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Pye CR, Green DC, Anderson JR, Phelan MM, Fitzgerald MM, Comerford EJ, Peffers MJ. Determining predictive metabolomic biomarkers of meniscal injury in dogs with cranial cruciate ligament rupture. J Small Anim Pract 2024; 65:90-103. [PMID: 38013167 DOI: 10.1111/jsap.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/21/2023] [Accepted: 11/05/2023] [Indexed: 11/29/2023]
Abstract
OBJECTIVES This study used hydrogen nuclear magnetic resonance spectroscopy for the first time to examine differences in the metabolomic profile of stifle joint synovial fluid from dogs with cranial cruciate ligament rupture with and without meniscal injuries, in order to identify biomarkers of meniscal injury. Identifying a biomarker of meniscal injury could then ultimately be used to design a minimally invasive diagnostic test for meniscal injuries in dogs. MATERIALS AND METHODS Stifle joint synovial fluid was collected from dogs undergoing stifle joint surgery or arthrocentesis for lameness investigations. We used multi-variate statistical analysis using principal component analysis and univariate statistical analysis using one-way analysis of variance and analysis of co-variance to identify differences in the metabolomic profile between dogs with cranial cruciate ligament rupture and meniscal injury, cranial cruciate ligament rupture without meniscal injury, and neither cranial cruciate ligament rupture nor meniscal injury, taking into consideration clinical variables. RESULTS A total of 154 samples of canine synovial fluid were included in the study. Sixty-four metabolites were annotated to the hydrogen nuclear magnetic resonance spectroscopy spectra. Six spectral regions were found to be significantly altered (false discovery rate adjusted P-value <0.05) between groups with cranial cruciate ligament rupture with and without meniscal injury, including three attributed to nuclear magnetic resonance mobile lipids [mobile lipid -CH3 (P=0.016), mobile lipid -n(CH3 )3 (P=0.017), mobile unsaturated lipid (P=0.031)]. CLINICAL SIGNIFICANCE We identified an increase in nuclear magnetic resonance mobile lipids in the synovial fluid of dogs with meniscal injury which are of interest as potential biomarkers of meniscal injury.
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Affiliation(s)
- C R Pye
- Institute of Life Course and Medical Science, University of Liverpool, Liverpool, UK
| | - D C Green
- Institute of Life Course and Medical Science, University of Liverpool, Liverpool, UK
| | - J R Anderson
- Institute of Life Course and Medical Science, University of Liverpool, Liverpool, UK
| | - M M Phelan
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - M M Fitzgerald
- Institute of Life Course and Medical Science, University of Liverpool, Liverpool, UK
| | - E J Comerford
- Institute of Life Course and Medical Science, University of Liverpool, Liverpool, UK
| | - M J Peffers
- Institute of Life Course and Medical Science, University of Liverpool, Liverpool, UK
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Ersoy U, Kanakis I, Alameddine M, Pedraza-Vazquez G, Ozanne SE, Peffers MJ, Jackson MJ, Goljanek-Whysall K, Vasilaki A. Lifelong dietary protein restriction accelerates skeletal muscle loss and reduces muscle fibre size by impairing proteostasis and mitochondrial homeostasis. Redox Biol 2024; 69:102980. [PMID: 38064763 PMCID: PMC10755587 DOI: 10.1016/j.redox.2023.102980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 01/01/2024] Open
Abstract
The early life environment significantly affects the development of age-related skeletal muscle disorders. However, the long-term effects of lactational protein restriction on skeletal muscle are still poorly defined. Our study revealed that male mice nursed by dams fed a low-protein diet during lactation exhibited skeletal muscle growth restriction. This was associated with a dysregulation in the expression levels of genes related to the ribosome, mitochondria and skeletal muscle development. We reported that lifelong protein restriction accelerated loss of type-IIa muscle fibres and reduced muscle fibre size by impairing mitochondrial homeostasis and proteostasis at 18 months of age. However, feeding a normal-protein diet following lactational protein restriction prevented accelerated fibre loss and fibre size reduction in later life. These findings provide novel insight into the mechanisms by which lactational protein restriction hinders skeletal muscle growth and includes evidence that lifelong dietary protein restriction accelerated skeletal muscle loss in later life.
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Affiliation(s)
- Ufuk Ersoy
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Ioannis Kanakis
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK; Chester Medical School, Faculty of Medicine and Life Sciences, University of Chester, Chester, UK
| | - Moussira Alameddine
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Gibran Pedraza-Vazquez
- Department of Physiology, School of Medicine and REMEDI, CMNHS, University of Galway, Galway, Ireland
| | - Susan E Ozanne
- MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, University of Cambridge Metabolic Research Laboratories, Cambridge, UK
| | - Mandy Jayne Peffers
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Malcolm J Jackson
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK
| | - Katarzyna Goljanek-Whysall
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK; Department of Physiology, School of Medicine and REMEDI, CMNHS, University of Galway, Galway, Ireland
| | - Aphrodite Vasilaki
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences (ILCaMS), The MRC - Versus Arthritis Centre for Integrated Research Into Musculoskeletal Ageing (CIMA), University of Liverpool, Liverpool, UK.
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Stassen RHMJ, van den Akker GGH, Surtel DAM, Housmans BAC, Cremers A, Caron MMJ, Smagul A, Peffers MJ, van Rhijn LW, Welting TJM. Unravelling the Basic Calcium Phosphate crystal-dependent chondrocyte protein secretome; a role for TGF-β signaling. Osteoarthritis Cartilage 2023; 31:1035-1046. [PMID: 37075856 DOI: 10.1016/j.joca.2023.02.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 04/21/2023]
Abstract
OBJECTIVE Basic Calcium Phosphate (BCP) crystals play an active role in the progression of osteoarthritis (OA). However, the cellular consequences remain largely unknown. Therefore, we characterized for the first time the changes in the protein secretome of human OA articular chondrocytes as a result of BCP stimulation using two unbiased proteomic analysis methods. METHOD Isolated human OA articular chondrocytes were stimulated with BCP crystals and examined by Quantitative Reverse Transcription PCR (RT-qPCR) and enzyme-linked immune sorbent assay (ELISA) after twenty-four and forty-eight hours. Forty-eight hours conditioned media were analyzed by label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) and an antibody array. The activity of BCP dependent Transforming Growth Factor Beta (TGF-β) signaling was analyzed by RT-qPCR and luciferase reporter assays. The molecular consequences regarding BCP-dependent TGF-β signaling on BCP-dependent Interleukin 6 (IL-6) were investigated using specific pathway inhibitors. RESULTS Synthesized BCP crystals induced IL-6 expression and secretion upon stimulation of human articular chondrocytes. Concomitant induction of catabolic gene expression was observed. Analysis of conditioned media revealed a complex and diverse response with a large number of proteins involved in TGF-β signaling, both in activation of latent TGF-β and TGF-β superfamily members, which were increased compared to non-stimulated OA chondrocytes. Activity of this BCP driven TGF-β signaling was confirmed by increased activity of expression of TGF-β target genes and luciferase reporters. Inhibition of BCP driven TGF-β signaling resulted in decreased IL-6 expression and secretion with a moderate effect on catabolic gene expression. CONCLUSION BCP crystal stimulation resulted in a complex and diverse chondrocyte protein secretome response. An important role for BCP-dependent TGF-β signaling was identified in development of a pro-inflammatory environment.
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Affiliation(s)
- R H M J Stassen
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, The Netherlands
| | - G G H van den Akker
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, The Netherlands
| | - D A M Surtel
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, The Netherlands
| | - B A C Housmans
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, The Netherlands
| | - A Cremers
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, The Netherlands
| | - M M J Caron
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, The Netherlands
| | - A Smagul
- Department of Musculoskeletal Biology, Life Course and Medical Sciences, University of Liverpool, UK
| | - M J Peffers
- Department of Musculoskeletal Biology, Life Course and Medical Sciences, University of Liverpool, UK
| | - L W van Rhijn
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center +, Maastricht, The Netherlands
| | - T J M Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, The Netherlands; Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center +, Maastricht, The Netherlands.
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Timur UT, Jahr H, Anderson J, Green DC, Emans PJ, Smagul A, van Rhijn LW, Peffers MJ, Welting TJM. Identification of tissue-dependent proteins in knee OA synovial fluid. Osteoarthritis Cartilage 2021; 29:124-133. [PMID: 33166667 DOI: 10.1016/j.joca.2020.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/10/2020] [Accepted: 09/29/2020] [Indexed: 02/02/2023]
Abstract
OBJECTIVE For many proteins from osteoarthritic synovial fluid, their intra-articular tissue of origin remains unknown. In this study we performed comparative proteomics to identify osteoarthritis-specific and joint tissue-dependent secreted proteins that may serve as candidates for osteoarthritis biomarker development on a tissue-specific basis. DESIGN Protein secretomes of cartilage, synovium, Hoffa's fat pad and meniscus from knee osteoarthritis patients were determined using liquid chromatography tandem mass spectrometry, followed by label-free quantification. Validation of tissue-dependent protein species was conducted by ELISA on independent samples. Differential proteomes of osteoarthritic and non-osteoarthritic knee synovial fluids were obtained via similar proteomics approach, followed by ELISA validation. RESULTS Proteomics revealed 64 proteins highly secreted from cartilage, 94 from synovium, 37 from Hoffa's fat pad and 21 from meniscus. Proteomic analyses of osteoarthritic vs non-osteoarthritic knee synovial fluid revealed 70 proteins with a relatively higher abundance and 264 proteins with a relatively lower abundance in osteoarthritic synovial fluid. Of the 70 higher abundance proteins, 23 were amongst the most highly expressed in the secretomes of a specific intra-articular tissue measured. Tissue-dependent release was validated for SLPI, C8, CLU, FN1, RARRES2, MATN3, MMP3 and TNC. Abundance in synovial fluid of tissue-dependent proteins was validated for IGF2, AHSG, FN1, CFB, KNG and C8. CONCLUSIONS We identified proteins with a tissue-dependent release from intra-articular human knee OA tissues. A number of these proteins also had an osteoarthritis-specific abundance in knee synovial fluid. These proteins may serve as novel candidates for osteoarthritis biomarker development on a tissue-specific basis.
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Affiliation(s)
- U T Timur
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands; Department of Orthopedic Surgery, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands
| | - H Jahr
- Department of Anatomy and Cell Biology, RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany; Department of Orthopedic Surgery, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands
| | - J Anderson
- Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - D C Green
- Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - P J Emans
- Department of Orthopedic Surgery, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands
| | - A Smagul
- Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - L W van Rhijn
- Department of Orthopedic Surgery, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands
| | - M J Peffers
- Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - T J M Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands; Department of Orthopedic Surgery, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands.
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Paraskevaidi M, Hook PD, Morais CLM, Anderson JR, White R, Martin-Hirsch PL, Peffers MJ, Martin FL. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy to diagnose osteoarthritis in equine serum. Equine Vet J 2019; 52:46-51. [PMID: 30900769 DOI: 10.1111/evj.13115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 03/15/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Reliable and validated biomarkers for osteoarthritis (OA) are currently lacking. OBJECTIVES To develop an accurate and minimally invasive method to assess OA-affected horses and provide potential spectral markers indicative of disease. STUDY DESIGN Observational, cross-sectional study. METHODS Our cohort consisted of 15 horses with OA and 48 without clinical signs of the disease, which were used as controls. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy was used to investigate serum samples (50 μL) collected from these horses. Spectral processing and multivariate analysis revealed differences and similarities, allowing for detection of spectral biomarkers that discriminated between the two cohorts. A supervised classification algorithm, namely principal component analysis coupled with quadratic discriminant analysis (PCA-QDA), was applied to evaluate the diagnostic accuracy. RESULTS Segregation between the two different cohorts, OA-affected and controls, was achieved with 100% sensitivity and specificity. The six most discriminatory peaks were attributed to proteins and lipids. Four of the spectral peaks were elevated in OA horses, which could be potentially due to an increase in lipids, protein expression levels and collagen, all of which have been previously reported in OA. Two peaks were found decreased and were tentatively assigned to the reduction of proteoglycan content that is observed during OA. MAIN LIMITATIONS The control group had a wide range of ages and breeds. Presymptomatic OA cases were not included. Therefore, it remains unknown whether this test could also be used as an early diagnostic tool. CONCLUSIONS This spectrochemical approach could provide an accurate and cost-effective blood test, facilitating point-of-care diagnosis of equine OA.
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Affiliation(s)
- M Paraskevaidi
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, UK
| | - P D Hook
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - C L M Morais
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, UK
| | - J R Anderson
- Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - R White
- Myerscough College, Preston, UK
| | - P L Martin-Hirsch
- Sharoe Green Unit, Lancashire Teaching Hospitals NHS Foundation, Preston, UK
| | - M J Peffers
- Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - F L Martin
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, UK
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Bardell D, Milner PI, Goljanek-Whysall K, Peffers MJ. Differences in plasma and peritoneal fluid proteomes identifies potential biomarkers associated with survival following strangulating small intestinal disease. Equine Vet J 2019; 51:727-732. [PMID: 30854696 DOI: 10.1111/evj.13094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 03/02/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Strangulating small intestinal disease (SSID) carries a poor prognosis for survival in comparison to other types of colic, particularly if resection is required. Identification of markers which aid early diagnosis may prevent the need for resection, assist with more accurate prognostication and/or support the decision on whether surgical intervention is likely to be successful, would be of significant welfare benefit. OBJECTIVES To apply an unbiased methodology to investigate the plasma and peritoneal fluid proteomes in horses diagnosed with SSID requiring resection, to identify novel biomarkers which may be of diagnostic or prognostic value. STUDY DESIGN Prospective clinical study. METHODS Plasma and peritoneal fluid from horses presented with acute abdominal signs consistent with SSID was collected at initial clinical examination. Samples from eight horses diagnosed with SSID at surgery in which resection of affected bowel was performed and four control horses subjected to euthanasia for orthopaedic conditions were submitted for liquid chromatography tandem mass spectrometry. Protein expression profiles were determined using label-free quantification. Data were analysed using analysis of variance to identify differentially expressed proteins between control and all SSID horses and SSID horses which survived to hospital discharge and those which did not. Significance was assumed at P≤0.05. RESULTS A greater number of proteins were identified in peritoneal fluid than plasma of both SSID cases and controls, with 123 peritoneal fluid and 13 plasma proteins significantly differentially expressed (DE) between cases and controls (P<0.05, ≥2 fold change). Twelve peritoneal fluid proteins (P<0.036) and four plasma proteins (P<0.05) were significantly DE between SSID horses which survived and those which did not. MAIN LIMITATIONS A low number of samples were analysed, there was variation in duration and severity of SSID and only short-term outcome was considered. CONCLUSIONS Changes in peritoneal fluid proteome may provide a sensitive indicator of small intestinal strangulation and provide biomarkers relevant to prognosis.
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Affiliation(s)
- D Bardell
- Institute of Ageing and Chronic Disease, Department of Musculoskeletal Biology, University of Liverpool, Liverpool, UK.,Institute of Veterinary Science, University of Liverpool, Neston, Wirral, UK
| | - P I Milner
- Institute of Ageing and Chronic Disease, Department of Musculoskeletal Biology, University of Liverpool, Liverpool, UK.,Institute of Veterinary Science, University of Liverpool, Neston, Wirral, UK
| | - K Goljanek-Whysall
- Institute of Ageing and Chronic Disease, Department of Musculoskeletal Biology, University of Liverpool, Liverpool, UK
| | - M J Peffers
- Institute of Ageing and Chronic Disease, Department of Musculoskeletal Biology, University of Liverpool, Liverpool, UK
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Abstract
INTRODUCTION Synovial fluid (SF) is in close proximity to tissues which are primarily altered during articular disease and has significant potential to better understand the underlying disease pathogeneses of articular pathologies and biomarker discovery. Although development of mass spectrometry-based methods has allowed faster and higher sensitivity techniques, interrogation of the SF proteome has been hindered by its large protein concentration dynamic range, impeding quantification of lower abundant proteins. Areas covered: Recent advances have developed methodologies to reduce the large protein concentration dynamic range of SF and subsequently allow deeper exploration of the SF proteome. This review concentrates on methods to overcome biofluid complexity, mass spectrometry proteomics methodologies, extracellular vesicles proteomics and the application of advances within the field in clinical disease, including osteoarthritis, rheumatoid arthritis, spondyloarthritis and juvenile arthritis. A narrative review was conducted with articles searched using PubMed, 1991-2018. Expert opinion: The SF proteomics field faces various challenges, including the requirement for rigorous and standardised methods of sample collection/storage, the sensitivity and specificity of proteomic assays, techniques to combat the large protein concentration dynamic range and comprehensive data analysis to reduce falsely identified markers. Additionally, there are challenges in developing multi 'omic' integration techniques, with computational integration enhancing analysis.
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Affiliation(s)
- Mandy Jayne Peffers
- a Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease , University of Liverpool , Liverpool , UK
| | - Aibek Smagul
- a Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease , University of Liverpool , Liverpool , UK
| | - James Ross Anderson
- a Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease , University of Liverpool , Liverpool , UK
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Abstract
OBJECTIVE The purpose of this review is to describe highlights from original research publications related to osteoarthritis (OA), epigenetics and genomics with the intention of recognising significant advances. DESIGN To identify relevant papers a Pubmed literature search was conducted for articles published between April 2016 and April 2017 using the search terms 'osteoarthritis' together with 'genetics', 'genomics', 'epigenetics', 'microRNA', 'lncRNA', 'DNA methylation' and 'histone modification'. RESULTS The search term OA generated almost 4000 references. Publications using the combination of descriptors OA and genetics provided the most references (82 references). However this was reduced compared to the same period in the previous year; 8.1-2.1% (expressed as a percentage of the total publications combining the terms OA and genetics). Publications combining the terms OA with genomics (29 references), epigenetics (16 references), long non-coding RNA (lncRNA) (11 references; including the identification of novel lncRNAs in OA), DNA methylation (21 references), histone modification (3 references) and microRNA (miR) (79 references) were reviewed. Potential OA therapeutics such as histone deacetylase (HDAC) inhibitors have been identified. A number of non-coding RNAs may also provide targets for future treatments. CONCLUSION There continues to be a year on year increase in publications researching miRs in OA (expressed as a percentage of the total publications), with a doubling over the last 4 years. An overview on the last year's progress within the fields of epigenetics and genomics with respect to OA will be given.
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Affiliation(s)
- M J Peffers
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - P Balaskas
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - A Smagul
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
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Rubio-Martínez LM, Rioja E, Castro Martins M, Wipawee S, Clegg P, Peffers MJ. Local anaesthetics or their combination with morphine and/or magnesium sulphate are toxic for equine chondrocytes and synoviocytes in vitro. BMC Vet Res 2017; 13:318. [PMID: 29115971 PMCID: PMC5678813 DOI: 10.1186/s12917-017-1244-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 10/30/2017] [Indexed: 12/11/2022] Open
Abstract
Background Chondrotoxic effects of local anaesthetics are well reported in humans and some animal species but knowledge on their toxic effects on synoviocytes or equine chondrocytes or the effects on cellular production of inflammatory cytokines is limited. The purpose of this study was to evaluate the in vitro effects of local anaesthetics, morphine, magnesium sulphate (MgSO4) or their combinations on cell viability and pro-inflammatory cytokine gene expression of equine synoviocytes and chondrocytes. Equine synoviocytes and cartilage explants harvested from normal joints in a co-culture system were exposed to mepivacaine (4.4 mg/ml), bupivacaine (2.2 mg/ml), morphine (2.85 mg/ml) and MgSO4 (37 mg/ml) alone or each local anaesthetic plus morphine or MgSO4 or both together. Chondrocyte and synoviocyte cell viability was assessed by CellTiter-Glo Luminescent Cell Viability Assay. Synoviocyte gene expression of IL-1β, IL-6 or TNF-α was measured and compared using the ∆∆CT method. Results Morphine alone, MgSO4 alone or their combination did not alter cell viability or the expression of IL-1β, IL-6 or TNF-α. However, local anaesthetics alone or in combination with morphine and/or MgSO4 reduced cell viability and increased the gene expression of IL-1β, IL-6 or TNF-α. Single short exposure to local anaesthetics is toxic to both chondrocytes and synoviocytes and their combination with morphine and/or MgSO4 enhanced the cytotoxic effects. Conclusions This in vitro study gives further evidence of the absence of cytotoxic effects of morphine alone, MgSO4 alone or their combination on normal articular tissues. However, local anaesthetics alone or in combination with morphine and/or MgSO4 have cytotoxic effects on equine articular tissues. Electronic supplementary material The online version of this article (10.1186/s12917-017-1244-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- L M Rubio-Martínez
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Chester High Road, CH647TE, Neston, UK.
| | - E Rioja
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Chester High Road, CH647TE, Neston, UK
| | - M Castro Martins
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Chester High Road, CH647TE, Neston, UK
| | - S Wipawee
- Faculty of Veterinary Science, Rajamangala University of Technology Srivijaya (Thailand) and Institute of Aging and Chronic Disease, University of Liverpool, Liverpool, UK
| | - P Clegg
- Institute of Aging and Chronic Disease, University of Liverpool, Liverpool, UK
| | - M J Peffers
- Institute of Aging and Chronic Disease, University of Liverpool, Liverpool, UK
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Peffers MJ, Goljanek-Whysall K, Collins J, Fang Y, Rushton M, Loughlin J, Proctor C, Clegg PD. Decoding the Regulatory Landscape of Ageing in Musculoskeletal Engineered Tissues Using Genome-Wide DNA Methylation and RNASeq. PLoS One 2016; 11:e0160517. [PMID: 27533049 PMCID: PMC4988628 DOI: 10.1371/journal.pone.0160517] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/20/2016] [Indexed: 12/11/2022] Open
Abstract
Mesenchymal stem cells (MSC) are capable of multipotent differentiation into connective tissues and as such are an attractive source for autologous cell-based regenerative medicine and tissue engineering. Epigenetic mechanisms, like DNA methylation, contribute to the changes in gene expression in ageing. However there was a lack of sufficient knowledge of the role that differential methylation plays during chondrogenic, osteogenic and tenogenic differentiation from ageing MSCs. This study undertook genome level determination of the effects of DNA methylation on expression in engineered tissues from chronologically aged MSCs. We compiled unique DNA methylation signatures from chondrogenic, osteogenic, and tenogenic engineered tissues derived from young; n = 4 (21.8 years ± 2.4 SD) and old; n = 4 (65.5 years±8.3SD) human MSCs donors using the Illumina HumanMethylation 450 Beadchip arrays and compared these to gene expression by RNA sequencing. Unique and common signatures of global DNA methylation were identified. There were 201, 67 and 32 chondrogenic, osteogenic and tenogenic age-related DE protein-coding genes respectively. Findings inferred the nature of the transcript networks was predominantly for 'cell death and survival', 'cell morphology', and 'cell growth and proliferation'. Further studies are required to validate if this gene expression effect translates to cell events. Alternative splicing (AS) was dysregulated in ageing with 119, 21 and 9 differential splicing events identified in chondrogenic, osteogenic and tenogenic respectively, and enrichment in genes associated principally with metabolic processes. Gene ontology analysis of differentially methylated loci indicated age-related enrichment for all engineered tissue types in 'skeletal system morphogenesis', 'regulation of cell proliferation' and 'regulation of transcription' suggesting that dynamic epigenetic modifications may occur in genes associated with shared and distinct pathways dependent upon engineered tissue type. An altered phenotype in engineered tissues was observed with ageing at numerous levels. These changes represent novel insights into the ageing process, with implications for stem cell therapies in older patients. In addition we have identified a number of tissue-dependant pathways, which warrant further studies.
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Affiliation(s)
- Mandy Jayne Peffers
- Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, UK, CH64 7TE
| | - Katarzyna Goljanek-Whysall
- Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, UK, CH64 7TE
| | - John Collins
- Thurston Arthritis Research Centre, School Of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA, 27599
| | - Yongxiang Fang
- Centre for Genomic Research, Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, UK, L69 7ZB
| | - Michael Rushton
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK, NE2 4HH
| | - John Loughlin
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK, NE2 4HH
| | - Carole Proctor
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK, NE2 4HH
- Newcastle University Institute for Ageing, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, UK, NE4 5PL
| | - Peter David Clegg
- Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, UK, CH64 7TE
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Peffers MJ, Collins J, Fang Y, Goljanek-Whysall K, Rushton M, Loughlin J, Proctor C, Clegg PD, Clegg PD. Age-related changes in mesenchymal stem cells identified using a multi-omics approach. Eur Cell Mater 2016; 31:136-59. [PMID: 26853623 DOI: 10.22203/ecm.v031a10] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Mesenchymal stem cells (MSC) are capable of multipotent differentiation into connective tissues and as such are an attractive source for autologous cell-based treatments for many clinical diseases and injuries. Ageing is associated with various altered cellular phenotypes coupled with a variety of transcriptional, epigenetic and translational changes. Furthermore, the regeneration potential of MSCs is reduced with increasing age and is correlated with changes in cellular functions. This study used a systems biology approach to investigate the transcriptomic (RNASeq), epigenetic (miRNASeq and DNA methylation) and protein alterations in ageing MSCs in order to understand the age-related functional and biological variations, which may affect their applications to regenerative medicine. We identified no change in expression of the cellular senescence markers. Alterations were evident at both the transcriptional and post-transcriptional level in a number of transcription factors. There was enrichment in genes involved in developmental disorders at mRNA and differential methylated loci (DML) level. Alterations in energy metabolism were apparent at the DML and protein level. The microRNA miR-199b-5p, whose expression was reduced in old MSCs, had predicted gene targets involved in energy metabolism and cell survival. Additionally, enrichment of DML and proteins in cell survival was evident. Enrichment in metabolic processes was revealed at the protein level and in genes identified as undergoing alternate splicing. Overall, an altered phenotype in MSC ageing at a number of levels implicated roles for inflamm-ageing and mitochondrial ageing. Identified changes represent novel insights into the ageing process, with implications for stem cell therapies in older patients.
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Affiliation(s)
- M J Peffers
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, The University of Liverpool, Leahurst, Neston, CH64 7TE,
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Abstract
Osteoarthritis is characterized by a loss of extracellular matrix that leads to cartilage degradation and joint space narrowing. Specific proteases, including the aggrecanases ADAMTS-4 and matrix metalloproteinase 3, are important in initiating and promoting cartilage degradation in osteoarthritis. This study investigated protease-specific and disease-specific cleavage patterns of particular extracellular matrix proteins by comparing new peptide fragments, neopeptides, in specific exogenous protease-driven digestion of a crude cartilage proteoglycan extract and an in-vitro model of early osteoarthritis. Additionally, equine cartilage explants were treated with interleukin-1 and the media collected. Proteolytic cleavage products following trypsin digestion were then identified using tandem mass spectrometry. Complete sequences of proteolytically cleaved neopeptides were determined for the major cartilage proteoglycans aggrecan, biglycan, decorin, fibromodulin plus cartilage oligomeric matrix protein. The generation of neopeptides varied with enzyme specificity; however, some peptides were common to all samples. Previous known and novel cleavage sites were identifies. The identification of novel peptide fragments provides a platform for the development of antibodies that could assist in the identification of biomarkers for osteoarthritis (OA), as well as the identification of basic biochemical processes underlying OA.
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Affiliation(s)
- Mandy Jayne Peffers
- Department of Musculoskeletal BiologyInstitute of Ageing and Chronic DiseaseUniversity of Liverpool, LeahurstChester High RoadNestonWirralCH64 7TEUK
| | - David James Thornton
- Wellcome Trust Centre for Cell Matrix ResearchFaculty of Life SciencesMichael Smith BuildingOxford RoadManchesterM13 9PTUK
| | - Peter David Clegg
- Department of Musculoskeletal BiologyInstitute of Ageing and Chronic DiseaseUniversity of Liverpool, LeahurstChester High RoadNestonWirralCH64 7TEUK
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Peffers MJ, McDermott B, Clegg PD, Riggs CM. Comprehensive protein profiling of synovial fluid in osteoarthritis following protein equalization. Osteoarthritis Cartilage 2015; 23:1204-13. [PMID: 25819577 PMCID: PMC4528073 DOI: 10.1016/j.joca.2015.03.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/30/2015] [Accepted: 03/16/2015] [Indexed: 02/02/2023]
Abstract
OBJECTIVE The aim of the study was to characterise the protein complement of synovial fluid (SF) in health and osteoarthritis (OA) using liquid chromatography mass spectrometry (LC-MS/MS) following peptide-based depletion of high abundance proteins. DESIGN SF was used from nine normal and nine OA Thoroughbred horses. Samples were analysed with LC-MS/MS using a NanoAcquity™ LC coupled to an LTQ Orbitrap Velos. In order to enrich the lower-abundance protein fractions protein equalisation was first undertaken using ProteoMiner™. Progenesis-QI™ LC-MS software was used for label-free quantification. In addition immunohistochemistry, western blotting and mRNA expression analysis was undertaken on selected joint tissues. RESULTS The number of protein identifications was increased by 33% in the ProteoMiner™ treated SF compared to undepleted SF. A total of 764 proteins (462 with≥2 significant peptides) were identified in SF. A subset of 10 proteins were identified which were differentially expressed in OA SF. S100-A10, a calcium binding protein was upregulated in OA and validated with western blotting and immunohistochemistry. Several new OA specific peptide fragments (neopeptides) were identified. CONCLUSION The protein equalisation method compressed the dynamic range of the synovial proteins identifying the most comprehensive SF proteome to date. A number of proteins were identified for the first time in SF which may be involved in the pathogenesis of OA. We identified a distinct set of proteins and neopeptides that may act as potential biomarkers to distinguish between normal and OA joints.
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Affiliation(s)
- M J Peffers
- Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, CH64 7TE, UK.
| | - B McDermott
- Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, CH64 7TE, UK.
| | - P D Clegg
- Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, CH64 7TE, UK.
| | - C M Riggs
- Hong Kong Jockey Club, Equine Hospital, Sha Tin Racecourse, New Territories, Hong Kong.
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Peffers MJ, Fang Y, Cheung K, Wei TKJ, Clegg PD, Birch HL. Transcriptome analysis of ageing in uninjured human Achilles tendon. Arthritis Res Ther 2015; 17:33. [PMID: 25888722 PMCID: PMC4355574 DOI: 10.1186/s13075-015-0544-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 01/26/2015] [Indexed: 01/02/2023] Open
Abstract
INTRODUCTION The risk of tendon injury and disease increases significantly with increasing age. The aim of the study was to characterise transcriptional changes in human Achilles tendon during the ageing process in order to identify molecular signatures that might contribute to age-related degeneration. METHODS RNA for gene expression analysis using RNA-Seq and quantitative real-time polymerase chain reaction analysis was isolated from young and old macroscopically normal human Achilles tendon. RNA sequence libraries were prepared following ribosomal RNA depletion, and sequencing was undertaken by using the Illumina HiSeq 2000 platform. Expression levels among genes were compared by using fragments per kilobase of exon per million fragments mapped. Differentially expressed genes were defined by using Benjamini-Hochberg false discovery rate approach (P<0.05, expression ratios 1.4 log2 fold change). Alternative splicing of exon variants were also examined by using Cufflinks. The functional significance of genes that showed differential expression between young and old tendon was determined by using ingenuity pathway analysis. RESULTS In total, the expression of 325 transcribed elements, including protein-coding transcripts and non-coding transcripts (small non-coding RNAs, pseudogenes, long non-coding RNAs and a single microRNA), was significantly different in old compared with young tendon (±1.4 log2 fold change, P<0.05). Of these, 191 were at higher levels in older tendon and 134 were at lower levels in older tendon. The top networks for genes differentially expressed with tendon age were from cellular function, cellular growth, and cellular cycling pathways. Notable differential transcriptome changes were also observed in alternative splicing patterns. Several of the top gene ontology terms identified in downregulated isoforms in old tendon related to collagen and post-translational modification of collagen. CONCLUSIONS This study demonstrates dynamic alterations in RNA with age at numerous genomic levels, indicating changes in the regulation of transcriptional networks. The results suggest that ageing is not primarily associated with loss of ability to synthesise matrix proteins and matrix-degrading enzymes. In addition, we have identified non-coding RNA genes and differentially expressed transcript isoforms of known matrix components with ageing which require further investigation.
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Affiliation(s)
- Mandy Jayne Peffers
- Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, CH64 7TE, UK.
| | - Yongxiang Fang
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK.
| | - Kathleen Cheung
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Tim Koh Jia Wei
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, 535 Clementi Road, Singapore, 599489, Singapore.
| | - Peter David Clegg
- Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, CH64 7TE, UK.
| | - Helen Lucy Birch
- Institute of Orthopaedics and Musculoskeletal Science, University College London, Stanmore Campus, Royal National Orthopaedic Hospital, Brockley Hill, Stanmore, HA7 4LP, UK.
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Abstract
The musculoskeletal system is severely affected by the ageing process, with many tissues undergoing changes that lead to loss of function and frailty. Articular cartilage is susceptible to age related diseases, such as osteoarthritis. Applying RNA-Seq to young and old equine cartilage, we identified an over-representation of genes with reduced expression relating to extracellular matrix, degradative proteases, matrix synthetic enzymes, cytokines and growth factors in cartilage from older donors. Here we describe the contents and quality controls in detail for the gene expression and related results published by Peffers and colleagues in Arthritis Research and Therapy 2013 associated with the data uploaded to ArrayExpress (E-MTAB-1386).
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Affiliation(s)
- Mandy Jayne Peffers
- Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral CH64 7TE, United Kingdom
| | - Xuan Liu
- Centre for Genomic Research, Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Peter David Clegg
- Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral CH64 7TE, United Kingdom
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Tew SR, Vasieva O, Peffers MJ, Clegg PD. Post-transcriptional gene regulation following exposure of osteoarthritic human articular chondrocytes to hyperosmotic conditions. Osteoarthritis Cartilage 2011; 19:1036-46. [PMID: 21640843 DOI: 10.1016/j.joca.2011.04.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 04/26/2011] [Accepted: 04/30/2011] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Osmolarity is a major biophysical regulator of chondrocyte function. Modulation of chondrocytic marker gene expression occurs at the post-transcriptional level following exposure of human articular chondrocytes (HAC) to hyperosmotic conditions. This study aims to further characterise the post-transcriptional response of HAC to hyperosmolarity. METHODS Gene expression and microRNA (miRNA) levels in freshly isolated HAC after 5h under control or hyperosmotic conditions were measured using microarrays. Regulated genes were checked for the presence of AU rich elements (AREs) in their 3' untranslated regions (3'UTR), whilst gene ontology was examined using Ingenuity Pathway Analysis (IPA). RNA decay rates of candidate ARE-containing genes were determined in HAC using actinomycin D chase experiments and the involvement of the p38 mitogen-activated protein kinase (MAPK) and extracellular signal-regulated kinases 1 and 2 (ERK1/2) pathways were investigated using pharmacological inhibitors. RESULTS Hyperosmolarity led to the regulation of a wide variety of genes. IPA identified enrichment of genes involved with cell stress responses, cell signalling and transforming growth factor β (TGFβ) signalling. Importantly, upregulated genes were over-represented with those containing AREs, and RNA decay analysis demonstrated that many of these were regulated post-transcriptionally by hyperosmolarity in HAC. Analysis of miRNA levels in HAC indicated that they are only modestly regulated by hyperosmotic conditions, whilst inhibitor studies showed that p38 MAPK and ERK1/2 were able to block hyperosmotic induction of many of these genes. CONCLUSION Through microarray and bioinformatics analysis we have identified genes which are post-transcriptionally regulated in HAC following exposure to hyperosmotic conditions. These genes have a range of functions, and their regulation involves transduction through the p38 MAPK and ERK1/2 pathways. Interestingly, our results suggest that miRNA regulation is not key to the process. Overall, this work illustrates the range of processes regulated in chondrocytes by changes in their osmotic environment, and underlines the importance of post-transcriptional mRNA regulation to chondrocyte function.
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Affiliation(s)
- S R Tew
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst Campus, Neston, Cheshire, UK.
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