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Roberts JB, Rice SJ. Osteoarthritis as an Enhanceropathy: Gene Regulation in Complex Musculoskeletal Disease. Curr Rheumatol Rep 2024; 26:222-234. [PMID: 38430365 PMCID: PMC11116181 DOI: 10.1007/s11926-024-01142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2024] [Indexed: 03/03/2024]
Abstract
PURPOSE OF REVIEW Osteoarthritis is a complex and highly polygenic disease. Over 100 reported osteoarthritis risk variants fall in non-coding regions of the genome, ostensibly conferring functional effects through the disruption of regulatory elements impacting target gene expression. In this review, we summarise the progress that has advanced our knowledge of gene enhancers both within the field of osteoarthritis and more broadly in complex diseases. RECENT FINDINGS Advances in technologies such as ATAC-seq have facilitated our understanding of chromatin states in specific cell types, bolstering the interpretation of GWAS and the identification of effector genes. Their application to osteoarthritis research has revealed enhancers as the principal regulatory element driving disease-associated changes in gene expression. However, tissue-specific effects in gene regulatory mechanisms can contribute added complexity to biological interpretation. Understanding gene enhancers and their altered activity in specific cell and tissue types is the key to unlocking the genetic complexity of osteoarthritis. The use of single-cell technologies in osteoarthritis research is still in its infancy. However, such tools offer great promise in improving our functional interpretation of osteoarthritis GWAS and the identification of druggable targets. Large-scale collaborative efforts will be imperative to understand tissue and cell-type specific molecular mechanisms underlying enhancer function in disease.
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Affiliation(s)
- Jack B Roberts
- Skeletal Research Group, International Centre for Life, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, UK
| | - Sarah J Rice
- Skeletal Research Group, International Centre for Life, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, UK.
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He Q, Lin Y, Chen B, Chen C, Zeng J, Dou X, Cai D, Zhou C, Wang H. Vitamin K2 ameliorates osteoarthritis by suppressing ferroptosis and extracellular matrix degradation through activation GPX4's dual functions. Biomed Pharmacother 2024; 175:116697. [PMID: 38759289 DOI: 10.1016/j.biopha.2024.116697] [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: 02/15/2024] [Revised: 04/23/2024] [Accepted: 05/01/2024] [Indexed: 05/19/2024] Open
Abstract
Vitamin K2 (VK2) is an effective compound for anti-ferroptosis and anti-osteoporosis, and Semen sojae praeparatum (Dandouchi in Chinese) is the main source of VK2. Chondrocyte ferroptosis and extracellular matrix (ECM) degradation playing a role in the pathogenesis of osteoarthritis (OA). Glutathione peroxidase 4 (GPX4) is the intersection of two mechanisms in regulating OA progression. But no studies have elucidated the therapeutic effects and mechanisms of VK2 on OA. This study utilized an in vivo rat OA model created via anterior cruciate ligament transection (ACLT) and an in vitro chondrocyte oxidative damage model induced by TBHP to investigate the protective effects and mechanisms of action of VK2 in OA. Knee joint pain in mice was evaluated using the Von Frey test. Micro-CT and Safranin O-Fast Green staining were employed to observe the extent of damage to the tibial cartilage and subchondral bone, while immunohistochemistry and PCR were used to examine GPX4 levels in joint cartilage. The effects of VK2 on rat chondrocyte viability were assessed using CCK-8 and flow cytometry assays, and chondrocyte morphology was observed with toluidine blue and alcian blue staining. The impact of VK2 on intracellular ferroptosis-related markers was observed using fluorescent staining and flow cytometry. Protein expression changes were detected by immunofluorescence and Western blot analysis. Furthermore, specific protein inhibitors were applied to confirm the dual-regulatory effects of VK2 on GPX4. VK2 can increase bone mass and cartilage thickness in the subchondral bone of the tibia, and reduce pain and the OARSI score induced by OA. Immunohistochemistry results indicate that VK2 exerts its anti-OA effects by regulating GPX4 to delay ECM degradation. VK2 can inhibit the activation of the MAPK/NFκB signaling pathway caused by reduced expression of intracellular GPX4, thereby decreasing ECM degradation. Additionally, VK2 can reverse the inhibitory effect of RSL3 on GPX4, increase intracellular GSH content and the GSH/GSSG ratio, reduce MDA content, and rescue chondrocyte ferroptosis. The protective mechanism of VK2 may involve its dual-target regulation of GPX4, reducing chondrocyte ferroptosis and inhibiting the MAPK/NFκB signaling pathway to decelerate the degradation of the chondrocyte extracellular matrix.
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Affiliation(s)
- Qi He
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, 12 Jichang Road, Baiyun Area, Guangzhou 510405, PR China; The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, PR China; Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuewei Lin
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, 12 Jichang Road, Baiyun Area, Guangzhou 510405, PR China; The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, PR China
| | - Baihao Chen
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, 12 Jichang Road, Baiyun Area, Guangzhou 510405, PR China; The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, PR China
| | - Chuyi Chen
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, 12 Jichang Road, Baiyun Area, Guangzhou 510405, PR China; The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, PR China
| | - Jiaxu Zeng
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, 12 Jichang Road, Baiyun Area, Guangzhou 510405, PR China; The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, PR China
| | - Xiangyun Dou
- First School of Clinical Medicine, Guangzhou University of Chinese Medicine, 12 Jichang Road, Baiyun Area, Guangzhou 510405, PR China; The Laboratory of Orthopaedics and Traumatology of Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, PR China
| | - Dongling Cai
- Department of Orthopedics, Panyu Hospital of Chinese Medicine, Guangzhou 510405, PR China.
| | - Chi Zhou
- Department of Orthopaedics, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 16 Jichang Road, Baiyun Area, Guangzhou 510405, PR China; Department of Orthopaedics, Maoming Hospital of Guangzhou University of Chinese Medicine, Maoming 525000, PR China.
| | - Haibin Wang
- Department of Orthopaedics, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 16 Jichang Road, Baiyun Area, Guangzhou 510405, PR China.
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3
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Qi B, Wang Z, Cao Y, Zhao H. Study on the treatment of osteoarthritis by acupuncture combined with traditional Chinese medicine based on pathophysiological mechanism: A review. Medicine (Baltimore) 2024; 103:e37483. [PMID: 38579081 PMCID: PMC10994424 DOI: 10.1097/md.0000000000037483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/13/2024] [Indexed: 04/07/2024] Open
Abstract
Osteoarthritis (OA) is a major contributor to disability and social costs in the elderly. As the population ages and becomes increasingly obese, the incidence of the disease is higher than in previous decades. In recent years, important progress has been made in the causes and pathogenesis of OA pain. Modern medical treatment modalities mainly include the specific situation of the patient and focus on the core treatment, including self-management and education, exercise, and related weight loss. As an important part of complementary and alternative medicine, TCM has remarkable curative effect, clinical safety, and diversity of treatment methods in the treatment of OA. Traditional Chinese Medicine treatment of OA has attracted worldwide attention. Therefore, this article will study the pathophysiological mechanism of OA based on modern medicine, and explore the treatment of OA by acupuncture combined with Chinese Medicine.
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Affiliation(s)
- Biao Qi
- Shenzhen Baoan District Shiyan People’s Hospital, Shenzhen, China
| | - Zeyu Wang
- Shenzhen Pingshan District Hospital of Traditional Chinese Medicine, Shenzhen, China
| | - Ying Cao
- Shenzhen Pingshan District Hospital of Traditional Chinese Medicine, Shenzhen, China
| | - Haishen Zhao
- Community Health Service Center of Nanhui New Town, Shanghai, China
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Loughlin J. Three decades of osteoarthritis molecular genetics research: From early discussions to impressive breakthroughs. Osteoarthritis Cartilage 2024; 32:352-354. [PMID: 37972686 DOI: 10.1016/j.joca.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/03/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Affiliation(s)
- J Loughlin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
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5
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Kreitmaier P, Park YC, Swift D, Gilly A, Wilkinson JM, Zeggini E. Epigenomic profiling of the infrapatellar fat pad in osteoarthritis. Hum Mol Genet 2024; 33:501-509. [PMID: 37975894 PMCID: PMC10939427 DOI: 10.1093/hmg/ddad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/13/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Osteoarthritis is a prevalent, complex disease of the joints, and affects multiple intra-articular tissues. Here, we have examined genome-wide DNA methylation profiles of primary infrapatellar fat pad and matched blood samples from 70 osteoarthritis patients undergoing total knee replacement surgery. Comparing the DNA methylation profiles between these tissues reveal widespread epigenetic differences. We produce the first genome-wide methylation quantitative trait locus (mQTL) map of fat pad, and make the resource available to the wider community. Using two-sample Mendelian randomization and colocalization analyses, we resolve osteoarthritis GWAS signals and provide insights into the molecular mechanisms underpinning disease aetiopathology. Our findings provide the first view of the epigenetic landscape of infrapatellar fat pad primary tissue in osteoarthritis.
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Affiliation(s)
- Peter Kreitmaier
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine and Health, Ismaninger Str. 22, Munich 81675, Germany
- Graduate School of Experimental Medicine, TUM School of Medicine and Health, Technical University of Munich, Ismaninger Str. 22, Munich 81675, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
| | - Young-Chan Park
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
| | - Diane Swift
- Department of Oncology and Metabolism, The University of Sheffield, Beech Hill Rd, Sheffield S10 2RX, United Kingdom
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
| | - J Mark Wilkinson
- Department of Oncology and Metabolism, The University of Sheffield, Beech Hill Rd, Sheffield S10 2RX, United Kingdom
| | - Eleftheria Zeggini
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine and Health, Ismaninger Str. 22, Munich 81675, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
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Ramos YFM, Rice SJ, Ali SA, Pastrello C, Jurisica I, Rai MF, Collins KH, Lang A, Maerz T, Geurts J, Ruiz-Romero C, June RK, Thomas Appleton C, Rockel JS, Kapoor M. Evolution and advancements in genomics and epigenomics in OA research: How far we have come. Osteoarthritis Cartilage 2024:S1063-4584(24)00054-2. [PMID: 38428513 DOI: 10.1016/j.joca.2024.02.656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/29/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
OBJECTIVE Osteoarthritis (OA) is the most prevalent musculoskeletal disease affecting articulating joint tissues, resulting in local and systemic changes that contribute to increased pain and reduced function. Diverse technological advancements have culminated in the advent of high throughput "omic" technologies, enabling identification of comprehensive changes in molecular mediators associated with the disease. Amongst these technologies, genomics and epigenomics - including methylomics and miRNomics, have emerged as important tools to aid our biological understanding of disease. DESIGN In this narrative review, we selected articles discussing advancements and applications of these technologies to OA biology and pathology. We discuss how genomics, deoxyribonucleic acid (DNA) methylomics, and miRNomics have uncovered disease-related molecular markers in the local and systemic tissues or fluids of OA patients. RESULTS Genomics investigations into the genetic links of OA, including using genome-wide association studies, have evolved to identify 100+ genetic susceptibility markers of OA. Epigenomic investigations of gene methylation status have identified the importance of methylation to OA-related catabolic gene expression. Furthermore, miRNomic studies have identified key microRNA signatures in various tissues and fluids related to OA disease. CONCLUSIONS Sharing of standardized, well-annotated omic datasets in curated repositories will be key to enhancing statistical power to detect smaller and targetable changes in the biological signatures underlying OA pathogenesis. Additionally, continued technological developments and analysis methods, including using computational molecular and regulatory networks, are likely to facilitate improved detection of disease-relevant targets, in-turn, supporting precision medicine approaches and new treatment strategies for OA.
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Affiliation(s)
- Yolande F M Ramos
- Dept. Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Sarah J Rice
- Biosciences Institute, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Shabana Amanda Ali
- Henry Ford Health + Michigan State University Health Sciences, Detroit, MI, USA
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada; Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Muhammad Farooq Rai
- Department of Biological Sciences, Center for Biotechnology, College of Medicine & Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Kelsey H Collins
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Annemarie Lang
- Departments of Orthopaedic Surgery and Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Tristan Maerz
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Jeroen Geurts
- Rheumatology, Department of Musculoskeletal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Cristina Ruiz-Romero
- Grupo de Investigación de Reumatología (GIR), Unidad de Proteómica, INIBIC -Hospital Universitario A Coruña, SERGAS, A Coruña, Spain
| | - Ronald K June
- Department of Mechanical & Industrial Engineering, Montana State University, Bozeman, MT, USA
| | - C Thomas Appleton
- Department of Medicine, University of Western Ontario, London, Ontario, Canada
| | - Jason S Rockel
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada
| | - Mohit Kapoor
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada.
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Jiang F, Hu SY, Tian W, Wang NN, Yang N, Dong SS, Song HM, Zhang DJ, Gao HW, Wang C, Wu H, He CY, Zhu DL, Chen XF, Guo Y, Yang Z, Yang TL. A landscape of gene expression regulation for synovium in arthritis. Nat Commun 2024; 15:1409. [PMID: 38360850 PMCID: PMC10869817 DOI: 10.1038/s41467-024-45652-x] [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: 05/09/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
The synovium is an important component of any synovial joint and is the major target tissue of inflammatory arthritis. However, the multi-omics landscape of synovium required for functional inference is absent from large-scale resources. Here we integrate genomics with transcriptomics and chromatin accessibility features of human synovium in up to 245 arthritic patients, to characterize the landscape of genetic regulation on gene expression and the regulatory mechanisms mediating arthritic diseases predisposition. We identify 4765 independent primary and 616 secondary cis-expression quantitative trait loci (cis-eQTLs) in the synovium and find that the eQTLs with multiple independent signals have stronger effects and heritability than single independent eQTLs. Integration of genome-wide association studies (GWASs) and eQTLs identifies 84 arthritis related genes, revealing 38 novel genes which have not been reported by previous studies using eQTL data from the GTEx project or immune cells. We further develop a method called eQTac to identify variants that could affect gene expression by affecting chromatin accessibility and identify 1517 regions with potential regulatory function of chromatin accessibility. Altogether, our study provides a comprehensive synovium multi-omics resource for arthritic diseases and gains new insights into the regulation of gene expression.
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Affiliation(s)
- Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Shou-Ye Hu
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, P.R. China
| | - Wen Tian
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Nai-Ning Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Ning Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Hui-Miao Song
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Da-Jin Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Hui-Wu Gao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Chen Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Chang-Yi He
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Zhi Yang
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, P.R. China.
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China.
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Su H, Yan Q, Du W, Hu E, Yang Z, Zhang W, Li Y, Tang T, Zhao S, Wang Y. Calycosin ameliorates osteoarthritis by regulating the imbalance between chondrocyte synthesis and catabolism. BMC Complement Med Ther 2024; 24:48. [PMID: 38254101 PMCID: PMC10804771 DOI: 10.1186/s12906-023-04314-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Osteoarthritis (OA) is a severe chronic inflammatory disease. As the main active component of Astragalus mongholicus Bunge, a classic traditional ethnic herb, calycosin exhibits anti-inflammatory action and its mechanism of exact targets for OA have yet to be determined. In this study, we established an anterior cruciate ligament transection (ACLT) mouse model. Mice were randomized to sham, OA, and calycosin groups. Cartilage synthesis markers type II collagen (Col-2) and SRY-Box Transcription Factor 9 (Sox-9) increased significantly after calycosin gavage. While cartilage matrix degradation index cyclooxygenase-2 (COX-2), phosphor-epidermal growth factor receptor (p-EGFR), and matrix metalloproteinase-9 (MMP9) expression were decreased. With the help of network pharmacology and molecular docking, these results were confirmed in chondrocyte ADTC5 cells. Our results indicated that the calycosin treatment significantly improved cartilage damage, this was probably attributed to reversing the imbalance between chondrocyte synthesis and catabolism.
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Affiliation(s)
- Hong Su
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China
| | - Qiuju Yan
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China
| | - Wei Du
- Department of Orthopedics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan Province, China
- Department of Rehabilitation Medicine, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan Province, China
| | - En Hu
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China
| | - Zhaoyu Yang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China
| | - Wei Zhang
- The College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Yusheng Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China
- Department of Orthopedics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan Province, China
| | - Tao Tang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China
| | - Shushan Zhao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China.
- Department of Orthopedics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan Province, China.
| | - Yang Wang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P.R. China.
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9
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Kenny J, Mullin BH, Tomlinson W, Robertson B, Yuan J, Chen W, Zhao J, Pavlos NJ, Walsh JP, Wilson SG, Tickner J, Morahan G, Xu J. Age-dependent genetic regulation of osteoarthritis: independent effects of immune system genes. Arthritis Res Ther 2023; 25:232. [PMID: 38041181 PMCID: PMC10691153 DOI: 10.1186/s13075-023-03216-2] [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: 08/16/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023] Open
Abstract
OBJECTIVES Osteoarthritis (OA) is a joint disease with a heritable component. Genetic loci identified via genome-wide association studies (GWAS) account for an estimated 26.3% of the disease trait variance in humans. Currently, there is no method for predicting the onset or progression of OA. We describe the first use of the Collaborative Cross (CC), a powerful genetic resource, to investigate knee OA in mice, with follow-up targeted multi-omics analysis of homologous regions of the human genome. METHODS We histologically screened 275 mice for knee OA and conducted quantitative trait locus (QTL) mapping in the complete cohort (> 8 months) and the younger onset sub-cohort (8-12 months). Multi-omic analysis of human genetic datasets was conducted to investigate significant loci. RESULTS We observed a range of OA phenotypes. QTL mapping identified a genome-wide significant locus on mouse chromosome 19 containing Glis3, the human equivalent of which has been identified as associated with OA in recent GWAS. Mapping the younger onset sub-cohort identified a genome-wide significant locus on chromosome 17. Multi-omic analysis of the homologous region of the human genome (6p21.32) indicated the presence of pleiotropic effects on the expression of the HLA - DPB2 gene and knee OA development risk, potentially mediated through the effects on DNA methylation. CONCLUSIONS The significant associations at the 6p21.32 locus in human datasets highlight the value of the CC model of spontaneous OA that we have developed and lend support for an immune role in the disease. Our results in mice also add to the accumulating evidence of a role for Glis3 in OA.
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Affiliation(s)
- Jacob Kenny
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia.
| | - Benjamin H Mullin
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - William Tomlinson
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Brett Robertson
- Australian Institute of Robotic Orthopaedics, Crawley, WA, Australia
| | - Jinbo Yuan
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Weiwei Chen
- Research Centre for Regenerative Medicine, and Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Guangxi, China
| | - Jinmin Zhao
- Research Centre for Regenerative Medicine, and Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Guangxi, China
| | - Nathan J Pavlos
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - John P Walsh
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
- Medical School, University of Western Australia, Crawley, WA, Australia
| | - Scott G Wilson
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jennifer Tickner
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute for Medical Research, Nedlands, WA, Australia.
| | - Jiake Xu
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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10
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Kaya S, Alliston T, Evans DS. Genetic and Gene Expression Resources for Osteoporosis and Bone Biology Research. Curr Osteoporos Rep 2023; 21:637-649. [PMID: 37831357 PMCID: PMC11098148 DOI: 10.1007/s11914-023-00821-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Abstract
PURPOSE OF REVIEW The integration of data from multiple genomic assays from humans and non-human model organisms is an effective approach to identify genes involved in skeletal fragility and fracture risk due to osteoporosis and other conditions. This review summarizes genome-wide genetic variation and gene expression data resources relevant to the discovery of genes contributing to skeletal fragility and fracture risk. RECENT FINDINGS Genome-wide association studies (GWAS) of osteoporosis-related traits are summarized, in addition to gene expression in bone tissues in humans and non-human organisms, with a focus on rodent models related to skeletal fragility and fracture risk. Gene discovery approaches using these genomic data resources are described. We also describe the Musculoskeletal Knowledge Portal (MSKKP) that integrates much of the available genomic data relevant to fracture risk. The available genomic resources provide a wealth of knowledge and can be analyzed to identify genes related to fracture risk. Genomic resources that would fill particular scientific gaps are discussed.
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Affiliation(s)
- Serra Kaya
- Department of Orthopedic Surgery, University of California, San Francisco, CA, USA
| | - Tamara Alliston
- Department of Orthopedic Surgery, University of California, San Francisco, CA, USA
| | - Daniel S Evans
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
- California Pacific Medical Center Research Institute, San Francisco, CA, USA.
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11
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Mullin BH, Zhu K, Brown SJ, Mullin S, Dudbridge F, Pavlos NJ, Richards JB, Grundberg E, Bell JT, Zeggini E, Walsh JP, Xu J, Wilson SG. Leveraging osteoclast genetic regulatory data to identify genes with a role in osteoarthritis. Genetics 2023; 225:iyad150. [PMID: 37579195 PMCID: PMC10550309 DOI: 10.1093/genetics/iyad150] [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: 06/28/2023] [Revised: 06/28/2023] [Accepted: 08/08/2023] [Indexed: 08/16/2023] Open
Abstract
There has been a growing interest in the role of the subchondral bone and its resident osteoclasts in the progression of osteoarthritis (OA). A recent genome-wide association study (GWAS) identified 100 independent association signals for OA traits. Most of these signals are led by noncoding variants, suggesting that genetic regulatory effects may drive many of the associations. We have generated a unique human osteoclast-like cell-specific expression quantitative trait locus (eQTL) resource for studying the genetics of bone disease. Considering the potential role of osteoclasts in the pathogenesis of OA, we performed an integrative analysis of this dataset with the recently published OA GWAS results. Summary data-based Mendelian randomization (SMR) and colocalization analyses identified 38 genes with a potential role in OA, including some that have been implicated in Mendelian diseases with joint/skeletal abnormalities, such as BICRA, EIF6, CHST3, and FBN2. Several OA GWAS signals demonstrated colocalization with more than one eQTL peak, including at 19q13.32 (hip OA with BCAM, PRKD2, and BICRA eQTL). We also identified a number of eQTL signals colocalizing with more than one OA trait, including FAM53A, GCAT, HMGN1, MGAT4A, RRP7BP, and TRIOBP. An SMR analysis identified 3 loci with evidence of pleiotropic effects on OA-risk and gene expression: LINC01481, CPNE1, and EIF6. Both CPNE1 and EIF6 are located at 20q11.22, a locus harboring 2 other strong OA candidate genes, GDF5 and UQCC1, suggesting the presence of an OA-risk gene cluster. In summary, we have used our osteoclast-specific eQTL dataset to identify genes potentially involved with the pathogenesis of OA.
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Affiliation(s)
- Benjamin H Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Kun Zhu
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Medical School, University of Western Australia, Crawley, WA 6009, Australia
| | - Suzanne J Brown
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
| | - Shelby Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Frank Dudbridge
- Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Nathan J Pavlos
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - J Brent Richards
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
- Department of Medicine, Human Genetics, Epidemiology, and Biostatistics, Jewish General Hospital, McGill University, Montreal H3A 0G4, Canada
| | - Elin Grundberg
- Genomic Medicine Center, Children’s Mercy Kansas City, Children’s Mercy Research Institute, Kansas City, MO 64108, USA
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Eleftheria Zeggini
- Helmholtz Zentrum München—German Research Center for Environmental Health, Institute of Translational Genomics, Neuherberg 85764, Germany
- TUM School of Medicine, Technical University of Munich (TUM) and Klinikum Rechts der Isar, Munich 81675, Germany
| | - John P Walsh
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Medical School, University of Western Australia, Crawley, WA 6009, Australia
| | - Jiake Xu
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Chinese Academy of Sciences, Shenzhen Institute of Advanced Technology, Shenzhen 518055, China
| | - Scott G Wilson
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
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12
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Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs. PLoS Genet 2023; 19:e1010932. [PMID: 37721944 PMCID: PMC10538656 DOI: 10.1371/journal.pgen.1010932] [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: 04/17/2023] [Revised: 09/28/2023] [Accepted: 08/22/2023] [Indexed: 09/20/2023] Open
Abstract
The eQTL Catalogue is an open database of uniformly processed human molecular quantitative trait loci (QTLs). We are continuously updating the resource to further increase its utility for interpreting genetic associations with complex traits. Over the past two years, we have increased the number of uniformly processed studies from 21 to 31 and added X chromosome QTLs for 19 compatible studies. We have also implemented Leafcutter to directly identify splice-junction usage QTLs in all RNA sequencing datasets. Finally, to improve the interpretability of transcript-level QTLs, we have developed static QTL coverage plots that visualise the association between the genotype and average RNA sequencing read coverage in the region for all 1.7 million fine mapped associations. To illustrate the utility of these updates to the eQTL Catalogue, we performed colocalisation analysis between vitamin D levels in the UK Biobank and all molecular QTLs in the eQTL Catalogue. Although most GWAS loci colocalised both with eQTLs and transcript-level QTLs, we found that visual inspection could sometimes be used to distinguish primary splicing QTLs from those that appear to be secondary consequences of large-effect gene expression QTLs. While these visually confirmed primary splicing QTLs explain just 6/53 of the colocalising signals, they are significantly less pleiotropic than eQTLs and identify a prioritised causal gene in 4/6 cases.
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Affiliation(s)
- Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ralf Tambets
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - James D. Hayhurst
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ida Rahu
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Peep Kolberg
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Uku Raudvere
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Ivan Kuzmin
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Anshika Chowdhary
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Andreas Vija
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Hans J. Teras
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jacob Ulirsch
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - John Hardy
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sebastian Guelfi
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Daniah Trabzuni
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sarah Kim-Hellmuth
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital LMU Munich, Munich, Germany
| | - William Rayner
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Hilary Finucane
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Abayomi Mosaku
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Helen Parkinson
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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13
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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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14
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Arruda AL, Hartley A, Katsoula G, Smith GD, Morris AP, Zeggini E. Genetic underpinning of the comorbidity between type 2 diabetes and osteoarthritis. Am J Hum Genet 2023; 110:1304-1318. [PMID: 37433298 PMCID: PMC10432145 DOI: 10.1016/j.ajhg.2023.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/13/2023] Open
Abstract
Multimorbidity is a rising public health challenge with important implications for health management and policy. The most common multimorbidity pattern is the combination of cardiometabolic and osteoarticular diseases. Here, we study the genetic underpinning of the comorbidity between type 2 diabetes and osteoarthritis. We find genome-wide genetic correlation between the two diseases and robust evidence for association-signal colocalization at 18 genomic regions. We integrate multi-omics and functional information to resolve the colocalizing signals and identify high-confidence effector genes, including FTO and IRX3, which provide proof-of-concept insights into the epidemiologic link between obesity and both diseases. We find enrichment for lipid metabolism and skeletal formation pathways for signals underpinning the knee and hip osteoarthritis comorbidities with type 2 diabetes, respectively. Causal inference analysis identifies complex effects of tissue-specific gene expression on comorbidity outcomes. Our findings provide insights into the biological basis for the type 2 diabetes-osteoarthritis disease co-occurrence.
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Affiliation(s)
- Ana Luiza Arruda
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; Munich School of Data Science, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; Technical University of Munich (TUM), School of Medicine, Graduate School of Experimental Medicine, 81675 Munich, Germany
| | - April Hartley
- MRC Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK
| | - Georgia Katsoula
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; Technical University of Munich (TUM), School of Medicine, Graduate School of Experimental Medicine, 81675 Munich, Germany
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK
| | - Andrew P Morris
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, M13 9PT Manchester, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; TUM School of Medicine, Technical University Munich and Klinikum Rechts der Isar, 81675 Munich, Germany.
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15
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He L, Xu Z, Niu X, Li R, Wang F, You Y, Gao J, Zhao L, Shah KM, Fan J, Liu M, Luo J. GPRC5B protects osteoarthritis by regulation of autophagy signaling. Acta Pharm Sin B 2023; 13:2976-2989. [PMID: 37521864 PMCID: PMC10372909 DOI: 10.1016/j.apsb.2023.05.014] [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: 11/30/2022] [Revised: 01/17/2023] [Accepted: 03/14/2023] [Indexed: 08/01/2023] Open
Abstract
Osteoarthritis (OA) is one of the most common chronic diseases in the world. However, current treatment modalities mainly relieve pain and inhibit cartilage degradation, but do not promote cartilage regeneration. In this study, we show that G protein-coupled receptor class C group 5 member B (GPRC5B), an orphan G-protein-couple receptor, not only inhibits cartilage degradation, but also increases cartilage regeneration and thereby is protective against OA. We observed that Gprc5b deficient chondrocytes had an upregulation of cartilage catabolic gene expression, along with downregulation of anabolic genes in vitro. Furthermore, mice deficient in Gprc5b displayed a more severe OA phenotype in the destabilization of the medial meniscus (DMM) induced OA mouse model, with upregulation of cartilage catabolic factors and downregulation of anabolic factors, consistent with our in vitro findings. Overexpression of Gprc5b by lentiviral vectors alleviated the cartilage degeneration in DMM-induced OA mouse model by inhibiting cartilage degradation and promoting regeneration. We also assessed the molecular mechanisms downstream of Gprc5b that may mediate these observed effects and identify the role of protein kinase B (AKT)-mammalian target of rapamycin (mTOR)-autophagy signaling pathway. Thus, we demonstrate an integral role of GPRC5B in OA pathogenesis, and activation of GPRC5B has the potential in preventing the progression of OA.
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Affiliation(s)
- Liang He
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai 201613, China
| | - Ziwei Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xin Niu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Rong Li
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai 201613, China
| | - Fanhua Wang
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai 201613, China
| | - Yu You
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jingduo Gao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Lei Zhao
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai 201613, China
| | - Karan M. Shah
- Department of Oncology and Metabolism, the Medical School, the University of Sheffield, Sheffield S10 2TN, UK
| | - Jian Fan
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai 200092, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jian Luo
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai 201613, China
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16
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Bocher O, Willer CJ, Zeggini E. Unravelling the genetic architecture of human complex traits through whole genome sequencing. Nat Commun 2023; 14:3520. [PMID: 37316478 DOI: 10.1038/s41467-023-39259-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 06/06/2023] [Indexed: 06/16/2023] Open
Affiliation(s)
- Ozvan Bocher
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Ismaninger Str. 22, 81675, Munich, Germany.
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17
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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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18
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Faber BG, Frysz M, Hartley AE, Ebsim R, Boer CG, Saunders FR, Gregory JS, Aspden RM, Harvey NC, Southam L, Giles W, Le Maitre CL, Wilkinson JM, van Meurs JBJ, Zeggini E, Cootes T, Lindner C, Kemp JP, Davey Smith G, Tobias JH. A Genome-Wide Association Study Meta-Analysis of Alpha Angle Suggests Cam-Type Morphology May Be a Specific Feature of Hip Osteoarthritis in Older Adults. Arthritis Rheumatol 2023; 75:900-909. [PMID: 36662418 PMCID: PMC10374163 DOI: 10.1002/art.42451] [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: 08/02/2022] [Revised: 11/08/2022] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
OBJECTIVE To examine the genetic architecture of cam morphology using alpha angle (AA) as a proxy measure and conduct an AA genome-wide association study (GWAS) followed by Mendelian randomization (MR) to evaluate its causal relationship with hip osteoarthritis (OA). METHODS Observational analyses examined associations between AA measurements derived from hip dual x-ray absorptiometry (DXA) scans from the UK Biobank study and radiographic hip OA outcomes and subsequent total hip replacement. Following these analyses, an AA GWAS meta-analysis was performed (N = 44,214) using AA measurements previously derived in the Rotterdam Study. Linkage disequilibrium score regression assessed the genetic correlation between AA and hip OA. Genetic associations considered significant (P < 5 × 10-8 ) were used as AA genetic instrument for 2-sample MR analysis. RESULTS DXA-derived AA showed expected associations between AA and radiographic hip OA (adjusted odds ratio [OR] 1.63 [95% confidence interval (95% CI) 1.58, 1.67]) and between AA and total hip replacement (adjusted hazard ratio 1.45 [95% CI 1.33, 1.59]) in the UK Biobank study cohort. The heritability of AA was 10%, and AA had a moderate genetic correlation with hip OA (rg = 0.26 [95% CI 0.10, 0.43]). Eight independent genetic signals were associated with AA. Two-sample MR provided weak evidence of causal effects of AA on hip OA risk (inverse variance weighted OR 1.84 [95% CI 1.14, 2.96], P = 0.01). In contrast, genetic predisposition for hip OA had stronger evidence of a causal effect on increased AA (inverse variance weighted β = 0.09 [95% CI 0.04, 0.13], P = 4.58 × 10-5 ). CONCLUSION Expected observational associations between AA and related clinical outcomes provided face validity for the DXA-derived AA measurements. Evidence of bidirectional associations between AA and hip OA, particularly for risk of hip OA on AA, suggests that hip shape modeling secondary to a genetic predisposition to hip OA contributes to the well-established relationship between hip OA and cam morphology in older adults.
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Affiliation(s)
- Benjamin G. Faber
- Musculoskeletal Research Unit, Translational Health Sciences, and Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolUK
| | - Monika Frysz
- Musculoskeletal Research Unit, Translational Health Sciences, and Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolUK
| | - April E. Hartley
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolUK
| | - Raja Ebsim
- Division of Informatics, Imaging and Data ScienceThe University of ManchesterUK
| | - Cindy G. Boer
- Department of Internal Medicine, Erasmus MCUniversity Medical CenterRotterdamThe Netherlands
| | - Fiona R. Saunders
- Centre for Arthritis and Musculoskeletal HealthUniversity of AberdeenUK
| | | | - Richard M. Aspden
- Centre for Arthritis and Musculoskeletal HealthUniversity of AberdeenUK
| | - Nicholas C. Harvey
- Medical Research Council Lifecourse Epidemiology Centre, University of Southampton, UK, and NIHR Southampton Biomedical Research CentreUniversity of Southampton and University Hospital Southampton NHS Foundation TrustUK
| | - Lorraine Southam
- Institute of Translational Genomics, Helmholtz Zentrum München–German Research Center for Environmental HealthNeuherbergGermany
| | - William Giles
- Department of Oncology and MetabolismThe University of SheffieldUK
| | | | | | - Joyce B. J. van Meurs
- Department of Internal Medicine and Department of Orthopaedics & Sports Medicine, Erasmus MCRotterdamThe Netherlands
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany, and TUM School of MedicineTechnical University of Munich and Klinikum Rechts der IsarGermany
| | - Timothy Cootes
- Division of Informatics, Imaging and Data ScienceThe University of ManchesterUK
| | - Claudia Lindner
- Division of Informatics, Imaging and Data ScienceThe University of ManchesterUK
| | - John P. Kemp
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, UK, and The University of Queensland Diamantina Institute and Institute for Molecular Bioscience, The University of QueenslandQueenslandAustralia
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolUK
| | - Jonathan H. Tobias
- Musculoskeletal Research Unit, Translational Health Sciences, and Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolUK
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19
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Li C, Wei P, Wang L, Wang Q, Wang H, Zhang Y. Integrated Analysis of Transcriptome Changes in Osteoarthritis: Gene Expression, Pathways and Alternative Splicing. Cartilage 2023; 14:235-246. [PMID: 36799242 PMCID: PMC10416206 DOI: 10.1177/19476035231154511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/24/2022] [Accepted: 01/06/2023] [Indexed: 02/18/2023] Open
Abstract
OBJECTIVE Osteoarthritis (OA) is the most prevalent joint disease characterized by the degeneration of articular cartilage and the remodeling of its underlying bones, resulting in pain and loss of function in the knees and hips. As far as we know, no curative treatments are available except for the joint replacement. The precise molecular mechanisms which are involved in the degradation of cartilage matrix and development of osteoarthritis are still unclear. DESIGN By analyzing RNA-seq data, we found the molecular changes at the transcriptome level such as alternative splicing, gene expression, and molecular pathways in OA knees cartilage. RESULTS Expression analysis have identified 457 differential expressed genes including 266 up-regulated genes such as TNFSF15, ST6GALNAC5, TGFBI, ASPM, and TYM, and 191 down-regulated genes such as ADM, JUN, IRE2, PIGA, and MAFF. Gene set enrichment analysis (GSEA) analysis identified down-regulated pathways related to translation, transcription, immunity, PI3K/AKT, and circadian as well as disturbed pathways related to extracellular matrix and collagen. Splicing analysis identified 442 differential alternative splicing events within 284 genes in osteoarthritis, including genes involved in extracellular matrix (ECM) and alternative splicing, and TIA1 was identified as a key regulator of these splicing events. CONCLUSIONS These findings provide insights into disease etiology, and offer favorable information to support the development of more effective interventions in response to the global clinical challenge of osteoarthritis.
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Affiliation(s)
- Congming Li
- Department of Orthopedic Surgery, Yijishan Hospital, The First Affiliated Hospital of Wannan Medical College, Wuhu, P.R. China
| | - Pengli Wei
- Department of Emergency, Yijishan Hospital, The First Affiliated Hospital of Wannan Medical College, Wuhu, P.R. China
| | - Lei Wang
- Department of Orthopedic Surgery, Yijishan Hospital, The First Affiliated Hospital of Wannan Medical College, Wuhu, P.R. China
| | - Qiang Wang
- Department of Orthopedic Surgery, Yijishan Hospital, The First Affiliated Hospital of Wannan Medical College, Wuhu, P.R. China
| | - Hong Wang
- Department of Orthopedic Surgery, Yijishan Hospital, The First Affiliated Hospital of Wannan Medical College, Wuhu, P.R. China
| | - Yangjun Zhang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, P.R. China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, P.R. China
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20
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Kehayova YS, Wilkinson JM, Rice SJ, Loughlin J. Osteoarthritis genetic risk acting on the galactosyltransferase gene COLGALT2 has opposing functional effects in articulating joint tissues. Arthritis Res Ther 2023; 25:83. [PMID: 37208701 DOI: 10.1186/s13075-023-03066-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/10/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Investigation of cartilage and chondrocytes has revealed that the osteoarthritis risk marked by the independent DNA variants rs11583641 and rs1046934 mediate their effects by decreasing the methylation status of CpG dinucleotides in enhancers and increasing the expression of shared target gene COLGALT2. We set out to investigate if these functional effects operate in a non-cartilaginous joint tissue. METHODS Nucleic acids were extracted from the synovium of osteoarthritis patients. Samples were genotyped, and DNA methylation was quantified by pyrosequencing at CpGs within the COLGALT2 enhancers. CpGs were tested for enhancer effects using a synovial cell line and a reporter gene assay. DNA methylation was altered using epigenetic editing, with the impact on gene expression determined using quantitative polymerase chain reaction. In silico analysis complemented laboratory experiments. RESULTS The rs1046934 genotype did not associate with DNA methylation or COLGALT2 expression in the synovium, whereas the rs11583641 genotype did. Surprisingly, the effects for rs11583641 were opposite to those previously observed in cartilage. Epigenetic editing in synovial cells revealed that enhancer methylation is causally linked to COLGALT2 expression. CONCLUSIONS This is the first direct demonstration for osteoarthritis genetic risk of a functional link between DNA methylation and gene expression operating in opposite directions between articular joint tissues. It highlights pleiotropy in the action of osteoarthritis risk and provides a cautionary note in the application of future genetically based osteoarthritis therapies: an intervention that decreases the detrimental effect of a risk allele in one joint tissue may inadvertently increase its detrimental effect in another joint tissue.
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Affiliation(s)
- Yulia S Kehayova
- Newcastle University, Biosciences Institute, International Centre for Life, Newcastle Upon Tyne, NE1 3BZ, UK
| | - J Mark Wilkinson
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Sarah J Rice
- Newcastle University, Biosciences Institute, International Centre for Life, Newcastle Upon Tyne, NE1 3BZ, UK.
| | - John Loughlin
- Newcastle University, Biosciences Institute, International Centre for Life, Newcastle Upon Tyne, NE1 3BZ, UK.
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21
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Rizzo MG, Best TM, Huard J, Philippon M, Hornicek F, Duan Z, Griswold AJ, Kaplan LD, Hare JM, Kouroupis D. Therapeutic Perspectives for Inflammation and Senescence in Osteoarthritis Using Mesenchymal Stem Cells, Mesenchymal Stem Cell-Derived Extracellular Vesicles and Senolytic Agents. Cells 2023; 12:1421. [PMID: 37408255 DOI: 10.3390/cells12101421] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/08/2023] [Accepted: 05/13/2023] [Indexed: 07/07/2023] Open
Abstract
Osteoarthritis (OA) is the most common cause of disability worldwide among the elderly. Alarmingly, the incidence of OA in individuals less than 40 years of age is rising, likely due to the increase in obesity and post-traumatic osteoarthritis (PTOA). In recent years, due to a better understanding of the underlying pathophysiology of OA, several potential therapeutic approaches targeting specific molecular pathways have been identified. In particular, the role of inflammation and the immune system has been increasingly recognized as important in a variety of musculoskeletal diseases, including OA. Similarly, higher levels of host cellular senescence, characterized by cessation of cell division and the secretion of a senescence-associated secretory phenotype (SASP) within the local tissue microenvironments, have also been linked to OA and its progression. New advances in the field, including stem cell therapies and senolytics, are emerging with the goal of slowing disease progression. Mesenchymal stem/stromal cells (MSCs) are a subset of multipotent adult stem cells that have demonstrated the potential to modulate unchecked inflammation, reverse fibrosis, attenuate pain, and potentially treat patients with OA. Numerous studies have demonstrated the potential of MSC extracellular vesicles (EVs) as cell-free treatments that comply with FDA regulations. EVs, including exosomes and microvesicles, are released by numerous cell types and are increasingly recognized as playing a critical role in cell-cell communication in age-related diseases, including OA. Treatment strategies for OA are being developed that target senescent cells and the paracrine and autocrine secretions of SASP. This article highlights the encouraging potential for MSC or MSC-derived products alone or in combination with senolytics to control patient symptoms and potentially mitigate the progression of OA. We will also explore the application of genomic principles to the study of OA and the potential for the discovery of OA phenotypes that can motivate more precise patient-driven treatments.
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Affiliation(s)
- Michael G Rizzo
- Department of Orthopedics, UHealth Sports Medicine Institute, University of Miami Miller School of Medicine, Miami, FL 33146, USA
| | - Thomas M Best
- Department of Orthopedics, UHealth Sports Medicine Institute, University of Miami Miller School of Medicine, Miami, FL 33146, USA
| | - Johnny Huard
- Center for Regenerative and Personalized Medicine (CRPM), Steadman Philippon Research Institute, Vail, CO 81657, USA
| | - Marc Philippon
- Center for Regenerative and Personalized Medicine (CRPM), Steadman Philippon Research Institute, Vail, CO 81657, USA
| | - Francis Hornicek
- Department of Orthopedics, Sarcoma Biology Laboratory, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Zhenfeng Duan
- Department of Orthopedics, Sarcoma Biology Laboratory, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lee D Kaplan
- Department of Orthopedics, UHealth Sports Medicine Institute, University of Miami Miller School of Medicine, Miami, FL 33146, USA
| | - Joshua M Hare
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33101, USA
| | - Dimitrios Kouroupis
- Department of Orthopedics, UHealth Sports Medicine Institute, University of Miami Miller School of Medicine, Miami, FL 33146, USA
- Diabetes Research Institute, Cell Transplant Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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22
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Richard D, Capellini TD, Diekman BO. Epigenetics as a mediator of genetic risk in osteoarthritis: role during development, homeostasis, aging, and disease progression. Am J Physiol Cell Physiol 2023; 324:C1078-C1088. [PMID: 36971423 PMCID: PMC10191130 DOI: 10.1152/ajpcell.00574.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
The identification of genomic loci that are associated with osteoarthritis (OA) has provided a starting point for understanding how genetic variation activates catabolic processes in the joint. However, genetic variants can only alter gene expression and cellular function when the epigenetic environment is permissive to these effects. In this review, we provide examples of how epigenetic shifts at distinct life stages can alter the risk for OA, which we posit is critical for the proper interpretation of genome-wide association studies (GWAS). During development, intensive work on the growth and differentiation factor 5 (GDF5) locus has revealed the importance of tissue-specific enhancer activity in controlling both joint development and the subsequent risk for OA. During homeostasis in adults, underlying genetic risk factors may help establish beneficial or catabolic "set points" that dictate tissue function, with a strong cumulative effect on OA risk. During aging, methylation changes and the reorganization of chromatin can "unmask" the effects of genetic variants. The destructive function of variants that alter aging would only mediate effects after reproductive competence and thus avoid any evolutionary selection pressure, as consistent with larger frameworks of biological aging and its relationship to disease. A similar "unmasking" may occur during OA progression, which is supported by the finding of distinct expression quantitative trait loci (eQTLs) in chondrocytes depending on the degree of tissue degradation. Finally, we propose that massively parallel reporter assays (MPRAs) will be a valuable tool to test the function of putative OA GWAS variants in chondrocytes from different life stages.
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Affiliation(s)
- Daniel Richard
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
| | - Brian O Diekman
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, and North Carolina State University, Raleigh, North Carolina, United States
- Thurston Arthritis Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
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23
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Donnenfield JI, Proffen BL, Fleming BC, Murray MM. Responding to ACL Injury and its Treatments: Comparative Gene Expression between Articular Cartilage and Synovium. Bioengineering (Basel) 2023; 10:bioengineering10050527. [PMID: 37237597 DOI: 10.3390/bioengineering10050527] [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: 04/04/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
The relationship between cartilage and synovium is a rapidly growing area of osteoarthritis research. However, to the best of our knowledge, the relationships in gene expression between these two tissues have not been explored in mid-stage disease development. The current study compared the transcriptomes of these two tissues in a large animal model one year following posttraumatic osteoarthritis induction and multiple surgical treatment modalities. Thirty-six Yucatan minipigs underwent transection of the anterior cruciate ligament. Subjects were randomized to no further intervention, ligament reconstruction, or ligament repair augmented with an extracellular matrix (ECM) scaffold, followed by RNA sequencing of the articular cartilage and synovium at 52 weeks after harvest. Twelve intact contralateral knees served as controls. Across all treatment modalities, the primary difference in the transcriptomes was that the articular cartilage had greater upregulation of genes related to immune activation compared to the synovium-once baseline differences between cartilage and synovium were adjusted for. Oppositely, synovium featured greater upregulation of genes related to Wnt signaling compared to articular cartilage. After adjusting for expression differences between cartilage and synovium seen following ligament reconstruction, ligament repair with an ECM scaffold upregulated pathways related to ion homeostasis, tissue remodeling, and collagen catabolism in cartilage relative to synovium. These findings implicate inflammatory pathways within cartilage in the mid-stage development of posttraumatic osteoarthritis, independent of surgical treatment. Moreover, use of an ECM scaffold may exert a chondroprotective effect over gold-standard reconstruction through preferentially activating ion homeostatic and tissue remodeling pathways within cartilage.
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Affiliation(s)
- Jonah I Donnenfield
- Division of Sports Medicine, Department of Orthopaedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Benedikt L Proffen
- Division of Sports Medicine, Department of Orthopaedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Braden C Fleming
- Department of Orthopaedics, Warren Alpert Medical School of Brown University/Rhode Island Hospital, Providence, RI 02903, USA
| | - Martha M Murray
- Division of Sports Medicine, Department of Orthopaedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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24
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Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535816. [PMID: 37066341 PMCID: PMC10104061 DOI: 10.1101/2023.04.06.535816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Splicing quantitative trait loci (QTLs) have been implicated as a common mechanism underlying complex trait associations. However, utilising splicing QTLs in target discovery and prioritisation has been challenging due to extensive data normalisation which often renders the direction of the genetic effect as well as its magnitude difficult to interpret. This is further complicated by the fact that strong expression QTLs often manifest as weak splicing QTLs and vice versa, making it difficult to uniquely identify the underlying molecular mechanism at each locus. We find that these ambiguities can be mitigated by visualising the association between the genotype and average RNA sequencing read coverage in the region. Here, we generate these QTL coverage plots for 1.7 million molecular QTL associations in the eQTL Catalogue identified with five quantification methods. We illustrate the utility of these QTL coverage plots by performing colocalisation between vitamin D levels in the UK Biobank and all molecular QTLs in the eQTL Catalogue. We find that while visually confirmed splicing QTLs explain just 6/53 of the colocalising signals, they are significantly less pleiotropic than eQTLs and identify a prioritised causal gene in 4/6 cases. All our association summary statistics and QTL coverage plots are freely available at https://www.ebi.ac.uk/eqtl/.
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Affiliation(s)
- Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ralf Tambets
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - James D Hayhurst
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ida Rahu
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Peep Kolberg
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Uku Raudvere
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Ivan Kuzmin
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Anshika Chowdhary
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Andreas Vija
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Hans J Teras
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob Ulirsch
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - John Hardy
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Sebastian Guelfi
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Daniah Trabzuni
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Sarah Kim-Hellmuth
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany
| | - Will Rayner
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Hilary Finucane
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Abayomi Mosaku
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Parkinson
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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25
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Kim M, Rubab A, Chan WC, Chan D. Osteoarthritis year in review: genetics, genomics and epigenetics. Osteoarthritis Cartilage 2023:S1063-4584(23)00725-2. [PMID: 36924918 DOI: 10.1016/j.joca.2023.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023]
Abstract
This "year in review" provides a summary of the research findings on the topic of genetics, genomics and epigenetics for osteoarthritis (OA) between Mar 2021-Apr 2022. A search routine of the literature in PubMed for the keyword, osteoarthritis, together with topics on genetics, genomics, epigenetics, polymorphism, DNA methylation, noncoding RNA, lncRNA, proteomics, and single cell RNA sequencing, returned key research articles and relevant reviews. Following filtering of duplicates across search routines, 695 unique research articles and 112 reviews were identified. We manually curated these articles and selected 90 as references for this review. However, we were unable to refer to all these articles, and only used selected articles to highlight key outcomes and trends. The trend in genetics is on the meta-analysis of existing cohorts with comparable genetic and phenotype characterisation of OA; in particular, clear definition of endophenotypes to enhance the genetic power. Further, many researchers are realizing the power of big data and multi-omics approaches to gain molecular insights for OA, and this has opened innovative approaches to include transcriptomics and epigenetics data as quantitative trait loci (QTLs). Given that most of the genetic loci for OA are not located within coding regions of genes, implying the impact is likely to be on gene regulation, epigenetics is a hot topic, and there is a surge in studies relating to the role of miRNA and long non-coding RNA on cartilage biology and pathology. The findings are exciting and new insights are provided in this review to summarize a year of research and the road map to capture all new innovations to achieve the desired goal in OA prevention and treatment.
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Affiliation(s)
- Minyeong Kim
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Aqsa Rubab
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Wilson Cw Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Danny Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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26
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Han BX, Yan SS, Yu Han, Xu Q, Zhao QG, Ma XL, Ni JJ, Zhang L, Pei YF. Causal Effects of Plasma Proteome on Osteoporosis and Osteoarthritis. Calcif Tissue Int 2023; 112:350-358. [PMID: 36576504 DOI: 10.1007/s00223-022-01049-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 12/13/2022] [Indexed: 12/29/2022]
Abstract
The two-sample Mendelian randomization (MR) study revealed a causal association of plasma proteins with osteoporosis (OP) and osteoarthritis (OA). Bone mineral density (BMD) is the gold standard for the clinical assessment of OP. Recent studies have shown that plasma proteins play an essential role in the regulation of bone development. However, the causal association of plasma proteins with BMD and OA remains unclear. We estimated the effects of 2889 plasma proteins on 2 BMD phenotypes and 6 OA phenotypes using two-sample MR analysis based on the genome-wide association study summary statistics. Then, we performed sensitivity analysis and reverse-direction MR analysis to evaluate the robustness of the MR analysis results, followed by gene ontology (GO) enrichment analysis and KEGG pathway analysis to explore the functional relevance of the identified plasma proteins. Overall, we observed a total of 257 protein-estimated heel BMD associations, 17 protein-total-body BMD associations, 2 protein-all-OA associations, and 2 protein-knee-OA associations at PFDR < 0.05. Reverse-direction MR analysis demonstrated that there was little evidence of the causal association of BMD and OA with plasma proteins. GO enrichment analysis and KEGG pathway analysis identified multiple pathways, which may be involved in the development of OP and OA. Our findings recognized plasma proteins that could be used to regulate changes in OP and OA, thus, providing new insights into protein-mediated mechanisms of bone development.
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Affiliation(s)
- Bai-Xue Han
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, 199 Ren-Ai Rd., SuZhou City, 215123, Jiangsu Province, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, SuZhou, Jiangsu, People's Republic of China
| | - Shan-Shan Yan
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, 199 Ren-Ai Rd., SuZhou City, 215123, Jiangsu Province, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, SuZhou, Jiangsu, People's Republic of China
| | - Yu Han
- Laboratory of Molecular Neuropathology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Suzhou Medical College of Soochow University, SuZhou, Jiangsu, People's Republic of China
| | - Qian Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, 199 Ren-Ai Rd., SuZhou City, 215123, Jiangsu Province, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, SuZhou, Jiangsu, People's Republic of China
| | - Qi-Gang Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, 199 Ren-Ai Rd., SuZhou City, 215123, Jiangsu Province, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, SuZhou, Jiangsu, People's Republic of China
| | - Xin-Ling Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, 199 Ren-Ai Rd., SuZhou City, 215123, Jiangsu Province, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, SuZhou, Jiangsu, People's Republic of China
| | - Jing-Jing Ni
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, SuZhou, Jiangsu, People's Republic of China
- Center for Genetic Epidemiology and Genomics, School of Public Health, Suzhou Medical College of Soochow University, 199 Ren-Ai Rd., SuZhou City, 215123, JiangSu Province, People's Republic of China
| | - Lei Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, SuZhou, Jiangsu, People's Republic of China.
- Center for Genetic Epidemiology and Genomics, School of Public Health, Suzhou Medical College of Soochow University, 199 Ren-Ai Rd., SuZhou City, 215123, JiangSu Province, People's Republic of China.
| | - Yu-Fang Pei
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, 199 Ren-Ai Rd., SuZhou City, 215123, Jiangsu Province, People's Republic of China.
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, SuZhou, Jiangsu, People's Republic of China.
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Xue A, Yazar S, Neavin D, Powell JE. Pitfalls and opportunities for applying latent variables in single-cell eQTL analyses. Genome Biol 2023; 24:33. [PMID: 36823676 PMCID: PMC9948363 DOI: 10.1186/s13059-023-02873-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Using latent variables in gene expression data can help correct unobserved confounders and increase statistical power for expression quantitative trait Loci (eQTL) detection. The probabilistic estimation of expression residuals (PEER) and principal component analysis (PCA) are widely used methods that can remove unwanted variation and improve eQTL discovery power in bulk RNA-seq analysis. However, their performance has not been evaluated extensively in single-cell eQTL analysis, especially for different cell types. Potential challenges arise due to the structure of single-cell RNA-seq data, including sparsity, skewness, and mean-variance relationship. Here, we show by a series of analyses that PEER and PCA require additional quality control and data transformation steps on the pseudo-bulk matrix to obtain valid latent variables; otherwise, it can result in highly correlated factors (Pearson's correlation r = 0.63 ~ 0.99). Incorporating valid PFs/PCs in the eQTL association model would identify 1.7 ~ 13.3% more eGenes. Sensitivity analysis showed that the pattern of change between the number of eGenes detected and fitted PFs/PCs varied significantly in different cell types. In addition, using highly variable genes to generate latent variables could achieve similar eGenes discovery power as using all genes but save considerable computational resources (~ 6.2-fold faster).
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Affiliation(s)
- Angli Xue
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia. .,School of Biomedical Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Seyhan Yazar
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Drew Neavin
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia. .,UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, 2052, Australia.
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28
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Insights from multi-omics integration in complex disease primary tissues. Trends Genet 2023; 39:46-58. [PMID: 36137835 DOI: 10.1016/j.tig.2022.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/23/2022]
Abstract
Genome-wide association studies (GWAS) have provided insights into the genetic basis of complex diseases. In the next step, integrative multi-omics approaches can characterize molecular profiles in relevant primary tissues to reveal the mechanisms that underlie disease development. Here, we highlight recent progress in four examples of complex diseases generated by integrative studies: type 2 diabetes (T2D), osteoarthritis, Alzheimer's disease (AD), and systemic lupus erythematosus (SLE). High-resolution methodologies such as single-cell and spatial omics techniques will become even more important in the future. Furthermore, we emphasize the urgent need to include as yet understudied cell types and increase the diversity of studied populations.
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29
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Thulson E, Davis ES, D’Costa S, Coryell PR, Kramer NE, Mohlke KL, Loeser RF, Diekman BO, Phanstiel DH. 3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes. Genetics 2022; 222:iyac141. [PMID: 36099032 PMCID: PMC9713432 DOI: 10.1093/genetics/iyac141] [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: 05/16/2022] [Accepted: 08/29/2022] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have identified over 100 loci associated with osteoarthritis risk, but the majority of osteoarthritis risk variants are noncoding, making it difficult to identify the impacted genes for further study and therapeutic development. To address this need, we used a multiomic approach and genome editing to identify and functionally characterize potential osteoarthritis risk genes. Computational analysis of genome-wide association studies and ChIP-seq data revealed that chondrocyte regulatory loci are enriched for osteoarthritis risk variants. We constructed a chondrocyte-specific regulatory network by mapping 3D chromatin structure and active enhancers in human chondrocytes. We then intersected these data with our previously collected RNA-seq dataset of chondrocytes responding to fibronectin fragment, a known osteoarthritis trigger. Integration of the 3 genomic datasets with recently reported osteoarthritis genome-wide association study variants revealed a refined set of putative causal osteoarthritis variants and their potential target genes. One of the putative target genes identified was SOCS2, which was connected to a putative causal variant by a 170-kb loop and is differentially regulated in response to fibronectin fragment. CRISPR-Cas9-mediated deletion of SOCS2 in primary human chondrocytes from 3 independent donors led to heightened expression of inflammatory markers after fibronectin fragment treatment. These data suggest that SOCS2 plays a role in resolving inflammation in response to cartilage matrix damage and provides a possible mechanistic explanation for its influence on osteoarthritis risk. In total, we identified 56 unique putative osteoarthritis risk genes for further research and potential therapeutic development.
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Affiliation(s)
- Eliza Thulson
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Susan D’Costa
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Philip R Coryell
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nicole E Kramer
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Richard F Loeser
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Division of Rheumatology, Allergy and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Brian O Diekman
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Joint Department of Biomedical Engineering, University of North Carolina and North Carolina State University, Raleigh, NC 27695, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Douglas H Phanstiel
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA
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30
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Brumwell A, Aubourg G, Hussain J, Parker E, Deehan DJ, Rice SJ, Loughlin J. Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk. Arthritis Res Ther 2022; 24:189. [PMID: 35941660 PMCID: PMC9358880 DOI: 10.1186/s13075-022-02882-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Osteoarthritis is highly heritable and genome-wide studies have identified single nucleotide polymorphisms (SNPs) associated with the disease. One such locus is marked by SNP rs11732213 (T > C). Genotype at rs11732213 correlates with the methylation levels of nearby CpG dinucleotides (CpGs), forming a methylation quantitative trait locus (mQTL). This study investigated the regulatory activity of the CpGs to identify a target gene of the locus. METHODS Nucleic acids were extracted from the articular cartilage of osteoarthritis patients. Samples were genotyped, and DNA methylation was quantified by pyrosequencing at 14 CpGs within a 259-bp interval. CpGs were tested for enhancer effects in immortalised chondrocytes using a reporter gene assay. DNA methylation at the locus was altered using targeted epigenome editing, with the impact on gene expression determined using quantitative polymerase chain reaction. RESULTS rs11732213 genotype correlated with DNA methylation at nine CpGs, which formed a differentially methylated region (DMR), with the osteoarthritis risk allele T corresponding to reduced levels of methylation. The DMR acted as an enhancer and demethylation of the CpGs altered expression of TMEM129. Allelic imbalance in TMEM129 expression was identified in cartilage, with under-expression of the risk allele. CONCLUSIONS TMEM129 is a target of osteoarthritis genetic risk at this locus. Genotype at rs11732213 impacts DNA methylation at the enhancer, which, in turn, modulates TMEM129 expression. TMEM129 encodes an enzyme involved in protein degradation within the endoplasmic reticulum, a process previously implicated in osteoarthritis. TMEM129 is a compelling osteoarthritis susceptibility target.
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Affiliation(s)
- Abby Brumwell
- Newcastle University, Biosciences Institute, International Centre for Life, Newcastle upon Tyne, UK
| | - Guillaume Aubourg
- Newcastle University, Biosciences Institute, International Centre for Life, Newcastle upon Tyne, UK
| | - Juhel Hussain
- Newcastle University, Biosciences Institute, International Centre for Life, Newcastle upon Tyne, UK
| | - Eleanor Parker
- Newcastle University, Biosciences Institute, International Centre for Life, Newcastle upon Tyne, UK
| | - David J Deehan
- Freeman Hospital, Newcastle University Teaching Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - Sarah J Rice
- Newcastle University, Biosciences Institute, International Centre for Life, Newcastle upon Tyne, UK
| | - John Loughlin
- Newcastle University, Biosciences Institute, International Centre for Life, Newcastle upon Tyne, UK.
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An epigenome-wide view of osteoarthritis in primary tissues. Am J Hum Genet 2022; 109:1255-1271. [PMID: 35679866 PMCID: PMC9300761 DOI: 10.1016/j.ajhg.2022.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/11/2022] [Indexed: 12/16/2022] Open
Abstract
Osteoarthritis is a complex degenerative joint disease. Here, we investigate matched genotype and methylation profiles of primary chondrocytes from macroscopically intact (low-grade) and degraded (high-grade) osteoarthritis cartilage and from synoviocytes collected from 98 osteoarthritis-affected individuals undergoing knee replacement surgery. We perform an epigenome-wide association study of knee cartilage degeneration and report robustly replicating methylation markers, which reveal an etiologic mechanism linked to the migration of epithelial cells. Using machine learning, we derive methylation models of cartilage degeneration, which we validate with 82% accuracy in independent data. We report a genome-wide methylation quantitative trait locus (mQTL) map of articular cartilage and synovium and identify 18 disease-grade-specific mQTLs in osteoarthritis cartilage. We resolve osteoarthritis GWAS loci through causal inference and colocalization analyses and decipher the epigenetic mechanisms that mediate the effect of genotype on disease risk. Together, our findings provide enhanced insights into epigenetic mechanisms underlying osteoarthritis in primary tissues.
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32
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Jia Z, Kang B, Cai Y, Chen C, Yu Z, Li W, Zhang W. Cell-free fat extract attenuates osteoarthritis via chondrocytes regeneration and macrophages immunomodulation. Stem Cell Res Ther 2022; 13:133. [PMID: 35365233 PMCID: PMC8973552 DOI: 10.1186/s13287-022-02813-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/02/2022] [Indexed: 01/15/2023] Open
Abstract
Background The prevalence of osteoarthritis (OA) is increasing, yet clinically effective and economical treatments are unavailable. We have previously proposed a cell-free fat extract (CEFFE) containing multiple cytokines, which possessed antiapoptotic, anti-oxidative, and proliferation promotion functions, as a “cell-free” strategy. In this study, we aimed to evaluate the therapeutic effect of CEFFE in vivo and in vitro. Methods In vivo study, sodium iodoacetate-induced OA rats were treated with CEFFE by intra-articular injections for 8 weeks. Behavioral experiments were performed every two weeks. Histological analyses, anti-type II collagen, and toluidine staining provided structural evaluation. Macrophage infiltration was assessed by anti-CD68 and anti-CD206 staining. In vitro study, the effect of CEFFE on macrophage polarization and secretory factors was evaluated by flow cytometry, immunofluorescence, and quantitative reverse-transcription polymerase chain reaction (qRT-PCR). The effect of CEFFE on cartilage regeneration was accessed by cell counting kit-8 assay and qRT-PCR. The generation of reactive oxygen species (ROS) and levels of ROS-related enzymes were investigated by qRT-PCR and western blotting. Results In rat models with sodium iodoacetate (MIA)-induced OA, CEFFE increased claw retraction pressure while decreasing bipedal pressure in a dose-dependent manner. Moreover, CEFFE promoted cartilage structure restoration and increased the proportion of CD206+ macrophages in the synovium. In vitro, CEFFE decreased the proportion of CD86+ cells and reduced the expression of pro-inflammatory factors in LPS + IFN-γ induced Raw 264.7. In addition, CEFFE decreased the expression of interleukin-6 and ADAMTs-5 and promoted the expression of SOX-9 in mouse primary chondrocytes. Besides, CEFFE reduced the intracellular levels of reactive oxygen species in both in vitro models through regulating ROS-related enzymes. Conclusions CEFFE inhibits the progression of OA by promoting cartilage regeneration and limiting low-grade joint inflammation. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02813-3.
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Affiliation(s)
- Zhuoxuan Jia
- Department of Plastic and Reconstructive Surgery, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Tissue Engineering, National Tissue Engineering Center of China, 639 ZhiZaoJu Road, Shanghai, 200011, China
| | - Bijun Kang
- Department of Plastic and Reconstructive Surgery, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Tissue Engineering, National Tissue Engineering Center of China, 639 ZhiZaoJu Road, Shanghai, 200011, China
| | - Yizuo Cai
- Department of Plastic and Reconstructive Surgery, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Tissue Engineering, National Tissue Engineering Center of China, 639 ZhiZaoJu Road, Shanghai, 200011, China
| | - Chingyu Chen
- Department of Plastic and Reconstructive Surgery, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Tissue Engineering, National Tissue Engineering Center of China, 639 ZhiZaoJu Road, Shanghai, 200011, China
| | - Zheyuan Yu
- Department of Plastic and Reconstructive Surgery, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Tissue Engineering, National Tissue Engineering Center of China, 639 ZhiZaoJu Road, Shanghai, 200011, China.
| | - Wei Li
- Department of Plastic and Reconstructive Surgery, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Tissue Engineering, National Tissue Engineering Center of China, 639 ZhiZaoJu Road, Shanghai, 200011, China.
| | - Wenjie Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Tissue Engineering, National Tissue Engineering Center of China, 639 ZhiZaoJu Road, Shanghai, 200011, China.
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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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34
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Young D, Barter M, Soul J. Osteoarthritis year in review: genetics, genomics, epigenetics. Osteoarthritis Cartilage 2022; 30:216-225. [PMID: 34774787 PMCID: PMC8811265 DOI: 10.1016/j.joca.2021.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/18/2021] [Accepted: 11/02/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVE In this review, we have highlighted the advances over the past year in genetics, genomics and epigenetics in the field of osteoarthritis (OA). METHODS A literature search of PubMed was performed using the criteria: "osteoarthritis" and one of the following terms "genetic(s), genomic(s), epigenetic(s), polymorphism, noncoding ribonucleic acid (RNA), microRNA, long noncoding RNA, lncRNA, circular RNA, RNA sequencing (RNA-seq), single cell sequencing, transcriptomics, or deoxyribonucleic acid (DNA) methylation between April 01, 2020 and April 30, 2021. RESULTS In total we identified 765 unique publications, which eventually reduced to 380 of relevance to the field as judged by two assessors. Many of these studies included multiple search terms. We summarised advances relating to genetics, functional genetics, genomics and epigenetics, focusing on our personal key papers during the year. CONCLUSIONS This year few studies have identified new genetic variants contributing to OA susceptibility, but a focus has been on refining risk loci or their functional validation. The use of new technologies together with investigating the cross-talk between multiple tissue types, greater sample sizes and/or better patient classification (OA subtypes) will continue to increase our knowledge of disease mechanisms and progress towards understanding and treating OA.
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Affiliation(s)
- D.A. Young
- Address correspondence and reprint requests to: D.A. Young, Skeletal Research Group, Biosciences Institute, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK. Tel.: 44-191-2418831.
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35
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Katsoula G, Steinberg J, Tuerlings M, de Almeida RC, Southam L, Swift D, Meulenbelt I, Wilkinson JM, Zeggini E. A molecular map of long non-coding RNA expression, isoform switching and alternative splicing in osteoarthritis. Hum Mol Genet 2022; 31:2090-2105. [PMID: 35088088 PMCID: PMC9239745 DOI: 10.1093/hmg/ddac017] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/22/2021] [Accepted: 01/10/2022] [Indexed: 11/30/2022] Open
Abstract
Osteoarthritis is a prevalent joint disease and a major cause of disability worldwide with no curative therapy. Development of disease-modifying therapies requires a better understanding of the molecular mechanisms underpinning disease. A hallmark of osteoarthritis is cartilage degradation. To define molecular events characterizing osteoarthritis at the whole transcriptome level, we performed deep RNA sequencing in paired samples of low- and high-osteoarthritis grade knee cartilage derived from 124 patients undergoing total joint replacement. We detected differential expression between low- and high-osteoarthritis grade articular cartilage for 365 genes and identified a 38-gene signature in osteoarthritis cartilage by replicating our findings in an independent dataset. We also found differential expression for 25 novel long non-coding RNA genes (lncRNAs) and identified potential lncRNA interactions with RNA-binding proteins in osteoarthritis. We assessed alterations in the relative usage of individual gene transcripts and identified differential transcript usage for 82 genes, including ABI3BP, coding for an extracellular matrix protein, AKT1S1, a negative regulator of the mTOR pathway and TPRM4, coding for a transient receptor potential channel. We further assessed genome-wide differential splicing, for the first time in osteoarthritis, and detected differential splicing for 209 genes, which were enriched for extracellular matrix, proteoglycans and integrin surface interactions terms. In the largest study of its kind in osteoarthritis, we find that isoform and splicing changes, in addition to extensive differences in both coding and non-coding sequence expression, are associated with disease and demonstrate a novel layer of genomic complexity to osteoarthritis pathogenesis.
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Affiliation(s)
- Georgia Katsoula
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,TUM School of Medicine, Technical University of Munich, Graduate School of Experimental Medicine, Ismaninger Str. 22, 81675 Munich, Germany
| | - Julia Steinberg
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,Daffodil Centre, University of Sydney, a joint venture with Cancer Council NSW, PO Box 572, Kings Cross, NSW 1340, Sydney, Australia
| | - Margo Tuerlings
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Einthovenweg 20 2333 ZC, Leiden, The Netherlands
| | - Rodrigo Coutinho de Almeida
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Einthovenweg 20 2333 ZC, Leiden, The Netherlands
| | - Lorraine Southam
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Diane Swift
- Department of Oncology and Metabolism, University of Sheffield, Metabolic Bone Unit, Sorby Wing Northern General Hospital Sheffield, S5 7AU, United Kingdom
| | - Ingrid Meulenbelt
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Einthovenweg 20 2333 ZC, Leiden, The Netherlands
| | - J Mark Wilkinson
- Department of Oncology and Metabolism, University of Sheffield, Metabolic Bone Unit, Sorby Wing Northern General Hospital Sheffield, S5 7AU, United Kingdom
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.,TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Ismaninger Str. 22, 81675 Munich, Germany
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36
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Abstract
PURPOSE OF REVIEW To provide an overview of recent developments in the field of osteoarthritis research with a focus on insights gleaned from the application of different -omic technologies. RECENT FINDINGS We searched for osteoarthritis-relevant studies focusing on transcriptomics, epigenomics, proteomics and metabolomics, published since November of 2019. Study designs showed a trend towards characterizing the genomic profile of osteoarthritis-relevant tissues with high resolution, for example either by using single-cell technologies or by considering several -omic levels and disease stages. SUMMARY Multitissue interactions (cartilage-subchondral bone; cartilage-synovium) are prevalent in the pathophysiology of osteoarthritis, which is characterized by substantial matrix remodelling in an inflammatory milieu. Subtyping approaches using -omic technologies have contributed to the identification of at least two osteoarthritis endotypes. Studies using data integration approaches have provided molecular maps that are tissue-specific for osteoarthritis and pave the way for expanding these data integration approaches towards a more comprehensive view of disease aetiopathogenesis.
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Affiliation(s)
- Georgia Katsoula
- Technical University of Munich (TUM), School of Medicine, Graduate School of Experimental Medicine
- Institute of Translational Genomics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Peter Kreitmaier
- Technical University of Munich (TUM), School of Medicine, Graduate School of Experimental Medicine
- Institute of Translational Genomics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Eleftheria Zeggini
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Munich
- Institute of Translational Genomics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
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37
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Qiao J, Zhang M, Wang T, Huang S, Zeng P. Evaluating Causal Relationship Between Metabolites and Six Cardiovascular Diseases Based on GWAS Summary Statistics. Front Genet 2021; 12:746677. [PMID: 34721534 PMCID: PMC8554206 DOI: 10.3389/fgene.2021.746677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/29/2021] [Indexed: 01/23/2023] Open
Abstract
Cardiovascular diseases (CVDs) remain the main cause of morbidity and mortality worldwide. The pathological mechanism and underlying biological processes of these diseases with metabolites remain unclear. In this study, we conducted a two-sample Mendelian randomization (MR) analysis to evaluate the causal effect of metabolites on these diseases by making full use of the latest GWAS summary statistics for 486 metabolites and six major CVDs. Extensive sensitivity analyses were implemented to validate our MR results. We also conducted linkage disequilibrium score regression (LDSC) and colocalization analysis to investigate whether MR findings were driven by genetic similarity or hybridization between LD and disease-associated gene loci. We identified a total of 310 suggestive associations across all metabolites and CVDs, and finally obtained four significant associations, including bradykinin, des-arg(9) (odds ratio [OR] = 1.160, 95% confidence intervals [CIs]: 1.080-1.246, false discovery rate [FDR] = 0.022) on ischemic stroke, N-acetylglycine (OR = 0.946, 95%CIs: 0.920-0.973, FDR = 0.023), X-09026 (OR = 0.845, 95%CIs: 0.779-0.916, FDR = 0.021) and X-14473 (OR = 0.938, 95%CIs = 0.907-0.971, FDR = 0.040) on hypertension. Sensitivity analyses showed that these causal associations were robust, the LDSC and colocalization analyses demonstrated that the identified associations were unlikely confused by LD. Moreover, we identified 15 important metabolic pathways might be involved in the pathogenesis of CVDs. Overall, our work identifies several metabolites that have a causal relationship with CVDs, and improves our understanding of the pathogenesis and treatment strategies for these diseases.
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Affiliation(s)
- Jiahao Qiao
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Meng Zhang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Ting Wang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Shuiping Huang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
- Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, China
- Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, China
| | - Ping Zeng
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
- Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, China
- Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, China
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Yu P, Liu Y, Xie J, Li J. Spatiotemporally controlled calcitonin delivery: Long-term and targeted therapy of skeletal diseases. J Control Release 2021; 338:486-504. [PMID: 34481022 DOI: 10.1016/j.jconrel.2021.08.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 02/05/2023]
Abstract
Bone is a connective tissue that support the entire body and protect the internal organs. However, there are great challenges on curing intractable skeletal diseases such as hypercalcemia, osteoporosis and osteoarthritis. To address these issues, calcitonin (CT) therapy is an effective treatment alternative to regulate calcium metabolism and suppress inflammation response, which are closely related to skeletal diseases. Traditional calcitonin formulation requires frequent administration due to the low bioavailability resulting from the short half-life and abundant calcitonin receptors distributed through the whole body. Therefore, long-term and targeted calcitonin delivery systems (LCDS and TCDS) have been widely explored as the popular strategies to overcome the intrinsic limitations of calcitonin and improve the functions of calcium management and inflammation inhibition in recent years. In this review, we first explain the physiological effects of calcitonin on bone remodeling: (i) inhibitory effects on osteoclasts and (ii) facilitated effects on osteoblasts. Then we summarized four strategies for spatiotemporally controlled delivery of calcitonin: micro-/nanomedicine (e.g. inorganic micro-/nanomedicine, polymeric micro-/nanomedicine and supramolecular assemblies), hydrogels (especially thermosensitive hydrogels), prodrug (PEGylation and targeting design) and hybrid biomaterials. Subsequently, we discussed the application of LCDS and TCDS in treating hypercalcemia, osteoporosis, and arthritis. Understanding and analyzing these advanced calcitonin delivery applications are essential for future development of calcitonin therapies toward skeletal diseases with superior efficacy in clinic.
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Affiliation(s)
- Peng Yu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, PR China
| | - Yanpeng Liu
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, PR China
| | - Jing Xie
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, PR China.
| | - Jianshu Li
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, PR China; State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, PR China; Med-X Center for Materials, Sichuan University, Chengdu 610041, PR China.
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Distinct Concentration-Dependent Molecular Pathways Regulate Bone Cell Responses to Cobalt and Chromium Exposure from Joint Replacement Prostheses. Int J Mol Sci 2021; 22:ijms22105225. [PMID: 34069294 PMCID: PMC8156984 DOI: 10.3390/ijms22105225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/27/2022] Open
Abstract
Systemic cobalt (Co) and chromium (Cr) concentrations may be elevated in patients with metal joint replacement prostheses. Several studies have highlighted the detrimental effects of this exposure on bone cells in vitro, but the underlying mechanisms remain unclear. In this study, we use whole-genome microarrays to comprehensively assess gene expression in primary human osteoblasts, osteoclast precursors and mature resorbing osteoclasts following exposure to clinically relevant circulating versus local periprosthetic tissue concentrations of Co2+ and Cr3+ ions and CoCr nanoparticles. We also describe the gene expression response in osteoblasts on routinely used prosthesis surfaces in the presence of metal exposure. Our results suggest that systemic levels of metal exposure have no effect on osteoblasts, and primarily inhibit osteoclast differentiation and function via altering the focal adhesion and extracellular matrix interaction pathways. In contrast, periprosthetic levels of metal exposure inhibit both osteoblast and osteoclast activity by altering HIF-1α signaling and endocytic/cytoskeletal genes respectively, as well as increasing inflammatory signaling with mechanistic implications for adverse reactions to metal debris. Furthermore, we identify gene clusters and KEGG pathways for which the expression correlates with increasing Co2+:Cr3+ concentrations, and has the potential to serve as early markers of metal toxicity. Finally, our study provides a molecular basis for the improved clinical outcomes for hydroxyapatite-coated prostheses that elicit a pro-survival osteogenic gene signature compared to grit-blasted and plasma-sprayed titanium-coated surfaces in the presence of metal exposure.
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