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Woods S, Charlton S, Cheung K, Hao Y, Soul J, Reynard LN, Crowe N, Swingler TE, Skelton AJ, Piróg KA, Miles CG, Tsompani D, Jackson RM, Dalmay T, Clark IM, Barter MJ, Young DA. microRNA-seq of cartilage reveals an overabundance of miR-140-3p which contains functional isomiRs. RNA 2020; 26:1575-1588. [PMID: 32660984 PMCID: PMC7566571 DOI: 10.1261/rna.075176.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/06/2020] [Indexed: 05/15/2023]
Abstract
miR-140 is selectively expressed in cartilage. Deletion of the entire Mir140 locus in mice results in growth retardation and early-onset osteoarthritis-like pathology; however, the relative contribution of miR-140-5p or miR-140-3p to the phenotype remains to be determined. An unbiased small RNA sequencing approach identified miR-140-3p as significantly more abundant (>10-fold) than miR-140-5p in human cartilage. Analysis of these data identified multiple miR-140-3p isomiRs differing from the miRBase annotation at both the 5' and 3' end, with >99% having one of two seed sequences (5' bases 2-8). Canonical (miR-140-3p.2) and shifted (miR-140-3p.1) seed isomiRs were overexpressed in chondrocytes and transcriptomics performed to identify targets. miR-140-3p.1 and miR-140-3p.2 significantly down-regulated 694 and 238 genes, respectively, of which only 162 genes were commonly down-regulated. IsomiR targets were validated using 3'UTR luciferase assays. miR-140-3p.1 targets were enriched within up-regulated genes in rib chondrocytes of Mir140-null mice and within down-regulated genes during human chondrogenesis. Finally, through imputing the expression of miR-140 from the expression of the host gene WWP2 in 124 previously published data sets, an inverse correlation with miR-140-3p.1 predicted targets was identified. Together these data suggest the novel seed containing isomiR miR-140-3p.1 is more functional than original consensus miR-140-3p seed containing isomiR.
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Affiliation(s)
- Steven Woods
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Sarah Charlton
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Kat Cheung
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Yao Hao
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
- Orthopedics Department, First Hospital of Shanxi Medical University, Yingze District, Taiyuan, 030000, China
| | - Jamie Soul
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Louise N Reynard
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Natalie Crowe
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Tracey E Swingler
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Andrew J Skelton
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Katarzyna A Piróg
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Colin G Miles
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Dimitra Tsompani
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Robert M Jackson
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Ian M Clark
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Matt J Barter
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - David A Young
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
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Swingler TE, Niu L, Smith P, Paddy P, Le L, Barter MJ, Young DA, Clark IM. The function of microRNAs in cartilage and osteoarthritis. Clin Exp Rheumatol 2019; 37 Suppl 120:40-47. [PMID: 31621575] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
MicroRNAs are small double-stranded RNAs, which negatively regulate gene expression and have been shown to have key roles in both chondrocyte development and cartilage homeostasis with age. Deletion of all microRNAs in chondrocytes leads to skeletal growth defects in mice, whilst deletion of specific microRNAs, e.g. miR-140, leads to premature articular cartilage degradation and increased susceptibility to posttraumatic osteoarthritis. Studies comparing microRNA expression in normal human articular cartilage compared to osteoarthritic cartilage show differential expression, but varying sample groups make interpretation difficult. MicroRNAs have been proposed as circulating biomarkers of osteoarthritis, but again, this differs amongst patient cohorts. Many micro-RNAs have been shown to have roles in chondrocyte phenotype via signalling pathways, apoptosis, autophagy and senescence. Modulating microRNAs in the joint has been shown to reduce osteoarthritis in animal models and translating this to man as a novel therapeutic strategy will be key.
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Affiliation(s)
| | - Lingzi Niu
- School of Biological Sciences, University of East Anglia, UK
| | - Perry Smith
- School of Biological Sciences, University of East Anglia, UK
| | - Paige Paddy
- School of Biological Sciences, University of East Anglia, UK
| | - Linh Le
- Biotechnology Department, Ho Chi Minh City Open University, Vietnam
| | | | - David A Young
- Institute of Genetic Medicine, Newcastle University, UK
| | - Ian M Clark
- School of Biological Sciences, University of East Anglia, UK.
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Snelling SJB, Davidson RK, Swingler TE, Le LTT, Barter MJ, Culley KL, Price A, Carr AJ, Clark IM. Dickkopf-3 is upregulated in osteoarthritis and has a chondroprotective role. Osteoarthritis Cartilage 2016; 24:883-91. [PMID: 26687825 PMCID: PMC4863878 DOI: 10.1016/j.joca.2015.11.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [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: 09/03/2015] [Revised: 11/06/2015] [Accepted: 11/24/2015] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Dickkopf-3 (Dkk3) is a non-canonical member of the Dkk family of Wnt antagonists and its upregulation has been reported in microarray analysis of cartilage from mouse models of osteoarthritis (OA). In this study we assessed Dkk3 expression in human OA cartilage to ascertain its potential role in chondrocyte signaling and cartilage maintenance. METHODS Dkk3 expression was analysed in human adult OA cartilage and synovial tissues and during chondrogenesis of ATDC5 and human mesenchymal stem cells. The role of Dkk3 in cartilage maintenance was analysed by incubation of bovine and human cartilage explants with interleukin-1β (IL1β) and oncostatin-M (OSM). Dkk3 gene expression was measured in cartilage following murine hip avulsion. Whether Dkk3 influenced Wnt, TGFβ and activin cell signaling was assessed in primary human chondrocytes and SW1353 chondrosarcoma cells using qRT-PCR and luminescence assays. RESULTS Increased gene and protein levels of Dkk3 were detected in human OA cartilage, synovial tissue and synovial fluid. DKK3 gene expression was decreased during chondrogenesis of both ATDC5 cells and humans MSCs. Dkk3 inhibited IL1β and OSM-mediated proteoglycan loss from human and bovine cartilage explants and collagen loss from bovine cartilage explants. Cartilage DKK3 expression was decreased following hip avulsion injury. TGFβ signaling was enhanced by Dkk3 whilst Wnt3a and activin signaling were inhibited. CONCLUSIONS We provide evidence that Dkk3 is upregulated in OA and may have a protective effect on cartilage integrity by preventing proteoglycan loss and helping to restore OA-relevant signaling pathway activity. Targeting Dkk3 may be a novel approach in the treatment of OA.
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Affiliation(s)
- S J B Snelling
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
| | - R K Davidson
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - T E Swingler
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - L T T Le
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - M J Barter
- Institute of Cellular Medicine, Newcastle University, Newcastle, UK
| | - K L Culley
- Hospital for Special Surgery and Weill Cornell Medical College, New York, NY, USA
| | - A Price
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - A J Carr
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - I M Clark
- School of Biological Sciences, University of East Anglia, Norwich, UK
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Le LTT, Swingler TE, Crowe N, Vincent TL, Barter MJ, Donell ST, Delany AM, Dalmay T, Young DA, Clark IM. The microRNA-29 family in cartilage homeostasis and osteoarthritis. J Mol Med (Berl) 2015; 94:583-96. [PMID: 26687115 PMCID: PMC4856728 DOI: 10.1007/s00109-015-1374-z] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [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] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/30/2015] [Indexed: 12/21/2022]
Abstract
Abstract MicroRNAs have been shown to function in cartilage development and homeostasis, as well as in progression of osteoarthritis. The objective of the current study was to identify microRNAs involved in the onset or early progression of osteoarthritis and characterise their function in chondrocytes. MicroRNA expression in mouse knee joints post-DMM surgery was measured over 7 days. Expression of miR-29b-3p was increased at day 1 and regulated in the opposite direction to its potential targets. In a mouse model of cartilage injury and in end-stage human OA cartilage, the miR-29 family was also regulated. SOX9 repressed expression of miR-29a-3p and miR-29b-3p via the 29a/b1 promoter. TGFβ1 decreased expression of miR-29a, b, and c (3p) in primary chondrocytes, whilst IL-1β increased (but LPS decreased) their expression. The miR-29 family negatively regulated Smad, NFκB, and canonical WNT signalling pathways. Expression profiles revealed regulation of new WNT-related genes. Amongst these, FZD3, FZD5, DVL3, FRAT2, and CK2A2 were validated as direct targets of the miR-29 family. These data identify the miR-29 family as microRNAs acting across development and progression of OA. They are regulated by factors which are important in OA and impact on relevant signalling pathways. Key messages Expression of the miR-29 family is regulated in cartilage during osteoarthritis. SOX9 represses expression of the miR-29 family in chondrocytes. The miR-29 family is regulated by TGF-β1 and IL-1 in chondrocytes. The miR-29 family negatively regulates Smad, NFκB, and canonical Wnt signalling. Several Wnt-related genes are direct targets of the miR-29 family.
Electronic supplementary material The online version of this article (doi:10.1007/s00109-015-1374-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Linh T T Le
- Biomedical Research Centre, School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Tracey E Swingler
- Biomedical Research Centre, School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Natalie Crowe
- Biomedical Research Centre, School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Tonia L Vincent
- Department of Cell Signalling, Kennedy Institute of Rheumatology, University of Oxford, Oxfordshire, UK
| | - Matthew J Barter
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Simon T Donell
- Institute of Orthopaedics, Norfolk and Norwich University Hospital, Norfolk, UK
| | - Anne M Delany
- Center for Molecular Medicine, University of Connecticut Health Center, Farmington, CT, USA
| | - Tamas Dalmay
- Biomedical Research Centre, School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - David A Young
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Ian M Clark
- Biomedical Research Centre, School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
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Soond SM, Smith PG, Wahl L, Swingler TE, Clark IM, Hemmings AM, Chantry A. Novel WWP2 ubiquitin ligase isoforms as potential prognostic markers and molecular targets in cancer. Biochim Biophys Acta Mol Basis Dis 2013; 1832:2127-35. [DOI: 10.1016/j.bbadis.2013.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/08/2013] [Accepted: 08/02/2013] [Indexed: 11/27/2022]
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Le LTT, Swingler TE, Clark IM. Review: the role of microRNAs in osteoarthritis and chondrogenesis. ACTA ACUST UNITED AC 2013; 65:1963-74. [PMID: 23666813 DOI: 10.1002/art.37990] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 04/23/2013] [Indexed: 12/21/2022]
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Culley KL, Hui W, Barter MJ, Davidson RK, Swingler TE, Destrument APM, Scott JL, Donell ST, Fenwick S, Rowan AD, Young DA, Clark IM. Class I histone deacetylase inhibition modulates metalloproteinase expression and blocks cytokine-induced cartilage degradation. ACTA ACUST UNITED AC 2013; 65:1822-30. [PMID: 23575963 DOI: 10.1002/art.37965] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 04/02/2013] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To examine the ability of a broad-spectrum histone deacetylase (HDAC) inhibitor to protect cartilage in vivo, and to explore the effects of class-selective HDAC inhibitors and small interfering RNA (siRNA)-induced knockdown of HDACs on metalloproteinase expression and cartilage degradation in vitro. METHODS A destabilization of the medial meniscus (DMM) model was used to assess the in vivo activity of the HDAC inhibitor trichostatin A (TSA). Human articular chondrocytes (HACs) and SW-1353 chondrosarcoma cells were treated with cytokines and TSA, valproic acid, MS-275, or siRNA, and quantitative reverse transcription-polymerase chain reaction was performed to determine the effect of treatment on metalloproteinase expression. HDAC inhibitor activity was detected by Western blotting. A bovine nasal cartilage (BNC) explant assay was performed to measure cartilage resorption in vitro. RESULTS Systemically administered TSA protected cartilage in the DMM model. TSA, valproic acid, and MS-275 repressed cytokine-induced MMP1 and MMP13 expression in HACs. Knockdown of each class I HDAC diminished interleukin-1-induced MMP13 expression. All of the HDAC inhibitors prevented degradation of BNC, in which TSA and MS-275 repressed cytokine-induced MMP expression. CONCLUSION Inhibition of class I HDACs (HDAC-1, HDAC-2, HDAC-3) by MS-275 or by specific depletion of HDACs is capable of repressing cytokine-induced metalloproteinase expression in cartilage cells and BNC explants, resulting in inhibition of cartilage resorption. These observations indicate that specific inhibition of class I HDACs is a possible therapeutic strategy in the arthritides.
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Wilkinson JM, Davidson RK, Swingler TE, Jones ER, Corps AN, Johnston P, Riley GP, Chojnowski AJ, Clark IM. MMP-14 and MMP-2 are key metalloproteases in Dupuytren's disease fibroblast-mediated contraction. Biochim Biophys Acta Mol Basis Dis 2012; 1822:897-905. [DOI: 10.1016/j.bbadis.2012.02.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 02/02/2012] [Accepted: 02/03/2012] [Indexed: 02/07/2023]
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Swingler TE, Wheeler G, Carmont V, Elliott HR, Barter MJ, Abu-Elmagd M, Donell ST, Boot-Handford RP, Hajihosseini MK, Münsterberg A, Dalmay T, Young DA, Clark IM. The expression and function of microRNAs in chondrogenesis and osteoarthritis. ACTA ACUST UNITED AC 2011; 64:1909-19. [PMID: 22143896 DOI: 10.1002/art.34314] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To use an in vitro model of chondrogenesis to identify microRNAs (miRNAs) with a functional role in cartilage homeostasis. METHODS The expression of miRNAs was measured in the ATDC5 cell model of chondrogenesis using microarray and was verified using quantitative reverse transcription-polymerase chain reaction. MicroRNA expression was localized by in situ hybridization. Predicted miRNA target genes were validated using 3'-untranslated region-Luc reporter plasmids containing either wild-type sequences or mutants of the miRNA target sequence. Signaling through the Smad pathway was measured using a (CAGA)(12) -Luc reporter. RESULTS The expression of several miRNAs was regulated during chondrogenesis. These included 39 miRNAs that are coexpressed with miRNA-140 (miR-140), which is known to be involved in cartilage homeostasis and osteoarthritis (OA). Of these miRNAs, miR-455 resides within an intron of COL27A1 that encodes a cartilage collagen. When human OA cartilage was compared with cartilage obtained from patients with femoral neck fractures, the expression of both miR-140-5p and miR-455-3p was increased in OA cartilage. In situ hybridization showed miR-455-3p expression in the developing limbs of chicks and mice and in human OA cartilage. The expression of miR-455-3p was regulated by transforming growth factor β (TGFβ) ligands, and miRNA regulated TGFβ signaling. ACVR2B, SMAD2, and CHRDL1 were direct targets of miR-455-3p and may mediate its functional impact on TGFβ signaling. CONCLUSION MicroRNA-455 is expressed during chondrogenesis and in adult articular cartilage, where it can regulate TGFβ signaling, suppressing the Smad2/3 pathway. Diminished signaling through this pathway during the aging process and in OA chondrocytes is known to contribute to cartilage destruction. We propose that the increased expression of miR-455 in OA exacerbates this process and contributes to disease pathology.
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Milner JM, Patel A, Davidson RK, Swingler TE, Desilets A, Young DA, Kelso EB, Donell ST, Cawston TE, Clark IM, Ferrell WR, Plevin R, Lockhart JC, Leduc R, Rowan AD. Matriptase is a novel initiator of cartilage matrix degradation in osteoarthritis. ACTA ACUST UNITED AC 2010; 62:1955-66. [PMID: 20506309 DOI: 10.1002/art.27476] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE Increasing evidence implicates serine proteinases in pathologic tissue turnover. The aim of this study was to assess the role of the transmembrane serine proteinase matriptase in cartilage destruction in osteoarthritis (OA). METHODS Serine proteinase gene expression in femoral head cartilage obtained from either patients with hip OA or patients with fracture to the neck of the femur (NOF) was assessed using a low-density array. The effect of matriptase on collagen breakdown was determined in cartilage degradation models, while the effect on matrix metalloproteinase (MMP) expression was analyzed by real-time polymerase chain reaction. ProMMP processing was determined using sodium dodecyl sulfate-polyacrylamide gel electrophoresis/N-terminal sequencing, while its ability to activate proteinase-activated receptor 2 (PAR-2) was determined using a synovial perfusion assay in mice. RESULTS Matriptase gene expression was significantly elevated in OA cartilage compared with NOF cartilage, and matriptase was immunolocalized to OA chondrocytes. We showed that matriptase activated proMMP-1 and processed proMMP-3 to its fully active form. Exogenous matriptase significantly enhanced cytokine-stimulated cartilage collagenolysis, while matriptase alone caused significant collagenolysis from OA cartilage, which was metalloproteinase-dependent. Matriptase also induced MMP-1, MMP-3, and MMP-13 gene expression. Synovial perfusion data confirmed that matriptase activates PAR-2, and we demonstrated that matriptase-dependent enhancement of collagenolysis from OA cartilage is blocked by PAR-2 inhibition. CONCLUSION Elevated matriptase expression in OA and the ability of matriptase to activate selective proMMPs as well as induce collagenase expression make this serine proteinase a key initiator and inducer of cartilage destruction in OA. We propose that the indirect effects of matriptase are mediated by PAR-2, and a more detailed understanding of these mechanisms may highlight important new therapeutic targets for OA treatment.
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Scott JL, Gabrielides C, Davidson RK, Swingler TE, Clark IM, Wallis GA, Boot-Handford RP, Kirkwood TBL, Taylor RW, Talyor RW, Young DA. Superoxide dismutase downregulation in osteoarthritis progression and end-stage disease. Ann Rheum Dis 2010; 69:1502-10. [PMID: 20511611 DOI: 10.1136/ard.2009.119966] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Oxidative stress is proposed as an important factor in osteoarthritis (OA). OBJECTIVE To investigate the expression of the three superoxide dismutase (SOD) antioxidant enzymes in OA. METHODS SOD expression was determined by real-time PCR and immunohistochemistry using human femoral head cartilage. SOD2 expression in Dunkin-Hartley guinea pig knee articular cartilage was determined by immunohistochemistry. The DNA methylation status of the SOD2 promoter was determined using bisulphite sequencing. RNA interference was used to determine the consequence of SOD2 depletion on the levels of reactive oxygen species (ROS) using MitoSOX and collagenases, matrix metalloproteinase 1 (MMP-1) and MMP-13, gene expression. RESULTS All three SOD were abundantly expressed in human cartilage but were markedly downregulated in end-stage OA cartilage, especially SOD2. In the Dunkin-Hartley guinea pig spontaneous OA model, SOD2 expression was decreased in the medial tibial condyle cartilage before, and after, the development of OA-like lesions. The SOD2 promoter had significant DNA methylation alterations in OA cartilage. Depletion of SOD2 in chondrocytes increased ROS but decreased collagenase expression. CONCLUSION This is the first comprehensive expression profile of all SOD genes in cartilage and, importantly, using an animal model, it has been shown that a reduction in SOD2 is associated with the earliest stages of OA. A decrease in SOD2 was found to be associated with an increase in ROS but a reduction of collagenase gene expression, demonstrating the complexities of ROS function.
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Affiliation(s)
- Jenny L Scott
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, UK
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Pais H, Nicolas FE, Soond SM, Swingler TE, Clark IM, Chantry A, Moulton V, Dalmay T. Analyzing mRNA expression identifies Smad3 as a microRNA-140 target regulated only at protein level. RNA 2010; 16:489-494. [PMID: 20071455 PMCID: PMC2822914 DOI: 10.1261/rna.1701210] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 11/23/2009] [Indexed: 05/28/2023]
Abstract
mRNA profiling is routinely used to identify microRNA targets, however, this high-throughput technology is not suitable for identifying targets regulated only at protein level. Here, we have developed and validated a novel methodology based on computational analysis of promoter sequences combined with mRNA microarray experiments to reveal transcription factors that are direct microRNA targets at the protein level. Using this approach we identified Smad3, a key transcription factor in the TGFbeta signaling pathway, as a direct miR-140 target. We showed that miR-140 suppressed the TGFbeta pathway through repression of Smad3 and that TGFbeta suppressed the accumulation of miR-140 forming a double negative feedback loop. Our findings establish a valid strategy for the discovery of microRNA targets regulated only at protein level, and we propose that additional targets could be identified by re-analysis of existing microarray datasets.
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Affiliation(s)
- Helio Pais
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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Surridge AK, Rodgers UR, Swingler TE, Davidson RK, Kevorkian L, Norton R, Waters JG, Goldring MB, Parker AE, Clark IM. Characterization and regulation of ADAMTS-16. Matrix Biol 2009; 28:416-24. [PMID: 19635554 PMCID: PMC2789966 DOI: 10.1016/j.matbio.2009.07.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 06/26/2009] [Accepted: 07/17/2009] [Indexed: 11/25/2022]
Abstract
The ADAMTS (a disintegrin and metalloproteinase domain with thrombospondin motifs) family includes 19 secreted proteinases in man. ADAMTS16 is a recently cloned gene expressed at high levels in fetal lung and kidney and adult brain and ovary. The ADAMTS-16 protein currently has no known function. ADAMTS16 is also expressed in human cartilage and synovium where its expression is increased in tissues from osteoarthritis patients compared to normal tissues. In this study, we ascertained that the full length ADAMTS16 mRNA was expressed in chondrocytes and cloned the appropriate cDNA. Stable over-expression of ADAMTS16 in chondrosarcoma cells led to a decrease in cell proliferation and migration, though not adhesion, as well as a decrease in the expression of matrix metalloproteinase-13 (MMP13). The transcription start point of the human ADAMTS16 gene was experimentally identified as 138 bp upstream of the translation start ATG and the basal promoter was mapped out to − 1802 bp. Overexpression of Egr1 induced ADAMTS16 promoter constructs of − 157/+138 or longer whilst Sp1 induced all ADAMTS16 promoter constructs. Transforming growth factor beta (TGFβ) stimulated expression of endogenous ADAMTS16 gene expression in chondrocyte cell lines.
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Affiliation(s)
- Alison K Surridge
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Ursula R Rodgers
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Tracey E Swingler
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Rose K Davidson
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Lara Kevorkian
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Rosemary Norton
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Jasmine G Waters
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Mary B Goldring
- Hospital for Special Surgery, 535 East 70th Street, New York, USA
| | - Andrew E Parker
- Respiratory and Inflammation Department, AstraZeneca Pharmaceuticals, Cheshire, UK
| | - Ian M Clark
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
- Respiratory and Inflammation Department, AstraZeneca Pharmaceuticals, Cheshire, UK
- Corresponding author. Cellular Protease Group, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK. Tel.: +44 1603 592760; fax: +44 1603 592250.
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Swingler TE, Waters JG, Davidson RK, Pennington CJ, Puente XS, Darrah C, Cooper A, Donell ST, Guile GR, Wang W, Clark IM. Degradome expression profiling in human articular cartilage. Arthritis Res Ther 2009; 11:R96. [PMID: 19549314 PMCID: PMC2714152 DOI: 10.1186/ar2741] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [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: 04/16/2009] [Revised: 06/10/2009] [Accepted: 06/23/2009] [Indexed: 12/26/2022] Open
Abstract
Introduction The molecular mechanisms underlying cartilage destruction in osteoarthritis are poorly understood. Proteolysis is a key feature in the turnover and degradation of cartilage extracellular matrix where the focus of research has been on the metzincin family of metalloproteinases. However, there is strong evidence to indicate important roles for other catalytic classes of proteases, with both extracellular and intracellular activities. The aim of this study was to profile the expression of the majority of protease genes in all catalytic classes in normal human cartilage and that from patients with osteoarthritis (OA) using a quantitative method. Methods Human cartilage was obtained from femoral heads at joint replacement for either osteoarthritis or following fracture to the neck of femur (NOF). Total RNA was purified, and expression of genes assayed using Taqman® low-density array quantitative RT-PCR. Results A total of 538 protease genes were profiled, of which 431 were expressed in cartilage. A total of 179 genes were differentially expressed in OA versus NOF cartilage: eight aspartic proteases, 44 cysteine proteases, 76 metalloproteases, 46 serine proteases and five threonine proteases. Wilcoxon ranking as well as the LogitBoost-NR machine learning approach were used to assign significance to each gene, with the most highly ranked genes broadly similar using each method. Conclusions This study is the most complete quantitative analysis of protease gene expression in cartilage to date. The data help give direction to future research on the specific function(s) of individual proteases or protease families in cartilage and may help to refine anti-proteolytic strategies in OA.
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Affiliation(s)
- Tracey E Swingler
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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Rodgers UR, Kevorkian L, Surridge AK, Waters JG, Swingler TE, Culley K, Illman S, Lohi J, Parker AE, Clark IM. Expression and function of matrix metalloproteinase (MMP)-28. Matrix Biol 2009; 28:263-72. [PMID: 19375502 PMCID: PMC2724077 DOI: 10.1016/j.matbio.2009.04.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 04/03/2009] [Accepted: 04/07/2009] [Indexed: 12/27/2022]
Abstract
Matrix metalloproteinase-28 (MMP-28, epilysin) is highly expressed in the skin by keratinocytes, the developing and regenerating nervous system and a number of other normal human tissues. In epithelial cells, over-expression of MMP-28 mediates irreversible epithelial to mesenchymal transition concomitant with loss of E-cadherin from the cell surface and an increase in active transforming growth factor beta. We recently reported the expression of MMP-28 in both cartilage and synovium where expression is increased in patients with osteoarthritis. In human chondrosarcoma cells MMP-28 was activated by proprotein convertases and the active form of the enzyme preferentially associated with the extracellular matrix in a C-terminal independent manner. over-expression of MMP-28 in chondrosarcoma cells led to altered cell morphology with increased organisation of actin. Adhesion to type II collagen and fibronectin was increased, and migration across the former was decreased. MMP-28 was localised to the cell surface, at least transiently, in a C-terminal dependent manner. Heparin prevented both extracellular matrix association and cell surface binding of MMP-28 suggesting that both are via heparan sulphate proteoglycans. Over-expression of activatable MMP-28, but not catalytically inactive EA mutant increased the expression and activity of MMP-2, and all forms of MMP-28 tested increased expression of MMP19 and TIMP3 mRNA. These data demonstrate that expression of MMP28 alters cell phenotype towards a more adhesive, less migratory behaviour. Further, MMP-28 activity may reside predominantly in the extracellular matrix, and we are currently searching for substrates in this compartment.
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Affiliation(s)
- Ursula R Rodgers
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, UK
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Clark IM, Swingler TE, Sampieri CL, Edwards DR. The regulation of matrix metalloproteinases and their inhibitors. Int J Biochem Cell Biol 2007; 40:1362-78. [PMID: 18258475 DOI: 10.1016/j.biocel.2007.12.006] [Citation(s) in RCA: 401] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Accepted: 12/14/2007] [Indexed: 01/12/2023]
Abstract
The matrix metalloproteinases (MMP) are a family of 23 enzymes in man. These enzymes were originally described as cleaving extracellular matrix (ECM) substrates with a predominant role in ECM homeostasis, but it is now clear that they have much wider functionality. Control over MMP and/or tissue inhibitor of metalloproteinases (TIMP) activity in vivo occurs at different levels and involves factors such as regulation of gene expression, activation of zymogens and inhibition of active enzymes by specific inhibitors. Whilst these enzymes and inhibitors have clear roles in physiological tissue turnover and homeostasis, if control of their expression or activity is lost, they contribute to a number of pathologies including e.g. cancer, arthritis and cardiovascular disease. The expression of many MMPs and TIMPs is regulated at the level of transcription by a variety of growth factors, cytokines and chemokines, though post-transcriptional pathways may contribute to this regulation in specific cases. The contribution of epigenetic modifications has also been uncovered in recent years. The promoter regions of many of these genes have been, at least partly, characterised including the role of identified single nucleotide polymorphisms. This article aims to review current knowledge across these gene families and use a bioinformatic approach to fill the gaps where no functional data are available.
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Affiliation(s)
- Ian M Clark
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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Clark IM, Swingler TE, Young DA. Acetylation in the regulation of metalloproteinase and tissue inhibitor of metalloproteinases gene expression. FRONT BIOSCI-LANDMRK 2007; 12:528-35. [PMID: 17127314 DOI: 10.2741/2079] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [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] [Indexed: 11/22/2022]
Abstract
Together, the matrix metalloproteinases (MMPs) are capable of degrading every component of the extracellular matrix (ECM). Besides degradation of the ECM, MMPs release bioactive molecules from the matrix or cell surface and play important role in tissue repair after injury, development and in a number of pathologies including arthritis and cancer metastasis. Small molecules that inhibit a broad spectrum of metalloproteinases have not proved useful in the treatment of various diseases, probably due to the diverse roles of this large family of enzymes. An alternative therapeutic approach for a number of pathologies is to modulate the expression of specific metalloproteinase genes. Acetylation represents a recently identified covalent protein modification that is strongly implicated in transcriptional regulation. Histones were the first proteins demonstrated to show variable acetylation leading to gene activation. Subsequently, a large number of molecules including structural proteins, intracellular signaling molecules, nuclear membrane receptors and transcription factors were shown to be acetylated. Acetylation, like phosphorylation, is a reversible modification. Acetyl groups are added by a family of histone acetyl transferase enzymes (HATs) and are removed by histone deacetylases (HDACs). Inhibitors of HDACs (HDACi) have potent anti-proliferative and pro-apoptotic activities in cancer cells and may be used as cancer therapeutics. In this review, we examine the impact of changes in acetylation on the expression of the MMPs and their inhibitors (tissue inhibitors of metalloproteinases, TIMPs). We discuss the suggestion that HDACi may act in a dual fashion: selectively decreasing cancer cell viability and reducing metastatic potential by decreasing stromal cell expression of specific metalloproteinases. Furthermore, we consider the possibility that selective HDACi have a potential as anti-inflammatory agents and in a range of degradative diseases such as arthritis.
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Affiliation(s)
- Ian M Clark
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.
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Swingler TE, Bess KL, Yao J, Stifani S, Jayaraman PS. The proline-rich homeodomain protein recruits members of the Groucho/Transducin-like enhancer of split protein family to co-repress transcription in hematopoietic cells. J Biol Chem 2004; 279:34938-47. [PMID: 15187083 DOI: 10.1074/jbc.m404488200] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proline-rich homeodomain protein (PRH/Hex) is important in the control of cell proliferation and differentiation and in the regulation of multiple processes in embryonic development. We have shown previously that PRH contains two domains that can independently bring about transcriptional repression. The PRH homeodomain represses transcription by binding to TATA box sequences, whereas the proline-rich N-terminal domain of PRH can repress transcription when attached to a heterologous DNA-binding domain. The Groucho/transducin-like enhancer of split (TLE) family of proteins are transcriptional co-repressors that interact with a number of DNA-bound transcription factors and play multiple roles in development. Here we demonstrate that the proline-rich N-terminal domain of PRH binds to TLE1 in vitro and in yeast two-hybrid assays. We show that PRH and TLE proteins are co-expressed in hematopoietic cells and interact in co-immunoprecipitation assays. We demonstrate that TLE1 increases repression by PRH in transient transfection assays and that titration of endogenous TLE proteins by co-expression of Grg5, a natural trans-dominant negative protein, alleviates transcriptional repression by PRH. Finally, we show that a mutation in the PRH N-terminal domain that blocks the PRH-TLE1 interaction in vitro eliminates co-repression. We discuss these results in terms of the roles of PRH and TLE in cell differentiation and development.
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Affiliation(s)
- Tracey E Swingler
- Department of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
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Bess KL, Swingler TE, Rivett AJ, Gaston K, Jayaraman PS. The transcriptional repressor protein PRH interacts with the proteasome. Biochem J 2003; 374:667-75. [PMID: 12826010 PMCID: PMC1223646 DOI: 10.1042/bj20030769] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2003] [Accepted: 06/25/2003] [Indexed: 02/07/2023]
Abstract
PRH (proline-rich homeodomain protein)/Hex is important in the control of cell proliferation and differentiation. We have shown previously that PRH contains two domains that can bring about transcriptional repression independently; the PRH homeodomain represses transcription by binding to TATA box sequences, whereas the proline-rich N-terminal domain can repress transcription by interacting with members of the Groucho/TLE (transducin-like enhancer of split) family of co-repressor proteins. The proteasome is a multi-subunit protein complex involved in the processing and degradation of proteins. Some proteasome subunits have been suggested to play a role in the regulation of transcription. In the present study, we show that PRH interacts with the HC8 subunit of the proteasome in the context of both 20 and 26 S proteasomes. Moreover, we show that PRH is associated with the proteasome in haematopoietic cells and that the proline-rich PRH N-terminal domain is responsible for this interaction. Whereas PRH can be cleaved by the proteasome, it does not appear to be degraded rapidly in vitro or in vivo, and the proteolytic activity of the proteasome is not required for transcriptional repression by PRH. However, proteasomal digestion of PRH can liberate truncated PRH proteins that retain the ability to bind to DNA. We discuss these findings in terms of the biological role of PRH in gene regulation and the control of cell proliferation.
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Affiliation(s)
- Kirstin L Bess
- Department of Biochemistry, University of Bristol, University Walk, Bristol BS81TD, UK
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