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Clarke E, Varela L, Jenkins RE, Lozano-Andrés E, Cywińska A, Przewozny M, van Weeren PR, van de Lest CH, Peffers M, Wauben MH. Proteome and phospholipidome interrelationship of synovial fluid-derived extracellular vesicles in equine osteoarthritis: An exploratory 'multi-omics' study to identify composite biomarkers. Biochem Biophys Rep 2024; 37:101635. [PMID: 38298208 PMCID: PMC10828605 DOI: 10.1016/j.bbrep.2023.101635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/15/2023] [Accepted: 12/29/2023] [Indexed: 02/02/2024] Open
Abstract
Osteoarthritis causes progressive joint deterioration, severe morbidity, and reduced mobility in both humans and horses. Currently, osteoarthritis is diagnosed at late stages through clinical examination and radiographic imaging, hence it is challenging to address and provide timely therapeutic interventions to slow disease progression or ameliorate symptoms. Extracellular vesicles are cell-derived vesicles that play a key role in cell-to-cell communication and are potential sources for specific composite biomarker panel discovery. We here used a multi-omics strategy combining proteomics and phospholipidomics in an integral approach to identify composite biomarkers associated to purified extracellular vesicles from synovial fluid of healthy, mildly and severely osteoarthritic equine joints. Although the number of extracellular vesicles was unaffected by osteoarthritis, proteome profiling of extracellular vesicles by mass spectrometry identified 40 differentially expressed proteins (non-adjusted p < 0.05) in osteoarthritic joints associated with 7 significant canonical pathways in osteoarthritis. Moreover, pathway analysis unveiled changes in disease and molecular functions during osteoarthritis development. Phospholipidome profiling by mass spectrometry showed a relative increase in sphingomyelin and a decrease in phosphatidylcholine, phosphatidylinositol, and phosphatidylserine in extracellular vesicles derived from osteoarthritic joints compared to healthy joints. Unsupervised data integration revealed positive correlations between the proteome and the phospholipidome. Comprehensive analysis showed that some phospholipids and their related proteins increased as the severity of osteoarthritis progressed, while others decreased or remained stable. Altogether our data show interrelationships between synovial fluid extracellular vesicle-associated phospholipids and proteins responding to osteoarthritis pathology and which could be explored as potential composite diagnostic biomarkers of disease.
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Affiliation(s)
- Emily Clarke
- Department of Musculoskeletal Biology and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Laura Varela
- Division Equine Sciences, Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Division Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Rosalind E. Jenkins
- Centre for Drug Safety Science Bioanalytical Facility, Liverpool Shared Research Facilities, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Estefanía Lozano-Andrés
- Division Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Division of Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Anna Cywińska
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland
| | | | - P. René van Weeren
- Division Equine Sciences, Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Chris H.A. van de Lest
- Division Equine Sciences, Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Division Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Mandy Peffers
- Department of Musculoskeletal Biology and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Marca H.M. Wauben
- Division Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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Curry PDK, Morris AP, Barton A, Bluett J. Do genetics contribute to TNF inhibitor response prediction in Psoriatic Arthritis? THE PHARMACOGENOMICS JOURNAL 2023; 23:1-7. [PMID: 36243888 PMCID: PMC9925377 DOI: 10.1038/s41397-022-00290-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 09/09/2022] [Accepted: 09/22/2022] [Indexed: 02/15/2023]
Abstract
Psoriatic arthritis (PsA) is a heterogeneous chronic musculoskeletal disease, affecting up to 30% of people with psoriasis. Research into PsA pathogenesis has led to the development of targeted therapies, including Tumor Necrosis Factor inhibitors (TNF-i). Good response is only achieved by ~60% of patients leading to 'trial and error' drug management approaches, adverse reactions and increasing healthcare costs. Robust and well-validated biomarker identification, and subsequent development of sensitive and specific assays, would facilitate the implementation of a stratified approach into clinical care. This review will summarise potential genetic biomarkers for TNF-i (adalimumab, etanercept and infliximab) response that have been reported to date. It will also comment upon the importance of managing clinical confounders when understanding drug response prediction. Variants in multiple gene regions including TNF-A, FCGR2A, TNFAIP3, TNFR1/TNFR1A/TNFRSF1A, TRAIL-R1/TNFRSF10A, FCGR3A have been reported to correlate with TNF-i response at various levels of statistical significance in patients with PsA. However, results were often from heterogenous and underpowered cohorts and none are currently implemented into clinical practice. External validation of genetic biomarkers in large, well-documented cohorts is required, and assessment of the predictive value of combining multiple genetic biomarkers with clinical measures is essential to clinically embed pharmacogenomics into PsA drug management.
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Affiliation(s)
- Philippa D K Curry
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Andrew P Morris
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Anne Barton
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK.,NIHR Manchester Biomedical Research Centre, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - James Bluett
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK. .,NIHR Manchester Biomedical Research Centre, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
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Eder L, Li Q, Rahmati S, Rahman P, Jurisica I, Chandran V. Defining imaging sub-phenotypes of psoriatic arthritis: integrative analysis of imaging data and gene expression in a PsA patient cohort. Rheumatology (Oxford) 2022; 61:4952-4961. [PMID: 35157043 PMCID: PMC9707284 DOI: 10.1093/rheumatology/keac078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/07/2022] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVES To define imaging sub-phenotypes in patients with PsA; determine their association with whole blood gene expression and identify biological pathways characterizing the sub-phenotypes. METHODS Fifty-five patients with PsA ready to initiate treatment for active disease were prospectively recruited. We performed musculoskeletal ultrasound assessment of the extent of inflammation in the following domains: synovitis, peritenonitis, tenosynovitis and enthesitis. Peripheral whole blood was profiled with RNAseq, and gene expression data were obtained. First, unsupervised cluster analysis was performed to define imaging sub-phenotypes that reflected the predominant tissue involved. Subsequently, principal component analysis was used to determine the association between imaging-defined sub-phenotypes and peripheral blood gene expression profile. Pathway enrichment analysis was performed to identify underlying mechanisms that characterize individual sub-phenotypes. RESULTS Cluster analysis revealed three imaging sub-phenotypes: (i) synovitis predominant [n = 31 (56%)]; (ii) enthesitis predominant [n = 13 (24%)]; (iii) peritenonitis predominant [n = 11 (20%)]. The peritenonitis-predominant sub-phenotype had the most severe clinical joint involvement, whereas the enthesitis-predominant sub-phenotype had the highest tender entheseal count. Unsupervised clustering of gene expression data identified three sub-phenotypes that partially overlapped with the imaging sub-phenotypes suggesting biological and clinical relevance of these sub-phenotypes. We therefore characterized enriched differential pathways, which included: immune system (innate system, B cells and neutrophil degranulation), complement system, platelet activation and coagulation function. CONCLUSIONS We identified three sub-phenotypes based on the predominant tissue involved in patients with active PsA. Distinct biological pathways may underlie these imaging sub-phenotypes seen in PsA, suggesting their biological and clinical importance.
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Affiliation(s)
- Lihi Eder
- Correspondence to: Lihi Eder, Women’s College Research Institute, Room 6326, Women’s College Hospital, 76 Grenville Street, Toronto, Ontario M5S 1B2, Canada. E-mail:
| | - Quan Li
- Princess Margaret Cancer Centre, University Health Network, University of Toronto
| | - Sara Rahmati
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON
| | - Proton Rahman
- Rheumatology Division, Department of Medicine, Memorial University, St. John’s, NL
| | - Igor Jurisica
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON,Departments of Medical Biophysics and Computer Science, Faculty of Dentistry University of Toronto, ON, Canada,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vinod Chandran
- Rheumatology Division, Department of Medicine,Institute of Medical Science,Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON,Rheumatology Division, Department of Medicine, Memorial University, St. John’s, NL,Department of Laboratory Medicine and Pathobiology, University of Toronto, ON, Canada
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O'Rielly DD, Rahman P. Clinical and molecular significance of genetic loci associated with psoriatic arthritis. Best Pract Res Clin Rheumatol 2021; 35:101691. [PMID: 34020887 DOI: 10.1016/j.berh.2021.101691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Psoriatic arthritis (PsA) is caused by a combination of environmental and multiple genetic factors, with clear evidence for a strong genetic basis. The remarkable accumulation of knowledge gained from genetic, pharmacogenetic, and therapeutic response of biologic agents in PsA has fundamentally changed and advanced our understanding of disease pathogenesis and has identified key signalling pathways. However, only one-quarter of the genetic contribution of PsA has been accounted for; and dissecting the genetic contributors of the cutaneous disease from those that would identify joint disease has been challenging. More importantly, the clinical utility of multiple proposed loci is unclear. In this review, we summarize the potential clinical relevance from established genetic associations and provide insight on the proposed molecular pathways that arise from these associations.
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Affiliation(s)
- Darren D O'Rielly
- Faculty of Medicine, Memorial University, Craig L Dobbin Genetics Research Centre, Suite 3M500, 300 Prince Philip Drive, St. John's, NL, A1B3V6, Canada
| | - Proton Rahman
- St. Clare's Mercy Hospital, 154 LeMarchant Rd, St. John's, Newfoundland, A1C5B8, Canada.
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