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An X, Wang R, Lv Z, Wu W, Sun Z, Wu R, Yan W, Jiang Q, Xu X. WTAP-mediated m 6A modification of FRZB triggers the inflammatory response via the Wnt signaling pathway in osteoarthritis. Exp Mol Med 2024; 56:156-167. [PMID: 38172596 PMCID: PMC10834961 DOI: 10.1038/s12276-023-01135-5] [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: 04/18/2023] [Revised: 09/16/2023] [Accepted: 10/01/2023] [Indexed: 01/05/2024] Open
Abstract
Osteoarthritis (OA) is the most common form of arthritis. However, the exact pathogenesis remains unclear. Emerging evidence shows that N6-methyladenosine (m6A) modification may have an important role in OA pathogenesis. This study aimed to investigate the role of m6A writers and the underlying mechanisms in osteoarthritic cartilage. Among m6A methyltransferases, Wilms tumor 1-associated protein (WTAP) expression most significantly differed in clinical osteoarthritic cartilage. WTAP regulated extracellular matrix (ECM) degradation, inflammation and antioxidation in human chondrocytes. Mechanistically, the m6A modification and relative downstream targets in osteoarthritic cartilage were assessed by methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing, which indicated that the expression of frizzled-related protein (FRZB), a secreted Wnt antagonist, was abnormally decreased and accompanied by high m6A modification in osteoarthritic cartilage. In vitro dysregulated WTAP had positive effects on β-catenin expression by targeting FRZB, which finally contributed to the cartilage injury phenotype in chondrocytes. Intra-articular injection of adeno-associated virus-WTAP alleviated OA progression in a mouse model, while this protective effect could be reversed by the application of a Wnt/β-catenin activator. In summary, this study revealed that WTAP-dependent RNA m6A modification contributed to Wnt/β-catenin pathway activation and OA progression through post-transcriptional regulation of FRZB mRNA, thus providing a potentially effective therapeutic strategy for OA treatment.
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Affiliation(s)
- Xueying An
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, Jiangsu, P.R. China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Nanjing, P.R. China
| | - Rongliang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, Jiangsu, P.R. China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Nanjing, P.R. China
| | - Zhongyang Lv
- Department of Orthopedic, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, P.R. China
| | - Wenshu Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, Jiangsu, P.R. China
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Nanjing, P.R. China
| | - Ziying Sun
- Department of Orthopedic, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, P.R. China
| | - Rui Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, Jiangsu, P.R. China
| | - Wenjin Yan
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, Jiangsu, P.R. China.
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Nanjing, P.R. China.
| | - Qing Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, Jiangsu, P.R. China.
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Nanjing, P.R. China.
| | - Xingquan Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, Jiangsu, P.R. China.
- Branch of National Clinical Research Center for Orthopedics, Sports Medicine and Rehabilitation, Nanjing, P.R. China.
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Chun JM, Kim JS, Kim C. Integrated Analysis of DNA Methylation and Gene Expression Profiles in a Rat Model of Osteoarthritis. Int J Mol Sci 2024; 25:594. [PMID: 38203768 PMCID: PMC10778961 DOI: 10.3390/ijms25010594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Osteoarthritis (OA) is common and affected by several factors, such as age, weight, sex, and genetics. The pathogenesis of OA remains unclear. Therefore, using a rat model of monosodium iodoacetate (MIA)-induced OA, we examined genomic-wide DNA methylation using methyl-seq and characterized the transcriptome using RNA-seq in the articular cartilage tissue from a negative control (NC) and MIA-induced rats. We identified 170 genes (100 hypomethylated and upregulated genes and 70 hypermethylated and downregulated genes) regulated by DNA methylation in OA. DNA methylation-regulated genes were enriched in functions related to focal adhesion, extracellular matrix (ECM)-receptor interaction and the PI3K-Akt and Hippo signaling pathways. Functions related to extracellular matrix organization, extracellular matrix proteoglycans, and collagen formation were involved in OA. A molecular and protein-protein network was constructed using methylated expression-correlated genes. Erk1/2 was a downstream target of OA-induced changes in DNA methylation and RNA expression. We found that the integrin subunit alpha 2 (ITGA2) gene is important in focal adhesion, alpha6-beta4 integrin signaling, and the inflammatory response pathway in OA. Overall, gene expression changes because DNA methylation influences OA pathogenesis. ITGA2, whose gene expression changes are regulated by DNA methylation during OA onset, is a candidate gene. Our findings provide insights into the epigenetic targets of OA processes in rats.
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Affiliation(s)
- Jin Mi Chun
- Digital Health Research Division, Korea Institute of Oriental Medicine, Yuseong-daero 1672, Daejeon 34054, Republic of Korea;
| | - Joong-Sun Kim
- College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Chul Kim
- KM Data Division, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea
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Chen S, Zhu X, Ou W, Kang L, Situ J, Liao Z, Huang L, Qi W, Ni S. ETS2 overexpression ameliorates cartilage injury in osteoarthritis by the ETS2/miR-155/STAT1/DNMT1 feedback loop pathway. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194965. [PMID: 37524226 DOI: 10.1016/j.bbagrm.2023.194965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/14/2023] [Accepted: 07/26/2023] [Indexed: 08/02/2023]
Abstract
Osteoarthritis (OA) is the most common irreversible chronic joint dysfunction disease, which is pathologically characterized by disturbance of articular cartilage homeostasis leading to subsequent inflammatory response and cartilage extracellular matrix (ECM) degradation. Increasing evidence has demonstrated the dysregulation of transcription factors play crucial roles in the occurrence and development of osteoarthritis (OA), but the potential functions and mechanism of most transcription factors in OA has not been completely illuminated. In this study, we identified that transcription factor V-ets erythroblastosis virus E26 oncogene homolog 2 (ETS2) was significantly down-regulated in OA cartilage and IL-1β-induced OA chondrocytes. Functional experiments in vitro demonstrated that the overexpressed ETS2 strikingly enhanced proliferation, outstandingly suppressed apoptosis, and dramatically reduced inflammation and ECM degradation in IL-1β-induced OA chondrocytes, whereas the knockdown of ETS2 led to the opposite effects. Further in vivo studies have shown that up-regulated ETS2 dramatically ameliorates cartilage injury in DMM-induced OA mice. Mechanical studies have disclosed that DNMT1-mediated downregulation of ETS2 dramatically promotes STAT1 by inhibiting miR-155 transcription, and increased STAT1 initiates a feedback loop that may enhance DNMT1-mediated hypermethylation of ETS2 to inhibit ETS2 expression, thus forming a DNMT1/ETS2/miR-155/STAT1 feedback loop that inhibits MAPK signaling pathways and aggravates OA cartilage injury. In all, our results revealed that overexpression of ETS2 markedly ameliorated OA cartilage injury through the ETS2/miR-155/STAT1/DNMT1 feedback loop, providing a new perspective on the pathogenesis and therapeutic strategies for OA.
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Affiliation(s)
- Shuxiang Chen
- Department of Orthopaedic, Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, Guangdong, China
| | - Xiaotong Zhu
- Department of Rheumatology and Clinical Immunology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Wenhuan Ou
- Department of Orthopaedic, Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, Guangdong, China
| | - Le Kang
- Department of Orthopaedic, Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, Guangdong, China
| | - Jian Situ
- Department of Orthopaedic, Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, Guangdong, China
| | - Zhipeng Liao
- Department of Orthopaedic, Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, Guangdong, China
| | - Li Huang
- Department of Orthopaedic, Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, Guangdong, China
| | - Weizhong Qi
- Department of Orthopaedic, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Songjia Ni
- Department of Orthopaedic, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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Zhu YS, Yan H, Mo TT, Zhang JN, Jiang C. Identification of Diagnostic Markers in Synovial Tissue of Osteoarthritis by Weighted Gene Coexpression Network. Biochem Genet 2023; 61:2056-2075. [PMID: 36929359 DOI: 10.1007/s10528-023-10359-z] [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: 09/29/2022] [Accepted: 02/23/2023] [Indexed: 03/18/2023]
Abstract
Osteoarthritis (OA) is a serious threat to human health. However, the etiology and pathogenesis of the disease are not fully understood. Most researchers believe that the degeneration and imbalance of articular cartilage, extracellular matrix, and subchondral bone are the fundamental causes of osteoarthritis. However, recent studies have shown that synovial lesions may precede cartilage, which may be an important precipitating factor in the early stage of OA and the whole course of the disease. This study aimed to conduct an analysis based on sequence data from the Gene Expression Omnibus (GEO) database to investigate the presence of effective biomarkers in the synovial tissue of osteoarthritis for the diagnosis and control of OA progression. In this study, the differentially expressed OA-related genes (DE-OARGs) in osteoarthritis synovial tissues were extracted in the GSE55235 and GSE55457 datasets using the Weighted Gene Co-expression Network Analysis (WGCNA) and limma. Least-Absolute Shrinkage and Selection Operator (LASSO) algorithm was used to select the diagnostic genes based on the DE-OARGs by glmnet package. 7 genes were selected as diagnostic genes including SAT1, RLF, MAFF, SIK1, RORA, ZNF529, and EBF2. Subsequently, the diagnostic model was constructed and the results of the Area Under the Curve (AUC) demonstrated that the diagnostic model had high diagnostic performance for OA. Additionally, among the 22 immune cells of the Cell type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) and the 24 immune cells of the single sample Gene Set Enrichment Analysis (ssGSEA), 3 immune cells and 5 immune cells were different between the OA and normal samples, respectively. The expression trends of the 7 diagnostic genes were consistent in the GEO datasets and the results of the real-time reverse transcription PCR (qRT-PCR). The results of this study demonstrate that these diagnostic markers have important significance in the diagnosis and treatment of OA, and will provide further evidence for the clinical and functional studies of OA.
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Affiliation(s)
- Yun-Sen Zhu
- Department of Orthopaedic Surgery, The First People's Hospital of Wenling, Wenzhou Medical University Affiliated Wenling Hospital, Chuan'an Nan Road NO 333, Wenling, 317500, Zhejiang, China
| | - Hong Yan
- Department of Orthopaedic Surgery, The First People's Hospital of Wenling, Wenzhou Medical University Affiliated Wenling Hospital, Chuan'an Nan Road NO 333, Wenling, 317500, Zhejiang, China
| | - Ting-Ting Mo
- Department of Orthopaedic Surgery, The First People's Hospital of Wenling, Wenzhou Medical University Affiliated Wenling Hospital, Chuan'an Nan Road NO 333, Wenling, 317500, Zhejiang, China
| | - Jiang-Nan Zhang
- Department of Orthopaedic Surgery, The First People's Hospital of Wenling, Wenzhou Medical University Affiliated Wenling Hospital, Chuan'an Nan Road NO 333, Wenling, 317500, Zhejiang, China
| | - Chang Jiang
- Department of Orthopaedic Surgery, The First People's Hospital of Wenling, Wenzhou Medical University Affiliated Wenling Hospital, Chuan'an Nan Road NO 333, Wenling, 317500, Zhejiang, China.
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Chen Z, Wang W, Zhang Y, Xue X, Hua Y. Identification of four-gene signature to diagnose osteoarthritis through bioinformatics and machine learning methods. Cytokine 2023; 169:156300. [PMID: 37454542 DOI: 10.1016/j.cyto.2023.156300] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/02/2023] [Accepted: 07/08/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Although osteoarthritis (OA) is one of the most prevalent joint disorders, effective biomarkers to diagnose OA are still unavailable. This study aimed to acquire some key synovial biomarkers (hub genes) and analyze their correlation with immune infiltration in OA. METHODS Gene expression profiles and clinical characteristics of OA and healthy synovial samples were retrieved from the Gene Expression Omnibus (GEO) database. Hub genes for OA were mined based on a combination of weighted gene co-expression network analysis (WGCNA), the least absolute shrinkage and selection operator (LASSO), support vector machine recursive feature elimination (SVM-RFE), and random forest (RF) algorithms. A diagnostic nomogram model for OA prediction was developed based on the hub genes. Receiver operating characteristic curves (ROC) were performed to confirm the abnormal expression of hub genes in the experimemtal and validation datasets. qRT-PCR using patients' samples were conducted as well. In addition, the infiltration level of 28 immune cells in the expression profile and their relationship with hub genes were analyzed using single-sample GSEA (ssGSEA). RESULTS 4 hub genes (ZBTB16, TNFSF11, SCRG1 and KDELR3) were obtained by WGCNA, lasso, SVM-RFE, RF algorithms as potential biomarkers for OA. The immune infiltration analyses revealed that hub genes were most correlated with regulatory T cell and natural killer cell. CONCLUSION A machine learning model to diagnose OA based on ZBTB16, TNFSF11, SCRG1 and KDELR3 using synovial tissue was constructed, providing theoretical foundation and guideline for diagnostic and treatment targets in OA.
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Affiliation(s)
- Ziyi Chen
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenjuan Wang
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yuwen Zhang
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Xiao'ao Xue
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yinghui Hua
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai, China.
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Cai Q, He B, Tu G, Peng W, Shi S, Qian B, Liang Q, Peng S, Tao Y, Wang X. Whole-genome DNA methylation and DNA methylation-based biomarkers in lung squamous cell carcinoma. iScience 2023; 26:107013. [PMID: 37389184 PMCID: PMC10300376 DOI: 10.1016/j.isci.2023.107013] [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: 09/14/2022] [Revised: 03/11/2023] [Accepted: 05/29/2023] [Indexed: 07/01/2023] Open
Abstract
Exploring early detection methods through comprehensive evaluation of DNA methylation for lung squamous cell carcinoma (LUSC) patients is of great significance. By using different machine learning algorithms for feature selection and model construction based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, five methylation biomarkers in LUSC (along with mapped genes) were identified including cg14823851 (TBX4), cg02772121 (TRIM15), cg10424681 (C6orf201), cg12910906 (ARHGEF4), and cg20181079 (OR4D11), achieving extremely high sensitivity and specificity in distinguishing LUSC from normal samples in independent cohorts. Pyrosequencing assay verified DNA methylation levels, meanwhile qRT-PCR and immunohistochemistry results presented their accordant methylation-related gene expression statuses in paired LUSC and normal lung tissues. The five methylation-based biomarkers proposed in this study have great potential for the diagnosis of LUSC and could guide studies in methylation-regulated tumor development and progression.
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Affiliation(s)
- Qidong Cai
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Boxue He
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Guangxu Tu
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Weilin Peng
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Shuai Shi
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Banglun Qian
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Qingchun Liang
- Department of Pathology, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Shaoliang Peng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, China
- School of Computer Science, National University of Defense Technology, Changsha 410073, China
- Peng Cheng Lab, Shenzhen 518000, China
| | - Yongguang Tao
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, Hunan 410078, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, Hunan 410078, China
| | - Xiang Wang
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, Second Xiangya Hospital, Central South University, Changsha 410011, China
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Kiełbowski K, Herian M, Bakinowska E, Banach B, Sroczyński T, Pawlik A. The Role of Genetics and Epigenetic Regulation in the Pathogenesis of Osteoarthritis. Int J Mol Sci 2023; 24:11655. [PMID: 37511413 PMCID: PMC10381003 DOI: 10.3390/ijms241411655] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Osteoarthritis (OA) is progressive disease characterised by cartilage degradation, subchondral bone remodelling and inflammation of the synovium. The disease is associated with obesity, mechanical load and age. However, multiple pro-inflammatory immune mediators regulate the expression of metalloproteinases, which take part in cartilage degradation. Furthermore, genetic factors also contribute to OA susceptibility. Recent studies have highlighted that epigenetic mechanisms may regulate the expression of OA-associated genes. This review aims to present the mechanisms of OA pathogenesis and summarise current evidence regarding the role of genetics and epigenetics in this process.
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Affiliation(s)
| | | | | | | | | | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.K.); (M.H.); (E.B.); (B.B.); (T.S.)
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Xiong B, Chen L, Huang Y, Lu G, Chen C, Nong J, Pan H. ZBTB16 eases lipopolysaccharide‑elicited inflammation, apoptosis and degradation of extracellular matrix in chondrocytes during osteoarthritis by suppressing GRK2 transcription. Exp Ther Med 2023; 25:276. [PMID: 37206562 PMCID: PMC10189728 DOI: 10.3892/etm.2023.11975] [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: 09/26/2022] [Accepted: 01/23/2023] [Indexed: 05/21/2023] Open
Abstract
Osteoarthritis (OA) is a chronic degenerative disease of the bone that is a major contributor of disability in the elderly population. Zinc finger and BTB domain-containing 16 (ZBTB16) is a transcription factor that has been previously revealed to be impaired in human OA tissues. The present study was designed to elaborate the potential impact of ZBTB16 on OA and to possibly assess any latent regulatory mechanism. ZBTB16 expression in human OA tissues was examined using the Gene Expression Series (GSE) database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169077) whereas ZBTB16 expression in chondrocytes was examined using reverse transcription-quantitative PCR (RT-qPCR) and western blotting. Cell viability was examined using a Cell Counting Kit-8 assay. A TUNEL assay and western blotting were used to assess cell apoptosis and apoptosis-related markers, including Bcl-2, Bax and cleaved caspase-3. The levels and expression of inflammatory factors, including TNF-α, IL-1β and IL-6, were determined by ELISA and western blotting. RT-qPCR and western blotting were also used to analyze the expression levels of extracellular matrix (ECM)-degrading enzymes, including MMP-13, a disintegrin-like and metalloproteinase with thrombospondin type-1 motifs-5, aggrecan and collagen type II α1. After the potential binding of ZBTB16 with the G protein coupled receptor kinase type 2 (GRK2) promoter was predicted using the Cistrome DB database, GRK2 expression was confirmed by RT-qPCR and western blotting. Chromatin immunoprecipitation and luciferase reporter assays were then used to determine the potential interaction between ZBTB16 and the GRK2 promoter. Following GRK2 overexpression in ZBTB16-overexpressing chondrocytes by co-transfection of GRK2 and ZBTB16 overexpression plasmids, the aforementioned functional experiments were performed again. ZBTB16 expression was found to be reduced in human OA tissues compared with in normal cartilage tissues and lipopolysaccharide (LPS)-stimulated chondrocytes. ZBTB16 overexpression increased cell viability whilst decreasing apoptosis, inflammation and ECM degradation by LPS-treated chondrocytes. In addition, GRK2 expression was found to be increased in LPS-stimulated chondrocytes. ZBTB16 successfully bound to the GRK2 promoter, which negatively modulated GRK2 expression. GRK2 upregulation reversed the effects of ZBTB16 overexpression on the viability, apoptosis, inflammation and ECM degradation by LPS-challenged chondrocytes. In conclusion, these data suggest that ZBTB16 may inhibit the development of OA through the transcriptional inactivation of GRK2.
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Affiliation(s)
- Bo Xiong
- Department of Orthopaedics and Traumatology, First Affiliated Hospital of The Guangxi University of Chinese Medicine, Nanning, Guangxi 530000, P.R. China
| | - Lihua Chen
- Department of Orthopaedics and Traumatology, First Affiliated Hospital of The Guangxi University of Chinese Medicine, Nanning, Guangxi 530000, P.R. China
| | - Yue Huang
- Department of Orthopaedics and Traumatology, First Affiliated Hospital of The Guangxi University of Chinese Medicine, Nanning, Guangxi 530000, P.R. China
| | - Guanyu Lu
- Department of Orthopaedics and Traumatology, First Affiliated Hospital of The Guangxi University of Chinese Medicine, Nanning, Guangxi 530000, P.R. China
| | - Cai Chen
- Department of Orthopaedics and Traumatology, First Affiliated Hospital of The Guangxi University of Chinese Medicine, Nanning, Guangxi 530000, P.R. China
| | - Jiao Nong
- Teaching Department, First Affiliated Hospital of The Guangxi University of Chinese Medicine, Nanning, Guangxi 530000, P.R. China
| | - Haida Pan
- Department of Orthopaedics and Traumatology, Yongjia County Traditional Chinese Medicine Hospital, Wenzhou, Zhejiang 325100, P.R. China
- Correspondence to: Dr Haida Pan, Department of Orthopaedics and Traumatology, Yongjia County Traditional Chinese Medicine Hospital, 6 Park Road, Jiangbei Street, Yongjia, Wenzhou, Zhejiang 325100, P.R. China
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Zhou J, Xiao L, Huang R, Song F, Li L, Li P, Fang Y, Lu W, Lv C, Quan M, Zhang D, Du Q. Local diversity of drought resistance and resilience in Populus tomentosa correlates with the variation of DNA methylation. PLANT, CELL & ENVIRONMENT 2023; 46:479-497. [PMID: 36385613 DOI: 10.1111/pce.14490] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Little information is known about DNA methylation variation in shaping environment-specific drought resistance and resilience for tree adaptation. In this study, we leveraged RNA sequencing and whole-genome bisulfite sequencing data to dissect the distinction of epigenetic regulation under drought stress and rewater condition of Populus tomentosa accessions from three geographical regions. We demonstrated low resistance and high resilience for accessions from South. Non-CG methylation levels in promoter regions of Southern accessions were lower than accessions from higher latitudes and negatively regulated gene expression. CHH context methylation was more sensitive to drought stress, and the geographical-specific differentially methylated regions were scarcely changed by environmental fluctuation. We identified 60 conserved hub genes within the co-expression networks that correlate with photosynthetic and stomatal morphological traits. Epigenome-wide association studies and genome-wide association studies of these 60 hub genes revealed the interdependency between genetic and epigenetic variation in GATA9 and LECRK-VIII.2, which was associated with stomatal morphology and chlorophyll content. The natural epigenetic variation in GATA9 was also faithfully transmitted to progenies in two family-based F1 populations. This study indicates a functional relationship of DNA methylation diversity with drought resistance and resilience which offers new insights into plants' local adaptation to a stressful environment.
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Affiliation(s)
- Jiaxuan Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Liang Xiao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Rui Huang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Fangyuan Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Lianzheng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Peng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Yuanyuan Fang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Wenjie Lu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Chenfei Lv
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Mingyang Quan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Deqiang Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Qingzhang Du
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
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10
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Lafont JE, Moustaghfir S, Durand AL, Mallein-Gerin F. The epigenetic players and the chromatin marks involved in the articular cartilage during osteoarthritis. Front Physiol 2023; 14:1070241. [PMID: 36733912 PMCID: PMC9887161 DOI: 10.3389/fphys.2023.1070241] [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: 10/14/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Epigenetics defines the modifications of the genome that do not involve a change in the nucleotide sequence of DNA. These modifications constitute a mechanism of gene regulation poorly explored in the context of cartilage physiology. They are now intensively studied by the scientific community working on articular cartilage and its related pathology such as osteoarthritis. Indeed, epigenetic regulations can control the expression of crucial gene in the chondrocytes, the only resident cells of cartilage. Some epigenetic changes are considered as a possible cause of the abnormal gene expression and the subsequent alteration of the chondrocyte phenotype (hypertrophy, proliferation, senescence…) as observed in osteoarthritic cartilage. Osteoarthritis is a joint pathology, which results in impaired extracellular matrix homeostasis and leads ultimately to the progressive destruction of cartilage. To date, there is no pharmacological treatment and the exact causes have yet to be defined. Given that the epigenetic modifying enzymes can be controlled by pharmacological inhibitors, it is thus crucial to describe the epigenetic marks that enable the normal expression of extracellular matrix encoding genes, and those associated with the abnormal gene expression such as degradative enzyme or inflammatory cytokines encoding genes. In this review, only the DNA methylation and histone modifications will be detailed with regard to normal and osteoarthritic cartilage. Although frequently referred as epigenetic mechanisms, the regulatory mechanisms involving microRNAs will not be discussed. Altogether, this review will show how this nascent field influences our understanding of the pathogenesis of OA in terms of diagnosis and how controlling the epigenetic marks can help defining epigenetic therapies.
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11
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Cao H, Fu Y, Zhang Z, Guo W. Unbiased transcriptome mapping and modeling identify candidate genes and compounds of osteoarthritis. Front Pharmacol 2022; 13:888533. [PMID: 36034872 PMCID: PMC9399521 DOI: 10.3389/fphar.2022.888533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/29/2022] [Indexed: 11/21/2022] Open
Abstract
Osteoarthritis (OA) is a chronic degenerative joint disease characterized by progressive cartilage loss, subchondral bone remodeling, and synovial inflammation. Given that the current therapies for advanced OA patients are limited, the understanding of mechanisms and novel therapies are urgently needed. In this study, we employed the weighted gene co-expression network (WGCNA) method and the connectivity map (CMap) database to identify the candidate target genes and potential compounds. Four groups of co-expressing genes were identified as the OA-related modules. The biological annotations of these modules indicated some critical hallmarks of OA and aging, such as mitochondrial dysfunctions and abnormal energy metabolism, and the signaling pathways, such as MAPK, TNF, and PI3K/Akt signaling pathways. Some genes, such as RELA and GADD45B, were predicted to extensively involve these critical pathways, indicating their potential functions in OA mechanisms. Moreover, we constructed the co-expressing networks of modules and identified the hub genes based on network topology. GADD45B, MAFF, and MYC were identified and validated as the hub genes. Finally, anisomycin and MG-262 were predicted to target these OA-related modules, which may be the potential drugs for OA therapy. In conclusion, this study identified the significant modules, signaling pathways, and hub genes relevant to OA and highlighted the potential clinical value of anisomycin and MG-262 as novel therapies in OA management.
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Affiliation(s)
- Hui Cao
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yifan Fu
- The First Clinical School, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhenzhen Zhang
- Department of Rehabilitation, Hankou Hospital, Wuhan, China
- *Correspondence: Zhenzhen Zhang, ; Weichun Guo,
| | - Weichun Guo
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Zhenzhen Zhang, ; Weichun Guo,
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12
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Li J, Yang X, Chu Q, Xie L, Ding Y, Xu X, Timko MP, Fan L. Multi-omics molecular biomarkers and database of osteoarthritis. Database (Oxford) 2022; 2022:6631109. [PMID: 35788653 PMCID: PMC9254640 DOI: 10.1093/database/baac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/15/2022] [Accepted: 06/28/2022] [Indexed: 12/05/2022]
Abstract
Osteoarthritis (OA) is the most common form of arthritis in the adult population and is a leading cause of disability. OA-related genetic loci may play an important role in clinical diagnosis and disease progression. With the rapid development of diverse technologies and omics methods, many OA-related public data sets have been accumulated. Here, we retrieved a diverse set of omics experimental results from 159 publications, including genome-wide association study, differentially expressed genes and differential methylation regions, and 2405 classified OA-related gene markers. Meanwhile, based on recent single-cell RNA-seq data from different joints, 5459 cell-type gene markers of joints were collected. The information has been integrated into an online database named OAomics and molecular biomarkers (OAOB). The database (http://ibi.zju.edu.cn/oaobdb/) provides a web server for OA marker genes, omics features and so on. To our knowledge, this is the first database of molecular biomarkers for OA.
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Affiliation(s)
- Jianhua Li
- Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, Zhejiang 310016, China
| | - Xiaotian Yang
- Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, Zhejiang 310016, China
| | - Qinjie Chu
- Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lingjuan Xie
- Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuwen Ding
- Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaoxu Xu
- Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Michael P Timko
- Department of Biology, University of Virginia, and Department of Public Health Sciences, UVA School of Medicine, Charlottesville, VA 22904, USA
| | - Longjiang Fan
- Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, Zhejiang 310016, China.,Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang 310058, China
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13
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Yang C, Dong Z, Ling Z, Chen Y. The crucial mechanism and therapeutic implication of RNA methylation in bone pathophysiology. Ageing Res Rev 2022; 79:101641. [PMID: 35569786 DOI: 10.1016/j.arr.2022.101641] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 04/19/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022]
Abstract
Methylation is the most common posttranscriptional modification in cellular RNAs, which has been reported to modulate the alteration of RNA structure for initiating relevant functions such as nuclear translocation and RNA degradation. Recent studies found that RNA methylation especially N6-methyladenosine (m6A) regulates the dynamic balance of bone matrix and forms a complicated network in bone metabolism. The modulation disorder of RNA methylation contributes to several pathological bone diseases including osteoporosis (OP), osteoarthritis (OA), rheumatoid arthritis (RA), and so on. In the review, we will discuss advanced technologies for detecting RNA methylation, summarize RNA methylation-related biological impacts on regulating bone homeostasis and pathological bone diseases. In addition, we focus on the promising roles of RNA methylation in early diagnosis and therapeutic implications for bone-related diseases. Then, we aim to establish a theoretical basis for further investigation in this meaningful field.
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14
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Izda V, Martin J, Sturdy C, Jeffries MA. DNA methylation and noncoding RNA in OA: Recent findings and methodological advances. OSTEOARTHRITIS AND CARTILAGE OPEN 2022; 3. [PMID: 35360044 PMCID: PMC8966627 DOI: 10.1016/j.ocarto.2021.100208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Introduction: Osteoarthritis (OA) is a chronic musculoskeletal disease characterized by progressive loss of joint function. Historically, it has been characterized as a disease caused by mechanical trauma, so-called ‘wear and tear’. Over the past two decades, it has come to be understood as a complex systemic disorder involving gene-environmental interactions. Epigenetic changes have been increasingly implicated. Recent improvements in microarray and next-generation sequencing (NGS) technologies have allowed for ever more complex evaluations of epigenetic aberrations associated with the development and progression of OA. Methods: A systematic review was conducted in the Pubmed database. We curated studies that presented the results of DNA methylation and noncoding RNA research in human OA and OA animal models since 1985. Results: Herein, we discuss recent findings and methodological advancements in OA epigenetics, including a discussion of DNA methylation, including microarray and NGS studies, and noncoding RNAs. Beyond cartilage, we also highlight studies in subchondral bone and peripheral blood mononuclear cells, which highlight widespread and potentially clinically important alterations in epigenetic patterns seen in OA patients. Finally, we discuss epigenetic editing approaches in the context of OA. Conclusions: Although a substantial body of literature has already been published in OA, much is still unknown. Future OA epigenetics studies will no doubt continue to broaden our understanding of underlying pathophysiology and perhaps offer novel diagnostics and/or treatments for human OA.
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Affiliation(s)
- Vladislav Izda
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, OK, USA
| | - Jake Martin
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, OK, USA
| | - Cassandra Sturdy
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, OK, USA
| | - Matlock A. Jeffries
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, OK, USA
- University of Oklahoma Health Sciences Center, Department of Internal Medicine, Division of Rheumatology, Immunology, And Allergy, Oklahoma City, OK, USA
- Corresponding author. Oklahoma Medical Research Foundation, 825 NE 13th Street, Laboratory MC400, Oklahoma City, OK, 73104, USA.
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15
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Kenney HM, Wu CL, Loiselle AE, Xing L, Ritchlin CT, Schwarz EM. Single-cell transcriptomics of popliteal lymphatic vessels and peripheral veins reveals altered lymphatic muscle and immune cell populations in the TNF-Tg arthritis model. Arthritis Res Ther 2022; 24:64. [PMID: 35255954 PMCID: PMC8900348 DOI: 10.1186/s13075-022-02730-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/21/2022] [Indexed: 11/23/2022] Open
Abstract
Background Lymphatic dysfunction exists in tumor necrosis factor transgenic (TNF-Tg) mice and rheumatoid arthritis (RA) patients. While joint-draining TNF-Tg popliteal lymphatic vessels (PLVs) have deficits in contractility during end-stage arthritis, the nature of lymphatic muscle cells (LMCs) and their TNF-altered transcriptome remain unknown. Thus, we performed single-cell RNA-sequencing (scRNAseq) on TNF-Tg LMCs in PLVs efferent to inflamed joints versus wild-type (WT) controls. Methods Single-cell suspensions of PLVs were sorted for smooth muscle cells (SMCs), which was validated by Cspg4-Cre;tdTomato reporter gene expression. Single-cell RNA-seq was performed on a 10x Genomics platform and analyzed using the Seurat R package. Uniform Manifold Approximation and Projections (UMAPs) and Ingenuity Pathway Analysis software were used to assess cell clusters and functional genomics in WT vs. TNF-Tg populations. Results Fluorescent imaging of Cspg4-Cre;tdTomato vessels demonstrated dim PLVs and strong reporter gene expression in the adjacent superficial saphenous vein, which was corroborated by flow cytometry of LMCs and vascular smooth muscle cells (VSMCs) from these vessels. Due to their unique morphology, these populations could also be readily detected by scatter analysis of cells from non-fluorescent mice. Bioinformatics analysis of flow sorted WT and TNF-Tg cells identified 20 unique cell clusters that together were 22.4% LMCs, 15.0% VSMCs, and 62.6% non-muscle cells of 8879 total cells. LMCs and M2-macrophages were decreased, while inflammatory monocytes were increased in TNF-Tg lower limb vasculature. SMC populations were defined by Cald1, Tpm1, and Pdgfrb expression and were enriched in myofibroblast-like gene expression. TNF-Tg LMCs exhibited enhanced functional genomics associated with cell death, phagocyte recruitment, and joint inflammation. Among the most prominent TNF-induced genes in SMCs were Mmp3, Cxcl12, and Ccl19, and the most downregulated genes were Zbtb16, Galnt15, and Apod. Conclusions Single-cell RNA-seq can be used to investigate functional genomics of lower limb vasculature in mice. Our findings confirm the inflammatory transcriptome of TNF-Tg vessels and altered gene expression in SMC populations. This study further supports a potential role of mesenchymal stromal cells in inflammatory-erosive arthritis pathogenesis, and warrants future studies to define the effects of this TNF-altered transcriptome on PLV function and joint homeostasis. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-022-02730-z.
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Affiliation(s)
- H Mark Kenney
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Ave, Box 665, Rochester, NY, 14642, USA.,Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Chia-Lung Wu
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Ave, Box 665, Rochester, NY, 14642, USA.,Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY, USA
| | - Alayna E Loiselle
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Ave, Box 665, Rochester, NY, 14642, USA.,Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA.,Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY, USA
| | - Lianping Xing
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Ave, Box 665, Rochester, NY, 14642, USA.,Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Christopher T Ritchlin
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Ave, Box 665, Rochester, NY, 14642, USA.,Department of Medicine, Division of Allergy, Immunology, Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Edward M Schwarz
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Ave, Box 665, Rochester, NY, 14642, USA. .,Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA. .,Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY, USA. .,Department of Medicine, Division of Allergy, Immunology, Rheumatology, University of Rochester Medical Center, Rochester, NY, USA.
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16
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Nuottamo ME, Häppölä P, Artto V, Hautakangas H, Pirinen M, Hiekkalinna T, Ellonen P, Lepistö M, Hämäläinen E, Siren A, Lehesjoki AE, Kallela M, Palotie A, Kaunisto MA, Wessman M. NCOR2 is a novel candidate gene for migraine-epilepsy phenotype. Cephalalgia 2022; 42:631-644. [PMID: 35166138 DOI: 10.1177/03331024211068065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
HYPOTHESIS To identify genetic factors predisposing to migraine-epilepsy phenotype utilizing a multi-generational family with known linkage to chr12q24.2-q24.3. METHODS We used single nucleotide polymorphism (SNP) genotyping and next-generation sequencing technologies to perform linkage, haplotype, and variant analyses in an extended Finnish migraine-epilepsy family (n = 120). In addition, we used a large genome-wide association study (GWAS) dataset of migraine and two biobank studies, UK Biobank and FinnGen, to test whether variants within the susceptibility region associate with migraine or epilepsy related phenotypes in a population setting. RESULTS The family showed the highest evidence of linkage (LOD 3.42) between rs7966411 and epilepsy. The haplotype shared among 12 out of 13 epilepsy patients in the family covers almost the entire NCOR2 and co-localizes with one of the risk loci of the recent GWAS on migraine. The haplotype harbors nine low-frequency variants with potential regulatory functions. Three of them, in addition to two common variants, show nominal associations with neurological disorders in either UK Biobank or FinnGen. CONCLUSION We provide several independent lines of evidence supporting association between migraine-epilepsy phenotype and NCOR2. Our study suggests that NCOR2 may have a role in both migraine and epilepsy and thus would provide evidence for shared pathophysiology underlying these two diseases.
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Affiliation(s)
- Marjo Eveliina Nuottamo
- Folkhälsan Research Center, Helsinki, Finland.,Institute for Molecular Medicine Finland FIMM, HiLIFE, 3835University of Helsinki, University of Helsinki, Helsinki, Finland
| | - Paavo Häppölä
- Institute for Molecular Medicine Finland FIMM, HiLIFE, 3835University of Helsinki, University of Helsinki, Helsinki, Finland
| | - Ville Artto
- Department of Neurology, Helsinki University Hospital and University of Helsinki, Finland
| | - Heidi Hautakangas
- Institute for Molecular Medicine Finland FIMM, HiLIFE, 3835University of Helsinki, University of Helsinki, Helsinki, Finland
| | - Matti Pirinen
- Institute for Molecular Medicine Finland FIMM, HiLIFE, 3835University of Helsinki, University of Helsinki, Helsinki, Finland.,Department of Mathematics and Statistics, 3835University of Helsinki, University of Helsinki, Helsinki, Finland.,Department of Public Health, 3835University of Helsinki, University of Helsinki, Helsinki, Finland
| | - Tero Hiekkalinna
- Genomics and Biobank Unit, Department of Public Health Solutions, 3837National Institute for Health and Welfare, National Institute for Health and Welfare, Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland FIMM, HiLIFE, 3835University of Helsinki, University of Helsinki, Helsinki, Finland
| | - Maija Lepistö
- Institute for Molecular Medicine Finland FIMM, HiLIFE, 3835University of Helsinki, University of Helsinki, Helsinki, Finland
| | - Eija Hämäläinen
- Institute for Molecular Medicine Finland FIMM, HiLIFE, 3835University of Helsinki, University of Helsinki, Helsinki, Finland
| | | | - Auli Siren
- Child Neurology Outpatient Clinic, Kanta-Häme Central Hospital, Hämeenlinna, Finland
| | - Anna-Elina Lehesjoki
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, 3835University of Helsinki, University of Helsinki, Helsinki, Finland
| | - Mikko Kallela
- Department of Neurology, Helsinki University Hospital and University of Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland FIMM, HiLIFE, 3835University of Helsinki, University of Helsinki, Helsinki, Finland.,Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mari Anneli Kaunisto
- Institute for Molecular Medicine Finland FIMM, HiLIFE, 3835University of Helsinki, University of Helsinki, Helsinki, Finland
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17
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BMP-2 and asporin expression regulate 5-aza-dC-mediated osteoblast/cementoblast differentiation of periodontal dental ligament mesenchymal progenitor cells. Differentiation 2022; 124:17-27. [DOI: 10.1016/j.diff.2022.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 12/27/2022]
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18
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Vesela B, Zapletalova M, Svandova E, Ramesova A, Doubek J, Lesot H, Matalova E. General Caspase Inhibition in Primary Chondrogenic Cultures Impacts Their Transcription Profile Including Osteoarthritis-Related Factors. Cartilage 2021; 13:1144S-1154S. [PMID: 34496641 PMCID: PMC8804802 DOI: 10.1177/19476035211044823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE The knowledge about functions of caspases, usually associated with cell death and inflammation, keeps expanding also regarding cartilage. Active caspases are present in the growth plate, and caspase inhibition in limb-derived chondroblasts altered the expression of osteogenesis-related genes. Caspase inhibitors were reported to reduce the severity of cartilage lesions in osteoarthritis (OA), and caspase-3 might represent a promising biomarker for OA prognosis. The objective of this investigation was to decipher the transcriptomic regulation of caspase inhibition in chondrogenic cells. DESIGN Limb-derived chondroblasts were cultured in the presence of 2 different inhibitors: Z-VAD-FMK (FMK) and Q-VD-OPH (OPH). A whole transcriptome RNA sequencing was performed as the key analysis. RESULTS The analysis revealed a statistically significant increase in the expression of 252 genes in the FMK samples and 163 genes in the OPH samples compared with controls. Conversely, there was a significant decrease in the expression of 290 genes in the FMK group and 188 in the OPH group. Among the top up- and downregulated genes (more than 10 times changed), almost half of them were associated with OA. Both inhibitors displayed the highest upregulation of the inflammatory chemokine Ccl5, the most downregulated gene was the one for mannose receptors Mrc1. CONCLUSIONS The obtained datasets pointed to a significant impact of caspase inhibition on the expression of several chondro-/osteogenesis-related markers in an in vitro model of endochondral ossification. Notably, the list of these genes included some encoding for factors associated with cartilage/bone pathologies such as OA.
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Affiliation(s)
- Barbora Vesela
- Department of Physiology, University of
Veterinary Sciences, Brno, Czech Republic,Institute of Animal Physiology and
Genetics, Czech Academy of Sciences, Brno, Czech Republic,Barbora Vesela, Institute of Animal
Physiology and Genetics, Czech Academy of Sciences, v.v.i., Veveri 97, Brno 602
00, Czech Republic.
| | - Martina Zapletalova
- Institute of Animal Physiology and
Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Eva Svandova
- Department of Physiology, University of
Veterinary Sciences, Brno, Czech Republic,Institute of Animal Physiology and
Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Alice Ramesova
- Department of Physiology, University of
Veterinary Sciences, Brno, Czech Republic
| | - Jaroslav Doubek
- Department of Physiology, University of
Veterinary Sciences, Brno, Czech Republic
| | - Hervé Lesot
- Institute of Animal Physiology and
Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Eva Matalova
- Department of Physiology, University of
Veterinary Sciences, Brno, Czech Republic,Institute of Animal Physiology and
Genetics, Czech Academy of Sciences, Brno, Czech Republic
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19
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Candler T, Kessler N, Gunasekara C, Ward K, James P, Laritsky E, Baker M, Dyer R, Elango R, Jeffries D, Waterland R, Moore S, Ludgate M, Prentice A, Silver M. DNA methylation at a nutritionally sensitive region of the PAX8 gene is associated with thyroid volume and function in Gambian children. SCIENCE ADVANCES 2021; 7:eabj1561. [PMID: 34739318 PMCID: PMC8570597 DOI: 10.1126/sciadv.abj1561] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/16/2021] [Indexed: 05/13/2023]
Abstract
PAX8 is a key thyroid transcription factor implicated in thyroid gland differentiation and function, and PAX8 gene methylation is reported to be sensitive to the periconceptional environment. Using a novel recall-by-epigenotype study in Gambian children, we found that PAX8 hypomethylation at age 2 years is associated with a 21% increase in thyroid volume and an increase in free thyroxine (T4) at 5 to 8 years, the latter equivalent to 8.4% of the normal range. Free T4 was associated with a decrease in DXA-derived body fat and bone mineral density. Furthermore, offspring PAX8 methylation was associated with periconceptional maternal nutrition, and methylation variability was influenced by genotype, suggesting that sensitivity to environmental exposures may be under partial genetic control. Together, our results demonstrate a possible link between early environment, PAX8 gene methylation and thyroid gland development and function, with potential implications for early embryonic programming of thyroid-related health and disease.
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Affiliation(s)
- Toby Candler
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Noah Kessler
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Chathura Gunasekara
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Kate Ward
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
- MRC Lifecourse Epidemiology, University of Southampton, Southampton, UK
| | - Philip James
- Department of Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Eleonora Laritsky
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Maria Baker
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Roger Dyer
- British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Rajavel Elango
- British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - David Jeffries
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Robert Waterland
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sophie Moore
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
- Department of Women and Children’s Health, King’s College London, London, UK
| | - Marian Ludgate
- Thyroid Research Group, School of Medicine, Cardiff University, Cardiff, UK
| | - Andrew Prentice
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Matt Silver
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
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20
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Housman G, Quillen EE, Stone AC. An evolutionary perspective of DNA methylation patterns in skeletal tissues using a baboon model of osteoarthritis. J Orthop Res 2021; 39:2260-2269. [PMID: 33325553 PMCID: PMC8206284 DOI: 10.1002/jor.24957] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/24/2020] [Accepted: 12/14/2020] [Indexed: 02/04/2023]
Abstract
Epigenetic factors, such as DNA methylation, play an influential role in the development of the degenerative joint disease osteoarthritis (OA). These molecular mechanisms have been heavily studied in humans, and although OA affects several other animals in addition to humans, few efforts have taken an evolutionary perspective. This study explores the evolution of OA epigenetics by assessing the relationship between DNA methylation variation and knee OA development in baboons (Papio spp.) and by comparing these findings to human OA epigenetic associations. Genome-wide DNA methylation patterns were identified in bone and cartilage of the right distal femora from 56 pedigreed, adult baboons (28 with and 28 without knee OA) using the Illumina Infinium MethylationEPIC BeadChip. Several significantly differentially methylated positions (DMPs) and regions were found between tissue types. Substantial OA-related differential methylation was also identified in cartilage, but not in bone, suggesting that cartilage epigenetics may be more influential in OA than bone epigenetics. Additionally, some genes containing OA-related DMPs overlap with and display methylation patterns similar to those previously identified in human OA, revealing a mixture of evolutionarily conserved and divergent OA-related methylation patterns in primates. Overall, these findings reinforce the current etiological perspectives of OA and enhance our evolutionary understanding of epigenetic mechanisms associated with OA. This study further establishes baboons as a valuable nonhuman primate model of OA, and continued investigations in baboons will help to disentangle the molecular mechanisms contributing to OA and their evolutionary histories.
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Affiliation(s)
- Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,Corresponding author: Genevieve Housman, Section of Genetic Medicine, University of Chicago, 920 East 58th Street, CLSC 317, Chicago, IL 60637, USA. Phone: 574-206-6564. Fax: 773-834-8470.
| | - Ellen E. Quillen
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Anne C. Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
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21
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Lee KI, Gamini R, Olmer M, Ikuta Y, Hasei J, Baek J, Alvarez-Garcia O, Grogan SP, D'Lima DD, Asahara H, Su AI, Lotz MK. Mohawk is a transcription factor that promotes meniscus cell phenotype and tissue repair and reduces osteoarthritis severity. Sci Transl Med 2021; 12:12/567/eaan7967. [PMID: 33115953 DOI: 10.1126/scitranslmed.aan7967] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 02/06/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022]
Abstract
Meniscus tears are common knee injuries and a major osteoarthritis (OA) risk factor. Knowledge gaps that limit the development of therapies for meniscus injury and degeneration concern transcription factors that control the meniscus cell phenotype. Analysis of RNA sequencing data from 37 human tissues in the Genotype-Tissue Expression database and RNA sequencing data from meniscus and articular cartilage showed that transcription factor Mohawk (MKX) is highly enriched in meniscus. In human meniscus cells, MKX regulates the expression of meniscus marker genes, OA-related genes, and other transcription factors, including Scleraxis (SCX), SRY Box 5 (SOX5), and Runt domain-related transcription factor 2 (RUNX2). In mesenchymal stem cells (MSCs), the combination of adenoviral MKX (Ad-MKX) and transforming growth factor-β3 (TGF-β3) induced a meniscus cell phenotype. When Ad-MKX-transduced MSCs were seeded on TGF-β3-conjugated decellularized meniscus scaffold (DMS) and inserted into experimental tears in meniscus explants, they increased glycosaminoglycan content, extracellular matrix interconnectivity, cell infiltration into the DMS, and improved biomechanical properties. Ad-MKX injection into mouse knee joints with experimental OA induced by surgical destabilization of the meniscus suppressed meniscus and cartilage damage, reducing OA severity. Ad-MKX injection into human OA meniscus tissue explants corrected pathogenic gene expression. These results identify MKX as a previously unidentified key transcription factor that regulates the meniscus cell phenotype. The combination of Ad-MKX with TGF-β3 is effective for differentiation of MSCs to a meniscus cell phenotype and useful for meniscus repair. MKX is a promising therapeutic target for meniscus tissue engineering, repair, and prevention of OA.
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Affiliation(s)
- Kwang Il Lee
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Ramya Gamini
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Merissa Olmer
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Yasunari Ikuta
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Joe Hasei
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Jihye Baek
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA.,Shiley Center for Orthopaedic Research and Education at Scripps Clinic, La Jolla, CA 92037, USA
| | | | - Shawn P Grogan
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA.,Shiley Center for Orthopaedic Research and Education at Scripps Clinic, La Jolla, CA 92037, USA
| | - Darryl D D'Lima
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA.,Shiley Center for Orthopaedic Research and Education at Scripps Clinic, La Jolla, CA 92037, USA
| | - Hiroshi Asahara
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Andrew I Su
- Department of Integrative, Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Martin K Lotz
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA.
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22
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Yi P, Xu X, Yao J, Qiu B. Effect of DNA methylation on gene transcription is associated with the distribution of methylation sites across the genome in osteoarthritis. Exp Ther Med 2021; 22:719. [PMID: 34007328 PMCID: PMC8120505 DOI: 10.3892/etm.2021.10151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
Genetics and epigenetics are important subjects in the field of osteoarthritis (OA) research. DNA methylation may affect gene transcription, but the specific mechanisms have remained to be fully elucidated. In the present study, the ChAMP methylation analysis package was used to identify differentially methylated genes (DMGs) from the dataset GSE63695 from the Gene Expression Omnibus (GEO) database. The distribution of differentially methylated sites (DMS) and the total array sites across the genome were analyzed by enrichment analysis. Subsequently, two mRNA expression profiling datasets, GSE114007 and GSE113825, were obtained from the GEO database and common differentially expressed genes (DEGs) were identified using the Limma package. Key genes were screened by analyzing the distribution of DMS across the genome consisting of DEGs and DMGs. A total of 1,662 and 1,986 DEGs were identified between OA and normal human cartilage from the GSE113825 and GSE114007 dataset, respectively. A further screening revealed 292 genes with common differences between the two datasets. A total of 574 DMS containing 394 DMGs were observed between OA and normal cartilage. Integrative analysis revealed a corresponding subset of 15 genes. Of these, 6 genes were verified by reverse transcription-quantitative PCR, confirming that the mRNA expression of 5 genes (MAP1B, FNDC1, ANLN, SCNN1A and STC2) in OA cartilage was consistent with the mRNA expression from the analysis of the datasets. Upon treatment with the DNA methylation inhibitor 5-aza-2'-deoxycytidine, the mRNA levels of FNDC1 and SCNN1A were decreased, and no significant alteration in the mRNA levels of MAP1B, ANLN, KCNN4 and STC2 was observed. The incidence of differential methylation varied in subregions of the genome and the effects on transcription were associated with the distribution of DEGs across the genome. The regulation of this appears more complex than initially postulated. Combining the data on epigenetic differences of OA with the genome or transcriptome data for analysis may improve the understanding of the pathophysiological processes of OA. FNDC1 and SCNN1A may potentially be valuable biomarkers for OA.
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Affiliation(s)
- Peng Yi
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Xiongfeng Xu
- Department of Emergency, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Jiawei Yao
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Bo Qiu
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
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23
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Wang G, Li Y, Yang G, Yang T, He L, Wang Y. Cathelicidin antimicrobial peptide (CAMP) gene promoter methylation induces chondrocyte apoptosis. Hum Genomics 2021; 15:24. [PMID: 33892795 PMCID: PMC8063489 DOI: 10.1186/s40246-021-00321-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/25/2021] [Indexed: 12/03/2022] Open
Abstract
Objective The occurrence of osteoarthritis is related to genetic and environmental factors. Among them, the change of chondrocyte gene expression pattern regulated by epigenetic modification is an important participant. This study analyzed the effect of CAMP gene methylation on the level of oxidative stress and inflammation of chondrocytes. Methods We analyzed the changes of the transcriptome in the articular cartilage tissue of osteoarthritis (OA) patients from the GSE117999 dataset. The GSE48422 dataset was used to analyze the changes in the methylation level of osteoarthritis cells. Cell Counting Kit-8 (CCK-8) and flow cytometry analysis of short hairpin RNA (shRNA) silencing CAMP gene and 5-μM 5-Aza-2’-Deoxycytidine (AZA) treatment on the proliferation and apoptosis of Human chondrocytes osteoarthritis (HC-OA) cells. The Dichloro-dihydro-fluorescein diacetate (DCFH-DA) assay was used to detect the level of reactive oxygen species (ROS), and the expression level of inflammatory factors was analyzed by Western Blot. Results The expression of CAMP in cartilage tissue of OA patients was upregulated, and the level of methylation was downregulated. CAMP was highly expressed in osteoarthritis articular cartilage cells. Silencing CAMP inhibited the proliferation of HC-OA cells and promoted their apoptosis. CAMP gene methylation inhibited ROS levels and tumor necrosis factor-α (TNF-α) expression levels in HC-OA cells, and promoted transforming growth factor beta (TGF-β) expression. CAMP gene methylation inhibited the proliferation of HC-OA cells and promoted their apoptosis. Conclusion CAMP gene promoter methylation inhibits ROS levels and inflammation and induces chondrocyte apoptosis.
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Affiliation(s)
- Guoliang Wang
- Department of Sports Medicine, First Affiliated Hospital of Kunming Medical University, Kunming, 650031, Yunnan, China
| | - Yanlin Li
- Department of Sports Medicine, First Affiliated Hospital of Kunming Medical University, Kunming, 650031, Yunnan, China
| | - Guang Yang
- Department of Sports Medicine, First Affiliated Hospital of Kunming Medical University, Kunming, 650031, Yunnan, China
| | - Tengyun Yang
- Department of Sports Medicine, First Affiliated Hospital of Kunming Medical University, Kunming, 650031, Yunnan, China
| | - Lu He
- Department of Sports Medicine, First Affiliated Hospital of Kunming Medical University, Kunming, 650031, Yunnan, China
| | - Yang Wang
- Department of Sports Medicine, First Affiliated Hospital of Kunming Medical University, Kunming, 650031, Yunnan, China.
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24
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Visconti VV, Cariati I, Fittipaldi S, Iundusi R, Gasbarra E, Tarantino U, Botta A. DNA Methylation Signatures of Bone Metabolism in Osteoporosis and Osteoarthritis Aging-Related Diseases: An Updated Review. Int J Mol Sci 2021; 22:ijms22084244. [PMID: 33921902 PMCID: PMC8072687 DOI: 10.3390/ijms22084244] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 01/03/2023] Open
Abstract
DNA methylation is one of the most studied epigenetic mechanisms that play a pivotal role in regulating gene expression. The epigenetic component is strongly involved in aging-bone diseases, such as osteoporosis and osteoarthritis. Both are complex multi-factorial late-onset disorders that represent a globally widespread health problem, highlighting a crucial point of investigations in many scientific studies. In recent years, new findings on the role of DNA methylation in the pathogenesis of aging-bone diseases have emerged. The aim of this systematic review is to update knowledge in the field of DNA methylation associated with osteoporosis and osteoarthritis, focusing on the specific tissues involved in both pathological conditions.
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Affiliation(s)
- Virginia Veronica Visconti
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (I.C.); (S.F.); (A.B.)
- Department of Orthopaedics and Traumatology, “Policlinico Tor Vergata” Foundation, Viale Oxford 81, 00133 Rome, Italy; (R.I.); (E.G.)
| | - Ida Cariati
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (I.C.); (S.F.); (A.B.)
- Department of Orthopaedics and Traumatology, “Policlinico Tor Vergata” Foundation, Viale Oxford 81, 00133 Rome, Italy; (R.I.); (E.G.)
| | - Simona Fittipaldi
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (I.C.); (S.F.); (A.B.)
| | - Riccardo Iundusi
- Department of Orthopaedics and Traumatology, “Policlinico Tor Vergata” Foundation, Viale Oxford 81, 00133 Rome, Italy; (R.I.); (E.G.)
| | - Elena Gasbarra
- Department of Orthopaedics and Traumatology, “Policlinico Tor Vergata” Foundation, Viale Oxford 81, 00133 Rome, Italy; (R.I.); (E.G.)
| | - Umberto Tarantino
- Department of Orthopaedics and Traumatology, “Policlinico Tor Vergata” Foundation, Viale Oxford 81, 00133 Rome, Italy; (R.I.); (E.G.)
- Department of Clinical Science and Translational Medicine, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
- Correspondence:
| | - Annalisa Botta
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy; (V.V.V.); (I.C.); (S.F.); (A.B.)
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25
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Zhang X, He J, Wang W. Progress in the use of mesenchymal stromal cells for osteoarthritis treatment. Cytotherapy 2021; 23:459-470. [PMID: 33736933 DOI: 10.1016/j.jcyt.2021.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/20/2020] [Accepted: 01/29/2021] [Indexed: 12/26/2022]
Abstract
LITERATURE REVIEW OF MSCS IN THE TREATMENT OF OSTEOARTHRITIS IN THE PAST FIVE YEARS: Osteoarthritis (OA) is one of the most common chronic joint diseases, with prominent symptoms caused by many factors. However, current medical interventions for OA have resulted in poor clinical outcomes, demonstrating that there are huge unmet medical needs in this area. Cell therapy has opened new avenues of OA treatment. Different sources of mesenchymal stromal cells (MSCs) may have different phenotypes and cellular functions. Pre-clinical and clinical studies have demonstrated the feasibility, safety and efficacy of MSC therapy. Mitogen-activated protein kinase, Wnt and Notch signaling pathways are involved in the chondrogenesis of MSC-mediated treatments. MSCs may also exert effective immunoregulatory and paracrine effects to stimulate tissue repair. Therapy with extracellular vesicles containing cytokines, which are secreted by MSCs, might be a potential treatment for OA.
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Affiliation(s)
- Xiaotian Zhang
- Department of Orthopedics, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jiyin He
- Department of Orthopedics, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Wen Wang
- Clinical Development, IASO Biotherapeutics Co., Ltd., Shanghai, China.
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26
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Long non-coding RNA CIR inhibits chondrogenic differentiation of mesenchymal stem cells by epigenetically suppressing ATOH8 via methyltransferase EZH2. Mol Med 2021; 27:12. [PMID: 33546582 PMCID: PMC7866678 DOI: 10.1186/s10020-021-00272-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/13/2021] [Indexed: 12/19/2022] Open
Abstract
Background Osteoarthritis (OA) is the most common articular disorder, leading to joint malfunction and disability. Although the incidence of OA is increasing globally, the treatment of OA is very limited. LncRNA CIR has been implicated in OA through unclear mechanisms. Here, we investigated the role of lncRNA CIR in chondrogenic differentiation. Methods Human umbilical-cord-derived mesenchymal stem cells (hUC-MSCs) were obtained from human umbilical cords. Flow cytometry was used to analyze the surface markers of hUC-MSCs. Various culture conditions and corresponding staining assays were employed to assess the differentiation abilities of hUC-MSC. qRT-PCR, western blot, and immunostaining were used to measure expression levels of related genes and proteins such as lncRNA CIR, ATOH8, EZH2, and H3K27me3. RNA immunoprecipitation assay, biotin pull-down, and chromatin immunoprecipitaion assay were performed to analyze the interactions of lncRNA CIR, EZH2, H3K27me3 and ATOH8 promoter. Results hUC-MSCs exhibited MSCs features and could differentiate into chondrocytes under specific conditions. LncRNA CIR was downregulated while ATOH8 was upregulated during the chondrogenic differentiation of hUC-MSCs. Knockdown lncRNA CIR or overexpression of ATOH8 promoted chondrogenic differentiation. Further, lncRNA CIR bound to EZH2 and repressed ATOH8 expression via EZH2-mediated H3K27me3, which promotes the methylation of ATOH8. Inhibition of ATOH8 reversed the effects of knockdown lncRNA CIR on chondrogenic differentiation. Conclusion LncRNA CIR suppresses chondrogenic differentiation of hUC-MSCs. Mechanistically, lncRNA CIR could inhibit ATOH8 expression that functions to promote chondrogenic differentiation through EZH2-mediated epigenetic modifications.
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27
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Yu S, Ruan X, Liu X, Zhang F, Wang D, Liu Y, Yang C, Shao L, Liu Q, Zhu L, Lin Y, Xue Y. HNRNPD interacts with ZHX2 regulating the vasculogenic mimicry formation of glioma cells via linc00707/miR-651-3p/SP2 axis. Cell Death Dis 2021; 12:153. [PMID: 33542193 PMCID: PMC7862279 DOI: 10.1038/s41419-021-03432-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/15/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022]
Abstract
Studies have found that RNA-binding proteins (RBPs) are dysfunctional and play a significant regulatory role in the development of glioma. Based on The Cancer Genome Atlas database and the previous studies, we selected heterogeneous nuclear ribonucleoprotein (HNRNPD) as the research candidate and sought its downstream targeted genes. In the present study, HNRNPD, linc00707, and specific protein 2 (SP2) were highly expressed, while zinc fingers and homeboxes 2 (ZHX2) and miR-651-3p were remarkedly downregulated in glioma tissues and cells. HNRNPD, linc00707, and SP2 knockdown or ZHX2 and miR-651-3p overexpression suppressed glioma cells proliferation, migration, and invasion and vasculogenic mimicry (VM) formation. Knockdown of HNRNPD increased the stability of ZHX2 mRNA. ZHX2 bound to the promoter region of linc00707 and negatively regulate its expression. Linc00707 could bind with miR-651-3p, while miR-651-3p bound to the 3' untranslated region (3'UTR) of SP2 mRNA to negatively regulate its expression. The transcription factor SP2 directly bound to the promoter regions of the VM formation-related proteins MMP2, MMP9, and VE-cadherin, playing a role in promoting transcription in order to regulate the VM formation ability of glioma cells.
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Affiliation(s)
- Sifei Yu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Xuelei Ruan
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
- Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang, 110004, People's Republic of China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, 110004, People's Republic of China
| | - Fangfang Zhang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Di Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
- Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang, 110004, People's Republic of China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, 110004, People's Republic of China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
- Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang, 110004, People's Republic of China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, 110004, People's Republic of China
| | - Chunqing Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
- Liaoning Research Center for Translational Medicine in Nervous System Disease, Shenyang, 110004, People's Republic of China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, 110004, People's Republic of China
| | - Lianqi Shao
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Qianshuo Liu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Lu Zhu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Yang Lin
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China
| | - Yixue Xue
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, People's Republic of China.
- Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, People's Republic of China.
- Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, People's Republic of China.
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28
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Lettini G, Condelli V, Pietrafesa M, Crispo F, Zoppoli P, Maddalena F, Laurenzana I, Sgambato A, Esposito F, Landriscina M. TRAP1 Regulates Wnt/β-Catenin Pathway through LRP5/6 Receptors Expression Modulation. Int J Mol Sci 2020; 21:E7526. [PMID: 33065966 PMCID: PMC7589514 DOI: 10.3390/ijms21207526] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/09/2020] [Accepted: 10/10/2020] [Indexed: 12/01/2022] Open
Abstract
Wnt/β-Catenin signaling is involved in embryonic development, regeneration, and cellular differentiation and is responsible for cancer stemness maintenance. The HSP90 molecular chaperone TRAP1 is upregulated in 60-70% of human colorectal carcinomas (CRCs) and favors stem cells maintenance, modulating the Wnt/β-Catenin pathway and preventing β-Catenin phosphorylation/degradation. The role of TRAP1 in the regulation of Wnt/β-Catenin signaling was further investigated in human CRC cell lines, patient-derived spheroids, and CRC specimens. TRAP1 relevance in the activation of Wnt/β-Catenin signaling was highlighted by a TCF/LEF Cignal Reporter Assay in Wnt-off HEK293T and CRC HCT116 cell lines. Of note, this regulation occurs through the modulation of Wnt ligand receptors LRP5 and LRP6 that are both downregulated in TRAP1-silenced cell lines. However, while LRP5 mRNA is significantly downregulated upon TRAP1 silencing, LRP6 mRNA is unchanged, suggesting independent mechanisms of regulation by TRAP1. Indeed, LRP5 is regulated upon promoter methylation in CRC cell lines and human CRCs, whereas LRP6 is controlled at post-translational level by protein ubiquitination/degradation. Consistently, human CRCs with high TRAP1 expression are characterized by the co-upregulation of active β-Catenin, LRP5 and LRP6. Altogether, these data suggest that Wnt/β-Catenin signaling is modulated at multiple levels by TRAP1.
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Affiliation(s)
- Giacomo Lettini
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, PZ, Italy; (G.L.); (V.C.); (M.P.); (F.C.); (P.Z.); (F.M.); (I.L.); (A.S.)
| | - Valentina Condelli
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, PZ, Italy; (G.L.); (V.C.); (M.P.); (F.C.); (P.Z.); (F.M.); (I.L.); (A.S.)
| | - Michele Pietrafesa
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, PZ, Italy; (G.L.); (V.C.); (M.P.); (F.C.); (P.Z.); (F.M.); (I.L.); (A.S.)
| | - Fabiana Crispo
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, PZ, Italy; (G.L.); (V.C.); (M.P.); (F.C.); (P.Z.); (F.M.); (I.L.); (A.S.)
| | - Pietro Zoppoli
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, PZ, Italy; (G.L.); (V.C.); (M.P.); (F.C.); (P.Z.); (F.M.); (I.L.); (A.S.)
| | - Francesca Maddalena
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, PZ, Italy; (G.L.); (V.C.); (M.P.); (F.C.); (P.Z.); (F.M.); (I.L.); (A.S.)
| | - Ilaria Laurenzana
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, PZ, Italy; (G.L.); (V.C.); (M.P.); (F.C.); (P.Z.); (F.M.); (I.L.); (A.S.)
| | - Alessandro Sgambato
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, PZ, Italy; (G.L.); (V.C.); (M.P.); (F.C.); (P.Z.); (F.M.); (I.L.); (A.S.)
| | - Franca Esposito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Matteo Landriscina
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, PZ, Italy; (G.L.); (V.C.); (M.P.); (F.C.); (P.Z.); (F.M.); (I.L.); (A.S.)
- Medical Oncology Unit, Department of Medical and Surgical Sciences, University of Foggia, 71100 Foggia, Italy
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Singh P, Lessard SG, Mukherjee P, Rourke B, Otero M. Changes in DNA methylation accompany changes in gene expression during chondrocyte hypertrophic differentiation in vitro. Ann N Y Acad Sci 2020; 1490:42-56. [PMID: 32978775 DOI: 10.1111/nyas.14494] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/29/2020] [Accepted: 08/27/2020] [Indexed: 12/26/2022]
Abstract
During osteoarthritis (OA), articular chondrocytes undergo phenotypic changes that resemble developmental patterns characteristic of growth plate chondrocytes. These phenotypic alterations lead to a hypertrophy-like phenotype characterized by altered production of extracellular matrix constituents and increased collagenase activity, which, in turn, results in cartilage destruction in OA disease. Recent studies have shown that the phenotypic instability and dysregulated gene expression in OA are associated with changes in DNA methylation patterns. Subsequent efforts have aimed to identify changes in DNA methylation with functional impact in OA disease, to potentially uncover therapeutic targets. Here, we paired an in vitro 3D/pellet culture system that mimics chondrocyte hypertrophy with RNA sequencing (RNA-Seq) and enhanced reduced representation of bisulfite sequencing (ERRBS) to identify transcriptomic and epigenomic changes in murine primary articular chondrocytes undergoing hypertrophy-like differentiation. We identified hypertrophy-associated changes in DNA methylation patterns in vitro. Integration of RNA-Seq and ERRBS datasets identified associations between changes in methylation and gene expression. Our integrative analyses showed that hypertrophic differentiation of articular chondrocytes is accompanied by transcriptomic and epigenomic changes in vitro. We believe that our integrative approaches have the potential to uncover new targets for therapeutic intervention.
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Affiliation(s)
- Purva Singh
- Research, Hospital for Special Surgery, HSS Research Institute, New York, New York
| | - Samantha G Lessard
- Research, Hospital for Special Surgery, HSS Research Institute, New York, New York
| | - Piali Mukherjee
- Epigenomics Core Facility, Weill Cornell Medicine, New York, New York
| | - Brennan Rourke
- Research, Hospital for Special Surgery, HSS Research Institute, New York, New York
| | - Miguel Otero
- Research, Hospital for Special Surgery, HSS Research Institute, New York, New York
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30
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Kadler S, Vural Ö, Rosowski J, Reiners-Schramm L, Lauster R, Rosowski M. Effects of 5-aza-2´-deoxycytidine on primary human chondrocytes from osteoarthritic patients. PLoS One 2020; 15:e0234641. [PMID: 32574164 PMCID: PMC7310740 DOI: 10.1371/journal.pone.0234641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/29/2020] [Indexed: 11/18/2022] Open
Abstract
Chondrocytes, comparable to many cells from the connective tissue, dedifferentiate and end up in a similar fibroblastoid cell type, marked by the loss of the specific expression pattern. Here, chondrocytes isolated from osteoarthritic (OA) patients were investigated. The OA chondrocytes used in this work were not affected by the loss of specific gene expression upon cell culture. The mRNA levels of known cartilage markers, such as SOX5, SOX6, SOX9, aggrecan and proteoglycan 4, remained unchanged. Since chondrocytes from OA and healthy tissue show different DNA methylation patterns, the underlying mechanisms of cartilage marker maintenance were investigated with a focus on the epigenetic modification by DNA methylation. The treatment of dedifferentiated chondrocytes with the DNA methyltransferase inhibitor 5-aza-2´-deoxycytidine (5-aza-dC) displayed no considerable impact on the maintenance of marker gene expression observed in the dedifferentiated state, while the chondrogenic differentiation capacity was compromised. On the other hand, the pre-cultivation with 5-aza-dC improved the osteogenesis and adipogenesis of OA chondrocytes. Contradictory to these effects, the DNA methylation levels were not reduced after treatment for four weeks with 1 μM 5-aza-dC. In conclusion, 5-aza-dC affects the differentiation capacity of OA chondrocytes, while the global DNA methylation level remains stable. Furthermore, dedifferentiated chondrocytes isolated from late-stage OA patients represent a reliable cell source for in vitro studies and disease models without the need for additional alterations.
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Affiliation(s)
- Shirin Kadler
- Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- * E-mail:
| | - Özlem Vural
- Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Jennifer Rosowski
- Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Luzia Reiners-Schramm
- Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Roland Lauster
- Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Mark Rosowski
- Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
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31
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Cheung K, Barter MJ, Falk J, Proctor CJ, Reynard LN, Young DA. Histone ChIP-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity. FASEB J 2020; 34:5317-5331. [PMID: 32058623 PMCID: PMC7187454 DOI: 10.1096/fj.201902061rr] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/27/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022]
Abstract
Epigenetic mechanisms are known to regulate gene expression during chondrogenesis. In this study, we have characterized the epigenome during the in vitro differentiation of human mesenchymal stem cells (hMSCs) into chondrocytes. Chromatin immunoprecipitation followed by next‐generation sequencing (ChIP‐seq) was used to assess a range of N‐terminal posttranscriptional modifications (marks) to histone H3 lysines (H3K4me3, H3K4me1, H3K27ac, H3K27me3, and H3K36me3) in both hMSCs and differentiated chondrocytes. Chromatin states were characterized using histone ChIP‐seq and cis‐regulatory elements were identified in chondrocytes. Chondrocyte enhancers were associated with chondrogenesis‐related gene ontology (GO) terms. In silico analysis and integration of DNA methylation data with chondrogenesis chromatin states revealed that enhancers marked by histone marks H3K4me1 and H3K27ac were de‐methylated during in vitro chondrogenesis. Similarity analysis between hMSC and chondrocyte chromatin states defined in this study with epigenomes of cell‐types defined by the Roadmap Epigenomics project revealed that enhancers are more distinct between cell‐types compared to other chromatin states. Motif analysis revealed that the transcription factor SOX9 is enriched in chondrocyte enhancers. Luciferase reporter assays confirmed that chondrocyte enhancers characterized in this study exhibited enhancer activity which may be modulated by DNA methylation and SOX9 overexpression. Altogether, these integrated data illustrate the cross‐talk between different epigenetic mechanisms during chondrocyte differentiation.
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Affiliation(s)
- Kathleen Cheung
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK.,Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew J Barter
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Julia Falk
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Carole J Proctor
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Louise N Reynard
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - David A Young
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
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Hu S, Sprintall J, Guan C, McPhaden MJ, Wang F, Hu D, Cai W. Deep-reaching acceleration of global mean ocean circulation over the past two decades. SCIENCE ADVANCES 2020; 105:108-123. [PMID: 32076640 DOI: 10.1111/tpj.15043] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 09/21/2020] [Indexed: 05/06/2023]
Abstract
Ocean circulation redistributes Earth's energy and water masses and influences global climate. Under historical greenhouse warming, regional ocean currents show diverse tendencies, but whether there is an emerging trend of the global mean ocean circulation system is not yet clear. Here, we show a statistically significant increasing trend in the globally integrated oceanic kinetic energy since the early 1990s, indicating a substantial acceleration of global mean ocean circulation. The increasing trend in kinetic energy is particularly prominent in the global tropical oceans, reaching depths of thousands of meters. The deep-reaching acceleration of the ocean circulation is mainly induced by a planetary intensification of surface winds since the early 1990s. Although possibly influenced by wind changes associated with the onset of a negative Pacific decadal oscillation since the late 1990s, the recent acceleration is far larger than that associated with natural variability, suggesting that it is principally part of a long-term trend.
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Affiliation(s)
- Shijian Hu
- CAS Key Laboratory of Ocean Circulation and Waves, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Janet Sprintall
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Cong Guan
- CAS Key Laboratory of Ocean Circulation and Waves, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Fan Wang
- CAS Key Laboratory of Ocean Circulation and Waves, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dunxin Hu
- CAS Key Laboratory of Ocean Circulation and Waves, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenju Cai
- Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- CSIRO Oceans and Atmosphere Flagship, Aspendale, Victoria 3195, Australia
- Centre for Southern Hemisphere Oceans Research (CSHOR), CSIRO Oceans and Atmosphere, Hobart, Tasmania 7004, Australia
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DNA hypomethylation during MSC chondrogenesis occurs predominantly at enhancer regions. Sci Rep 2020; 10:1169. [PMID: 31980739 PMCID: PMC6981252 DOI: 10.1038/s41598-020-58093-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/21/2019] [Indexed: 12/12/2022] Open
Abstract
Regulation of transcription occurs in a cell type specific manner orchestrated by epigenetic mechanisms including DNA methylation. Methylation changes may also play a key role in lineage specification during stem cell differentiation. To further our understanding of epigenetic regulation in chondrocytes we characterised the DNA methylation changes during chondrogenesis of mesenchymal stem cells (MSCs) by Infinium 450 K methylation array. Significant DNA hypomethylation was identified during chondrogenic differentiation including changes at many key cartilage gene loci. Integration with chondrogenesis gene expression data revealed an enrichment of significant CpGs in upregulated genes, while characterisation of significant CpG loci indicated their predominant localisation to enhancer regions. Comparison with methylation profiles of other tissues, including healthy and diseased adult cartilage, identified chondrocyte-specific regions of hypomethylation and the overlap with differentially methylated CpGs in osteoarthritis. Taken together we have associated DNA methylation levels with the chondrocyte phenotype. The consequences of which has potential to improve cartilage generation for tissue engineering purposes and also to provide context for observed methylation changes in cartilage diseases such as osteoarthritis.
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Chen H, Yang S, Shao R. Long non-coding XIST raises methylation of TIMP-3 promoter to regulate collagen degradation in osteoarthritic chondrocytes after tibial plateau fracture. Arthritis Res Ther 2019; 21:271. [PMID: 31815654 PMCID: PMC6902347 DOI: 10.1186/s13075-019-2033-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 10/17/2019] [Indexed: 02/07/2023] Open
Abstract
Background Hypermethylation of gene promoters has been regarded as an epigenetic regulator for gene inactivation in the development of several diseases. In the current study, we aimed to explore how long noncoding RNA X-inactive specific transcript (lncRNA XIST) function in collagen degradation in chondrocytes of osteoarthritis (OA) after tibial plateau fracture by regulating tissue inhibitor of metalloproteinase-3 (TIMP-3) promoter methylation. Methods In silico analysis was used to screen differentially expressed lncRNAs in cartilage tissues of OA. Chondrocytes were then successfully isolated from normal and OA cartilage tissues and identified, with the expressions of lncRNA XIST and TIMP-3 examined. The methylation levels of TIMP-3 promoter were determined by MS-PCR. The binding of lncRNA XIST to DNA methyltransferase and the binding of TIMP-3 promoter to DNA methyltransferase were determined by a series of experiments, including RIP, RNA pull-down, and ChIP assays. Results The differentially expressed lncRNA XIST was determined in OA. In addition, cartilage tissues of OA showed upregulation of lncRNA XIST and downregulation of TIMP-3. LncRNA XIST was primarily localized in the nucleus and was capable of binding to the promoter of TIMP-3. The silencing of lncRNA XIST decreased the methylation levels of TIMP-3 promoter and increased the expressions of TIMP-3, which consequently inhibited collagen degradation in OA chondrocytes. Furthermore, TIMP-3 over-expression reversed the effect of lncRNA XIST on collagen degradation in OA chondrocytes. Conclusion Collectively, lncRNA XIST raises collagen degradation in OA chondrocytes after tibial plateau fracture by accelerating the methylation of TIMP-3 promoter by recruiting DNA methyltransferase.
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Affiliation(s)
- Hongwei Chen
- Department of Orthopedic Surgery, Yiwu Central Hospital, the Affiliated Yiwu Hospital of Wenzhou Medical University, Yiwu, 322000, People's Republic of China
| | - Shengdi Yang
- Department of Hand-Foot Microsurgery, Lanshi Hospital, Lanzhou, 730050, People's Republic of China
| | - Ruyi Shao
- Department of Orthopedics, Zhuji People's Hospital, No. 9, Jianmin Road, Zhuji, 311800, Zhejiang Province, People's Republic of China.
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Genome-wide analysis of DNA methylation profile identifies differentially methylated loci associated with human intervertebral disc degeneration. PLoS One 2019; 14:e0222188. [PMID: 31513634 PMCID: PMC6742346 DOI: 10.1371/journal.pone.0222188] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/25/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Environmental and endogenous factors under genetic predisposition are considered to initiate the human intervertebral disc (IVD) degeneration. DNA methylation is an essential mechanism to ensure cell-specific gene expression for normal development and tissue stability. Aberrant epigenetic alterations play a pivotal role in several diseases, including osteoarthritis. However, epigenetic alternations, including DNA methylation, in IVD degeneration have not been evaluated. The purpose of this study was to comprehensively compare the genome-wide DNA methylation profiles of human IVD tissues, specifically nucleus pulpous (NP) tissues, with early and advanced stages of disc degeneration. METHODS Human NP tissues were used in this study. The samples were divided into two groups: early stage degeneration (n = 8, Pfirrmann's MRI grade: I-III) and advanced stage degeneration (n = 8, grade: IV). Genomic DNA was processed for genome-wide DNA methylation profiling using the Infinium MethylationEPIC BeadChip array. Extraction of raw methylation data, clustering and scatter plot of each group values of each sample were performed using a methylation module in GenomeStudio software. The identification of differentially methylated loci (DMLs) and the Gene Ontology (GO) analysis were performed using R software with the ChAMP package. RESULTS Unsupervised hierarchical clustering revealed that early and advanced stage degenerated IVD samples segregated into two main clusters by their DNA methylome. A total of 220 DMLs were identified between early and advanced disc degeneration stages. Among these, four loci were hypomethylated and 216 loci were hypermethylated in the advanced disc degeneration stage. The GO enrichment analysis of genes containing DMLs identified two significant GO terms for biological processes, hemophilic cell adhesion and cell-cell adhesion. CONCLUSIONS We conducted a genome-wide DNA methylation profile comparative study and observed significant differences in DNA methylation profiles between early and advanced stages of human IVD degeneration. These results implicate DNA methylation in the process of human IVD degeneration.
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36
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Whitney DG. Racial differences in skeletal fragility but not osteoarthritis among women and men with cerebral palsy. Bone Rep 2019; 11:100219. [PMID: 31417943 PMCID: PMC6690429 DOI: 10.1016/j.bonr.2019.100219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 02/04/2023] Open
Abstract
Background Adults with cerebral palsy (CP) have increased risk for skeletal fragility and osteoarthritis. However, racial differences in these outcomes have not been examined. Such knowledge could improve patient-specific clinical care for the prevention and management of these conditions. The purpose of this study was to determine if there were racial differences in the prevalence of osteoporosis, all-cause fracture, and osteoarthritis among young and middle-aged adults with CP. Methods Data from 2016 were extracted from a random 20% sample of the Medicare fee-for-service database. International Classification of Diseases, Tenth Revision, Clinical Modification codes were used to identify 18-64 year olds with CP, as well as osteoporosis, all-cause fracture, osteoarthritis, and neurodevelopmental and noncommunicable disease comorbidities. Results Of the 16,488 adults with CP, 13,334 were White, 2477 were Black, and 677 were Hispanic. The age-standardized prevalence of osteoporosis (women: 12.9%, 9.0%, 8.3%, respectively; men: 9.2%, 4.8%, 7.9%, respectively) and fracture (women: 7.4%, 4.2%, 9.9%; men: 6.0%, 2.3%, 6.0%) was lower for Black adults with CP compared to White adults with CP (all p < 0.005). No racial differences were observed for age-standardized prevalence of osteoarthritis (women: 13.6%, 14.4%, 9.6%; men: 10.7%, 10.4%, 12.7%). The racial differences between Black and White adults with CP remained even after adjusting for age, U.S. region, neurodevelopmental comorbidities, and several noncommunicable diseases for osteoporosis (women: OR = 0.66, 99.5% CI = 0.48-0.91; men: OR = 0.51, 99.5% CI = 0.35-0.75) and fracture (women: OR = 0.57, 99.5% CI = 0.37-0.89; men: OR = 0.39, 99.5% CI = 0.23-0.68). Conclusions Study findings suggest racial differences in skeletal fragility among young and middle-aged adults with CP, with White women and men with CP having greater risk compared to Black women and men with CP. This study found no evidence of racial differences in the prevalence of osteoarthritis.
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Affiliation(s)
- Daniel G. Whitney
- Department of Physical Medicine and Rehabilitation, University of Michigan, 325 E. Eisenhower, Ann Arbor, MI, United States of America
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Housman G, Havill LM, Quillen EE, Comuzzie AG, Stone AC. Assessment of DNA Methylation Patterns in the Bone and Cartilage of a Nonhuman Primate Model of Osteoarthritis. Cartilage 2019; 10:335-345. [PMID: 29457464 PMCID: PMC6585300 DOI: 10.1177/1947603518759173] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE Osteoarthritis (OA) affects humans and several other animals. Thus, the mechanisms underlying this disorder, such as specific skeletal tissue DNA methylation patterns, may be evolutionary conserved. However, associations between methylation and OA have not been readily studied in nonhuman animals. Baboons serve as important models of disease and develop OA at rates similar to those in humans. Therefore, this study investigated the associations between methylation and OA in baboons to advance the evolutionary understanding of OA. DESIGN Trabecular bone and cartilage was collected from the medial condyles of adult female baboon femora, 5 with and 5 without knee OA. The Infinium HumanMethylation450 BeadChip (450K array) was used to identify DNA methylation patterns in these tissues. RESULTS Approximately 44% of the 450K array probes reliably align to the baboon genome, contain a CpG site of interest, and maintain a wide distribution throughout the genome. Of the 2 filtering methods tested, both identified significantly differentially methylated positions (DMPs) between healthy and OA individuals in cartilage tissues, and some of these patterns overlap with those previously identified in humans. Conversely, no DMPs were found between tissue types or between disease states in bone tissues. CONCLUSIONS Overall, the 450K array can be used to measure genome-wide DNA methylation in baboon tissues and identify significant associations with complex traits. The results of this study indicate that some DNA methylation patterns associated with OA are evolutionarily conserved, while others are not. This warrants further investigation in a larger and more phylogenetically diverse sample set.
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Affiliation(s)
- Genevieve Housman
- School of Human Evolution and Social
Change, Arizona State University, Tempe, AZ, USA,Center for Evolution and Medicine,
Arizona State University, Tempe, AZ, USA,Genevieve Housman, Section of Genetic
Medicine, University of Chicago, 920 East 58th Street, CLSC 317, Chicago, IL
60637, USA.
| | - Lorena M. Havill
- Southwest National Primate Research
Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ellen E. Quillen
- Department of Genetics, Texas Biomedical
Research Institute, San Antonio, TX, USA
| | - Anthony G. Comuzzie
- Department of Genetics, Texas Biomedical
Research Institute, San Antonio, TX, USA
| | - Anne C. Stone
- School of Human Evolution and Social
Change, Arizona State University, Tempe, AZ, USA,Center for Evolution and Medicine,
Arizona State University, Tempe, AZ, USA
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Rice SJ, Aubourg G, Sorial AK, Almarza D, Tselepi M, Deehan DJ, Reynard LN, Loughlin J. Identification of a novel, methylation-dependent, RUNX2 regulatory region associated with osteoarthritis risk. Hum Mol Genet 2019; 27:3464-3474. [PMID: 30010910 PMCID: PMC6140783 DOI: 10.1093/hmg/ddy257] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 07/03/2018] [Indexed: 12/13/2022] Open
Abstract
Osteoarthritis (OA) is a common, multifactorial and polygenic skeletal disease that, in its severest form, requires joint replacement surgery to restore mobility and to relieve chronic pain. Using tissues from the articulating joints of 260 patients with OA and a range of in vitro experiments, including CRISPR-Cas9, we have characterized an intergenic regulatory element. Here, genotype at an OA risk locus correlates with differential DNA methylation, with altered gene expression of both a transcriptional regulator (RUNX2), and a chromatin remodelling protein (SUPT3H). RUNX2 is a strong candidate for OA susceptibility, with its encoded protein being essential for skeletogenesis and healthy joint function. The OA risk locus includes single nucleotide polymorphisms (SNPs) located within and flanking the differentially methylated region (DMR). The OA association SNP, rs10948172, demonstrates particularly strong correlation with methylation, and two intergenic SNPs falling within the DMR (rs62435998 and rs62435999) demonstrate genetic and epigenetic effects on the regulatory activity of this region. We therefore posit that the OA signal mediates its effect by modulating the methylation of the regulatory element, which then impacts on gene expression, with RUNX2 being the principal target. Our study highlights the interplay between DNA methylation, OA genetic risk and the downstream regulation of genes critical to normal joint function.
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Affiliation(s)
- Sarah J Rice
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, NE1 3BZ, UK
| | - Guillaume Aubourg
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, NE1 3BZ, UK
| | - Antony K Sorial
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, NE1 3BZ, UK
| | - David Almarza
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, NE1 3BZ, UK
| | - Maria Tselepi
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, NE1 3BZ, UK
| | - David J Deehan
- Newcastle University Teaching Hospitals NHS Trust, Freeman Hospital, High Heaton, NE1 7DN, UK
| | - Louise N Reynard
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, NE1 3BZ, UK
| | - John Loughlin
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, NE1 3BZ, UK
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Abstract
Metalloproteinases remain important players in arthritic disease, in part because members of this large enzymatic family, namely matrix metalloproteinase-1 (MMP-1) and MMP-13, are responsible for the irreversible degradation of articular cartilage collagen. Although direct inhibition of MMPs fell out of vogue with the initial clinical disappointment of the first generation of compounds, interest in other mechanisms that control these important enzymes has always been maintained. Since these enzymes are critically important for tissue homeostasis, their expression and activity are tightly regulated at many levels, not just by direct inhibition by their endogenous inhibitors the tissue inhibitors of metalloproteinases (TIMPs). Focussing on MMP-13, we discuss recent work that highlights new discoveries in the transcriptional regulation of this enzyme, from defined promoter functional analysis to how more global technologies can provide insight into the enzyme’s regulation, especially by epigenetic mechanisms, including non-coding RNAs. In terms of protein regulation, we highlight recent findings into enzymatic cascades involved in MMP-13 regulation and activation. Importantly, we highlight a series of recent studies that describe how MMP-13 activity, and in fact that of other metalloproteinases, is in part controlled by receptor-mediated endocytosis. Together, these new discoveries provide a plethora of novel regulatory mechanisms, besides direct inhibition, which with renewed vigour could provide further therapeutic opportunities for regulating the activity of this class of important enzymes.
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Affiliation(s)
- David A Young
- Skeletal Research Group, Institute of Genetic Medicine, Central Parkway, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Matt J Barter
- Skeletal Research Group, Institute of Genetic Medicine, Central Parkway, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - David J Wilkinson
- Skeletal Research Group, Institute of Genetic Medicine, Central Parkway, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
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van Meurs JB, Boer CG, Lopez-Delgado L, Riancho JA. Role of Epigenomics in Bone and Cartilage Disease. J Bone Miner Res 2019; 34:215-230. [PMID: 30715766 DOI: 10.1002/jbmr.3662] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/03/2018] [Accepted: 01/02/2019] [Indexed: 12/14/2022]
Abstract
Phenotypic variation in skeletal traits and diseases is the product of genetic and environmental factors. Epigenetic mechanisms include information-containing factors, other than DNA sequence, that cause stable changes in gene expression and are maintained during cell divisions. They represent a link between environmental influences, genome features, and the resulting phenotype. The main epigenetic factors are DNA methylation, posttranslational changes of histones, and higher-order chromatin structure. Sometimes non-coding RNAs, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are also included in the broad term of epigenetic factors. There is rapidly expanding experimental evidence for a role of epigenetic factors in the differentiation of bone cells and the pathogenesis of skeletal disorders, such as osteoporosis and osteoarthritis. However, different from genetic factors, epigenetic signatures are cell- and tissue-specific and can change with time. Thus, elucidating their role has particular difficulties, especially in human studies. Nevertheless, epigenomewide association studies are beginning to disclose some disease-specific patterns that help to understand skeletal cell biology and may lead to development of new epigenetic-based biomarkers, as well as new drug targets useful for treating diffuse and localized disorders. Here we provide an overview and update of recent advances on the role of epigenomics in bone and cartilage diseases. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
| | - Cindy G Boer
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Laura Lopez-Delgado
- Department of Internal Medicine, Hospital U M Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Jose A Riancho
- Department of Internal Medicine, Hospital U M Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
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Abstract
Owing to the development of new technologies, the epigenome, a second dimensional method for genome analysis has emerged. Epigenetic mechanisms, including DNA methylation, histone modifications and noncoding RNAs, regulate gene expression without changing the genetic sequence. These epigenetic mechanisms normally modulate gene expression, trans-generational effects and inherited expression states in various biological processes. Abnormal epigenetic patterns typically cause pathological conditions, including cancers, age-related diseases, and specific cartilage and bone diseases. Facing the rapidly developing epigenetic field, we reviewed epigenetic mechanisms and their involvement with the skeletal system and their role in skeletal development, homeostasis and degeneration. Finally, we discuss the prospects for the future of epigenetics.
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Singh P, Marcu KB, Goldring MB, Otero M. Phenotypic instability of chondrocytes in osteoarthritis: on a path to hypertrophy. Ann N Y Acad Sci 2018; 1442:17-34. [PMID: 30008181 DOI: 10.1111/nyas.13930] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/11/2018] [Accepted: 06/21/2018] [Indexed: 12/24/2022]
Abstract
Articular chondrocytes are quiescent, fully differentiated cells responsible for the homeostasis of adult articular cartilage by maintaining cellular survival functions and the fine-tuned balance between anabolic and catabolic functions. This balance requires phenotypic stability that is lost in osteoarthritis (OA), a disease that affects and involves all joint tissues and especially impacts articular cartilage structural integrity. In OA, articular chondrocytes respond to the accumulation of injurious biochemical and biomechanical insults by shifting toward a degradative and hypertrophy-like state, involving abnormal matrix production and increased aggrecanase and collagenase activities. Hypertrophy is a necessary, transient developmental stage in growth plate chondrocytes that culminates in bone formation; in OA, however, chondrocyte hypertrophy is catastrophic and it is believed to initiate and perpetuate a cascade of events that ultimately result in permanent cartilage damage. Emphasizing changes in DNA methylation status and alterations in NF-κB signaling in OA, this review summarizes the data from the literature highlighting the loss of phenotypic stability and the hypertrophic differentiation of OA chondrocytes as central contributing factors to OA pathogenesis.
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Affiliation(s)
- Purva Singh
- HSS Research Institute, Hospital for Special Surgery, New York, New York
| | - Kenneth B Marcu
- Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, New York
| | - Mary B Goldring
- HSS Research Institute, Hospital for Special Surgery, New York, New York.,Department of Cell and Developmental Biology, Weill Cornell Medical College and Weill Cornell Graduate School of Medical Sciences, New York, New York
| | - Miguel Otero
- HSS Research Institute, Hospital for Special Surgery, New York, New York
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Abstract
PURPOSE OF REVIEW 'Omics' technologies developed for the massive analysis of the major biologically relevant molecules (genes, proteins, metabolites) have been applied to the study of osteoarthritis (OA) for more than a decade. RECENT FINDINGS 'Omics' studies have undoubtedly contributed to increase the knowledge on pathogenic processes related with OA and have provided hundreds to thousands of molecules that might have a putative biomarker utility for this disease. SUMMARY This review describes the most recent 'omics' studies in OA research, their conclusions, and discuss those remaining challenges. Still many validation studies must be performed in large and well-characterized cohorts for the translation of the findings from 'omics' strategies to clinical applications. The development of tools for the intelligent integration of 'omics' data with clinical and imaging information is also mandatory to take full profit of the work that has been already performed.
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He A, Ning Y, Wen Y, Cai Y, Xu K, Cai Y, Han J, Liu L, Du Y, Liang X, Li P, Fan Q, Hao J, Wang X, Guo X, Ma T, Zhang F. Use of integrative epigenetic and mRNA expression analyses to identify significantly changed genes and functional pathways in osteoarthritic cartilage. Bone Joint Res 2018; 7:343-350. [PMID: 29922454 PMCID: PMC5987683 DOI: 10.1302/2046-3758.75.bjr-2017-0284.r1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Aim Osteoarthritis (OA) is caused by complex interactions between genetic and environmental factors. Epigenetic mechanisms control the expression of genes and are likely to regulate the OA transcriptome. We performed integrative genomic analyses to define methylation-gene expression relationships in osteoarthritic cartilage. Patients and Methods Genome-wide DNA methylation profiling of articular cartilage from five patients with OA of the knee and five healthy controls was conducted using the Illumina Infinium HumanMethylation450 BeadChip (Illumina, San Diego, California). Other independent genome-wide mRNA expression profiles of articular cartilage from three patients with OA and three healthy controls were obtained from the Gene Expression Omnibus (GEO) database. Integrative pathway enrichment analysis of DNA methylation and mRNA expression profiles was performed using integrated analysis of cross-platform microarray and pathway software. Gene ontology (GO) analysis was conducted using the Database for Annotation, Visualization and Integrated Discovery (DAVID). Results We identified 1265 differentially methylated genes, of which 145 are associated with significant changes in gene expression, such as DLX5, NCOR2 and AXIN2 (all p-values of both DNA methylation and mRNA expression < 0.05). Pathway enrichment analysis identified 26 OA-associated pathways, such as mitogen-activated protein kinase (MAPK) signalling pathway (p = 6.25 × 10-4), phosphatidylinositol (PI) signalling system (p = 4.38 × 10-3), hypoxia-inducible factor 1 (HIF-1) signalling pathway (p = 8.63 × 10-3 pantothenate and coenzyme A (CoA) biosynthesis (p = 0.017), ErbB signalling pathway (p = 0.024), inositol phosphate (IP) metabolism (p = 0.025), and calcium signalling pathway (p = 0.032). Conclusion We identified a group of genes and biological pathwayswhich were significantly different in both DNA methylation and mRNA expression profiles between patients with OA and controls. These results may provide new clues for clarifying the mechanisms involved in the development of OA. Cite this article: A. He, Y. Ning, Y. Wen, Y. Cai, K. Xu, Y. Cai, J. Han, L. Liu, Y. Du, X. Liang, P. Li, Q. Fan, J. Hao, X. Wang, X. Guo, T. Ma, F. Zhang. Use of integrative epigenetic and mRNA expression analyses to identify significantly changed genes and functional pathways in osteoarthritic cartilage. Bone Joint Res 2018;7:343–350. DOI: 10.1302/2046-3758.75.BJR-2017-0284.R1.
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Affiliation(s)
- A He
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Y Ning
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Y Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Y Cai
- Department of Orthopaedics, The First Affiliated Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - K Xu
- Department of Joint Surgery, Xi'an Hong-Hui Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Y Cai
- Department of Joint Surgery, Xi'an Hong-Hui Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - J Han
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - L Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Y Du
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - X Liang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - P Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Q Fan
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - J Hao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - X Wang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - X Guo
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - T Ma
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - F Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
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Peffers MJ, Balaskas P, Smagul A. Osteoarthritis year in review 2017: genetics and epigenetics. Osteoarthritis Cartilage 2018; 26:304-311. [PMID: 28989115 PMCID: PMC6292677 DOI: 10.1016/j.joca.2017.09.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/06/2017] [Accepted: 09/08/2017] [Indexed: 02/02/2023]
Abstract
OBJECTIVE The purpose of this review is to describe highlights from original research publications related to osteoarthritis (OA), epigenetics and genomics with the intention of recognising significant advances. DESIGN To identify relevant papers a Pubmed literature search was conducted for articles published between April 2016 and April 2017 using the search terms 'osteoarthritis' together with 'genetics', 'genomics', 'epigenetics', 'microRNA', 'lncRNA', 'DNA methylation' and 'histone modification'. RESULTS The search term OA generated almost 4000 references. Publications using the combination of descriptors OA and genetics provided the most references (82 references). However this was reduced compared to the same period in the previous year; 8.1-2.1% (expressed as a percentage of the total publications combining the terms OA and genetics). Publications combining the terms OA with genomics (29 references), epigenetics (16 references), long non-coding RNA (lncRNA) (11 references; including the identification of novel lncRNAs in OA), DNA methylation (21 references), histone modification (3 references) and microRNA (miR) (79 references) were reviewed. Potential OA therapeutics such as histone deacetylase (HDAC) inhibitors have been identified. A number of non-coding RNAs may also provide targets for future treatments. CONCLUSION There continues to be a year on year increase in publications researching miRs in OA (expressed as a percentage of the total publications), with a doubling over the last 4 years. An overview on the last year's progress within the fields of epigenetics and genomics with respect to OA will be given.
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Affiliation(s)
- M J Peffers
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - P Balaskas
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - A Smagul
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
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Sieker JT, Proffen BL, Waller KA, Chin K, Karamchedu NP, Akelman MR, Perrone GS, Kiapour AM, Konrad J, Murray MM, Fleming BC. Transcriptional profiling of articular cartilage in a porcine model of early post-traumatic osteoarthritis. J Orthop Res 2018; 36:318-329. [PMID: 28671352 PMCID: PMC5752630 DOI: 10.1002/jor.23644] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/25/2017] [Indexed: 02/04/2023]
Abstract
To identify the molecular pathophysiology present in early post-traumatic osteoarthritis (PTOA), the transcriptional profile of articular cartilage and its response to surgical PTOA induction were determined. Thirty six Yucatan minipigs underwent anterior cruciate ligament (ACL) transection and were randomly assigned in equal numbers to no further treatment, reconstruction or ligament repair. Cartilage was harvested at 1 and 4 weeks post-operatively and histology and RNA-sequencing were performed and compared to controls. Microscopic cartilage scores significantly worsened at 1 (p = 0.028) and 4 weeks (p = 0.001) post-surgery relative to controls, but did not differ between untreated, reconstruction or repair groups. Gene expression after ACL reconstruction and ACL transection were similar, with only 0.03% (including SERPINB7 and CR2) and 0.2% of transcripts (including INHBA) differentially expressed at 1 and 4 weeks respectively. COL2A1, COMP, SPARC, CHAD, and EF1ALPHA were the most highly expressed non ribosomal, non mitochondrial genes in the controls and remained abundant after surgery. A total of 1,275 genes were differentially expressed between 1 and 4 weeks post-surgery. With the treatment groups pooled, 682 genes were differentially expressed at both time-points, with the most significant changes observed in MMP1, COCH, POSTN, CYTL1, and PTGFR. This study confirmed the development of a microscopic PTOA stage after ACL surgery in the porcine model. Upregulation of multiple proteases (including MMP1 and ADAMTS4) were found; however, the level of expression remained orders of magnitude below that of extracellular matrix protein-coding genes (including COL2A1 and ACAN). In summary, genes with established roles in PTOA as well as novel targets for specific intervention were identified. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:318-329, 2018.
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Affiliation(s)
- Jakob T. Sieker
- Boston Children’s Hospital, Harvard Medical School, Boston, MA
| | | | - Kimberly A. Waller
- Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI
| | - Kaitlyn Chin
- Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI
| | - Naga P. Karamchedu
- Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI
| | - Matthew R. Akelman
- Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI
| | | | - Ata M. Kiapour
- Boston Children’s Hospital, Harvard Medical School, Boston, MA
| | - Johannes Konrad
- Boston Children’s Hospital, Harvard Medical School, Boston, MA
| | | | - Braden C. Fleming
- Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI
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TWIST1 induces MMP3 expression through up-regulating DNA hydroxymethylation and promotes catabolic responses in human chondrocytes. Sci Rep 2017; 7:42990. [PMID: 28220902 PMCID: PMC5318945 DOI: 10.1038/srep42990] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 01/18/2017] [Indexed: 02/05/2023] Open
Abstract
The objective was to investigate the levels of TWIST1 in normal and OA cartilage and examine its role in regulating gene expression in chondrocytes. Human cartilage tissues and chondrocytes were obtained at autopsy from normal knee joints and from OA-affected joints at the time of total knee arthroplasty. TWIST1 expression was increased in human OA knee cartilage compared to normal knee cartilage. TWIST1 induced matrix metalloproteinase 3 (MMP3) expression without direct binding to MMP3 promoter and increased the 5-hydroxymethylcytosine (5hmC) level at the MMP3 promoter. The effect of TWIST1 on expression of TET family (TET1, 2 and 3) was measured in stable TWIST1 transfected TC28 cells, and TET1 expression was up-regulated. TWIST1 dependent upregulation of Mmp3 expression was suppressed in Tet triple KO fibroblast derived from mouse ES cells. Increased TWIST1 expression is a feature of OA-affected cartilage. We identified a novel mechanism of catabolic reaction where TWIST1 up-regulates MMP3 expression by enriching 5hmC levels at the MMP3 promoter via TET1 induction. These findings implicate TWIST1 as an important factor regulating OA related gene expression. Clarifying epigenetic mechanisms of 5hmC induced by TWIST1 is a critical molecule to understanding OA pathogenesis.
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van Meurs JBJ. Osteoarthritis year in review 2016: genetics, genomics and epigenetics. Osteoarthritis Cartilage 2017; 25:181-189. [PMID: 28100422 DOI: 10.1016/j.joca.2016.11.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/20/2016] [Accepted: 11/02/2016] [Indexed: 02/02/2023]
Abstract
The purpose of this narrative review is to provide an overview of last year's publications in the field of genetics, genomics and epigenetics in the osteoarthritis (OA) field. Major themes arising from a Pubmed search on (epi)genetics in OA were identified. In addition, general developments in the fast evolving field of (epi)genetics are reviewed and relevance for the OA field is summarized. In the last 5 years, a number of genome-wide association studies have identified a modest number of genetic loci associated to OA. Continued functional research into these DNA variants is showing putative biological mechanisms underlying these associations. Over the last year, no additional large genome-wide association studies were published, but there clearly remains much to be discovered in the OA genetic field. A lot of research has been done into the epigenetics of OA over the last year. Several genome-wide screens examining the methylome of osteoarthritic cartilage were done. Pathway analysis confirmed deregulation of developmental and extracellular pathways in OA cartilage. Over the last year many microRNAs (miRNAs) have been identified that potentially play important roles in cartilage homeostasis and/or OA process. Continued research will learn whether these identified miRNAs are truly causal and can be used in clinical applications. Many of the epigenetic findings need further confirmation, but they highlight potential novel pathways involved in cartilage biology and OA.
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Affiliation(s)
- J B J van Meurs
- Department of Internal Medicine, Erasmus MC, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands.
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Reynard LN. Analysis of genetics and DNA methylation in osteoarthritis: What have we learnt about the disease? Semin Cell Dev Biol 2016; 62:57-66. [PMID: 27130636 DOI: 10.1016/j.semcdb.2016.04.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/25/2016] [Indexed: 01/30/2023]
Abstract
Osteoarthritis (OA) is a chronic musculoskeletal disease characterised by the destruction of articular cartilage, synovial inflammation and bone remodelling. Disease aetiology is complex and highly heritable, with genetic variation estimated to contribute to 50% of OA occurrence. Epigenetic alterations, including DNA methylation changes, have also been implicated in OA pathophysiology. This review examines what genetic and DNA methylation studies have taught us about the genes and pathways involved in OA pathology. The influence of DNA methylation on the molecular mechanisms underlying OA genetic risk and the consequence of this interaction on disease susceptibility and penetrance are also discussed.
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Affiliation(s)
- Louise N Reynard
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, NE2 4HH, UK.
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