{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T10:05:55Z","timestamp":1789985155849,"version":"4.0.1"},"reference-count":192,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Dalian Program for Distinguished Young Technological Talents","award":["2025RJ10"],"award-info":[{"award-number":["2025RJ10"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Osteoarthritis (OA) is a joint disease of unknown etiology that can occur in joints throughout the body, especially with articular cartilage lesions of the knee joint and hip joint. Osteoarthritis not only causes joint pain, deformity, and functional impairment, but also significantly increases the risk of cardiovascular events, deep vein thrombosis in the lower limbs, and hip fractures. Up to now, there have been no specific medications available for the treatment of osteoarthritis, and the disease remains incurable. Therefore, identifying reliable biomarkers is crucial for achieving a more accurate diagnosis of OA and for guiding the development of targeted treatment strategies. In this paper, we screen and synthesize articles that performed transcriptomics and proteomics analysis on tissue or cell samples taken from osteoarthritis cartilage. We identify common differentially expressed genes (co-DEGs) and proteins (co-DEPs) in cartilage samples from knee osteoarthritis (KOA) and hip osteoarthritis (HOA) and consolidate them into candidate molecules, while systematically delineating their expression trends and underlying mechanisms at both the transcriptomic and proteomic levels. This review establishes a theoretical foundation and identifies future research directions for functional validation and clinical translation of these candidate molecules as potential biomarkers and therapeutic targets for osteoarthritis.<\/jats:p>","DOI":"10.3390\/biom16091363","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T09:01:38Z","timestamp":1789981298000},"page":"1363","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Omics Studies in Osteoarthritis: A Review of Molecular Mechanisms and Candidate Molecules"],"prefix":"10.3390","volume":"16","author":[{"given":"Yimeng","family":"Sun","sequence":"first","affiliation":[{"name":"Zhongshan Clinical College, Dalian University, Dalian 116622, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qulong","family":"Xiao","sequence":"additional","affiliation":[{"name":"Zhongshan Clinical College, Dalian University, Dalian 116622, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming","family":"Jin","sequence":"additional","affiliation":[{"name":"Zhongshan Clinical College, Dalian University, Dalian 116622, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ge","family":"Liu","sequence":"additional","affiliation":[{"name":"Laboratory of Orthopedics, Affiliated Zhongshan Hospital of Dalian University, Dalian 116001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingzhong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Zhongshan Clinical College, Dalian University, Dalian 116622, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-2486-3814","authenticated-orcid":false,"given":"Xiaowei","family":"Wei","sequence":"additional","affiliation":[{"name":"Laboratory of Orthopedics, Affiliated Zhongshan Hospital of Dalian University, Dalian 116001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"147650","DOI":"10.1016\/j.ijbiomac.2025.147650","article-title":"DHA Laden Liposome Incorporated HA-Menthol-CD Host-Guest Hydrogels as Delivery System for Osteoarthritis Treatment","volume":"328","author":"Yang","year":"2025","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/s00223-020-00670-x","article-title":"Models of Osteoarthritis: Relevance and New Insights","volume":"109","author":"Samvelyan","year":"2021","journal-title":"Calcif. Tissue Int."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"157228","DOI":"10.1016\/j.phymed.2025.157228","article-title":"Yiqi Xugu HeJi Restores Cartilage Metabolic Homeostasis via AKT1-Thr473 Activation in Osteoarthritis","volume":"148","author":"Wu","year":"2025","journal-title":"Phytomedicine"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Gu, J., Rao, W., Huo, S., Fan, T., Qiu, M., Zhu, H., Chen, D., and Sheng, X. (2022). MicroRNAs and Long Non-Coding RNAs in Cartilage Homeostasis and Osteoarthritis. Front. Cell Dev. Biol., 10.","DOI":"10.3389\/fcell.2022.1092776"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1002\/cbin.11256","article-title":"SUMO-Modified Bone Marrow Mesenchymal Stem Cells Promoted the Repair of Articular Cartilage in Rats","volume":"44","author":"Liu","year":"2020","journal-title":"Cell Biol. Int."},{"key":"ref_6","first-page":"265","article-title":"Expression of MiR-204 in Patients with Osteoarthritis and Its Damage to Chondrocytes","volume":"20","author":"Liu","year":"2020","journal-title":"J. Musculoskelet. Neuronal Interact."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.1002\/art.39564","article-title":"Association of Osteoarthritis With Increased Risk of Cardiovascular Diseases in the Elderly: Findings From the Progetto Veneto Anziano Study Cohort","volume":"68","author":"Veronese","year":"2016","journal-title":"Arthritis Rheumatol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1177\/2047487315610663","article-title":"Association between Osteoarthritis and Cardiovascular Disease: Systematic Review and Meta-Analysis","volume":"23","author":"Hall","year":"2016","journal-title":"Eur. J. Prev. Cardiol."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Sun, W., Ai, D., Yao, Y., Ren, K., Lu, J., Sun, H., Wu, X., and Jiang, Q. (2022). The Application of Caprini Risk Assessment Model in Evaluation of Deep Vein Thrombosis for Patients with End-Stage Osteoarthritis before Arthroplasty. BMC Musculoskelet. Disord., 23.","DOI":"10.1186\/s12891-022-05712-z"},{"key":"ref_10","first-page":"e81776","article-title":"Epidemiological Study on the Prevalence and Severity of Knee Osteoarthritis in Geriatric Patients With Fragility Fractures of the Hip","volume":"17","author":"Hon","year":"2025","journal-title":"Cureus"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2179","DOI":"10.1016\/j.arth.2025.01.016","article-title":"High Prevalence of Symptomatic Knee Osteoarthritis Among Patients Who Have Fragility Hip Fractures","volume":"40","author":"Mekariya","year":"2025","journal-title":"J. Arthroplast."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1397","DOI":"10.1016\/j.joca.2024.07.014","article-title":"Osteoarthritis Year in Review 2024: Epidemiology and Therapy","volume":"32","author":"Courties","year":"2024","journal-title":"Osteoarthr. Cartil."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Xiong, Z., Peng, G., Deng, J., Liu, M., Ning, X., Zhuang, Y., Yang, H., and Sun, H. (2024). Therapeutic Targets and Potential Delivery Systems of Melatonin in Osteoarthritis. Front. Immunol., 15.","DOI":"10.3389\/fimmu.2024.1331934"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Li, H.-Z., Liang, X.-Z., Sun, Y.-Q., Jia, H.-F., Li, J.-C., and Li, G. (2024). Global, Regional, and National Burdens of Osteoarthritis from 1990 to 2021: Findings from the 2021 Global Burden of Disease Study. Front. Med., 11.","DOI":"10.3389\/fmed.2024.1476853"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e12028","DOI":"10.1002\/jfa2.12028","article-title":"Differences in Ankle and Knee Muscle Architecture and Plantar Pressure Distribution among Women with Knee Osteoarthritis","volume":"17","author":"Cigercioglu","year":"2024","journal-title":"J. Foot Ankle Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"194","DOI":"10.21037\/atm-22-4284","article-title":"Identification of CaMK4 as a Sex-Difference-Related Gene in Knee Osteoarthritis","volume":"11","author":"Feng","year":"2023","journal-title":"Ann. Transl. Med."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.1016\/S0140-6736(20)32230-3","article-title":"Osteoarthritis in 2020 and beyond: A Lancet Commission","volume":"396","author":"Hunter","year":"2020","journal-title":"Lancet"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"181","DOI":"10.2174\/1573397113666170425150133","article-title":"Clinical and Radiographic Features of Knee Osteoarthritis of Elderly Patients","volume":"14","author":"Hana","year":"2018","journal-title":"Curr. Rheumatol. Rev."},{"key":"ref_19","first-page":"769","article-title":"The GSK-3\u03b2\/\u0392-catenin Signaling Pathway Is Involved in HMGB1-induced Chondrocyte Apoptosis and Cartilage Matrix Degradation","volume":"45","author":"Shu","year":"2020","journal-title":"Int. J. Mol. Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/j.joca.2025.11.003","article-title":"Uncovering Causal Genetic Mediators Linking Redefined Obesity to Osteoarthritis: Multidimensional Analysis from Population to Genetic Mechanisms","volume":"34","author":"Yang","year":"2025","journal-title":"Osteoarthr. Cartil."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1136\/ard-2023-225324","article-title":"Global Burden of Early-Onset Osteoarthritis, 1990\u20132019: Results from the Global Burden of Disease Study 2019","volume":"83","author":"Weng","year":"2024","journal-title":"Ann. Rheum. Dis."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Laires, P.A., Canh\u00e3o, H., Rodrigues, A.M., Eus\u00e9bio, M., Gouveia, M., and Branco, J.C. (2018). The Impact of Osteoarthritis on Early Exit from Work: Results from a Population-Based Study. BMC Public Health, 18.","DOI":"10.1186\/s12889-018-5381-1"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/j.joca.2025.10.016","article-title":"Intersectional Racial, Ethnic, and Sex-Based Disparities in Length of Stay after Total Hip and Knee Arthroplasty: An Analysis of National Data","volume":"34","author":"Rumalla","year":"2025","journal-title":"Osteoarthr. Cartil."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.joca.2021.05.007","article-title":"The Burden of OA-Health Services and Economics","volume":"30","author":"Leifer","year":"2022","journal-title":"Osteoarthr. Cartil."},{"key":"ref_25","first-page":"A4","article-title":"Advances in Osteoarthritis Research: From Diagnosis, Treatment to Mechanism Studies","volume":"44","author":"Lv","year":"2024","journal-title":"J. Orthop. Transl."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Wu, J., Zhang, Z., Ma, X., and Liu, X. (2023). Advances in Research on the Regulatory Roles of LncRNAs in Osteoarthritic Cartilage. Biomolecules, 13.","DOI":"10.3390\/biom13040580"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"582","DOI":"10.3892\/etm.2021.10014","article-title":"Changes of Type II Collagenase Biomarkers on IL-1\u03b2-Induced Rat Articular Chondrocytes","volume":"21","author":"Ma","year":"2021","journal-title":"Exp. Ther. Med."},{"key":"ref_28","first-page":"323","article-title":"Chinese guidelines for diagnosis and treatment of osteoarthritis (2024 edition)","volume":"20","author":"Huang","year":"2024","journal-title":"Chin. J. Painol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e70114","DOI":"10.1111\/cbdd.70114","article-title":"A Comprehensive Review on the Advancements of Dual COX-2\/5-LOX Inhibitors as Anti-Inflammatory Drugs","volume":"105","author":"Agrawal","year":"2025","journal-title":"Chem. Biol. Drug Des."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"101827","DOI":"10.1016\/j.bonr.2025.101827","article-title":"Long-Term Effects of Infrapatellar Fat Pad SVF Infiltration in Knee Osteoarthritis Management: A Prospective Cohort Study","volume":"24","author":"Labarre","year":"2025","journal-title":"Bone Rep."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Qin, Y., Di, J., Guo, Z., Chen, S., and Xiang, C. (2025). Association of Organs-Crosstalk with the Pathogenesis of Osteoarthritis: Cartilage as a Key Player. Front. Endocrinol., 16.","DOI":"10.3389\/fendo.2025.1593658"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"pgac258","DOI":"10.1093\/pnasnexus\/pgac258","article-title":"Hip Osteoarthritis: A Novel Network Analysis of Subchondral Trabecular Bone Structures","volume":"1","author":"Dorraki","year":"2022","journal-title":"PNAS Nexus"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.12659\/MSM.898218","article-title":"Advantages of Pure Platelet-Rich Plasma Compared with Leukocyte- and Platelet-Rich Plasma in Treating Rabbit Knee Osteoarthritis","volume":"22","author":"Yin","year":"2016","journal-title":"Med. Sci. Monit."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1016\/j.joca.2024.01.005","article-title":"Molecular Pathogenesis of OA Pain: Past, Present, and Future","volume":"32","author":"Vincent","year":"2024","journal-title":"Osteoarthr. Cartil."},{"key":"ref_35","first-page":"CD010842","article-title":"Exercise Interventions and Patient Beliefs for People with Hip, Knee or Hip and Knee Osteoarthritis: A Mixed Methods Review","volume":"4","author":"Hurley","year":"2018","journal-title":"Cochrane Database Syst. Rev."},{"key":"ref_36","first-page":"CD004376","article-title":"Exercise for Osteoarthritis of the Knee","volume":"2015","author":"Fransen","year":"2015","journal-title":"Cochrane Database Syst. Rev."},{"key":"ref_37","first-page":"CD008963","article-title":"Self-Management Education Programmes for Osteoarthritis","volume":"2014","author":"Kroon","year":"2014","journal-title":"Cochrane Database Syst. Rev."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1016\/j.jbiomech.2010.02.001","article-title":"Kinematic and Dynamic Analysis of an Anatomically Based Knee Joint","volume":"43","author":"Lee","year":"2010","journal-title":"J. Biomech."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"ziae119","DOI":"10.1093\/jbmrpl\/ziae119","article-title":"Lower Limb Joint Loading during High-Impact Activities: Implication for Bone Health","volume":"8","author":"Altai","year":"2024","journal-title":"JBMR Plus"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2969","DOI":"10.1007\/s11999-015-4349-z","article-title":"What Are the Prognostic Factors for Radiographic Progression of Knee Osteoarthritis? A Meta-Analysis","volume":"473","author":"Bastick","year":"2015","journal-title":"Clin. Orthop. Relat. Res."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"836","DOI":"10.7326\/M14-0318","article-title":"Prioritization of Patient-Centered Comparative Effectiveness Research for Osteoarthritis","volume":"160","author":"Gierisch","year":"2014","journal-title":"Ann. Intern. Med."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1002\/art.24273","article-title":"Expressing Pain and Fatigue: A New Method of Analysis to Explore Differences in Osteoarthritis Experience","volume":"61","author":"French","year":"2009","journal-title":"Arthritis Rheum."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1093\/fampra\/cmw071","article-title":"Pain Distribution in Primary Care Patients with Hip Osteoarthritis","volume":"33","author":"Poulsen","year":"2016","journal-title":"Fam. Pract."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Ye, M., Lin, Y., Pan, S., Wang, Z.-W., and Zhu, X. (2021). Applications of Multi-Omics Approaches for Exploring the Molecular Mechanism of Ovarian Carcinogenesis. Front. Oncol., 11.","DOI":"10.3389\/fonc.2021.745808"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s13052-025-02174-6","article-title":"Advances in Multi-Omics and Therapeutic Studies of Henoch-Sch\u00f6nlein Purpura","volume":"52","author":"Xu","year":"2025","journal-title":"Ital. J. Pediatr."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Kuang, J., Lin, Y., Wang, L., Yan, Z., Wei, J., Du, J., and Li, Z. (2024). Effects of PEF on Cell and Transcriptomic of Escherichia Coli. Microorganisms, 12.","DOI":"10.3390\/microorganisms12071380"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.cbpa.2012.12.008","article-title":"Transcriptomics in the RNA-Seq Era","volume":"17","author":"McGettigan","year":"2013","journal-title":"Curr. Opin. Chem. Biol."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Lowe, R., Shirley, N., Bleackley, M., Dolan, S., and Shafee, T. (2017). Transcriptomics Technologies. PLoS Comput. Biol., 13.","DOI":"10.1371\/journal.pcbi.1005457"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1007\/s11427-013-4557-2","article-title":"Transcriptomics: Advances and Approaches","volume":"56","author":"Dong","year":"2013","journal-title":"Sci. China Life Sci."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1017\/S0033583502003797","article-title":"A Review of DNA Sequencing Techniques","volume":"35","author":"Carrilho","year":"2002","journal-title":"Q. Rev. Biophys."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.csbj.2019.11.002","article-title":"Long Walk to Genomics: History and Current Approaches to Genome Sequencing and Assembly","volume":"18","author":"Giani","year":"2020","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"8077664","DOI":"10.1155\/2022\/8077664","article-title":"K-Mer Spectrum-Based Error Correction Algorithm for Next-Generation Sequencing Data","volume":"2022","author":"AlEisa","year":"2022","journal-title":"Comput. Intell. Neurosci."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: A Revolutionary Tool for Transcriptomics","volume":"10","author":"Wang","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"ref_54","unstructured":"Santra, T.S., and Tseng, F.-G. (2018). Single-Cell Transcriptomics. Handbook of Single Cell Technologies, Springer."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1126\/science.aaw1219","article-title":"Slide-Seq: A Scalable Technology for Measuring Genome-Wide Expression at High Spatial Resolution","volume":"363","author":"Rodriques","year":"2019","journal-title":"Science"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1038\/s41588-025-02193-3","article-title":"High-Definition Spatial Transcriptomic Profiling of Immune Cell Populations in Colorectal Cancer","volume":"57","author":"Oliveira","year":"2025","journal-title":"Nat. Genet."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"3953","DOI":"10.1016\/j.cell.2024.05.055","article-title":"Open-ST: High-Resolution Spatial Transcriptomics in 3D","volume":"187","author":"Schott","year":"2024","journal-title":"Cell"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"102387","DOI":"10.1016\/j.gde.2025.102387","article-title":"Evolution of Comparative Transcriptomics: Biological Scales, Phylogenetic Spans, and Modeling Frameworks","volume":"94","author":"Zambon","year":"2025","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1093\/chromsci\/bmw167","article-title":"Proteomics: Technologies and Their Applications","volume":"55","author":"Aslam","year":"2017","journal-title":"J. Chromatogr. Sci."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"O\u2019Lone, C.E., Juh\u00e1sz, A., Nye-Wood, M., Dunn, H., Moody, D., Ral, J.-P., and Colgrave, M.L. (2023). Proteomic Exploration Reveals a Metabolic Rerouting Due to Low Oxygen during Controlled Germination of Malting Barley (Hordeum vulgare L.). Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1305381"},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"la Marca, G., Carling, R.S., Moat, S.J., Yahyaoui, R., Ranieri, E., Bonham, J.R., and Schielen, P.C.J.I. (2023). Current State and Innovations in Newborn Screening: Continuing to Do Good and Avoid Harm. Int. J. Neonatal Screen., 9.","DOI":"10.3390\/ijns9010015"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1038\/35015709","article-title":"Proteomics to Study Genes and Genomes","volume":"405","author":"Pandey","year":"2000","journal-title":"Nature"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"645","DOI":"10.21873\/cgp.20480","article-title":"Comparative Proteomics of CcRCC Cell Lines to Identify Kidney Cancer Progression Factors","volume":"21","author":"Park","year":"2024","journal-title":"Cancer Genom. Proteom."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"726869","DOI":"10.1155\/2011\/726869","article-title":"Lung Cancer Proteomics: Recent Advances in Biomarker Discovery","volume":"2011","author":"Indovina","year":"2011","journal-title":"Int. J. Proteom."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Teraiya, M., Perreault, H., and Chen, V.C. (2023). An Overview of Glioblastoma Multiforme and Temozolomide Resistance: Can LC-MS-Based Proteomics Reveal the Fundamental Mechanism of Temozolomide Resistance?. Front. Oncol., 13.","DOI":"10.3389\/fonc.2023.1166207"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Di Tucci, C., and Muzii, L. (2023). Chronic Pelvic Pain, Vulvar Pain Disorders, and Proteomics Profiles: New Discoveries, New Hopes. Biomedicines, 12.","DOI":"10.3390\/biomedicines12010001"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1111\/jre.13357","article-title":"Salivary Proteomics for Detecting Novel Biomarkers of Periodontitis: A Systematic Review","volume":"60","author":"Corana","year":"2025","journal-title":"J. Periodontal Res."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"3665","DOI":"10.1002\/pmic.200401031","article-title":"Current Two-dimensional Electrophoresis Technology for Proteomics","volume":"4","author":"Weiss","year":"2004","journal-title":"Proteomics"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"460763","DOI":"10.1016\/j.chroma.2019.460763","article-title":"The Evolution of Two-Dimensional Gel Electrophoresis\u2014From Proteomics to Emerging Alternative Applications","volume":"1615","author":"Lee","year":"2020","journal-title":"J. Chromatogr. A"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"4789","DOI":"10.1038\/s41598-024-55596-3","article-title":"Unveiling Molecular Mechanisms of Pepper Resistance to Phytophthora Capsici through Grafting Using ITRAQ-Based Proteomic Analysis","volume":"14","author":"Shi","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"2105","DOI":"10.1021\/pr060638v","article-title":"Comparing SILAC and Two-Dimensional Gel Electrophoresis Image Analysis for Profiling Urokinase Plasminogen Activator Signaling in Ovarian Cancer Cells","volume":"6","author":"Uitto","year":"2007","journal-title":"J. Proteome Res."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1007\/s44154-025-00268-z","article-title":"Temporal Proteomic Profiling via 4D-DIA Reveals Early Defense Mechanisms and Core Resistance Determinants in Soybean against Phakopsora Pachyrhizi","volume":"5","author":"Lu","year":"2025","journal-title":"Stress Biol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1007\/978-1-59745-255-7_7","article-title":"The Use of a Quantitative Cysteinyl-Peptide Enrichment Technology for High-Throughput Quantitative Proteomics","volume":"359","author":"Liu","year":"2007","journal-title":"Methods Mol. Biol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1089\/nsm.2020.0009","article-title":"Plasma Metabolomic Signatures of Chronic Obstructive Pulmonary Disease and the Impact of Genetic Variants on Phenotype-Driven Modules","volume":"3","author":"Gillenwater","year":"2020","journal-title":"Netw. Syst. Med."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1016\/j.jprot.2016.11.002","article-title":"LC-MS\/MS-Based Targeted Proteomics Quantitatively Detects the Interaction between P53 and MDM2 in Breast Cancer","volume":"152","author":"Zhang","year":"2017","journal-title":"J. Proteom."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"2100153","DOI":"10.1002\/pmic.202100153","article-title":"Targeted Liquid Chromatography-tandem Mass Spectrometry Analysis of Proteins: Basic Principles, Applications, and Perspectives","volume":"21","author":"Kulyyassov","year":"2021","journal-title":"Proteomics"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1074\/mcp.M900456-MCP200","article-title":"Synthetic Peptide Arrays for Pathway-Level Protein Monitoring by Liquid Chromatography-Tandem Mass Spectrometry","volume":"9","author":"Hewel","year":"2010","journal-title":"Mol. Cell. Proteom."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1074\/mcp.M300021-MCP200","article-title":"Mass Spectrometric Analysis of Protein Mixtures at Low Levels Using Cleavable 13C-Isotope-Coded Affinity Tag and Multidimensional Chromatography","volume":"2","author":"Hansen","year":"2003","journal-title":"Mol. Cell. Proteom."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1074\/mcp.M200066-MCP200","article-title":"Toward a Human Blood Serum Proteome","volume":"1","author":"Adkins","year":"2002","journal-title":"Mol. Cell. Proteom."},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Chen, Y., Liu, Y., and Gao, X. (2021). The Application of Single-Cell Technologies in Cardiovascular Research. Front. Cell Dev. Biol., 9.","DOI":"10.3389\/fcell.2021.751371"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1007\/978-1-4939-2987-0_5","article-title":"Genome-Wide Analysis of Protein and MRNA Copy Numbers in Single Escherichia Coli Cells with Single-Molecule Sensitivity","volume":"1346","author":"Taniguchi","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"0019","DOI":"10.34133\/research.0019","article-title":"Mass Spectrometry Imaging-Based Single-Cell Lipidomics Profiles Metabolic Signatures of Heart Failure","volume":"6","author":"Ren","year":"2023","journal-title":"Research"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1007\/978-1-0716-4402-7_9","article-title":"Functional Single-Cell Proteomics: Technology and Biological Applications","volume":"2902","author":"Su","year":"2025","journal-title":"Methods Mol. Biol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1038\/s41586-025-08584-0","article-title":"Mass-Spectrometry-Based Proteomics: From Single Cells to Clinical Applications","volume":"638","author":"Guo","year":"2025","journal-title":"Nature"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"1727","DOI":"10.1074\/mcp.M600162-MCP200","article-title":"Advances and Challenges in Liquid Chromatography-Mass Spectrometry-Based Proteomics Profiling for Clinical Applications","volume":"5","author":"Qian","year":"2006","journal-title":"Mol. Cell. Proteom."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1016\/j.joca.2012.05.006","article-title":"Identification of the Pathogenic Pathways in Osteoarthritic Hip Cartilage: Commonality and Discord between Hip and Knee OA","volume":"20","author":"Xu","year":"2012","journal-title":"Osteoarthr. Cartil."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"2208","DOI":"10.1136\/annrheumdis-2014-205980","article-title":"Knee and Hip Articular Cartilage Have Distinct Epigenomic Landscapes: Implications for Future Cartilage Regeneration Approaches","volume":"73","author":"Ramos","year":"2014","journal-title":"Ann. Rheum. Dis."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1016\/j.joca.2018.12.015","article-title":"Identification of Long Non-Coding RNAs Expressed in Knee and Hip Osteoarthritic Cartilage","volume":"27","author":"Ajekigbe","year":"2019","journal-title":"Osteoarthr. Cartil."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1021\/acs.jproteome.5b00946","article-title":"Elucidating the Molecular Composition of Cartilage by Proteomics","volume":"15","author":"Hsueh","year":"2016","journal-title":"J. Proteome Res."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1136\/annrheumdis-2017-211848","article-title":"A Novel Variant in GLIS3 Is Associated with Osteoarthritis","volume":"77","author":"Casalone","year":"2018","journal-title":"Ann. Rheum. Dis."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"110701","DOI":"10.1016\/j.intimp.2023.110701","article-title":"ANGPTL2 Aggravates LPS-Induced Septic Cardiomyopathy via NLRP3-Mediated Inflammasome in a DUSP1-Dependent Pathway","volume":"123","author":"Li","year":"2023","journal-title":"Int. Immunopharmacol."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"1784","DOI":"10.1158\/0008-5472.CAN-11-3878","article-title":"Tumor Cell\u2013Derived Angiopoietin-like Protein ANGPTL2 Is a Critical Driver of Metastasis","volume":"72","author":"Endo","year":"2012","journal-title":"Cancer Res."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1007\/s00774-019-01016-w","article-title":"Angiopoietin-like 2 Upregulation Promotes Human Chondrocyte Injury via NF-\u039aB and P38\/MAPK Signaling Pathway","volume":"37","author":"Shan","year":"2019","journal-title":"J. Bone Miner. Metab."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"2502108","DOI":"10.1002\/advs.202502108","article-title":"CCDC80 Protects against Aortic Dissection and Rupture by Maintaining the Contractile Smooth Muscle Cell Phenotype","volume":"12","author":"Xiao","year":"2025","journal-title":"Adv. Sci."},{"key":"ref_95","doi-asserted-by":"crossref","unstructured":"Yu, M., Peng, J., Lu, Y., Li, S., and Ding, K. (2024). Silencing Immune-Infiltrating Biomarker CCDC80 Inhibits Malignant Characterization and Tumor Formation in Gastric Cancer. BMC Cancer, 24.","DOI":"10.1186\/s12885-024-12451-y"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"2834","DOI":"10.1210\/jc.2012-2926","article-title":"Tumor Suppressor Role of the CL2\/DRO1\/CCDC80 Gene in Thyroid Carcinogenesis","volume":"98","author":"Ferraro","year":"2013","journal-title":"J. Clin. Endocrinol. Metab."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"203","DOI":"10.33549\/physiolres.934547","article-title":"Plasma Asprosin, CCDC80 and ANGPTL4 Levels Are Associated with Metabolic and Cardiovascular Risk in Patients with Inflammatory Bowel Disease","volume":"70","author":"Wang","year":"2021","journal-title":"Physiol. Res."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1186\/s13075-024-03326-5","article-title":"Thyroid Hormone Induces Ossification and Terminal Maturation in a Preserved OA Cartilage Biomimetic Model","volume":"26","author":"Korthagen","year":"2024","journal-title":"Arthritis Res. Ther."},{"key":"ref_99","first-page":"92","article-title":"Human HtrA1 in the Archived Eyes with Age-Related Macular Degeneration","volume":"105","author":"Chan","year":"2007","journal-title":"Trans. Am. Ophthalmol. Soc."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"1543","DOI":"10.1093\/hmg\/ddab140","article-title":"Human Photoreceptor Cells from Different Macular Subregions Have Distinct Transcriptional Profiles","volume":"30","author":"Voigt","year":"2021","journal-title":"Hum. Mol. Genet."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"1279","DOI":"10.1177\/002215540305101004","article-title":"Distribution of the Serine Protease HtrA1 in Normal Human Tissues","volume":"51","author":"Severino","year":"2003","journal-title":"J. Histochem. Cytochem."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1042\/bj20021569","article-title":"Identification and Cloning of Two Isoforms of Human High-Temperature Requirement Factor A3 (HtrA3), Characterization of Its Genomic Structure and Comparison of Its Tissue Distribution with HtrA1 and HtrA2","volume":"371","author":"Nie","year":"2003","journal-title":"Biochem. J."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"859","DOI":"10.17219\/acem\/135939","article-title":"Overexpression of HTRA1 Increases the Proliferation and Migration of Retinal Pigment Epithelium","volume":"30","author":"Zhou","year":"2021","journal-title":"Adv. Clin. Exp. Med."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1186\/s12967-024-05098-7","article-title":"HTRA1-Driven Detachment of Type I Collagen from Endoplasmic Reticulum Contributes to Myocardial Fibrosis in Dilated Cardiomyopathy","volume":"22","author":"Shi","year":"2024","journal-title":"J. Transl. Med."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/j.bone.2005.03.015","article-title":"Expression of Mouse HtrA1 Serine Protease in Normal Bone and Cartilage and Its Upregulation in Joint Cartilage Damaged by Experimental Arthritis","volume":"37","author":"Tsuchiya","year":"2005","journal-title":"Bone"},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1016\/j.joca.2022.03.010","article-title":"The Serine Proteinase HtrA1 Is Ubiquitous and Abundant in Osteoarthritic Joints, but What Is It Doing?","volume":"30","author":"Wilkinson","year":"2022","journal-title":"Osteoarthr. Cartil."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1242\/dev.00999","article-title":"HtrA1 Serine Protease Inhibits Signaling Mediated by Tgf\u03b2 Family Proteins","volume":"131","author":"Oka","year":"2004","journal-title":"Development"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/j.joca.2008.07.010","article-title":"Differential transcriptome analysis of intraarticular lesional vs intact cartilage reveals new candidate genes in osteoarthritis pathophysiology","volume":"17","author":"Geyer","year":"2009","journal-title":"Osteoarthr. Cartil."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1177\/1947603518796122","article-title":"A Microarray Study of Articular Cartilage in Relation to Obesity and Severity of Knee Osteoarthritis","volume":"11","author":"Rai","year":"2020","journal-title":"CARTILAGE"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"e16553","DOI":"10.7717\/peerj.16553","article-title":"PH-Sensing G Protein-Coupled Orphan Receptor GPR68 Is Expressed in Human Cartilage and Correlates with Degradation of Extracellular Matrix during OA Progression","volume":"11","author":"Khan","year":"2023","journal-title":"PeerJ"},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"e003255","DOI":"10.1136\/rmdopen-2023-003255","article-title":"Cartilage Tissue from Sites of Weight Bearing in Patients with Osteoarthritis Exhibits a Differential Phenotype with Distinct Chondrocytes Subests","volume":"9","author":"Di","year":"2023","journal-title":"RMD Open"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"4135","DOI":"10.7150\/thno.109468","article-title":"Free Glutaraldehyde Gelatin Microsphere Loaded Mesenchymal Stem Cells Alleviate Osteoarthritis by Promoting Ext1 Expression","volume":"15","author":"Yuan","year":"2025","journal-title":"Theranostics"},{"key":"ref_113","doi-asserted-by":"crossref","unstructured":"Winstanley-Zarach, P., Rot, G., Kuba, S., Smagul, A., Peffers, M.J., and Tew, S.R. (2023). Analysis of RNA Polyadenylation in Healthy and Osteoarthritic Human Articular Cartilage. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24076611"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"2090","DOI":"10.1093\/hmg\/ddac017","article-title":"A Molecular Map of Long Non-Coding RNA Expression, Isoform Switching and Alternative Splicing in Osteoarthritis","volume":"31","author":"Katsoula","year":"2022","journal-title":"Hum. Mol. Genet."},{"key":"ref_115","doi-asserted-by":"crossref","unstructured":"Han, L., Cheng, B., Wei, W., Liu, L., Cheng, S., Liu, H., Jia, Y., Wen, Y., and Zhang, F. (2024). Whole-Transcriptome Sequencing of Knee Joint Cartilage from Kashin\u2013Beck Disease and Osteoarthritis Patients. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25084348"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1186\/s13075-023-03164-x","article-title":"Identification of Candidate Genes and Chemicals Associated with Osteoarthritis by Transcriptome-Wide Association Study and Chemical-Gene Interaction Analysis","volume":"25","author":"Mei","year":"2023","journal-title":"Arthritis Res. Ther."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1186\/s13019-025-03462-2","article-title":"Elucidating the Role of LGALS3BP in Coronary Atherosclerosis: Integrating Bioinformatics and Machine Learning for Advanced Insights","volume":"20","author":"Zhao","year":"2025","journal-title":"J. Cardiothorac. Surg."},{"key":"ref_118","doi-asserted-by":"crossref","unstructured":"Guo, X., Ji, J., Jose Kumar Sreena, G.S., Hou, X., Luo, Y., Fu, X., Mei, Z., and Feng, Z. (2020). Computational Prediction of Antiangiogenesis Synergistic Mechanisms of Total Saponins of Panax Japonicus Against Rheumatoid Arthritis. Front. Pharmacol., 11.","DOI":"10.3389\/fphar.2020.566129"},{"key":"ref_119","doi-asserted-by":"crossref","unstructured":"Wang, T., He, C., Hu, M., Wu, H., Ou, S., Li, Y., and Fan, C. (2022). Subtyping Children with Asthma by Clustering Analysis of MRNA Expression Data. Front. Genet., 13.","DOI":"10.3389\/fgene.2022.974936"},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"e70201","DOI":"10.1111\/jcmm.70201","article-title":"Study on the Mechanism of Shenmai Injection in the Treatment of Sepsis","volume":"28","author":"Yang","year":"2024","journal-title":"J. Cell. Mol. Med."},{"key":"ref_121","doi-asserted-by":"crossref","unstructured":"Li, C., and Zheng, Z. (2021). Cartilage Targets of Knee Osteoarthritis Shared by Both Genders. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22020569"},{"key":"ref_122","doi-asserted-by":"crossref","unstructured":"Li, C., and Zheng, Z. (2021). Males and Females Have Distinct Molecular Events in the Articular Cartilage during Knee Osteoarthritis. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22157876"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"639","DOI":"10.2147\/IJGM.S444847","article-title":"Bioinformatics Analysis and Experimental Validation of Mitochondrial Autophagy Genes in Knee Osteoarthritis","volume":"17","author":"Tang","year":"2024","journal-title":"Int. J. Gen. Med."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"R91","DOI":"10.1186\/ar4535","article-title":"Genetic, Clinical and Radiographic Signs in Knee Osteoarthritis Susceptibility","volume":"16","author":"Minafra","year":"2014","journal-title":"Arthritis Res. Ther."},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"953","DOI":"10.2147\/JIR.S350432","article-title":"Chloride Channel and Inflammation-Mediated Pathogenesis of Osteoarthritis","volume":"15","author":"Lin","year":"2022","journal-title":"J. Inflamm. Res."},{"key":"ref_126","doi-asserted-by":"crossref","unstructured":"Bengue, M., Ferraris, P., Baronti, C., Diagne, C.T., Talignani, L., Wichit, S., Liegeois, F., Bisbal, C., Nougair\u00e8de, A., and Miss\u00e9, D. (2019). Mayaro Virus Infects Human Chondrocytes and Induces the Expression of Arthritis-Related Genes Associated with Joint Degradation. Viruses, 11.","DOI":"10.3390\/v11090797"},{"key":"ref_127","doi-asserted-by":"crossref","unstructured":"Chen, Y.-J., Chang, W.-A., Wu, L.-Y., Hsu, Y.-L., Chen, C.-H., and Kuo, P.-L. (2018). Systematic Analysis of Transcriptomic Profile of Chondrocytes in Osteoarthritic Knee Using Next-Generation Sequencing and Bioinformatics. J. Clin. Med., 7.","DOI":"10.3390\/jcm7120535"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"8935","DOI":"10.1038\/s41598-017-09335-6","article-title":"Integrative Epigenomics, Transcriptomics and Proteomics of Patient Chondrocytes Reveal Genes and Pathways Involved in Osteoarthritis","volume":"7","author":"Steinberg","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1016\/j.joca.2022.11.004","article-title":"Dysregulated Energy Metabolism Impairs Chondrocyte Function in Osteoarthritis","volume":"31","author":"Wu","year":"2023","journal-title":"Osteoarthr. Cartil."},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"6105","DOI":"10.2147\/JIR.S385648","article-title":"Single-Cell RNA Sequencing Reveals Transcriptional Changes in the Cartilage of Subchondral Insufficiency Fracture of the Knee","volume":"15","author":"Tang","year":"2022","journal-title":"J. Inflamm. Res."},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1136\/ard-2023-224420","article-title":"Unveiling Inflammatory and Prehypertrophic Cell Populations as Key Contributors to Knee Cartilage Degeneration in Osteoarthritis Using Multi-Omics Data Integration","volume":"83","author":"Fan","year":"2024","journal-title":"Ann. Rheum. Dis."},{"key":"ref_132","doi-asserted-by":"crossref","unstructured":"Sun, Z., Yan, M., Wang, J., Zhang, H., Ji, X., Xiao, Y., Wang, T., and Yu, T. (2024). Single-Cell RNA Sequencing Reveals Different Chondrocyte States in Femoral Cartilage between Osteoarthritis and Healthy Individuals. Front. Immunol., 15.","DOI":"10.3389\/fimmu.2024.1407679"},{"key":"ref_133","doi-asserted-by":"crossref","unstructured":"Sebastian, A., Murugesh, D.K., Mendez, M.E., Hum, N.R., Rios-Arce, N.D., McCool, J.L., Christiansen, B.A., and Loots, G.G. (2020). Global Gene Expression Analysis Identifies Age-Related Differences in Knee Joint Transcriptome during the Development of Post-Traumatic Osteoarthritis in Mice. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21010364"},{"key":"ref_134","doi-asserted-by":"crossref","unstructured":"Sebastian, A., McCool, J.L., Hum, N.R., Murugesh, D.K., Wilson, S.P., Christiansen, B.A., and Loots, G.G. (2021). Single-Cell RNA-Seq Reveals Transcriptomic Heterogeneity and Post-Traumatic Osteoarthritis-Associated Early Molecular Changes in Mouse Articular Chondrocytes. Cells, 10.","DOI":"10.3390\/cells10061462"},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"114785","DOI":"10.1016\/j.intimp.2025.114785","article-title":"Unveiling the Mechanisms of Mechanical Loading-Induced Knee Osteoarthritis through Transcriptomics","volume":"157","author":"Wu","year":"2025","journal-title":"Int. Immunopharmacol."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1177\/19476035231213174","article-title":"Analysis of Molecular Changes and Features in Rat Knee Osteoarthritis Cartilage: Progress From Cellular Changes to Structural Damage","volume":"16","author":"Zhao","year":"2025","journal-title":"CARTILAGE"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/j.joca.2022.10.003","article-title":"Transcriptomic Analyses of Joint Tissues during Osteoarthritis Development in a Rat Model Reveal Dysregulated Mechanotransduction and Extracellular Matrix Pathways","volume":"31","author":"Hu","year":"2023","journal-title":"Osteoarthr. Cartil."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"43514","DOI":"10.1074\/jbc.M407041200","article-title":"Proteomic Analysis of Articular Cartilage Shows Increased Type II Collagen Synthesis in Osteoarthritis and Expression of Inhibin \u0392A (Activin A), a Regulatory Molecule for Chondrocytes","volume":"279","author":"Hermansson","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1016\/j.jbspin.2007.12.003","article-title":"Proteomic Analysis of Human Articular Cartilage: Identification of Differentially Expressed Proteins in Knee Osteoarthritis","volume":"75","author":"Guo","year":"2008","journal-title":"Jt. Bone Spine"},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"2999","DOI":"10.1002\/rcm.2692","article-title":"Protein Profile of Osteoarthritic Human Articular Cartilage Using Tandem Mass Spectrometry","volume":"20","author":"Garcia","year":"2006","journal-title":"Rapid Commun. Mass Spectrom."},{"key":"ref_141","doi-asserted-by":"crossref","unstructured":"Chen, G., Zhang, H., and Bai, X. (2025). FGA Can Be Used as a Promising Therapeutic Target in Osteoarthritis. BMC Musculoskelet. Disord., 26.","DOI":"10.1186\/s12891-025-08738-1"},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1080\/03008207.2024.2440716","article-title":"Proteomic Characterization of Regenerated Cartilage Following Knee Joint Distraction; a Human Case-Study","volume":"65","author":"Steijns","year":"2024","journal-title":"Connect. Tissue Res."},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"e22142","DOI":"10.1096\/fj.202101449R","article-title":"The Deterioration of Calcified Cartilage Integrity Reflects the Severity of Osteoarthritis\u2014A Structural, Molecular, and Biochemical Analysis","volume":"36","author":"Fan","year":"2022","journal-title":"FASEB J."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"100664","DOI":"10.1016\/j.ocarto.2025.100664","article-title":"A Proteomics Investigation of Primary Human Articular Chondrocyte Isolation","volume":"7","author":"Brumwell","year":"2025","journal-title":"Osteoarthr. Cartil. Open"},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.joca.2007.06.005","article-title":"Differential Proteome Analysis of Normal and Osteoarthritic Chondrocytes Reveals Distortion of Vimentin Network in Osteoarthritis","volume":"16","author":"Lambrecht","year":"2008","journal-title":"Osteoarthr. Cartil."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.jprot.2014.01.016","article-title":"Proteomic Analysis of Osteoarthritic Chondrocyte Reveals the Hyaluronic Acid-Regulated Proteins Involved in Chondroprotective Effect under Oxidative Stress","volume":"99","author":"Yu","year":"2014","journal-title":"J. Proteom."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s12014-015-9085-6","article-title":"Comparative Proteomic Analysis of Hypertrophic Chondrocytes in Osteoarthritis","volume":"12","author":"Tsolis","year":"2015","journal-title":"Clin. Proteom."},{"key":"ref_148","doi-asserted-by":"crossref","unstructured":"Balaskas, P., Goljanek-Whysall, K., Clegg, P.D., Fang, Y., Cremers, A., Smagul, A., Welting, T.J.M., and Peffers, M.J. (2023). MicroRNA Signatures in Cartilage Ageing and Osteoarthritis. Biomedicines, 11.","DOI":"10.3390\/biomedicines11041189"},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1080\/14789450.2021.1962299","article-title":"Chondrocyte Protein Co-Synthesis Network Analysis Links ECM Mechanosensing to Metabolic Adaptation in Osteoarthritis","volume":"18","author":"Destouni","year":"2021","journal-title":"Expert Rev. Proteom."},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/j.jare.2024.11.009","article-title":"Increased Rab1a Accelerates Osteoarthritis by Inhibiting Autophagy via Activation of the MTORC1-S6K Pathway","volume":"75","author":"Chen","year":"2024","journal-title":"J. Adv. Res."},{"key":"ref_151","first-page":"e920104","article-title":"Proteomics and Bioinformatics Analysis of Cartilage in Post-Traumatic Osteoarthritis in a Mini-Pig Model of Anterior Cruciate Ligament Repair","volume":"26","author":"Li","year":"2020","journal-title":"Med. Sci. Monit."},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"11553","DOI":"10.1038\/s41598-024-62516-y","article-title":"Sericin promotes chondrogenic proliferation and differentiation via glycolysis and Smad2\/3 TGF-\u03b2 signaling inductions and alleviates inflammation in three-dimensional models","volume":"14","author":"Fongsodsri","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1097\/NOR.0b013e3181a46a1c","article-title":"Femoroacetabular Impingement in Adolescents and Young Adults","volume":"28","author":"Hart","year":"2009","journal-title":"Orthop. Nurs."},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"135","DOI":"10.2106\/JBJS.O.00443","article-title":"Inflammation and Degeneration in Cartilage Samples from Patients with Femoroacetabular Impingement","volume":"98","author":"Chinzei","year":"2016","journal-title":"J. Bone Jt. Surg."},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/j.csm.2005.12.006","article-title":"Arthroscopy for the Treatment of Femoroacetabular Impingement in the Athlete","volume":"25","author":"Philippon","year":"2006","journal-title":"Clin. Sports Med."},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"S391","DOI":"10.1016\/j.arth.2022.03.013","article-title":"Otto Aufranc Award: Identification of Key Molecular Players in the Progression of Hip Osteoarthritis Through Transcriptomes and Epigenetics","volume":"37","author":"Kamenaga","year":"2022","journal-title":"J. Arthroplast."},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"1517","DOI":"10.1002\/jor.25485","article-title":"Whole-genome RNA Sequencing Identifies Distinct Transcriptomic Profiles in Impingement Cartilage between Patients with Femoroacetabular Impingement and Hip Osteoarthritis","volume":"41","author":"Kuhns","year":"2023","journal-title":"J. Orthop. Res."},{"key":"ref_158","doi-asserted-by":"crossref","unstructured":"Huang, J., Liu, M., Zhang, H., Sun, G., Furey, A., Rahman, P., and Zhai, G. (2024). Multi-Omics Integrative Analyses Identified Two Endotypes of Hip Osteoarthritis. Metabolites, 14.","DOI":"10.3390\/metabo14090480"},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1093\/hmg\/ddae200","article-title":"Transcriptomic Analysis of Human Cartilage Identified Potential Therapeutic Targets for Hip Osteoarthritis","volume":"34","author":"Huang","year":"2025","journal-title":"Hum. Mol. Genet."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"1481","DOI":"10.1093\/rheumatology\/key101","article-title":"Widespread Epigenomic, Transcriptomic and Proteomic Differences between Hip Osteophytic and Articular Chondrocytes in Osteoarthritis","volume":"57","author":"Steinberg","year":"2018","journal-title":"Rheumatology"},{"key":"ref_161","doi-asserted-by":"crossref","unstructured":"Aki, T., Hashimoto, K., Ogasawara, M., and Itoi, E. (2018). A Whole-Genome Transcriptome Analysis of Articular Chondrocytes in Secondary Osteoarthritis of the Hip. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0199734"},{"key":"ref_162","doi-asserted-by":"crossref","unstructured":"Southan, J., McHugh, E., Walker, H., and Ismail, H.M. (2020). Metabolic Signature of Articular Cartilage Following Mechanical Injury: An Integrated Transcriptomics and Metabolomics Analysis. Front. Mol. Biosci., 7.","DOI":"10.3389\/fmolb.2020.592905"},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1002\/jor.24158","article-title":"Targeted Proteomics of Hip Articular Cartilage in OA and Fracture Patients","volume":"37","author":"Hosseininia","year":"2019","journal-title":"J. Orthop. Res."},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"70","DOI":"10.22203\/eCM.v034a05","article-title":"Cartilage Matrix Remodelling Differs by Disease State and Joint Type","volume":"34","author":"Hsueh","year":"2017","journal-title":"Eur. Cells Mater."},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1159\/000535651","article-title":"Clinical Characteristics of Pathogenic ACAN Variants and 3-Year Response to Growth Hormone Treatment: Real-World Data","volume":"97","author":"Renes","year":"2024","journal-title":"Horm. Res. Paediatr."},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1016\/S0021-9258(17)35257-2","article-title":"Complete Coding Sequence and Deduced Primary Structure of the Human Cartilage Large Aggregating Proteoglycan, Aggrecan. Human-Specific Repeats, and Additional Alternatively Spliced Forms","volume":"266","author":"Doege","year":"1991","journal-title":"J. Biol. Chem."},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/sj.cr.7290106","article-title":"Structure and Function of Aggrecan","volume":"12","author":"Kiani","year":"2002","journal-title":"Cell Res."},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1297\/cpe.26.119","article-title":"ACAN Mutations as a Cause of Familial Short Stature","volume":"26","author":"Dateki","year":"2017","journal-title":"Clin. Pediatr. Endocrinol."},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"3432","DOI":"10.1021\/bm2004912","article-title":"Articular Cartilage Proteoglycans As Boundary Lubricants: Structure and Frictional Interaction of Surface-Attached Hyaluronan and Hyaluronan\u2013Aggrecan Complexes","volume":"12","author":"Seror","year":"2011","journal-title":"Biomacromolecules"},{"key":"ref_170","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/s41419-022-04919-1","article-title":"Synovial Mesenchymal Progenitor Derived Aggrecan Regulates Cartilage Homeostasis and Endogenous Repair Capacity","volume":"13","author":"Krawetz","year":"2022","journal-title":"Cell Death Dis."},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1097\/BOR.0000000000000845","article-title":"Blood and Urine Biomarkers in Osteoarthritis\u2014An Update on Cartilage Associated Type II Collagen and Aggrecan Markers","volume":"34","author":"Mobasheri","year":"2022","journal-title":"Curr. Opin. Rheumatol."},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"13646","DOI":"10.18632\/aging.205186","article-title":"Cabozantinib Prevents AGEs-Induced Degradation of Type 2 Collagen and Aggrecan in Human Chondrocytes","volume":"15","author":"Dong","year":"2023","journal-title":"Aging"},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"108968","DOI":"10.1016\/j.cbi.2020.108968","article-title":"The Protective Effects of Dulaglutide against Advanced Glycation End Products (AGEs)-Induced Degradation of Type II Collagen and Aggrecan in Human SW1353 Chondrocytes","volume":"322","author":"Li","year":"2020","journal-title":"Chem.-Biol. Interact."},{"key":"ref_174","doi-asserted-by":"crossref","first-page":"3668568","DOI":"10.1155\/2021\/3668568","article-title":"Effect of Resveratrol on Serum Levels of Type II Collagen and Aggrecan in Patients with Knee Osteoarthritis: A Pilot Clinical Study","volume":"2021","author":"Marouf","year":"2021","journal-title":"BioMed Res. Int."},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1016\/j.jid.2016.02.802","article-title":"Cartilage Oligomeric Matrix Protein Increases in Photodamaged Skin","volume":"136","author":"Kobayashi","year":"2016","journal-title":"J. Investig. Dermatol."},{"key":"ref_176","doi-asserted-by":"crossref","unstructured":"Cui, J., and Zhang, J. (2022). Cartilage Oligomeric Matrix Protein, Diseases, and Therapeutic Opportunities. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23169253"},{"key":"ref_177","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.matbio.2018.02.023","article-title":"Cartilage Oligomeric Matrix Protein: COMPopathies and Beyond","volume":"71\u201372","author":"Posey","year":"2018","journal-title":"Matrix Biol."},{"key":"ref_178","doi-asserted-by":"crossref","unstructured":"Maly, K., Andres Sastre, E., Farrell, E., Meurer, A., and Zaucke, F. (2021). COMP and TSP-4: Functional Roles in Articular Cartilage and Relevance in Osteoarthritis. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22052242"},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"107183","DOI":"10.1016\/j.jmbbm.2025.107183","article-title":"Therapeutic Potential of COMP and TIMP-3 in Preserving Cartilage Integrity Compromised by Proteases: A Histo-Mechanical Study","volume":"172","author":"Istiak","year":"2025","journal-title":"J. Mech. Behav. Biomed. Mater."},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"37758","DOI":"10.1074\/jbc.M111.248039","article-title":"Cartilage Intermediate Layer Protein 2 (CILP-2) Is Expressed in Articular and Meniscal Cartilage and Down-Regulated in Experimental Osteoarthritis","volume":"286","author":"Bernardo","year":"2011","journal-title":"J. Biol. Chem."},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/s10616-025-00856-x","article-title":"CHRDL2 Inhibits the Progression of Osteoarthritis by Regulating the Balance of Th17\/Treg","volume":"77","author":"Li","year":"2025","journal-title":"Cytotechnology"},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"15337","DOI":"10.1523\/JNEUROSCI.3467-10.2010","article-title":"Metzincin Proteases and Their Inhibitors: Foes or Friends in Nervous System Physiology?","volume":"30","author":"Rivera","year":"2010","journal-title":"J. Neurosci."},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1016\/j.bbadis.2011.08.009","article-title":"Proteoglycan Degradation by the ADAMTS Family of Proteinases","volume":"1812","author":"Stanton","year":"2011","journal-title":"Biochim. Biophys. Acta (BBA) -Mol. Basis Dis."},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.matbio.2024.12.005","article-title":"Cleavage of Cartilage Oligomeric Matrix Protein (COMP) by ADAMTS4 Generates a Neoepitope Associated with Osteoarthritis and Other Forms of Degenerative Joint Disease","volume":"135","author":"Folgado","year":"2025","journal-title":"Matrix Biol."},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"7959","DOI":"10.1002\/jcb.26600","article-title":"IL-1\u03b2-induced MiR-34a Up-regulation Inhibits Cyr61 to Modulate Osteoarthritis Chondrocyte Proliferation through ADAMTS-4","volume":"119","author":"Yang","year":"2018","journal-title":"J. Cell. Biochem."},{"key":"ref_186","doi-asserted-by":"crossref","first-page":"R107","DOI":"10.1186\/ar2311","article-title":"SOX9 Transduction of a Human Chondrocytic Cell Line Identifies Novel Genes Regulated in Primary Human Chondrocytes and in Osteoarthritis","volume":"9","author":"Tew","year":"2007","journal-title":"Arthritis Res. Ther."},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/s00223-009-9311-1","article-title":"Cytokine Receptor-Like Factor 1 Is Highly Expressed in Damaged Human Knee Osteoarthritic Cartilage and Involved in Osteoarthritis Downstream of TGF-\u03b2","volume":"86","author":"Tsuritani","year":"2010","journal-title":"Calcif. Tissue Int."},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1186\/s10020-021-00369-1","article-title":"Suppression of CRLF1 Promotes the Chondrogenic Differentiation of Bone Marrow-Derived Mesenchymal Stem and Protects Cartilage Tissue from Damage in Osteoarthritis via Activation of MiR-320","volume":"27","author":"Xu","year":"2021","journal-title":"Mol. Med."},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"113643","DOI":"10.1016\/j.intimp.2024.113643","article-title":"Inhibition of CRLF1 Expression by MiR-8485 Alleviates IL-1\u03b2-Induced Chondrocyte Inflammation, Apoptosis, and Extracellular Matrix Degradation","volume":"144","author":"Yang","year":"2025","journal-title":"Int. Immunopharmacol."},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"102504","DOI":"10.1016\/j.tice.2024.102504","article-title":"ENO1 Regulates IL-1\u03b2-Induced Chondrocyte Inflammation, Apoptosis and Matrix Degradation Possibly through the Potential Binding to CRLF1","volume":"90","author":"Lu","year":"2024","journal-title":"Tissue Cell"},{"key":"ref_191","doi-asserted-by":"crossref","first-page":"112589","DOI":"10.1016\/j.celrep.2023.112589","article-title":"METTL3-Mediated M6A Modification of IGFBP7-OT Promotes Osteoarthritis Progression by Regulating the DNMT1\/DNMT3a-IGFBP7 Axis","volume":"42","author":"Tang","year":"2023","journal-title":"Cell Rep."},{"key":"ref_192","doi-asserted-by":"crossref","first-page":"2901","DOI":"10.1002\/art.22042","article-title":"Increase in Production of Matrix Metalloproteinase 13 by Human Articular Chondrocytes Due to Stimulation with S100A4: Role of the Receptor for Advanced Glycation End Products","volume":"54","author":"Yammani","year":"2006","journal-title":"Arthritis Rheum."}],"container-title":["Biomolecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2218-273X\/16\/9\/1363\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T09:57:53Z","timestamp":1789984673000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2218-273X\/16\/9\/1363"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,18]]},"references-count":192,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["biom16091363"],"URL":"https:\/\/doi.org\/10.3390\/biom16091363","relation":{},"ISSN":["2218-273X"],"issn-type":[{"value":"2218-273X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,18]]}}}