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Dai J, Jiang H, Yang Z, Chen C, Tang X. A functional variant of ALDH1A2 is associated with hand osteoarthritis in the Chinese population. Int J Immunogenet 2024; 51:157-163. [PMID: 38441233 DOI: 10.1111/iji.12662] [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: 11/07/2023] [Revised: 01/24/2024] [Accepted: 02/16/2024] [Indexed: 05/08/2024]
Abstract
Genome-wide association study identified common variants within the ALDH1A2 gene as the susceptible loci of hand osteoarthritis (HOA) in UK and Iceland populations. Located in chromosome 15, ALDH1A2 encodes aldehyde dehydrogenase family 1 member A2, which is an enzyme that catalyses the synthesis of retinoic acid from retinaldehyde. Our purposes were to replicate the association of functional variant in ALDH1A2 with the development of HOA in the Chinese population. Variant rs12915901 of ALDH1A2 was genotyped in 872 HOA patients and 1223 healthy controls. Subchondral bone samples were collected from 40 patients who had undergone a trapeziectomy, and the tissue expression of ALDH1A2 was analysed. The chi-square analysis was used to compare the frequency of genotype and risk allele between the HOA cases and controls. The Student t test was used to compare the mRNA expression of ALDH1A2 between patients with genotype AA/AG and those with genotype GG. The frequency of genotype AA was significantly higher in HOA patients than in the controls (7.6% vs. 5.1%, p = .01). The frequency of allele A was significantly higher in the patients than in the controls (28.9% vs. 24.6%, p = .005). The mRNA expression of ALDH1A2 was 1.31-folds higher in patients with genotype GG than in the patients with genotype AA/AG (0.000617 ± 0.000231 vs. 0.000471 ± 0.000198, p = .04). Variant rs12915901 of ALDH1A2 contributed to the susceptibility of HOA in the Chinese population. Allele A of rs12915901 can add to the risk of HOA possibly via down-regulation of ALDH1A2 expression.
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Affiliation(s)
- Jian Dai
- Department of Orthopedics Surgery, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
| | - Haitao Jiang
- Department of Orthopedics Surgery, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
| | - Zhaoqi Yang
- Postgraduate in Orthopedics Surgery, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chuan Chen
- Department of Orthopedics Surgery, Third People's Hospital of Jiujiang City, Jiujiang, Jiangxi, China
| | - Xiaoming Tang
- Department of Orthopedics Surgery, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
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Duan X, Hu H, Wang L, Chen L. Aldehyde dehydrogenase 1 family: A potential molecule target for diseases. Cell Biol Int 2024. [PMID: 38800962 DOI: 10.1002/cbin.12188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 04/22/2024] [Accepted: 05/04/2024] [Indexed: 05/29/2024]
Abstract
Aldehyde dehydrogenase 1 (ALDH1), a crucial aldehyde metabolizing enzyme, has six family members. The ALDH1 family is expressed in various tissues, with a significant presence in the liver. It plays a momentous role in several pathophysiological processes, including aldehyde detoxification, oxidative stress, and lipid peroxidation. Acetaldehyde detoxification is the fundamental function of the ALDH1 family in participating in vital pathological mechanisms. The ALDH1 family can catalyze retinal to retinoic acid (RA) that is a hormone-signaling molecule and plays a vital role in the development and adult tissues. Furthermore, there is a need for further and broader research on the role of the ALDH1 family as a signaling molecule. The ALDH1 family is widely recognized as a cancer stem cell (CSC) marker and plays a significant role in the proliferation, invasion, metastasis, prognosis, and drug resistance of cancer. The ALDH1 family also participates in other human diseases, such as neurodegenerative diseases, osteoarthritis, diabetes, and atherosclerosis. It can inhibit disease progression by inhibiting/promoting the expression/activity of the ALDH1 family. In this review, we comprehensively analyze the tissue distribution, and functions of the ALDH1 family. Additionally, we review the involvement of the ALDH1 family in diseases, focusing on the underlying pathological mechanisms and briefly talk about the current status and development of ALDH1 family inhibitors. The ALDH1 family presents new possibilities for treating diseases, with both its upstream and downstream pathways serving as promising targets for therapeutic intervention. This offers fresh perspectives for drug development in the field of disease research.
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Affiliation(s)
- Xiangning Duan
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang Medical School, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy and Pharmacology, University of South China, Hengyang, Hunan, China
| | - Haoliang Hu
- Changde Research Centre for Artificial Intelligence and Biomedicine, Zoology Key Laboratory of Hunan Higher Education, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Lingzhi Wang
- Department of Pharmacy, The First Affiliated Hospital of Jishou University, Jishou, Hunan, China
| | - Linxi Chen
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hengyang Medical School, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy and Pharmacology, University of South China, Hengyang, Hunan, China
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McDonnell E, Orr SE, Barter MJ, Rux D, Brumwell A, Wrobel N, Murphy L, Overmann LM, Sorial AK, Young DA, Soul J, Rice SJ. Epigenetic mechanisms of osteoarthritis risk in human skeletal development. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.05.24306832. [PMID: 38766055 PMCID: PMC11100852 DOI: 10.1101/2024.05.05.24306832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The epigenome, including the methylation of cytosine bases at CG dinucleotides, is intrinsically linked to transcriptional regulation. The tight regulation of gene expression during skeletal development is essential, with ~1/500 individuals born with skeletal abnormalities. Furthermore, increasing evidence is emerging to link age-associated complex genetic musculoskeletal diseases, including osteoarthritis (OA), to developmental factors including joint shape. Multiple studies have shown a functional role for DNA methylation in the genetic mechanisms of OA risk using articular cartilage samples taken from aged patients. Despite this, our knowledge of temporal changes to the methylome during human cartilage development has been limited. We quantified DNA methylation at ~700,000 individual CpGs across the epigenome of developing human articular cartilage in 72 samples ranging from 7-21 post-conception weeks, a time period that includes cavitation of the developing knee joint. We identified significant changes in 8% of all CpGs, and >9400 developmental differentially methylated regions (dDMRs). The largest hypermethylated dDMRs mapped to transcriptional regulators of early skeletal patterning including MEIS1 and IRX1. Conversely, the largest hypomethylated dDMRs mapped to genes encoding extracellular matrix proteins including SPON2 and TNXB and were enriched in chondrocyte enhancers. Significant correlations were identified between the expression of these genes and methylation within the hypomethylated dDMRs. We further identified 811 CpGs at which significant dimorphism was present between the male and female samples, with the majority (68%) being hypermethylated in female samples. Following imputation, we captured the genotype of these samples at >5 million variants and performed epigenome-wide methylation quantitative trait locus (mQTL) analysis. Colocalization analysis identified 26 loci at which genetic variants exhibited shared impacts upon methylation and OA genetic risk. This included loci which have been previously reported to harbour OA-mQTLs (including GDF5 and ALDH1A2), yet the majority (73%) were novel (including those mapping to CHST3, FGF1 and TEAD1). To our knowledge, this is the first extensive study of DNA methylation across human articular cartilage development. We identify considerable methylomic plasticity within the development of knee cartilage and report active epigenomic mediators of OA risk operating in prenatal joint tissues.
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Affiliation(s)
- Euan McDonnell
- Computational Biology Facility, University of Liverpool, MerseyBio, Crown Street, United Kingdom
| | - Sarah E Orr
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Matthew J Barter
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Danielle Rux
- Orthopaedic Surgery, UConn Health, Farmington, Connecticut, USA
| | - Abby Brumwell
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, United Kingdom
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, United Kingdom
| | - Lynne M Overmann
- Human Developmental Biology Resource, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Antony K Sorial
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - David A Young
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Jamie Soul
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sarah J Rice
- Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
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Molin AN, Contentin R, Angelozzi M, Karvande A, Kc R, Haseeb A, Voskamp C, de Charleroy C, Lefebvre V. Skeletal growth is enhanced by a shared role for SOX8 and SOX9 in promoting reserve chondrocyte commitment to columnar proliferation. Proc Natl Acad Sci U S A 2024; 121:e2316969121. [PMID: 38346197 PMCID: PMC10895259 DOI: 10.1073/pnas.2316969121] [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: 09/29/2023] [Accepted: 12/26/2023] [Indexed: 02/15/2024] Open
Abstract
SOX8 was linked in a genome-wide association study to human height heritability, but roles in chondrocytes for this close relative of the master chondrogenic transcription factor SOX9 remain unknown. We undertook here to fill this knowledge gap. High-throughput assays demonstrate expression of human SOX8 and mouse Sox8 in growth plate cartilage. In situ assays show that Sox8 is expressed at a similar level as Sox9 in reserve and early columnar chondrocytes and turned off when Sox9 expression peaks in late columnar and prehypertrophic chondrocytes. Sox8-/- mice and Sox8fl/flPrx1Cre and Sox9fl/+Prx1Cre mice (inactivation in limb skeletal cells) have a normal or near normal skeletal size. In contrast, juvenile and adult Sox8fl/flSox9fl/+Prx1Cre compound mutants exhibit a 15 to 20% shortening of long bones. Their growth plate reserve chondrocytes progress slowly toward the columnar stage, as witnessed by a delay in down-regulating Pthlh expression, in packing in columns and in elevating their proliferation rate. SOX8 or SOX9 overexpression in chondrocytes reveals not only that SOX8 can promote growth plate cell proliferation and differentiation, even upon inactivation of endogenous Sox9, but also that it is more efficient than SOX9, possibly due to greater protein stability. Altogether, these findings uncover a major role for SOX8 and SOX9 in promoting skeletal growth by stimulating commitment of growth plate reserve chondrocytes to actively proliferating columnar cells. Further, by showing that SOX8 is more chondrogenic than SOX9, they suggest that SOX8 could be preferred over SOX9 in therapies to promote cartilage formation or regeneration in developmental and degenerative cartilage diseases.
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Affiliation(s)
- Arnaud N. Molin
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Romain Contentin
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Marco Angelozzi
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Anirudha Karvande
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Ranjan Kc
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Abdul Haseeb
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Chantal Voskamp
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Charles de Charleroy
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Véronique Lefebvre
- Department of Surgery, Division of Orthopaedic Surgery, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
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Zhu L, Vincent TL. Genome-Wide Association Studies to Drug: Identifying Retinoic Acid Metabolism Blocking Agents to Suppress Mechanoflammation in Osteoarthritis. DNA Cell Biol 2023; 42:527-531. [PMID: 37418291 DOI: 10.1089/dna.2023.0197] [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] [Indexed: 07/08/2023] Open
Abstract
Osteoarthritis (OA) is a highly prevalent debilitating joint disease for which there are currently no licensed disease-modifying treatments. The pathogenesis of OA is complex, involving genetic, mechanical, biochemical, and environmental factors. Cartilage injury, arguably the most important driving factor in OA development, is able to activate both protective and inflammatory pathways within the tissue. Recently, >100 genetic risk variants for OA have been identified through Genome Wide Association Studies, which provide a powerful tool to validate existing putative disease pathways and discover new ones. Using such an approach, hypomorphic variants within the aldehyde dehydrogenase 1 family member A2 (ALDH1A2) gene were shown to be associated with increased risk of severe hand OA. ALDH1A2 encodes the enzyme that synthesizes all-trans retinoic acid (atRA), an intracellular signaling molecule. This review summarizes the influence of the genetic variants on expression and function of ALDH1A2 in OA cartilage, its role in the mechanical injury response of cartilage, and its potent anti-inflammatory effect after cartilage injury. In doing so it identifies atRA metabolism-blocking agents as potential treatments for suppressing mechanoflammation in OA.
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Affiliation(s)
- Linyi Zhu
- Centre for Osteoarthritis Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Tonia L Vincent
- Centre for Osteoarthritis Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
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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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Kaya S, Bailey KN, Schurman CA, Evans DS, Alliston T. Bone-cartilage crosstalk informed by aging mouse bone transcriptomics and human osteoarthritis genome-wide association studies. Bone Rep 2023; 18:101647. [PMID: 36636109 PMCID: PMC9830153 DOI: 10.1016/j.bonr.2022.101647] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/28/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
Subchondral bone participates in crosstalk with articular cartilage to maintain joint homeostasis, and disruption of either tissue results in overall joint degeneration. Among the subchondral bone changes observed in osteoarthritis (OA), subchondral bone plate (SBP) thickening has a time-dependent relationship with cartilage degeneration and has recently been shown to be regulated by osteocytes. Here, we evaluate the effect of age on SBP thickness and cartilage degeneration in aging mice. We find that SBP thickness significantly increases by 18-months of age, corresponding temporally with increased cartilage degeneration. To identify factors in subchondral bone that may participate in bone cartilage crosstalk or OA, we leveraged mouse transcriptomic data from one joint tissue compartment - osteocyte-enriched bone - to search for enrichment with human OA in UK Biobank and Arthritis Research UK Osteoarthritis Genetics (arcOGEN) GWAS using the mouse2human (M2H, www.mouse2human.org) strategy. Genes differentially expressed in aging mouse bone are significantly enriched for human OA, showing joint site-specific (knee vs. hip) relationships, exhibit temporal associations with age, and unique gene clusters are implicated in each type of OA. Application of M2H identifies genes with known and unknown functions in osteocytes and OA development that are clinically associated with human OA. Altogether, this work prioritizes genes with a potential role in bone/cartilage crosstalk for further mechanistic study based on their association with human OA in GWAS.
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Affiliation(s)
- Serra Kaya
- Department of Orthopaedic Surgery, University of California San Francisco, CA, United States of America
| | - Karsyn N. Bailey
- Department of Orthopaedic Surgery, University of California San Francisco, CA, United States of America
- UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, CA, United States of America
| | - Charles A. Schurman
- Department of Orthopaedic Surgery, University of California San Francisco, CA, United States of America
- UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, CA, United States of America
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, United States of America
| | - Tamara Alliston
- Department of Orthopaedic Surgery, University of California San Francisco, CA, United States of America
- UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, CA, United States of America
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Kehayova YS, Wilkinson JM, Rice SJ, Loughlin J. Mediation of the Same Epigenetic and Transcriptional Effect by Independent Osteoarthritis Risk-Conferring Alleles on a Shared Target Gene, COLGALT2. Arthritis Rheumatol 2023; 75:910-922. [PMID: 36538011 PMCID: PMC10952352 DOI: 10.1002/art.42427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Over 100 DNA variants have been associated with osteoarthritis (OA), including rs1046934, located within a linkage disequilibrium block encompassing part of COLGALT2 and TSEN15. The present study was undertaken to determine the target gene(s) and the mechanism of action of the OA locus using human fetal cartilage, cartilage from OA and femoral neck fracture arthroplasty patients, and a chondrocyte cell model. METHODS Genotyping and methylation array data of DNA from human OA cartilage samples (n = 87) were used to determine whether the rs1046934 genotype is associated with differential DNA methylation at proximal CpGs. Results were replicated in DNA from human arthroplasty (n = 132) and fetal (n = 77) cartilage samples using pyrosequencing. Allelic expression imbalance (AEI) measured the effects of genotype on COLGALT2 and TSEN15 expression. Reporter gene assays and epigenetic editing determined the functional role of regions harboring differentially methylated CpGs. In silico analyses complemented these experiments. RESULTS Three differentially methylated CpGs residing within regulatory regions were detected in the human OA cartilage array data, and 2 of these were replicated in human arthroplasty and fetal cartilage. AEI was detected for COLGALT2 and TSEN15, with associations between expression and methylation for COLGALT2. Reporter gene assays confirmed that the CpGs are in chondrocyte enhancers, with epigenetic editing results directly linking methylation with COLGALT2 expression. CONCLUSION COLGALT2 is a target of this OA locus. We previously characterized another OA locus, marked by rs11583641, that independently targets COLGALT2. The genotype of rs1046934, like rs11583641, mediates its effect by modulating expression of COLGALT2 via methylation changes to CpGs located in enhancers. Although the single-nucleotide polymorphisms, CpGs, and enhancers are distinct between the 2 independent OA risk loci, their effect on COLGALT2 is the same. COLGALT2 is the target of independent OA risk loci sharing a common mechanism of action.
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Affiliation(s)
| | - J. Mark Wilkinson
- Department of Oncology and MetabolismUniversity of SheffieldSheffieldUK
| | - Sarah J. Rice
- Biosciences Institute, Newcastle UniversityNewcastle upon TyneUK
| | - John Loughlin
- Biosciences Institute, Newcastle UniversityNewcastle upon TyneUK
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9
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Khosasih V, Liu KM, Huang CM, Liou LB, Hsieh MS, Lee CH, Tsai CY, Kuo SY, Hwa SY, Yu CL, Chang CH, Lin CJ, Hsieh SC, Cheng CY, Chen WM, Chen LK, Chuang HP, Chen YT, Tsai PC, Lu LS, H’ng WS, Zhang Y, Chen HC, Chen CH, Lee MTM, Wu JY. A Functional Polymorphism Downstream of Vitamin A Regulator Gene CYP26B1 Is Associated with Hand Osteoarthritis. Int J Mol Sci 2023; 24:ijms24033021. [PMID: 36769350 PMCID: PMC9918232 DOI: 10.3390/ijms24033021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
While genetic analyses have revealed ~100 risk loci associated with osteoarthritis (OA), only eight have been linked to hand OA. Besides, these studies were performed in predominantly European and Caucasian ancestries. Here, we conducted a genome-wide association study in the Han Chinese population to identify genetic variations associated with the disease. We recruited a total of 1136 individuals (n = 420 hand OA-affected; n = 716 unaffected control subjects) of Han Chinese ancestry. We carried out genotyping using Axiom Asia Precisi on Medicine Research Array, and we employed the RegulomeDB database and RoadMap DNase I Hypersensitivity Sites annotations to further narrow down our potential candidate variants. Genetic variants identified were tested in the Geisinger's hand OA cohort selected from the Geisinger MyCode community health initiative (MyCode®). We also performed a luciferase reporter assay to confirm the potential impact of top candidate single-nucleotide polymorphisms (SNPs) on hand OA. We identified six associated SNPs (p-value = 6.76 × 10-7-7.31 × 10-6) clustered at 2p13.2 downstream of the CYP26B1 gene. The strongest association signal identified was rs883313 (p-value = 6.76 × 10-7, odds ratio (OR) = 1.76), followed by rs12713768 (p-value = 1.36 × 10-6, OR = 1.74), near or within the enhancer region closest to the CYP26B1 gene. Our findings showed that the major risk-conferring CC haplotype of SNPs rs12713768 and rs10208040 [strong linkage disequilibrium (LD); D' = 1, r2 = 0.651] drives 18.9% of enhancer expression activity. Our findings highlight that the SNP rs12713768 is associated with susceptibility to and severity of hand OA in the Han Chinese population and that the suggested retinoic acid signaling pathway may play an important role in its pathogenesis.
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Affiliation(s)
- Vivia Khosasih
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 115, Taiwan
- National Center for Genome Medicine, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Kai-Ming Liu
- National Center for Genome Medicine, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Chung-Ming Huang
- Division of Immunology and Rheumatology, Department of Internal Medicine, China Medical University Hospital, Taichung 404, Taiwan
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung 404, Taiwan
- Correspondence: (C.-M.H.); (J.-Y.W.)
| | - Lieh-Bang Liou
- Division of Rheumatology, Allergy and Immunology, New Taipei Municipal Tucheng Hospital, New Taipei City 236, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Ming-Shium Hsieh
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Orthopedics, Taipei Medical University Hospital, Taipei 110, Taiwan
- Department of Orthopedics, En Chu Kong Hospital, New Taipei 237, Taiwan
| | - Chian-Her Lee
- Department of Orthopedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Orthopedics, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Chang-Youh Tsai
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - San-Yuan Kuo
- Division of Rheumatology, Immunology and Allergy, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Su-Yang Hwa
- Department of Orthopaedics, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Chia-Li Yu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Chih-Hao Chang
- Department of Orthopedics, College of Medicine, National Taiwan University and National Taiwan University Hospital, Taipei 100, Taiwan
- Department of Orthopedics, National Taiwan University Hospital Jin-Shan Branch, New Taipei City 208, Taiwan
| | - Cheng-Jyh Lin
- Department of Orthopedics, China Medical University Hospital, Taichung 404, Taiwan
| | - Song-Chou Hsieh
- Division of Allergy, Immunology, and Rheumatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Chun-Ying Cheng
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Orthopedic, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan
| | - Wei-Ming Chen
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Department of Orthopaedics and Traumatology, Taipei Veteran General Hospital, Taipei 112, Taiwan
| | - Liang-Kuang Chen
- Department of Diagnostic Radiology, Shin Kong Wu Ho-Su Memorial Hospital, Taipei 111, Taiwan
| | - Hui-Ping Chuang
- National Center for Genome Medicine, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Ying-Ting Chen
- National Center for Genome Medicine, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Pei-Chun Tsai
- National Center for Genome Medicine, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Liang-Suei Lu
- National Center for Genome Medicine, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Weng-Siong H’ng
- National Center for Genome Medicine, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yanfei Zhang
- Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA
| | - Hsiang-Cheng Chen
- Division of Rheumatology, Immunology and Allergy, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Chien-Hsiun Chen
- National Center for Genome Medicine, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- School of Chinese Medicine, China Medical University, Taichung 404, Taiwan
| | - Ming Ta Michael Lee
- Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA
- School of Chinese Medicine, China Medical University, Taichung 404, Taiwan
| | - Jer-Yuarn Wu
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 115, Taiwan
- National Center for Genome Medicine, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- School of Chinese Medicine, China Medical University, Taichung 404, Taiwan
- Correspondence: (C.-M.H.); (J.-Y.W.)
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10
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Zhu L, Kamalathevan P, Koneva LA, Zarebska JM, Chanalaris A, Ismail H, Wiberg A, Ng M, Muhammad H, Walsby-Tickle J, McCullagh JSO, Watt FE, Sansom SN, Furniss D, Gardiner MD, Vincent TL, Riley N, Spiteri M, McNab I, Little C, Cogswell L, Critchley P, Giele H, Shirley R. Variants in ALDH1A2 reveal an anti-inflammatory role for retinoic acid and a new class of disease-modifying drugs in osteoarthritis. Sci Transl Med 2022; 14:eabm4054. [PMID: 36542696 DOI: 10.1126/scitranslmed.abm4054] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
More than 40% of individuals will develop osteoarthritis (OA) during their lifetime, yet there are currently no licensed disease-modifying treatments for this disabling condition. Common polymorphic variants in ALDH1A2, which encodes the key enzyme for synthesis of all-trans retinoic acid (atRA), are associated with severe hand OA. Here, we sought to elucidate the biological significance of this association. We first confirmed that ALDH1A2 risk variants were associated with hand OA in the U.K. Biobank. Articular cartilage was acquired from 33 individuals with hand OA at the time of routine hand OA surgery. After stratification by genotype, RNA sequencing was performed. A reciprocal relationship between ALDH1A2 mRNA and inflammatory genes was observed. Articular cartilage injury up-regulated similar inflammatory genes by a process that we have previously termed mechanoflammation, which we believe is a primary driver of OA. Cartilage injury was also associated with a concomitant drop in atRA-inducible genes, which were used as a surrogate measure of cellular atRA concentration. Both responses to injury were reversed using talarozole, a retinoic acid metabolism blocking agent (RAMBA). Suppression of mechanoflammation by talarozole was mediated by a peroxisome proliferator-activated receptor gamma (PPARγ)-dependent mechanism. Talarozole was able to suppress mechano-inflammatory genes in articular cartilage in vivo 6 hours after mouse knee joint destabilization and reduced cartilage degradation and osteophyte formation after 26 days. These data show that boosting atRA suppresses mechanoflammation in the articular cartilage in vitro and in vivo and identifies RAMBAs as potential disease-modifying drugs for OA.
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Affiliation(s)
- Linyi Zhu
- Centre for Osteoarthritis Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford OX3 7FY, UK
| | - Pragash Kamalathevan
- Centre for Osteoarthritis Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford OX3 7FY, UK
| | - Lada A Koneva
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford OX3 7FY, UK
| | - Jadwiga Miotla Zarebska
- Centre for Osteoarthritis Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford OX3 7FY, UK
| | - Anastasios Chanalaris
- Centre for Osteoarthritis Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford OX3 7FY, UK
| | - Heba Ismail
- Centre for Osteoarthritis Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford OX3 7FY, UK
- Healthy Lifespan Institute (HELSI) and Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2TN, UK
| | - Akira Wiberg
- Botnar Research Centre, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Michael Ng
- Botnar Research Centre, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Hayat Muhammad
- Centre for Osteoarthritis Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford OX3 7FY, UK
| | - John Walsby-Tickle
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - James S O McCullagh
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Fiona E Watt
- Centre for Osteoarthritis Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford OX3 7FY, UK
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK
| | - Stephen N Sansom
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford OX3 7FY, UK
| | - Dominic Furniss
- Botnar Research Centre, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Matthew D Gardiner
- Centre for Osteoarthritis Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford OX3 7FY, UK
| | - Tonia L Vincent
- Centre for Osteoarthritis Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford OX3 7FY, UK
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11
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Chwastek J, Kędziora M, Borczyk M, Korostyński M, Starowicz K. Inflammation-Driven Secretion Potential Is Upregulated in Osteoarthritic Fibroblast-Like Synoviocytes. Int J Mol Sci 2022; 23:ijms231911817. [PMID: 36233118 PMCID: PMC9570304 DOI: 10.3390/ijms231911817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/24/2022] [Accepted: 09/30/2022] [Indexed: 11/25/2022] Open
Abstract
Osteoarthritis (OA) is one of the most common joint pathologies and a major cause of disability among the population of developed countries. It manifests as a gradual degeneration of the cartilage and subchondral part of the bone, leading to joint damage. Recent studies indicate that not only the cells that make up the articular cartilage but also the synoviocytes, which build the membrane surrounding the joint, contribute to the development of OA. Therefore, the aim of the study was to determine the response to inflammatory factors of osteoarthritic synoviocytes and to identify proteins secreted by them that may influence the progression of OA. This study demonstrated that fibroblast-like synoviocytes of OA patients (FLS-OA) respond more strongly to pro-inflammatory stimulation than cells obtained from control patients (FLS). These changes were observed at the transcriptome level and subsequently confirmed by protein analysis. FLS-OA stimulated by pro-inflammatory factors [such as lipopolysaccharide (LPS) and tumor necrosis factor alpha (TNFα) were shown to secrete significantly more chemokines (CXCL6, CXCL10, and CXCL16) and growth factors [angiopoietin-like protein 1 (ANGPTL1), fibroblast growth factor 5 (FGF5), and insulin-like growth factor 2 (IGF2)] than control cells. Moreover, the translation of proteolytic enzymes [matrix metalloprotease 3 (MMP3), cathepsin K (CTSK), and cathepsin S (CTSS)] by FLS-OA is increased under inflammatory conditions. Our data indicate that the FLS of OA patients are functionally altered, resulting in an enhanced response to the presence of pro-inflammatory factors in the environment, manifested by the increased production of the previously mentioned proteins, which may promote further disease progression.
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Affiliation(s)
- Jakub Chwastek
- Department of Neurochemistry, Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Krakow, Poland
| | - Marta Kędziora
- Department of Neurochemistry, Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Krakow, Poland
| | - Małgorzata Borczyk
- Laboratory of Pharmacogenomics, Department of Molecular Pharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Krakow, Poland
| | - Michał Korostyński
- Laboratory of Pharmacogenomics, Department of Molecular Pharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Krakow, Poland
| | - Katarzyna Starowicz
- Department of Neurochemistry, Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Krakow, Poland
- Correspondence:
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12
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Coutinho de Almeida R, Tuerlings M, Ramos Y, Den Hollander W, Suchiman E, Lakenberg N, Nelissen RGHH, Mei H, Meulenbelt I. Allelic expression imbalance in articular cartilage and subchondral bone refined genome-wide association signals in osteoarthritis. Rheumatology (Oxford) 2022; 62:1669-1676. [PMID: 36040165 PMCID: PMC10070069 DOI: 10.1093/rheumatology/keac498] [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: 05/19/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To present an unbiased approach to identify positional transcript single nucleotide polymorphisms (SNPs) of osteoarthritis (OA) risk loci by allelic expression imbalance (AEI) analyses using RNA sequencing of articular cartilage and subchondral bone from OA patients. METHODS RNA sequencing from 65 articular cartilage and 24 subchondral bone from OA patients was used for AEI analysis. AEI was determined for all genes present in the 100 regions reported by the GWAS catalog that were also expressed in cartilage or bone. The count fraction of the alternative allele (φ) was calculated for each heterozygous individual with the risk-SNP or with the SNP in linkage disequilibrium (LD) with it (r2 > 0.6). Furthermore, a meta-analysis was performed to generate a meta-φ (null hypothesis median φ = 0.49) and P-value for each SNP. RESULTS We identified 30 transcript SNPs (28 in cartilage and 2 in subchondral bone) subject to AEI in 29 genes. Notably, 10 transcript SNPs were located in genes not previously reported in the GWAS catalog, including two long intergenic non-coding RNAs (lincRNAs), MALAT1 (meta-φ = 0.54, FDR = 1.7x10-4) and ILF3-DT (meta-φ = 0.6, FDR = 1.75x10-5). Moreover, 12 drugs were interacting with 7 genes displaying AEI, of which 7 drugs have been already approved. CONCLUSIONS By prioritizing proxy transcript SNPs that mark AEI in cartilage and/or subchondral bone at loci harboring GWAS signals, we present an unbiased approach to identify the most likely functional OA risk-SNP and gene. We identified 10 new potential OA risk genes ready for further, translation towards underlying biological mechanisms.
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Affiliation(s)
- Rodrigo Coutinho de Almeida
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Margo Tuerlings
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Yolande Ramos
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Wouter Den Hollander
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eka Suchiman
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Nico Lakenberg
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rob G H H Nelissen
- Department of Orthopaedics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Dept. of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Ingrid Meulenbelt
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
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13
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Identification of candidate enhancers controlling the transcriptome during the formation of interphalangeal joints. Sci Rep 2022; 12:12835. [PMID: 35896673 PMCID: PMC9329285 DOI: 10.1038/s41598-022-16951-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
The formation of the synovial joint begins with the visible emergence of a stripe of densely packed mesenchymal cells located between distal ends of the developing skeletal anlagen called the interzone. Recently the transcriptome of the early synovial joint was reported. Knowledge about enhancers would complement these data and lead to a better understanding of the control of gene transcription at the onset of joint development. Using ChIP-sequencing we have mapped the H3-signatures H3K27ac and H3K4me1 to locate regulatory elements specific for the interzone and adjacent phalange, respectively. This one-stage atlas of candidate enhancers (CEs) was used to map the association between these respective joint tissue specific CEs and biological processes. Subsequently, integrative analysis of transcriptomic data and CEs identified new putative regulatory elements of genes expressed in interzone (e.g., GDF5, BMP2 and DACT2) and phalange (e.g., MATN1, HAPLN1 and SNAI1). We also linked such CEs to genes known as crucial in synovial joint hypermobility and osteoarthritis, as well as phalange malformations. These analyses show that the CE atlas can serve as resource for identifying, and as starting point for experimentally validating, putative disease-causing genomic regulatory regions in patients with synovial joint dysfunctions and/or phalange disorders, and enhancer-controlled synovial joint and phalange formation.
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14
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Cai Z, Long T, Zhao Y, Lin R, Wang Y. Epigenetic Regulation in Knee Osteoarthritis. Front Genet 2022; 13:942982. [PMID: 35873487 PMCID: PMC9304589 DOI: 10.3389/fgene.2022.942982] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/20/2022] [Indexed: 12/02/2022] Open
Abstract
Osteoarthritis (OA) is a complicated disease with both hereditary and environmental causes. Despite an increase in reports of possible OA risk loci, it has become clear that genetics is not the sole cause of osteoarthritis. Epigenetics, which can be triggered by environmental influences and result in transcriptional alterations, may have a role in OA pathogenesis. The majority of recent research on the epigenetics of OA has been focused on DNA methylation, histone modification, and non-coding RNAs. However, this study will explore epigenetic regulation in OA at the present stage. How genetics, environmental variables, and epigenetics interact will be researched, shedding light for future studies. Their possible interaction and control processes open up new avenues for the development of innovative osteoarthritis treatment and diagnostic techniques.
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Affiliation(s)
| | - Teng Long
- *Correspondence: Teng Long, ; You Wang,
| | | | | | - You Wang
- *Correspondence: Teng Long, ; You Wang,
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15
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Aubourg G, Rice SJ, Bruce-Wootton P, Loughlin J. Genetics of osteoarthritis. Osteoarthritis Cartilage 2022; 30:636-649. [PMID: 33722698 PMCID: PMC9067452 DOI: 10.1016/j.joca.2021.03.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/17/2021] [Accepted: 03/06/2021] [Indexed: 02/02/2023]
Abstract
Osteoarthritis genetics has been transformed in the past decade through the application of large-scale genome-wide association scans. So far, over 100 polymorphic DNA variants have been associated with this common and complex disease. These genetic risk variants account for over 20% of osteoarthritis heritability and the vast majority map to non-protein coding regions of the genome where they are presumed to act by regulating the expression of target genes. Statistical fine mapping, in silico analyses of genomics data, and laboratory-based functional studies have enabled the identification of some of these targets, which encode proteins with diverse roles, including extracellular signaling molecules, intracellular enzymes, transcription factors, and cytoskeletal proteins. A large number of the risk variants correlate with epigenetic factors, in particular cartilage DNA methylation changes in cis, implying that epigenetics may be a conduit through which genetic effects on gene expression are mediated. Some of the variants also appear to have been selected as humans adapted to bipedalism, suggesting that a proportion of osteoarthritis genetic susceptibility results from antagonistic pleiotropy, with risk variants having a positive role in joint formation but a negative role in the long-term health of the joint. Although data from an osteoarthritis genetic study has not yet directly led to a novel treatment, some of the osteoarthritis associated genes code for proteins that have available therapeutics. Genetic investigations are therefore revealing fascinating fundamental insights into osteoarthritis and can expose options for translational intervention.
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Affiliation(s)
- G Aubourg
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - S J Rice
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - P Bruce-Wootton
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - J Loughlin
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK.
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16
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Identifying Novel Osteoarthritis-Associated Genes in Human Cartilage Using a Systematic Meta-Analysis and a Multi-Source Integrated Network. Int J Mol Sci 2022; 23:ijms23084395. [PMID: 35457215 PMCID: PMC9030814 DOI: 10.3390/ijms23084395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
Osteoarthritis, the most common joint disorder, is characterised by deterioration of the articular cartilage. Many studies have identified potential therapeutic targets, yet no effective treatment has been determined. The aim of this study was to identify and rank osteoarthritis-associated genes and micro-RNAs to prioritise those most integral to the disease. A systematic meta-analysis of differentially expressed mRNA and micro-RNAs in human osteoarthritic cartilage was conducted. Ingenuity pathway analysis identified cellular senescence as an enriched pathway, confirmed by a significant overlap (p < 0.01) with cellular senescence drivers (CellAge Database). A co-expression network was built using genes from the meta-analysis as seed nodes and combined with micro-RNA targets and SNP datasets to construct a multi-source information network. This accumulated and connected 1689 genes which were ranked based on node and edge aggregated scores. These bioinformatic analyses were confirmed at the protein level by mass spectrometry of the different zones of human osteoarthritic cartilage (superficial, middle, and deep) compared to normal controls. This analysis, and subsequent experimental confirmation, revealed five novel osteoarthritis-associated proteins (PPIB, ASS1, LHDB, TPI1, and ARPC4-TTLL3). Focusing future studies on these novel targets may lead to new therapies for osteoarthritis.
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17
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Loughlin J. Translating osteoarthritis genetics research: challenging times ahead. Trends Mol Med 2022; 28:176-182. [PMID: 35033441 DOI: 10.1016/j.molmed.2021.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022]
Abstract
The ultimate goal of molecular genetic studies of human diseases is to translate the discoveries for patient benefit. For diseases that lack licensed disease-modifying therapeutics, such as osteoarthritis (OA), the need is acute. OA is polygenic and affects older individuals, with a recent genome-wide study of over 800 000 individuals adding 52 novel association signals to those already reported on for this common arthritis. Many of the predicted effector genes of these signals encode proteins that are targets of drugs for other indications, highlighting repurposing opportunities. Here, the potential for OA genetic data to translate is discussed, including whether the developmental origin of OA will limit the application of genetic risk data for disease-modification purposes.
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Affiliation(s)
- John Loughlin
- Newcastle University, Biosciences Institute, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK.
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18
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Zhang D, Li Q, Zhang D, Yang X, Wang C, Zhang R, Yang X, Li Z, Xiong Y. An eQTL variant of ALDH1A2 is associated with Kashin-Beck disease in Chinese population. J Bone Miner Metab 2022; 40:317-326. [PMID: 35059888 DOI: 10.1007/s00774-021-01287-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 10/28/2021] [Indexed: 11/29/2022]
Abstract
INTRODUCTION The aims of the study were to investigate the relationship between aldehyde dehydrogenase 1 family member A2 (ALDH1A2) and Kashin-Beck disease (KBD), explore the effects of the rs3204689 polymorphism and methylation status on the expression levels of ALDH1A2, and further clarify the pathogenesis of KBD. MATERIALS AND METHODS The genotype of ALDH1A2 rs3204689 was detected by PCR-RFLP in 103 KBD patients and 109 healthy controls in the whole blood. The mRNA level of ALDH1A2 was measured by qRT-PCR, and the protein expression was detected using IHC staining and Western blotting. The MSP-PCR was used to identify the ALDH1A2 methylation level. RESULTS There were significant differences in G/G, G/C, and C/C frequencies of ALDH1A2 rs3204689 between the KBD and control groups (χ2 = 7.113, P = 0.029); the minor allele G of ALDH1A2 was associated with the risk of KBD (χ2 = 5.984, P = 0.014). The mRNA and protein levels of ALDH1A2 were increased in the whole blood and cartilage of KBD patients compared with the controls (P = 0.049, P < 0.0001, P = 0.019). Meanwhile, a statistically significant difference was observed between G/G, G/C and C/C genotype on mRNA expression (P = 0.039). The methylation level of the ALDH1A2 gene promoter region showed no significant difference between the KBD and control groups (χ2 = 0.317, P = 0.573). CONCLUSION Our case-control study indicates that the common variant rs3204689 near ALDH1A2 is associated with KBD in Chinese population. The risk allele G of rs3204689 is statistically linked to the high expression of ALDH1A2, which is up-regulated in the cartilage and whole blood of KBD patients. Our findings suggest a potential role of ALDH1A2 in the pathogenesis of KBD.
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Affiliation(s)
- Di Zhang
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, School of Public Health, National Health Commission of the People's Republic of China, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Qiang Li
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, School of Public Health, National Health Commission of the People's Republic of China, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Dandan Zhang
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, School of Public Health, National Health Commission of the People's Republic of China, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Xiaoli Yang
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, School of Public Health, National Health Commission of the People's Republic of China, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Chen Wang
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, School of Public Health, National Health Commission of the People's Republic of China, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Rongqiang Zhang
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, School of Public Health, National Health Commission of the People's Republic of China, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, People's Republic of China
- Shaanxi University of Chinese Medicine, Xianyang, People's Republic of China
| | - Xuena Yang
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, School of Public Health, National Health Commission of the People's Republic of China, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Zhaofang Li
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, School of Public Health, National Health Commission of the People's Republic of China, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Yongmin Xiong
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, School of Public Health, National Health Commission of the People's Republic of China, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, People's Republic of China.
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19
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Takemoto G, Seki T, Takegami Y, Osawa Y, Makida K, Ochiai S, Ishizuka S, Suzuki K, Hasegawa Y, Imagama S. The development of knee osteoarthritis and serum carotenoid levels among community-dwelling people in Japan. Mod Rheumatol 2022; 32:205-212. [PMID: 33719826 DOI: 10.1080/14397595.2021.1900030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVES Carotenoids are plant pigments found in many vegetables, functioning as antioxidants scavenging singlet molecular oxygen and peroxyl radicals. No longitudinal study exists on the relationship between carotenoids and knee osteoarthritis (KOA) development. We aimed to determine the incidence of KOA development for 10 years in community-dwelling people in Japan and assess its association with serum carotenoids. METHODS Data of 440 participants (174 men, 266 women) with health-screening records for at least 10 years were analysed. We defined KOA development as advancing from K/L grade 0/1 at the initial check-up to grade ≥2 in a unilateral knee during a 10-year follow-up period. Serum carotenoid levels were measured using high-performance liquid chromatography. We used the Cox hazard model for multivariate analysis and investigated each carotenoid's impact on KOA development. RESULTS KOA developed in 33.4% of patients; the annual KOA development rate was significantly higher among women than among men (p < .01; 3.4% vs. 1.6%). Among the carotenoids measured, only retinol was associated with KOA development in women using multivariable analysis. KOA development was not associated with any carotenoids in men. CONCLUSION The annual rate of KOA development was higher in women, and retinol was associated with KOA development in women.
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Affiliation(s)
- Genta Takemoto
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taisuke Seki
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuhiko Takegami
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Osawa
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuya Makida
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoshi Ochiai
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinya Ishizuka
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koji Suzuki
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan
| | - Yukiharu Hasegawa
- Department of Rehabilitation, Kansai University of Welfare Sciences, Kashihara, Japan
| | - Shiro Imagama
- Department of Orthopedic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
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20
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Dickinson AJG, Turner SD, Wahl S, Kennedy AE, Wyatt BH, Howton DA. E-liquids and vanillin flavoring disrupts retinoic acid signaling and causes craniofacial defects in Xenopus embryos. Dev Biol 2022; 481:14-29. [PMID: 34543654 PMCID: PMC8665092 DOI: 10.1016/j.ydbio.2021.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 01/03/2023]
Abstract
Environmental teratogens such as smoking are known risk factors for developmental disorders such as cleft palate. While smoking rates have declined, a new type of smoking, called vaping is on the rise. Vaping is the use of e-cigarettes to vaporize and inhale an e-liquid containing nicotine and food-like flavors. There is the potential that, like smoking, vaping could also pose a danger to the developing human. Rather than waiting for epidemiological and mammalian studies, we have turned to an aquatic developmental model, Xenopus laevis, to more quickly assess whether e-liquids contain teratogens that could lead to craniofacial malformations. Xenopus, like zebrafish, has the benefit of being a well-established developmental model and has also been effective in predicting whether a chemical could be a teratogen. We have determined that embryonic exposure to dessert flavored e-liquids can cause craniofacial abnormalities, including an orofacial cleft in Xenopus. To better understand the underlying mechanisms contributing to these defects, transcriptomic analysis of the facial tissues of embryos exposed to a representative dessert flavored e-liquid vapor extract was performed. Analysis of differentially expressed genes in these embryos revealed several genes associated with retinoic acid metabolism or the signaling pathway. Consistently, retinoic acid receptor inhibition phenocopied the craniofacial defects as those embryos exposed to the vapor extract of the e-liquid. Such malformations also correlated with a group of common differentially expressed genes, two of which are associated with midface birth defects in humans. Further, e-liquid exposure sensitized embryos to forming craniofacial malformations when they already had depressed retinoic acid signaling. Moreover, 13-cis-retinoic acid treatment could significantly reduce the e-liquid induced malformation in the midface. Such results suggest the possibility of an interaction between retinoic acid signaling and e-liquid exposure. One of the most popular and concentrated flavoring chemicals in dessert flavored e-liquids is vanillin. Xenopus embryos exposed to this chemical closely resembled embryos exposed to dessert-like e-liquids and a retinoic acid receptor antagonist. In summary, we determined that e-liquid chemicals, in particular vanillin, can cause craniofacial defects potentially by dysregulating retinoic acid signaling. This work warrants the evaluation of vanillin and other such flavoring additives in e-liquids on mammalian development.
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Affiliation(s)
| | - Stephen D Turner
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA; Signature Science LLC, Charlottesville, VA, USA
| | - Stacey Wahl
- Research and Education Department, Tompkins-McCaw Library for the Health Sciences, Virginia Commonwealth University, Richmond, VA, USA
| | - Allyson E Kennedy
- Directorate for Computer and Information Science and Engineering, National Science Foundation, Alexandria, VA, USA
| | - Brent H Wyatt
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27607, USA
| | - Deborah A Howton
- Department of Biology, Virginia Commonwealth University, Richmond, VA, USA
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21
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Shepherd RF, Kerns JG, Ranganath LR, Gallagher JA, Taylor AM. "Lessons from Rare Forms of Osteoarthritis". Calcif Tissue Int 2021; 109:291-302. [PMID: 34417863 PMCID: PMC8403118 DOI: 10.1007/s00223-021-00896-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022]
Abstract
Osteoarthritis (OA) is one of the most prevalent conditions in the world, particularly in the developed world with a significant increase in cases and their predicted impact as we move through the twenty-first century and this will be exacerbated by the covid pandemic. The degeneration of cartilage and bone as part of this condition is becoming better understood but there are still significant challenges in painting a complete picture to recognise all aspects of the condition and what treatment(s) are most appropriate in individual causes. OA encompasses many different types and this causes some of the challenges in fully understanding the condition. There have been examples through history where much has been learnt about common disease(s) from the study of rare or extreme phenotypes, particularly where Mendelian disorders are involved. The often early onset of symptoms combined with the rapid and aggressive pathogenesis of these diseases and their predictable outcomes give an often-under-explored resource. It is these "rarer forms of disease" that William Harvey referred to that offer novel insights into more common conditions through their more extreme presentations. In the case of OA, GWAS analyses demonstrate the multiple genes that are implicated in OA in the general population. In some of these rarer forms, single defective genes are responsible. The extreme phenotypes seen in conditions such as Camptodactyly Arthropathy-Coxa Vara-pericarditis Syndrome, Chondrodysplasias and Alkaptonuria all present potential opportunities for greater understanding of disease pathogenesis, novel therapeutic interventions and diagnostic imaging. This review examines some of the rarer presenting forms of OA and linked conditions, some of the novel discoveries made whilst studying them, and findings on imaging and treatment strategies.
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Affiliation(s)
- Rebecca F Shepherd
- Lancaster Medical School, Faculty of Health & Medicine, Lancaster University, Lancaster, UK
| | - Jemma G Kerns
- Lancaster Medical School, Faculty of Health & Medicine, Lancaster University, Lancaster, UK
| | - Lakshminarayan R Ranganath
- Departments of Clinical Biochemistry and Metabolic Medicine, Royal Liverpool University Hospital, Liverpool, L7 8XP, UK
| | - James A Gallagher
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8T, UK
| | - Adam M Taylor
- Lancaster Medical School, Faculty of Health & Medicine, Lancaster University, Lancaster, UK.
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22
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Cheng B, Liang C, Yang X, Li P, Liu L, Cheng S, Jia Y, Zhang L, Ma M, Qi X, Yao Y, Chu X, Ye J, Lu C, Guo X, Wen Y, Zhang F. Genetic association scan of 32 osteoarthritis susceptibility genes identified TP63 associated with an endemic osteoarthritis, Kashin-Beck disease. Bone 2021; 150:115997. [PMID: 33964467 DOI: 10.1016/j.bone.2021.115997] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/20/2021] [Accepted: 04/15/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Kashin-Beck disease (KBD) is an endemic chronic osteochondropathy. The clinical manifestations and radiographic features of adult KBD were similar to those of osteoarthritis (OA). METHODS We first performed a genetic association scan of 32 OA susceptibility genes with KBD in 898 Han Chinese subjects. The MassARRAY genotyping system (Agena) was used for SNP genotyping. PLINK 1.9 was used for quality control and association testing. Using articular cartilage specimens from 7 adult KBD patients and 4 control subjects, lentivirus-mediated RNA interference (RNAi), qRT-PCR, Western blot and immunohistochemistry were employed to explore the functional relevance of TP63 to KBD chondrocyte. RESULTS SNP genotyping and association analysis identified TP63 (rs12107036, P = 0.005, OR = 0.71) and OARD1 (rs11280, P = 0.004, OR = 1.51) were significantly associated with KBD. It was also found that TP63 was significantly up-regulated in KBD articular cartilage in both mRNA and protein level compared with the controls (P < 0.05). TP63 suppression by lentivirus-mediated RNAi notably decreased the abundance of Caspase3 and SOX9 in chondrocytes. Most importantly, compared with the scrambled sequence (shControl) group, the protein level of ACAN was increased in the shTP63 group. The mRNA expression of chondrocyte marker genes (COL2A1 and ACAN) was not significantly changed after TP63 knockdown relative to shControl group. CONCLUSION Our study identifies TP63 as a novel susceptibility gene for KBD, and demonstrates that the inhibition of TP63 suppresses chondrocyte apoptosis and partly facilitates chondrogenesis. The combination of SNP genotyping and molecular biology techniques provides a useful tool for understanding the biological mechanism and differential diagnosis studies of KBD and OA.
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Affiliation(s)
- Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Chujun Liang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Ping Li
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Lu Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Mei Ma
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Xin Qi
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Yao Yao
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Xiaomeng Chu
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Jing Ye
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Chao Lu
- Department of Joint Surgery, Xi'an Honghui Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiong Guo
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China.
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, 710061, China.
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23
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Steinberg J, Southam L, Fontalis A, Clark MJ, Jayasuriya RL, Swift D, Shah KM, Brooks RA, McCaskie AW, Wilkinson JM, Zeggini E. Linking chondrocyte and synovial transcriptional profile to clinical phenotype in osteoarthritis. Ann Rheum Dis 2021; 80:1070-1074. [PMID: 33903094 PMCID: PMC8292595 DOI: 10.1136/annrheumdis-2020-219760] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/30/2021] [Accepted: 04/11/2021] [Indexed: 12/20/2022]
Abstract
OBJECTIVES To determine how gene expression profiles in osteoarthritis joint tissues relate to patient phenotypes and whether molecular subtypes can be reproducibly captured by a molecular classification algorithm. METHODS We analysed RNA sequencing data from cartilage and synovium in 113 osteoarthritis patients, applying unsupervised clustering and Multi-Omics Factor Analysis to characterise transcriptional profiles. We tested the association of the molecularly defined patient subgroups with clinical characteristics from electronic health records. RESULTS We detected two patient subgroups in low-grade cartilage (showing no/minimal degeneration, cartilage normal/softening only), with differences associated with inflammation, extracellular matrix-related and cell adhesion pathways. The high-inflammation subgroup was associated with female sex (OR 4.12, p=0.0024) and prescription of proton pump inhibitors (OR 4.21, p=0.0040). We identified two independent patient subgroupings in osteoarthritis synovium: one related to inflammation and the other to extracellular matrix and cell adhesion processes. A seven-gene classifier including MMP13, APOD, MMP2, MMP1, CYTL1, IL6 and C15orf48 recapitulated the main axis of molecular heterogeneity in low-grade knee osteoarthritis cartilage (correlation ρ=-0.88, p<10-10) and was reproducible in an independent patient cohort (ρ=-0.85, p<10-10). CONCLUSIONS These data support the reproducible stratification of osteoarthritis patients by molecular subtype and the exploration of new avenues for tailored treatments.
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Affiliation(s)
- Julia Steinberg
- Institute for Translational Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
- Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, New South Wales, Australia
- Wellcome Sanger Institute, Hinxton, UK
| | - Lorraine Southam
- Institute for Translational Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
- Wellcome Sanger Institute, Hinxton, UK
| | - Andreas Fontalis
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield, UK
| | - Matthew J Clark
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield, UK
| | - Raveen L Jayasuriya
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield, UK
| | - Diane Swift
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield, UK
| | - Karan M Shah
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield, UK
| | - Roger A Brooks
- Division of Trauma & Orthopaedic Surgery, University of Cambridge, Cambridge, UK
| | - Andrew W McCaskie
- Division of Trauma & Orthopaedic Surgery, University of Cambridge, Cambridge, UK
| | - Jeremy Mark Wilkinson
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield, UK
- Centre for Integrated Research into Musculoskeletal Ageing and Sheffield Healthy Lifespan Institute, University of Sheffield, Sheffield, UK
| | - Eleftheria Zeggini
- Institute for Translational Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
- Wellcome Sanger Institute, Hinxton, UK
- Translational Genomics, Klinikum rechts der Isar der Technischen Universitat Munchen, Munchen, Germany
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24
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Houtman E, Coutinho de Almeida R, Tuerlings M, Suchiman HED, Broekhuis D, Nelissen RGHH, Ramos YFM, van Meurs JBJ, Meulenbelt I. Characterization of dynamic changes in Matrix Gla Protein (MGP) gene expression as function of genetic risk alleles, osteoarthritis relevant stimuli, and the vitamin K inhibitor warfarin. Osteoarthritis Cartilage 2021; 29:1193-1202. [PMID: 33984465 DOI: 10.1016/j.joca.2021.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVE We here aimed to characterize changes of Matrix Gla Protein (MGP) expression in relation to its recently identified OA risk allele rs1800801-T in OA cartilage, subchondral bone and human ex vivo osteochondral explants subjected to OA related stimuli. Given that MGP function depends on vitamin K bioavailability, we studied the effect of frequently prescribed vitamin K antagonist warfarin. METHODS Differential (allelic) mRNA expression of MGP was analyzed using RNA-sequencing data of human OA cartilage and subchondral bone. Human osteochondral explants were used to study exposures to interleukin one beta (IL-1β; inflammation), triiodothyronine (T3; Hypertrophy), warfarin, or 65% mechanical stress (65%MS) as function of rs1800801 genotypes. RESULTS We confirmed that the MGP risk allele rs1800801-T was associated with lower expression and that MGP was significantly upregulated in lesioned as compared to preserved OA tissues, mainly in risk allele carriers, in both cartilage and subchondral bone. Moreover, MGP expression was downregulated in response to OA like triggers in cartilage and subchondral bone and this effect might be reduced in carriers of the rs1800801-T risk allele. Finally, warfarin treatment in cartilage increased COL10A1 and reduced SOX9 and MMP3 expression and in subchondral bone reduced COL1A1 and POSTN expression. DISCUSSION & CONCLUSIONS Our data highlights that the genetic risk allele lowers MGP expression and upon OA relevant triggers may hamper adequate dynamic changes in MGP expression, mainly in cartilage. The determined direct negative effect of warfarin on human explant cultures functionally underscores the previously found association between vitamin K deficiency and OA.
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Affiliation(s)
- E Houtman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - R Coutinho de Almeida
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - M Tuerlings
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - H E D Suchiman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - D Broekhuis
- Department of Orthopaedics, Leiden University Medical Center, Leiden, the Netherlands
| | - R G H H Nelissen
- Department of Orthopaedics, Leiden University Medical Center, Leiden, the Netherlands
| | - Y F M Ramos
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - J B J van Meurs
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - I Meulenbelt
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
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25
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Current Epidemiology and Risk Factors for the Development of Hand Osteoarthritis. Curr Rheumatol Rep 2021; 23:61. [PMID: 34216294 DOI: 10.1007/s11926-021-01025-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2021] [Indexed: 12/23/2022]
Abstract
PURPOSE OF REVIEW Hand osteoarthritis (hand OA), the most common peripheral arthritis in the world, is less studied than osteoarthritis (OA) of the knee and hip. However, it is uniquely situated to offer novel insight into OA as a disease process by removing weight-bearing as a confounder of systemic disease mechanisms. Here we review the epidemiology of hand OA and key risk factors for its development. RECENT FINDINGS Mounting evidence points to obesity as an important risk factor for hand OA development, with new evidence implicating a role for leptin and serum fatty acids. Disease progression in hand OA and specifically the erosive OA subtype may be associated with diabetes. New evidence supports an association between cardiovascular disease progression and symptomatic hand OA. Alcohol use may be associated with increased synovitis and erosive hand OA. Differences in ethnical distributions of hand OA have become more apparent, with a lower prevalence in Black patients compared to White patients. Novel genetic insights implicating the WNT gene pathway and IL-1β have led to novel potential targets in hand OA pathogenesis. Hand OA is a heterogeneous disease with many modifiable and non-modifiable risk factors that can determine disease severity and shed light on disease pathogenesis.
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26
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Abstract
PURPOSE OF REVIEW Osteoarthritis is a heterogeneous, multifactorial condition regulated by complex biological interactions at multiple levels. Comprehensive understanding of these regulatory interactions is required to develop feasible advances to improve patient outcomes. Improvements in technology have made extensive genomic, transcriptomic, epigenomic, proteomic, and metabolomic profiling possible. This review summarizes findings over the past 20 months related to omics technologies in osteoarthritis and examines how using a multiomics approach is necessary for advancing our understanding of osteoarthritis as a disease to improve precision osteoarthritis treatments. RECENT FINDINGS Using the search terms 'genomics' or 'transcriptomics' or 'epigenomics' or 'proteomics' or 'metabolomics' and 'osteoarthritis' from January 1, 2018 to August 31, 2019, we identified advances in omics approaches applied to osteoarthritis. Trends include untargeted whole genome, transcriptome, proteome, and metabolome analyses leading to identification of novel molecular signatures, cell subpopulations and multiomics validation approaches. SUMMARY To address the complexity of osteoarthritis, integration of multitissue analyses by multiomics approaches with the inclusion of longitudinal clinical data is necessary for a comprehensive understanding of the disease process, and for appropriate development of efficacious diagnostics, prognostics, and biotherapeutics.
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27
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Sorial AK, Hofer IMJ, Tselepi M, Cheung K, Parker E, Deehan DJ, Rice SJ, Loughlin J. Multi-tissue epigenetic analysis of the osteoarthritis susceptibility locus mapping to the plectin gene PLEC. Osteoarthritis Cartilage 2020; 28:1448-1458. [PMID: 32580029 PMCID: PMC7594932 DOI: 10.1016/j.joca.2020.06.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 02/02/2023]
Abstract
OBJECTIVE In cartilage, the osteoarthritis (OA) associated single nucleotide polymorphism (SNP) rs11780978 correlates with differential expression of PLEC, and with differential methylation of PLEC CpG dinucleotides, forming eQTLs and mQTLs respectively. This implies that methylation links chondrocyte genotype and phenotype, thus driving the functional effect of this genetic risk signal. PLEC encodes plectin, a cytoskeletal protein that enables tissues to respond to mechanical forces. We sought to assess whether these PLEC functional effects were cartilage specific. METHOD Cartilage, fat pad, synovium and peripheral blood were collected from patients undergoing arthroplasty. PLEC CpGs were analysed for mQTLs and allelic expression imbalance (AEI) was performed to test for eQTLs. Plectin was knocked down in a mesenchymal stem cell (MSC) line using CRISPR/Cas9 and cells phenotyped by RNA-sequencing. RESULTS mQTLs were discovered in fat pad, synovium and blood. Their effects were however stronger in the joint tissues and of comparable effect between these tissues. We observed AEI in synovium in the same direction as for cartilage and correlations between methylation and PLEC expression. Knocking-down plectin impacted on pathways reported to have a role in OA, including Wnt signalling, glycosaminoglycan biosynthesis and immune regulation. CONCLUSIONS Synovium is also a target of the rs11780978 OA association functionally operating on PLEC. In fat pad, mQTLs were identified but these did not correlate with PLEC expression, suggesting the functional effect is not joint-wide. Our study highlights interplay between genetic risk, DNA methylation and gene expression in OA, and reveals clear differences between tissues from the same diseased joint.
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MESH Headings
- Adipose Tissue/metabolism
- Adult
- Aged
- Aged, 80 and over
- Arthroplasty, Replacement
- CRISPR-Cas Systems
- Cartilage, Articular/metabolism
- Cell Line
- Chondrocytes/metabolism
- CpG Islands
- DNA Methylation
- Epigenesis, Genetic
- Female
- Gene Expression
- Gene Knockdown Techniques
- Genetic Predisposition to Disease
- Glycosaminoglycans/biosynthesis
- Humans
- Male
- Mesenchymal Stem Cells/metabolism
- Middle Aged
- Osteoarthritis, Hip/blood
- Osteoarthritis, Hip/genetics
- Osteoarthritis, Hip/metabolism
- Osteoarthritis, Hip/surgery
- Osteoarthritis, Knee/blood
- Osteoarthritis, Knee/genetics
- Osteoarthritis, Knee/metabolism
- Osteoarthritis, Knee/surgery
- Plectin/blood
- Plectin/genetics
- Plectin/metabolism
- Quantitative Trait Loci
- Sequence Analysis, RNA
- Synovial Membrane/metabolism
- Wnt Signaling Pathway/genetics
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Affiliation(s)
- A K Sorial
- Newcastle University, Biosciences Institute, Newcastle Upon Tyne, UK.
| | - I M J Hofer
- Newcastle University, Biosciences Institute, Newcastle Upon Tyne, UK.
| | - M Tselepi
- Newcastle University, Biosciences Institute, Newcastle Upon Tyne, UK.
| | - K Cheung
- Newcastle University, Biosciences Institute, Newcastle Upon Tyne, UK.
| | - E Parker
- Newcastle University, Biosciences Institute, Newcastle Upon Tyne, UK.
| | - D J Deehan
- Freeman Hospital, Newcastle Upon Tyne, UK.
| | - S J Rice
- Newcastle University, Biosciences Institute, Newcastle Upon Tyne, UK.
| | - J Loughlin
- Newcastle University, Biosciences Institute, Newcastle Upon Tyne, UK.
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28
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Rice SJ, Beier F, Young DA, Loughlin J. Interplay between genetics and epigenetics in osteoarthritis. Nat Rev Rheumatol 2020; 16:268-281. [PMID: 32273577 DOI: 10.1038/s41584-020-0407-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2020] [Indexed: 12/15/2022]
Abstract
Research into the molecular genetics of osteoarthritis (OA) has been substantially bolstered in the past few years by the implementation of powerful genome-wide scans that have revealed a large number of novel risk loci associated with the disease. This refreshing wave of discovery has occurred concurrently with epigenetic studies of joint tissues that have examined DNA methylation, histone modifications and regulatory RNAs. These epigenetic analyses have involved investigations of joint development, homeostasis and disease and have used both human samples and animal models. What has become apparent from a comparison of these two complementary approaches is that many OA genetic risk signals interact with, map to or correlate with epigenetic mediators. This discovery implies that epigenetic mechanisms, and their effect on gene expression, are a major conduit through which OA genetic risk polymorphisms exert their functional effects. This observation is particularly exciting as it provides mechanistic insight into OA susceptibility. Furthermore, this knowledge reveals avenues for attenuating the negative effect of risk-conferring alleles by exposing the epigenome as an exploitable target for therapeutic intervention in OA.
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Affiliation(s)
- Sarah J Rice
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Frank Beier
- Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada.,Western Bone and Joint Institute, The University of Western Ontario, London, ON, Canada
| | - David A Young
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - John Loughlin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
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Osteoarthritis year in review 2019: genetics, genomics and epigenetics. Osteoarthritis Cartilage 2020; 28:275-284. [PMID: 31874234 DOI: 10.1016/j.joca.2019.11.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 02/02/2023]
Abstract
Although osteoarthritis (OA) aetiology is complex, genetic, genomic and epigenetic studies published within the last decade have advanced our understanding of the molecular processes underlying this common musculoskeletal disease. The purpose of this narrative review is to highlight the key research articles within the OA genetics, genomics and epigenetics fields that were published between April 2018 and April 2019. The review focuses on the identification of new OA genetic risk loci, genomics techniques that have been used for the first time in human cartilage and new publicly available databases, and datasets that will aid OA functional studies. Fifty-six new OA susceptibility loci were identified by two large scale genome wide association study meta-analyses, increasing the number of genome-wide significant risk loci to 90. OA risk variants are enriched near genes involved in skeletal development and morphology, and show genetic overlap with height, hip shape, bone area and developmental dysplasia of the hip. Several functional studies of OA loci were published, including a genome-wide analysis of genetic variation on cartilage gene expression. A specialised data portal for exploring cross-species skeletal transcriptomic datasets has been developed, and the first use of cartilage single cell RNAseq analysis reported. This year also saw the systematic identification of all microRNAs, long non-coding RNAs and circular RNAs expressed in human OA cartilage. Putative transcriptional regulatory regions have been mapped in human chondrocytes genome-wide, providing a dataset that will facilitate the prioritisation and characterisation of OA genetic and epigenetic loci.
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Rice SJ, Cheung K, Reynard LN, Loughlin J. Discovery and analysis of methylation quantitative trait loci (mQTLs) mapping to novel osteoarthritis genetic risk signals. Osteoarthritis Cartilage 2019; 27:1545-1556. [PMID: 31173883 DOI: 10.1016/j.joca.2019.05.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Osteoarthritis (OA) is polygenic with over 90 independent genome-wide association loci so far reported. A key next step is the identification of target genes and the molecular mechanisms through which this genetic risk operates. The majority of OA risk-conferring alleles are predicted to act by modulating gene expression. DNA methylation at CpG dinucleotides may be a functional conduit through which this occurs and is detectable by mapping methylation quantitative trait loci, or mQTLs. This approach can therefore provide functional insight into OA risk and will prioritize genes for subsequent investigation. That was our goal, with a focus on the largest set of OA loci yet to be reported. METHOD We investigated DNA methylation, genotype and RNA sequencing data derived from the cartilage of patients who had undergone arthroplasty and combined this with in silico analyses of expression quantitative trait loci, epigenomes and chromatin interactions. RESULTS We investigated 42 OA risk loci and in ten of these we identified 24 CpGs in which methylation correlated with genotype (false discovery rate (FDR) P-values ranging from 0.049 to 1.73x10-25). In silico analyses of these mQTLs prioritised genes and regulatory elements at the majority of the ten loci, with COLGALT2 (encoding a collagen galactosyltransferase), COL11A2 (encoding a polypeptide chain of type XI collagen) and WWP2 (encoding a ubiquitin ligase active during chondrogenesis) emerging as particularly compelling target genes. CONCLUSION We have highlighted the pivotal role of DNA methylation as a link between genetic risk and OA and prioritized genes for further investigation.
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Affiliation(s)
- S J Rice
- Newcastle University, Institute of Genetic Medicine, Newcastle upon Tyne, UK.
| | - K Cheung
- Newcastle University, Institute of Genetic Medicine, Newcastle upon Tyne, UK; Newcastle University, Bioinformatics Support Unit, Newcastle upon Tyne, UK.
| | - L N Reynard
- Newcastle University, Institute of Genetic Medicine, Newcastle upon Tyne, UK.
| | - J Loughlin
- Newcastle University, Institute of Genetic Medicine, Newcastle upon Tyne, UK.
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Rice SJ, Tselepi M, Sorial AK, Aubourg G, Shepherd C, Almarza D, Skelton AJ, Pangou I, Deehan D, Reynard LN, Loughlin J. Prioritization of PLEC and GRINA as Osteoarthritis Risk Genes Through the Identification and Characterization of Novel Methylation Quantitative Trait Loci. Arthritis Rheumatol 2019; 71:1285-1296. [PMID: 30730609 PMCID: PMC6790675 DOI: 10.1002/art.40849] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 01/30/2019] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To identify methylation quantitative trait loci (mQTLs) correlating with osteoarthritis (OA) risk alleles and to undertake mechanistic characterization as a means of target gene prioritization. METHODS We used genome-wide genotyping and cartilage DNA methylation array data in a discovery screen of novel OA risk loci. This was followed by methylation, gene expression analysis, and genotyping studies in additional cartilage samples, accompanied by in silico analyses. RESULTS We identified 4 novel OA mQTLs. The most significant mQTL contained 9 CpG sites where methylation correlated with OA risk genotype, with 5 of the CpG sites having P values <1 × 10-10 . The 9 CpG sites reside in an interval of only 7.7 kb within the PLEC gene and form 2 distinct clusters. We were able to prioritize PLEC and the adjacent gene GRINA as independent targets of the OA risk. We identified PLEC and GRINA expression QTLs operating in cartilage, as well as methylation-expression QTLs operating on the 2 genes. GRINA and PLEC also demonstrated differential expression between OA hip and non-OA hip cartilage. CONCLUSION PLEC encodes plectin, a cytoskeletal protein that maintains tissue integrity by regulating intracellular signaling in response to mechanical stimuli. GRINA encodes the ionotropic glutamate receptor TMBIM3 (transmembrane BAX inhibitor 1 motif-containing protein family member 3), which regulates cell survival. Based on our results, we hypothesize that in a joint predisposed to OA, expression of these genes alters in order to combat aberrant biomechanics, and that this is epigenetically regulated. However, carriage of the OA risk-conferring allele at this locus hinders this response and contributes to disease development.
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Affiliation(s)
- Sarah J Rice
- International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - Maria Tselepi
- International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - Antony K Sorial
- International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - Guillaume Aubourg
- International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - Colin Shepherd
- International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - David Almarza
- International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew J Skelton
- International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - Ioanna Pangou
- International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | | | - Louise N Reynard
- International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - John Loughlin
- International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
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Klein JC, Keith A, Rice SJ, Shepherd C, Agarwal V, Loughlin J, Shendure J. Functional testing of thousands of osteoarthritis-associated variants for regulatory activity. Nat Commun 2019; 10:2434. [PMID: 31164647 PMCID: PMC6547687 DOI: 10.1038/s41467-019-10439-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 04/29/2019] [Indexed: 12/19/2022] Open
Abstract
To date, genome-wide association studies have implicated at least 35 loci in osteoarthritis but, due to linkage disequilibrium, the specific variants underlying these associations and the mechanisms by which they contribute to disease risk have yet to be pinpointed. Here, we functionally test 1,605 single nucleotide variants associated with osteoarthritis for regulatory activity using a massively parallel reporter assay. We identify six single nucleotide polymorphisms (SNPs) with differential regulatory activity between the major and minor alleles. We show that the most significant SNP, rs4730222, exhibits differential nuclear protein binding in electrophoretic mobility shift assays and drives increased expression of an alternative isoform of HBP1 in a heterozygote chondrosarcoma cell line, in a CRISPR-edited osteosarcoma cell line, and in chondrocytes derived from osteoarthritis patients. This study provides a framework for prioritization of GWAS variants and highlights a role of HBP1 and Wnt signaling in osteoarthritis pathogenesis.
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Affiliation(s)
- Jason C Klein
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Aidan Keith
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Sarah J Rice
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Colin Shepherd
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Vikram Agarwal
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - John Loughlin
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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Bortoluzzi A, Furini F, Scirè CA. Osteoarthritis and its management - Epidemiology, nutritional aspects and environmental factors. Autoimmun Rev 2018; 17:1097-1104. [DOI: 10.1016/j.autrev.2018.06.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 06/03/2018] [Indexed: 02/06/2023]
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Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis. Sci Rep 2018; 8:15499. [PMID: 30341348 PMCID: PMC6195601 DOI: 10.1038/s41598-018-33779-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/04/2018] [Indexed: 12/11/2022] Open
Abstract
Osteoarthritis (OA) is a common joint disorder with increasing impact in an aging society. While genetic and transcriptomic analyses have revealed some genes and non-coding loci associated to OA, the pathogenesis remains incompletely understood. Chromatin profiling, which provides insight into gene regulation, has not been reported in OA mainly due to technical difficulties. Here, we employed Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) to map the accessible chromatin landscape in articular knee cartilage of OA patients. We identified 109,215 accessible chromatin regions for cartilages, of which 71% were annotated as enhancers. By overlaying them with genetic and DNA methylation data, we have determined potential OA-relevant enhancers and their putative target genes. Furthermore, through integration with RNA-seq data, we characterized genes that are altered both at epigenomic and transcriptomic levels in OA. These genes are enriched in pathways regulating ossification and mesenchymal stem cell (MSC) differentiation. Consistently, the differentially accessible regions in OA are enriched for MSC-specific enhancers and motifs of transcription factor families involved in osteoblast differentiation. In conclusion, we demonstrate how direct chromatin profiling of clinical tissues can provide comprehensive epigenetic information for a disease and suggest candidate genes and enhancers of translational potential.
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Skarp S, Kämäräinen OP, Wei GH, Jakkula E, Kiviranta I, Kröger H, Auvinen J, Lehenkari P, Ala-Kokko L, Männikkö M. Whole exome sequencing in Finnish families identifies new candidate genes for osteoarthritis. PLoS One 2018; 13:e0203313. [PMID: 30157244 PMCID: PMC6114922 DOI: 10.1371/journal.pone.0203313] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/18/2018] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Osteoarthritis (OA) is the most common degenerative joint disease and one of the major causes of disability worldwide. It is a multifactorial disorder with a significant genetic component. The heritability of OA has been estimated to be 60% for hip OA and 39% for knee OA. Genetic factors behind OA are still largely unknown. Studying families with strong history of OA, facilitates examining the co-segregation of genetic variation and OA. The aim of this study was to identify new, rare genetic factors and novel candidate genes for OA. METHODS Eight patients from three Finnish families with hip and knee OA were studied using whole exome sequencing. We focused on rare exonic variants with predicted pathogenicity and variants located in active promoter or strong enhancer regions. Expression of identified candidate genes were studied in bone and cartilage tissues and the observed variants were investigated using bioinformatic analyses. RESULTS Two rare variants co-segregated with OA in two families. In Family 8 a missense variant (c.628C>G, p.Arg210Gly) was observed in the OLIG3 gene that encodes a transcription factor known to be associated with rheumatoid arthritis and inflammatory polyarthritis. The Arg210Gly variant was estimated to be pathogenic by Polyphen-2 and Mutation taster and the locus is conserved among mammals. In Family 12 the observed variant (c.-127G>T) was located in the transcription start site of the FIP1L1 gene. FIP1L1 participates in the regulation of polyadenylation. The c.-127G>T is located in the transcription start site and may alter the DNA-binding of transcription factors. Both, OLIG3 and FIP1L1 were observed in human bone and cartilage. CONCLUSION The identified variants revealed novel candidate genes for OA. OLIG3 and FIP1L1 have specific roles in transcription and may effect expression of other genes. Identified variants in these genes may thus have a role in the regulatory events leading to OA.
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Affiliation(s)
- Sini Skarp
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- * E-mail:
| | | | - Gong-Hong Wei
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Eveliina Jakkula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Ilkka Kiviranta
- Department of Orthopaedics and Traumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Orthopaedics and Traumatology, Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Heikki Kröger
- Department of Orthopaedics and Traumatology, Kuopio University Hospital and Kuopio Musculoskeletal Research Unit, University of Eastern Finland, Kuopio, Finland
| | - Juha Auvinen
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Petri Lehenkari
- Department of Anatomy and Cell biology and Surgery Clinic, Medical Research Center, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Leena Ala-Kokko
- Connective Tissue Gene Tests, Allentown, PA, United States of America
| | - Minna Männikkö
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Northern Finland Birth Cohort, Faculty of Medicine, University of Oulu, Oulu, Finland
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