lens cell elongation in vitro","volume":"2","author":"Ramaekers","year":"1982","journal-title":"Curr. Eye Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1002\/cm.21889","article-title":"Role of actin-binding proteins in cataract formation","volume":"82","author":"Karakosta","year":"2024","journal-title":"Cytoskeleton"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Shu, D.Y., Chaudhary, S., Cho, K.-S., Lennikov, A., Miller, W.P., Thorn, D.C., Yang, M., and McKay, T.B. (2023). Role of Oxidative Stress in Ocular Diseases: A Balancing Act. Metabolites, 13.","DOI":"10.3390\/metabo13020187"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1097\/IIO.0000000000000440","article-title":"The Post Vitrectomy Cataract","volume":"62","author":"Markatia","year":"2022","journal-title":"Int. Ophthalmol. Clin."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.ajo.2019.02.008","article-title":"Intraocular Oxygen and Antioxidant Status: New Insights on the Effect of Vitrectomy and Glaucoma Pathogenesis","volume":"203","author":"Siegfried","year":"2019","journal-title":"Am. J. Ophthalmol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e70028","DOI":"10.1111\/acel.70028","article-title":"Deep Characterization of Isomerization in the Human Eye Lens Proteome by Crystallin-Depleted Data-Independent Acquisition","volume":"24","author":"Hubbard","year":"2025","journal-title":"Aging Cell"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1021\/jasms.5c00087","article-title":"Data-Independent Acquisition Parallel Accumulation-Serial Fragmentation (diaPASEF) Analysis of the Separated Zebrafish Lens Improves Identifications","volume":"36","author":"Zelle","year":"2025","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1167\/iovs.66.5.34","article-title":"Identification of Age- and Cataract-Related Changes in High-Density Lens Protein Aggregates","volume":"66","author":"Wang","year":"2025","journal-title":"Investig. Ophthalmol. Vis. Sci."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"100453","DOI":"10.1016\/j.mcpro.2022.100453","article-title":"Proteome Remodeling of the Eye Lens at 50 Years Identified With Data-Independent Acquisition","volume":"22","author":"Cantrell","year":"2023","journal-title":"Mol. Cell Proteom."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Schey, K.L., Wang, Z., Rose, K.L., and Anderson, D.M.G. (2022). Imaging Cataract-Specific Peptides in Human Lenses. Cells, 11.","DOI":"10.3390\/cells11244042"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"D1539","DOI":"10.1093\/nar\/gkac1040","article-title":"The ProteomeXchange consortium at 10 years: 2023 update","volume":"51","author":"Deutsch","year":"2023","journal-title":"Nucleic Acids Res."}],"container-title":["Proteomes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2227-7382\/13\/4\/62\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,23]],"date-time":"2025-11-23T05:12:55Z","timestamp":1763874775000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2227-7382\/13\/4\/62"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,21]]},"references-count":46,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["proteomes13040062"],"URL":"https:\/\/doi.org\/10.3390\/proteomes13040062","relation":{},"ISSN":["2227-7382"],"issn-type":[{"value":"2227-7382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,21]]}}}