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Roberts JB, Rice SJ. Osteoarthritis as an Enhanceropathy: Gene Regulation in Complex Musculoskeletal Disease. Curr Rheumatol Rep 2024; 26:222-234. [PMID: 38430365 PMCID: PMC11116181 DOI: 10.1007/s11926-024-01142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2024] [Indexed: 03/03/2024]
Abstract
PURPOSE OF REVIEW Osteoarthritis is a complex and highly polygenic disease. Over 100 reported osteoarthritis risk variants fall in non-coding regions of the genome, ostensibly conferring functional effects through the disruption of regulatory elements impacting target gene expression. In this review, we summarise the progress that has advanced our knowledge of gene enhancers both within the field of osteoarthritis and more broadly in complex diseases. RECENT FINDINGS Advances in technologies such as ATAC-seq have facilitated our understanding of chromatin states in specific cell types, bolstering the interpretation of GWAS and the identification of effector genes. Their application to osteoarthritis research has revealed enhancers as the principal regulatory element driving disease-associated changes in gene expression. However, tissue-specific effects in gene regulatory mechanisms can contribute added complexity to biological interpretation. Understanding gene enhancers and their altered activity in specific cell and tissue types is the key to unlocking the genetic complexity of osteoarthritis. The use of single-cell technologies in osteoarthritis research is still in its infancy. However, such tools offer great promise in improving our functional interpretation of osteoarthritis GWAS and the identification of druggable targets. Large-scale collaborative efforts will be imperative to understand tissue and cell-type specific molecular mechanisms underlying enhancer function in disease.
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Affiliation(s)
- Jack B Roberts
- Skeletal Research Group, International Centre for Life, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, UK
| | - Sarah J Rice
- Skeletal Research Group, International Centre for Life, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, UK.
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Roberts JB, Boldvig OLG, Aubourg G, Kanchenapally ST, Deehan DJ, Rice SJ, Loughlin J. Specific isoforms of the ubiquitin ligase gene WWP2 are targets of osteoarthritis genetic risk via a differentially methylated DNA sequence. Arthritis Res Ther 2024; 26:78. [PMID: 38570801 PMCID: PMC10988806 DOI: 10.1186/s13075-024-03315-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Transitioning from a genetic association signal to an effector gene and a targetable molecular mechanism requires the application of functional fine-mapping tools such as reporter assays and genome editing. In this report, we undertook such studies on the osteoarthritis (OA) risk that is marked by single nucleotide polymorphism (SNP) rs34195470 (A > G). The OA risk-conferring G allele of this SNP associates with increased DNA methylation (DNAm) at two CpG dinucleotides within WWP2. This gene encodes a ubiquitin ligase and is the host gene of microRNA-140 (miR-140). WWP2 and miR-140 are both regulators of TGFβ signaling. METHODS Nucleic acids were extracted from adult OA (arthroplasty) and foetal cartilage. Samples were genotyped and DNAm quantified by pyrosequencing at the two CpGs plus 14 flanking CpGs. CpGs were tested for transcriptional regulatory effects using a chondrocyte cell line and reporter gene assay. DNAm was altered using epigenetic editing, with the impact on gene expression determined using RT-qPCR. In silico analysis complemented laboratory experiments. RESULTS rs34195470 genotype associates with differential methylation at 14 of the 16 CpGs in OA cartilage, forming a methylation quantitative trait locus (mQTL). The mQTL is less pronounced in foetal cartilage (5/16 CpGs). The reporter assay revealed that the CpGs reside within a transcriptional regulator. Epigenetic editing to increase their DNAm resulted in altered expression of the full-length and N-terminal transcript isoforms of WWP2. No changes in expression were observed for the C-terminal isoform of WWP2 or for miR-140. CONCLUSIONS As far as we are aware, this is the first experimental demonstration of an OA association signal targeting specific transcript isoforms of a gene. The WWP2 isoforms encode proteins with varying substrate specificities for the components of the TGFβ signaling pathway. Future analysis should focus on the substrates regulated by the two WWP2 isoforms that are the targets of this genetic risk.
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Affiliation(s)
- Jack B Roberts
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK.
| | - Olivia L G Boldvig
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - Guillaume Aubourg
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - S Tanishq Kanchenapally
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - David J Deehan
- Freeman Hospital, Newcastle University Teaching Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - Sarah J Rice
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - John Loughlin
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK.
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Wang Y, Huang X, Zhang Q, Cheng C, Qin Z, Lu L, Huang Q. The osteoporosis susceptibility SNP rs188303909 at 2q14.2 regulates EN1 expression by modulating DNA methylation and E2F6 binding. J Mol Med (Berl) 2024; 102:273-284. [PMID: 38153509 DOI: 10.1007/s00109-023-02412-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 12/29/2023]
Abstract
EN1 encodes a homeodomain-containing transcription factor and is a determinant of bone density and fracture. Previous powerful genome-wide association studies (GWASs) have identified multiple single-nucleotide polymorphisms (SNPs) near EN1 at 2q14.2 locus for osteoporosis, but the causal SNPs and functional mechanisms underlying these associations are poorly understood. The target genes regulated by the transcription factor EN1 are also unclear. In this study, we identified rs188303909, a functional CpG-SNP, as a causal SNP for osteoporosis at 2q14.2 through the integration of functional and epigenomic analyses. Functional experiments demonstrated that unmethylated rs188303909 acted as a strong allele-specific distal enhancer to regulate EN1 expression by modifying the binding of transcription factor E2F6, but rs188303909 methylation attenuated the active effect of E2F6 on EN1 expression. Importantly, transcription factor EN1 could differentially bind osteoporosis GWAS lead SNPs rs4869739-T and rs4355801-G to upregulate CCDC170 and COLEC10 expression, thus promoting bone formation. Our study provided a mechanistic insight into expression regulation of the osteoporosis susceptibility gene EN1, which could be a potential therapeutic target for osteoporosis precision medicine. KEY MESSAGES: CpG-SNP rs188303909 is a causal SNP at the osteoporosis susceptibility locus 2q14.2. Rs188303909 distally regulates EN1 expression by modulating DNA methylation and E2F6 binding. EN1 upregulates CCDC170 and COLEC10 expression through osteoporosis GWAS lead SNPs rs4869739 and rs4355801.
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Affiliation(s)
- Ya Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xinyao Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Qiongdan Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Chen Cheng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Zixuan Qin
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Li Lu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Qingyang Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.
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Cao N, Wang D, Liu B, Wang Y, Han W, Tian J, Xiang L, Wang Z. Silencing of STUB1 relieves osteoarthritis via inducing NRF2-mediated M2 macrophage polarization. Mol Immunol 2023; 164:112-122. [PMID: 37992540 DOI: 10.1016/j.molimm.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023]
Abstract
OBJECTIVES Shifting macrophages towards an anti-inflammatory state is key in treating osteoarthritis (OA) by reducing inflammation and tissue damage. However, the underlying mechanisms guiding this shift remain largely undefined. STUB1, an E3 ubiquitin ligase, known for its regulatory role in macrophage polarization. This study aims to explore the function and underlying action mechanisms of STUB1 in OA. METHODS An in vivo OA model was established in rats. Hematoxylin-Eosin and safranin O-fast green staining were performed to reveal the hispathological injuries in knee-joint tissues. Immunohistochemistry and flow cytometry were performed to detect the distribution of M1 and M2 macrophages. The inflammatory response (TNF-α and IL-6 levels) was evaluated by ELISA. In vitro, the interaction between STUB1 and NFR2 was determined by CO-IP and pull-down assays. After treated with LPS (an in vitro model of OA), the viability and apoptosis of chondrocytes were measured by CCK-8 and flow cytometry, respectively. RESULTS Silencing STUB1 alleviated OA in rats, as indicated by reduced subchondral bone thickness, knee synovitis score, histopathological damages, and inflammatory response. STUB1 silencing also decreased M1 macrophages and increased M2 macrophages in both in vivo and in vitro settings. NRF2 was identified as a target of STUB1, with STUB1 mediating its ubiquitination. Silencing NRF2 reversed the effects of STUB1 silencing on inducing M2 macrophage polarization. Furthermore, silencing STUB1 upregulated NRF2 expression in LPS-treated chondrocytes, promoting cell viability and inhibiting apoptosis. CONCLUSION Silencing STUB1 induces M2 macrophage polarization by inhibiting NRF2 ubiquitination, thereby contributing to the mitigation of OA.
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Affiliation(s)
- Nan Cao
- Department of Orthopedics, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Danni Wang
- Department of Orthopedics, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Bin Liu
- Department of Orthopedics, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Yu Wang
- Department of Orthopedics, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Wenfeng Han
- Department of Orthopedics, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Jing Tian
- Department of Orthopedics, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Liangbi Xiang
- Department of Orthopedics, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China.
| | - Zheng Wang
- Department of Orthopedics, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China.
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Faber BG, Frysz M, Boer CG, Evans DS, Ebsim R, Flynn KA, Lundberg M, Southam L, Hartley A, Saunders FR, Lindner C, Gregory JS, Aspden RM, Lane NE, Harvey NC, Evans DM, Zeggini E, Davey Smith G, Cootes T, Van Meurs J, Kemp JP, Tobias JH. The identification of distinct protective and susceptibility mechanisms for hip osteoarthritis: findings from a genome-wide association study meta-analysis of minimum joint space width and Mendelian randomisation cluster analyses. EBioMedicine 2023; 95:104759. [PMID: 37619450 PMCID: PMC10470292 DOI: 10.1016/j.ebiom.2023.104759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Hip minimum joint space width (mJSW) provides a proxy for cartilage thickness. This study aimed to conduct a genome-wide association study (GWAS) of mJSW to (i) identify new genetic determinants of mJSW and (ii) identify which mJSW loci convey hip osteoarthritis (HOA) risk and would therefore be of therapeutic interest. METHODS GWAS meta-analysis of hip mJSW derived from plain X-rays and DXA was performed, stratified by sex and adjusted for age and ancestry principal components. Mendelian randomisation (MR) and cluster analyses were used to examine causal effect of mJSW on HOA. FINDINGS 50,745 individuals were included in the meta-analysis. 42 SNPs, which mapped to 39 loci, were identified. Mendelian randomisation (MR) revealed little evidence of a causal effect of mJSW on HOA (ORIVW 0.98 [95% CI 0.82-1.18]). However, MR-Clust analysis suggested the null MR estimates reflected the net effect of two distinct causal mechanisms cancelling each other out, one of which was protective, whereas the other increased HOA susceptibility. For the latter mechanism, all loci were positively associated with height, suggesting mechanisms leading to greater height and mJSW increase the risk of HOA in later life. INTERPRETATIONS One group of mJSW loci reduce HOA risk via increased mJSW, suggesting possible utility as targets for chondroprotective therapies. The second group of mJSW loci increased HOA risk, despite increasing mJSW, but were also positively related to height, suggesting they contribute to HOA risk via a growth-related mechanism. FUNDING Primarily funded by the Medical Research Council and Wellcome Trust.
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Affiliation(s)
- Benjamin G Faber
- Musculoskeletal Research Unit, University of Bristol, UK; Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK.
| | - Monika Frysz
- Musculoskeletal Research Unit, University of Bristol, UK; Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK
| | - Cindy G Boer
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, USA
| | - Raja Ebsim
- Division of Informatics, Imaging and Data Sciences, The University of Manchester, UK
| | - Kaitlyn A Flynn
- Mater Research Institute, The University of Queensland, Woolloongabba, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Mischa Lundberg
- UQ Frazer Institute, The University of Queensland, Woolloongabba, Australia
| | - Lorraine Southam
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
| | - April Hartley
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK
| | - Fiona R Saunders
- Centre for Arthritis and Musculoskeletal Health, University of Aberdeen, UK
| | - Claudia Lindner
- Division of Informatics, Imaging and Data Sciences, The University of Manchester, UK
| | - Jennifer S Gregory
- Centre for Arthritis and Musculoskeletal Health, University of Aberdeen, UK
| | - Richard M Aspden
- Centre for Arthritis and Musculoskeletal Health, University of Aberdeen, UK
| | - Nancy E Lane
- Center for Musculoskeletal Health, University of California Davis, Sacramento, USA
| | - Nicholas C Harvey
- Medical Research Council Lifecourse Epidemiology Centre, University of Southampton, UK; NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, UK
| | - David M Evans
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia; UQ Frazer Institute, The University of Queensland, Woolloongabba, Australia
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany; Technical University of Munich and Klinikum Rechts der Isar, TUM School of Medicine, Germany
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK
| | - Timothy Cootes
- Division of Informatics, Imaging and Data Sciences, The University of Manchester, UK
| | - Joyce Van Meurs
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - John P Kemp
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK; Mater Research Institute, The University of Queensland, Woolloongabba, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Jonathan H Tobias
- Musculoskeletal Research Unit, University of Bristol, UK; Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK
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Kehayova YS, Wilkinson JM, Rice SJ, Loughlin J. Osteoarthritis genetic risk acting on the galactosyltransferase gene COLGALT2 has opposing functional effects in articulating joint tissues. Arthritis Res Ther 2023; 25:83. [PMID: 37208701 DOI: 10.1186/s13075-023-03066-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/10/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Investigation of cartilage and chondrocytes has revealed that the osteoarthritis risk marked by the independent DNA variants rs11583641 and rs1046934 mediate their effects by decreasing the methylation status of CpG dinucleotides in enhancers and increasing the expression of shared target gene COLGALT2. We set out to investigate if these functional effects operate in a non-cartilaginous joint tissue. METHODS Nucleic acids were extracted from the synovium of osteoarthritis patients. Samples were genotyped, and DNA methylation was quantified by pyrosequencing at CpGs within the COLGALT2 enhancers. CpGs were tested for enhancer effects using a synovial cell line and a reporter gene assay. DNA methylation was altered using epigenetic editing, with the impact on gene expression determined using quantitative polymerase chain reaction. In silico analysis complemented laboratory experiments. RESULTS The rs1046934 genotype did not associate with DNA methylation or COLGALT2 expression in the synovium, whereas the rs11583641 genotype did. Surprisingly, the effects for rs11583641 were opposite to those previously observed in cartilage. Epigenetic editing in synovial cells revealed that enhancer methylation is causally linked to COLGALT2 expression. CONCLUSIONS This is the first direct demonstration for osteoarthritis genetic risk of a functional link between DNA methylation and gene expression operating in opposite directions between articular joint tissues. It highlights pleiotropy in the action of osteoarthritis risk and provides a cautionary note in the application of future genetically based osteoarthritis therapies: an intervention that decreases the detrimental effect of a risk allele in one joint tissue may inadvertently increase its detrimental effect in another joint tissue.
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Affiliation(s)
- Yulia S Kehayova
- Newcastle University, Biosciences Institute, International Centre for Life, Newcastle Upon Tyne, NE1 3BZ, UK
| | - J Mark Wilkinson
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Sarah J Rice
- Newcastle University, Biosciences Institute, International Centre for Life, Newcastle Upon Tyne, NE1 3BZ, UK.
| | - John Loughlin
- Newcastle University, Biosciences Institute, International Centre for Life, Newcastle Upon Tyne, NE1 3BZ, UK.
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