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Liu W, Xiu L, Zhou M, Li T, Jiang N, Wan Y, Qiu C, Li J, Hu W, Zhang W, Wu J. The Critical Role of the Shroom Family Proteins in Morphogenesis, Organogenesis and Disease. PHENOMICS (CHAM, SWITZERLAND) 2024; 4:187-202. [PMID: 38884059 PMCID: PMC11169129 DOI: 10.1007/s43657-023-00119-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 06/18/2024]
Abstract
The Shroom (Shrm) family of actin-binding proteins has a unique and highly conserved Apx/Shrm Domain 2 (ASD2) motif. Shroom protein directs the subcellular localization of Rho-associated kinase (ROCK), which remodels the actomyosin cytoskeleton and changes cellular morphology via its ability to phosphorylate and activate non-muscle myosin II. Therefore, the Shrm-ROCK complex is critical for the cellular shape and the development of many tissues, including the neural tube, eye, intestines, heart, and vasculature system. Importantly, the structure and expression of Shrm proteins are also associated with neural tube defects, chronic kidney disease, metastasis of carcinoma, and X-link mental retardation. Therefore, a better understanding of Shrm-mediated signaling transduction pathways is essential for the development of new therapeutic strategies to minimize damage resulting in abnormal Shrm proteins. This paper provides a comprehensive overview of the various Shrm proteins and their roles in morphogenesis and disease.
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Affiliation(s)
- Wanling Liu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200438 China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Lei Xiu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Mingzhe Zhou
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200438 China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Tao Li
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Yanmin Wan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200438 China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Chao Qiu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200438 China
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Jian Li
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200438 China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Wei Hu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200438 China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Monglia University, Hohhot, 010030 China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200438 China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Huashen Institute of Microbes and Infections, Shanghai, 200052 China
| | - Jing Wu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200438 China
- Shanghai Huashen Institute of Microbes and Infections, Shanghai, 200052 China
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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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An epigenome-wide view of osteoarthritis in primary tissues. Am J Hum Genet 2022; 109:1255-1271. [PMID: 35679866 PMCID: PMC9300761 DOI: 10.1016/j.ajhg.2022.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/11/2022] [Indexed: 12/16/2022] Open
Abstract
Osteoarthritis is a complex degenerative joint disease. Here, we investigate matched genotype and methylation profiles of primary chondrocytes from macroscopically intact (low-grade) and degraded (high-grade) osteoarthritis cartilage and from synoviocytes collected from 98 osteoarthritis-affected individuals undergoing knee replacement surgery. We perform an epigenome-wide association study of knee cartilage degeneration and report robustly replicating methylation markers, which reveal an etiologic mechanism linked to the migration of epithelial cells. Using machine learning, we derive methylation models of cartilage degeneration, which we validate with 82% accuracy in independent data. We report a genome-wide methylation quantitative trait locus (mQTL) map of articular cartilage and synovium and identify 18 disease-grade-specific mQTLs in osteoarthritis cartilage. We resolve osteoarthritis GWAS loci through causal inference and colocalization analyses and decipher the epigenetic mechanisms that mediate the effect of genotype on disease risk. Together, our findings provide enhanced insights into epigenetic mechanisms underlying osteoarthritis in primary tissues.
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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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Szwedowski D, Szczepanek J, Paczesny Ł, Zabrzyński J, Gagat M, Mobasheri A, Jeka S. The Effect of Platelet-Rich Plasma on the Intra-Articular Microenvironment in Knee Osteoarthritis. Int J Mol Sci 2021; 22:5492. [PMID: 34071037 PMCID: PMC8197096 DOI: 10.3390/ijms22115492] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/07/2023] Open
Abstract
Knee osteoarthritis (KOA) represents a clinical challenge due to poor potential for spontaneous healing of cartilage lesions. Several treatment options are available for KOA, including oral nonsteroidal anti-inflammatory drugs, physical therapy, braces, activity modification, and finally operative treatment. Intra-articular (IA) injections are usually used when the non-operative treatment is not effective, and when the surgery is not yet indicated. More and more studies suggesting that IA injections are as or even more efficient and safe than NSAIDs. Recently, research to improve intra-articular homeostasis has focused on biologic adjuncts, such as platelet-rich plasma (PRP). The catabolic and inflammatory intra-articular processes that exists in knee osteoarthritis (KOA) may be influenced by the administration of PRP and its derivatives. PRP can induce a regenerative response and lead to the improvement of metabolic functions of damaged structures. However, the positive effect on chondrogenesis and proliferation of mesenchymal stem cells (MSC) is still highly controversial. Recommendations from in vitro and animal research often lead to different clinical outcomes because it is difficult to translate non-clinical study outcomes and methodology recommendations to human clinical treatment protocols. In recent years, significant progress has been made in understanding the mechanism of PRP action. In this review, we will discuss mechanisms related to inflammation and chondrogenesis in cartilage repair and regenerative processes after PRP administration in in vitro and animal studies. Furthermore, we review clinical trials of PRP efficiency in changing the OA biomarkers in knee joint.
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Affiliation(s)
- Dawid Szwedowski
- Orthopedic Arthroscopic Surgery International (O.A.S.I.) Bioresearch Foundation, Gobbi N.P.O., 20133 Milan, Italy
- Department of Orthopaedics and Trauma Surgery, Provincial Polyclinical Hospital, 87100 Torun, Poland
| | - Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87100 Torun, Poland;
| | - Łukasz Paczesny
- Orvit Clinic, Citomed Healthcare Center, 87100 Torun, Poland; (Ł.P.); (J.Z.)
| | - Jan Zabrzyński
- Orvit Clinic, Citomed Healthcare Center, 87100 Torun, Poland; (Ł.P.); (J.Z.)
| | - Maciej Gagat
- Department of Histology and Embryology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85067 Bydgoszcz, Poland;
| | - Ali Mobasheri
- Research Unit of Medical Imaging, Physics and Technology, Faculty of Medicine, University of Oulu, FI-90014 Oulu, Finland;
- Department of Regenerative Medicine, State Research Institute Centre for Innovative Medicine, Santariskiu 5, LT-08406 Vilnius, Lithuania
- Departments of Orthopedics, Rheumatology and Clinical Immunology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
- Department of Joint Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Sławomir Jeka
- Department and Clinic of Rheumatology and Connective Tissue Diseases, University Hospital No. 2, Collegium Medicum UMK, 85168 Bydgoszcz, Poland;
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Wuelling M, Neu C, Thiesen AM, Kitanovski S, Cao Y, Lange A, Westendorf AM, Hoffmann D, Vortkamp A. Epigenetic Mechanisms Mediating Cell State Transitions in Chondrocytes. J Bone Miner Res 2021; 36:968-985. [PMID: 33534175 DOI: 10.1002/jbmr.4263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 01/06/2023]
Abstract
Epigenetic modifications play critical roles in regulating cell lineage differentiation, but the epigenetic mechanisms guiding specific differentiation steps within a cell lineage have rarely been investigated. To decipher such mechanisms, we used the defined transition from proliferating (PC) into hypertrophic chondrocytes (HC) during endochondral ossification as a model. We established a map of activating and repressive histone modifications for each cell type. ChromHMM state transition analysis and Pareto-based integration of differential levels of mRNA and epigenetic marks revealed that differentiation-associated gene repression is initiated by the addition of H3K27me3 to promoters still carrying substantial levels of activating marks. Moreover, the integrative analysis identified genes specifically expressed in cells undergoing the transition into hypertrophy. Investigation of enhancer profiles detected surprising differences in enhancer number, location, and transcription factor binding sites between the two closely related cell types. Furthermore, cell type-specific upregulation of gene expression was associated with increased numbers of H3K27ac peaks. Pathway analysis identified PC-specific enhancers associated with chondrogenic genes, whereas HC-specific enhancers mainly control metabolic pathways linking epigenetic signature to biological functions. Since HC-specific enhancers show a higher conservation in postnatal tissues, the switch to metabolic pathways seems to be a hallmark of differentiated tissues. Surprisingly, the analysis of H3K27ac levels at super-enhancers revealed a rapid adaption of H3K27ac occupancy to changes in gene expression, supporting the importance of enhancer modulation for acute alterations in gene expression. © 2021 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Manuela Wuelling
- Developmental Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Christoph Neu
- Developmental Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Andrea M Thiesen
- Developmental Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Simo Kitanovski
- Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Yingying Cao
- Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Anja Lange
- Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Astrid M Westendorf
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Andrea Vortkamp
- Developmental Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
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Tao J, Xia L, Cai Z, Liang L, Chen Y, Meng J, Wang Z. Interaction Between microRNA and DNA Methylation in Atherosclerosis. DNA Cell Biol 2020; 40:101-115. [PMID: 33259723 DOI: 10.1089/dna.2020.6138] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Atherosclerosis (AS) is a chronic inflammatory disease accompanied by complex pathological changes, such as endothelial dysfunction, foam cell formation, and vascular smooth muscle cell proliferation. Many approaches, including regulating AS-related gene expression in the transcriptional or post-transcriptional level, contribute to alleviating AS development. The DNA methylation is a crucial epigenetic modification in regulating cell function by silencing the relative gene expression. The microRNA (miRNA) is a type of noncoding RNA that plays an important role in gene post-transcriptional regulation and disease development. The DNA methylation and the miRNA are important epigenetic factors in AS. However, recent studies have found a mutual regulation between these two factors in AS development. In this study, recent insights into the roles of miRNA and DNA methylation and their interaction in the AS progression are reviewed.
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Affiliation(s)
- Jun Tao
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical College, University of South China, Hengyang, China
| | - Linzhen Xia
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical College, University of South China, Hengyang, China
| | - Zemin Cai
- Department of Pediatrics and The First Affiliated Hospital of University of South China, Hengyang, China
| | - Lingli Liang
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical College, University of South China, Hengyang, China
| | - Yanjun Chen
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical College, University of South China, Hengyang, China
| | - Jun Meng
- Functional Department, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Zuo Wang
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical College, University of South China, Hengyang, China
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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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Yin Z, Zhang X, Li J, Jiao Y, Kong Q, Mu Y. Identification of Imprinted Genes and Their Differentially Methylated Regions in Porcine. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795419120135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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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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Lim JH, Kang YJ, Lee BY, Han YJ, Chung JH, Kim MY, Kim MH, Kim JW, Cho YH, Ryu HM. Epigenome-wide base-resolution profiling of DNA methylation in chorionic villi of fetuses with Down syndrome by methyl-capture sequencing. Clin Epigenetics 2019; 11:180. [PMID: 31801612 PMCID: PMC6894197 DOI: 10.1186/s13148-019-0756-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/06/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Epigenetic mechanisms provide an interface between environmental factors and the genome and are influential in various diseases. These mechanisms, including DNA methylation, influence the regulation of development, differentiation, and establishment of cellular identity. Here, we performed high-throughput methylome profiling to determine whether differential patterns of DNA methylation correlate with Down syndrome (DS). MATERIALS AND METHODS We extracted DNA from the chorionic villi cells of five normal and five DS fetuses at the early developmental stage (12-13 weeks of gestation). Methyl-capture sequencing (MC-Seq) was used to investigate the methylation levels of CpG sites distributed across the whole genome to identify differentially methylated CpG sites (DMCs) and regions (DMRs) in DS. New functional annotations of DMR genes using bioinformatics tools were predicted. RESULTS DNA hypermethylation was observed in DS fetal chorionic villi cells. Significant differences were evident for 4,439 DMCs, including hypermethylation (n = 4,261) and hypomethylation (n = 178). Among them, 140 hypermethylated DMRs and only 1 hypomethylated DMR were located on 121 genes and 1 gene, respectively. One hundred twenty-two genes, including 141 DMRs, were associated with heart morphogenesis and development of the ear, thyroid gland, and nervous systems. The genes were significantly associated with DS and various diseases, including hepatopulmonary syndrome, conductive hearing loss, holoprosencephaly, heart diseases, glaucoma, and musculoskeletal abnormalities. CONCLUSIONS This is the first study to compare the whole-epigenome DNA methylation pattern of the chorionic villi cells from normal and DS fetuses at the early developmental-stage using MC-seq. Overall, our results indicate that the chorionic villi cells of DS fetuses are hypermethylated in all autosomes and suggested that altered DNA methylation may be a recurrent and functionally relevant downstream response to DS in human cells. This study provides basic information for future research focused on the pathophysiology of the DS and its potential effects, as well as the role DNA methylation plays in the early developmental stage of DS fetuses.
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Affiliation(s)
- Ji Hyae Lim
- Center for Biomarker Research and Precision Medicine, CHA Advanced Research Institute, Gyeonggi-do, Republic of Korea.,Department of Medical Genetics, College of Medicine, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Yu-Jung Kang
- Center for Biomarker Research and Precision Medicine, CHA Advanced Research Institute, Gyeonggi-do, Republic of Korea
| | - Bom Yi Lee
- SD Genomics Co., Ltd., Seoul, Republic of Korea
| | - You Jung Han
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - Jin Hoon Chung
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - Moon Young Kim
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - Min Hyoung Kim
- Department of Obstetrics Gynecology, Mizmedi Hospital, Seoul, Republic of Korea
| | - Jin Woo Kim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Republic of Korea
| | - Youl-Hee Cho
- Department of Medical Genetics, College of Medicine, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.
| | - Hyun Mee Ryu
- Center for Biomarker Research and Precision Medicine, CHA Advanced Research Institute, Gyeonggi-do, Republic of Korea. .,Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, 59, Yatap-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13496, Republic of Korea.
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12
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Nemtsova MV, Zaletaev DV, Bure IV, Mikhaylenko DS, Kuznetsova EB, Alekseeva EA, Beloukhova MI, Deviatkin AA, Lukashev AN, Zamyatnin AA. Epigenetic Changes in the Pathogenesis of Rheumatoid Arthritis. Front Genet 2019; 10:570. [PMID: 31258550 PMCID: PMC6587113 DOI: 10.3389/fgene.2019.00570] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/31/2019] [Indexed: 01/06/2023] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease that affects about 1% of the world’s population. The etiology of RA remains unknown. It is considered to occur in the presence of genetic and environmental factors. An increasing body of evidence pinpoints that epigenetic modifications play an important role in the regulation of RA pathogenesis. Epigenetics causes heritable phenotype changes that are not determined by changes in the DNA sequence. The major epigenetic mechanisms include DNA methylation, histone proteins modifications and changes in gene expression caused by microRNAs and other non-coding RNAs. These modifications are reversible and could be modulated by diet, drugs, and other environmental factors. Specific changes in DNA methylation, histone modifications and abnormal expression of non-coding RNAs associated with RA have already been identified. This review focuses on the role of these multiple epigenetic factors in the pathogenesis and progression of the disease, not only in synovial fibroblasts, immune cells, but also in the peripheral blood of patients with RA, which clearly shows their high diagnostic potential and promising targets for therapy in the future.
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Affiliation(s)
- Marina V Nemtsova
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Dmitry V Zaletaev
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Irina V Bure
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Dmitry S Mikhaylenko
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ekaterina B Kuznetsova
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ekaterina A Alekseeva
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Marina I Beloukhova
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Andrei A Deviatkin
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Alexander N Lukashev
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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13
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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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14
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Ren G, Krawetz RJ. Biochemical Markers for the Early Identification of Osteoarthritis: Systematic Review and Meta-Analysis. Mol Diagn Ther 2018; 22:671-682. [PMID: 30377978 DOI: 10.1007/s40291-018-0362-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND There is a desperate need for the reliable detection of osteoarthritis (OA) at the early stage when patients are likely to benefit most from disease interventions. A variety of biochemical markers have been proposed, but their reliability varies among studies. OBJECTIVE In this review, we aimed to answer the following questions: (1) are there biochemical markers that are differentially expressed in early OA versus healthy subjects, and (2) if so, what is the diagnostic value of these biomarkers for early OA? METHODS Embase, PubMed, and Web of Science were searched to obtain all relevant studies up to March 2018, and studies comparing the biochemical markers between early OA and healthy controls were selected. The Downs and Black checklist was used to assess the risk of bias. Biomarkers that were investigated in five or more different populations were pooled for meta-analysis. A meta-regression analysis was performed to explore possible explanations for the heterogeneity of studies. RESULT In total, 26 articles met the criteria for the qualitative synthesis and 17 articles for the final quantitative synthesis. N-terminal crosslinked telopeptide of type I collagen (NTX-I) was the only biomarker found to be differently expressed in patients with early OA versus controls, without significant heterogeneity among studies (I2 = 0%, [Formula: see text] = 1.695, p = 0.792). The meta-regression analysis identified that sample size and affected joint possibly explained the heterogeneity among studies. CONCLUSION Although a wide range of biomarkers has been previously investigated in early OA, the diagnostic value of these biomarkers could not be determined because due to a low number of studies regarding any given biomarker. Large prospective and adequately powered studies are therefore required to validate these (and other) biomarkers for identifying early OA.
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Affiliation(s)
- Guomin Ren
- Cumming School of Medicine, McCaig Institute, University of Calgary, HRIC 3AA14, 3330 Hospital Dr. NW, Calgary, AB, T2N 4N1, Canada
- Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, Canada
| | - Roman J Krawetz
- Cumming School of Medicine, McCaig Institute, University of Calgary, HRIC 3AA14, 3330 Hospital Dr. NW, Calgary, AB, T2N 4N1, Canada.
- Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, Canada.
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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15
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Shen L, Zhu J, Robert Li SY, Fan X. Detect differentially methylated regions using non-homogeneous hidden Markov model for methylation array data. Bioinformatics 2018; 33:3701-3708. [PMID: 29036320 DOI: 10.1093/bioinformatics/btx467] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 07/18/2017] [Indexed: 12/12/2022] Open
Abstract
Motivation DNA methylation is an important epigenetic mechanism in gene regulation and the detection of differentially methylated regions (DMRs) is enthralling for many disease studies. There are several aspects that we can improve over existing DMR detection methods: (i) methylation statuses of nearby CpG sites are highly correlated, but this fact has seldom been modelled rigorously due to the uneven spacing; (ii) it is practically important to be able to handle both paired and unpaired samples; and (iii) the capability to detect DMRs from a single pair of samples is demanded. Results We present DMRMark (DMR detection based on non-homogeneous hidden Markov model), a novel Bayesian framework for detecting DMRs from methylation array data. It combines the constrained Gaussian mixture model that incorporates the biological knowledge with the non-homogeneous hidden Markov model that models spatial correlation. Unlike existing methods, our DMR detection is achieved without predefined boundaries or decision windows. Furthermore, our method can detect DMRs from a single pair of samples and can also incorporate unpaired samples. Both simulation studies and real datasets from The Cancer Genome Atlas showed the significant improvement of DMRMark over other methods. Availability and implementation DMRMark is freely available as an R package at the CRAN R package repository. Contact xfan@cuhk.edu.hk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Linghao Shen
- Department of Information Engineering, The Chinese University of Hong Kong, Hong Kong
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York University, New York, NY, USA
| | - Shuo-Yen Robert Li
- University of Electronic Science and Technology of China, Sichuan, China
| | - Xiaodan Fan
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong
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16
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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: 100] [Impact Index Per Article: 16.7] [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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17
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Karouzakis E, Raza K, Kolling C, Buckley CD, Gay S, Filer A, Ospelt C. Analysis of early changes in DNA methylation in synovial fibroblasts of RA patients before diagnosis. Sci Rep 2018; 8:7370. [PMID: 29743579 PMCID: PMC5943364 DOI: 10.1038/s41598-018-24240-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/26/2018] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an important epigenetic modification that is known to be altered in rheumatoid arthritis synovial fibroblasts (RASF). Here, we compared the status of promoter DNA methylation of SF from patients with very early RA with SF from patients with resolving arthritis, fully established RA and from non-arthritic patients. DNA was hybridized to Infinium Human methylation 450k and 850k arrays and differential methylated genes and pathways were identified. We could identify a significant number of CpG sites that differed between the SF of different disease stages, showing that epigenetic changes in SF occur early in RA development. Principal component analysis confirmed that the different groups of SF were separated according to their DNA methylation state. Furthermore, pathway analysis showed that important functional pathways were altered in both very early and late RASF. By focusing our analysis on CpG sites in CpG islands within promoters, we identified genes that have significant hypermethylated promoters in very early RASF. Our data show that changes in DNA methylation differ in RASF compared to other forms of arthritis and occur at a very early, clinically yet unspecific stage of disease. The identified differential methylated genes might become valuable prognostic biomarkers for RA development.
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Affiliation(s)
- Emmanuel Karouzakis
- Center of Experimental Rheumatology, Department of Rheumatology, University of Zurich, Zurich, CH-8952, Switzerland.
| | - Karim Raza
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, B15 2TT, UK.,Sandwell and West Birmingham Hospitals NHS Trust, West Bromwich, B71 4HJ, UK
| | | | - Christopher D Buckley
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Steffen Gay
- Center of Experimental Rheumatology, Department of Rheumatology, University of Zurich, Zurich, CH-8952, Switzerland
| | - Andrew Filer
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, B15 2TT, UK.,University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2 GW, UK
| | - Caroline Ospelt
- Center of Experimental Rheumatology, Department of Rheumatology, University of Zurich, Zurich, CH-8952, Switzerland
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18
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Steinberg J, Ritchie GRS, Roumeliotis TI, Jayasuriya RL, Clark MJ, Brooks RA, Binch ALA, Shah KM, Coyle R, Pardo M, Le Maitre CL, Ramos YFM, Nelissen RGHH, Meulenbelt I, McCaskie AW, Choudhary JS, Wilkinson JM, Zeggini E. Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis. Sci Rep 2017; 7:8935. [PMID: 28827734 PMCID: PMC5566454 DOI: 10.1038/s41598-017-09335-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/17/2017] [Indexed: 11/09/2022] Open
Abstract
Osteoarthritis (OA) is a common disease characterized by cartilage degeneration and joint remodeling. The underlying molecular changes underpinning disease progression are incompletely understood. We investigated genes and pathways that mark OA progression in isolated primary chondrocytes taken from paired intact versus degraded articular cartilage samples across 38 patients undergoing joint replacement surgery (discovery cohort: 12 knee OA, replication cohorts: 17 knee OA, 9 hip OA patients). We combined genome-wide DNA methylation, RNA sequencing, and quantitative proteomics data. We identified 49 genes differentially regulated between intact and degraded cartilage in at least two -omics levels, 16 of which have not previously been implicated in OA progression. Integrated pathway analysis implicated the involvement of extracellular matrix degradation, collagen catabolism and angiogenesis in disease progression. Using independent replication datasets, we showed that the direction of change is consistent for over 90% of differentially expressed genes and differentially methylated CpG probes. AQP1, COL1A1 and CLEC3B were significantly differentially regulated across all three -omics levels, confirming their differential expression in human disease. Through integration of genome-wide methylation, gene and protein expression data in human primary chondrocytes, we identified consistent molecular players in OA progression that replicated across independent datasets and that have translational potential.
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Affiliation(s)
- Julia Steinberg
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Cancer Research Division, Cancer Council NSW, Sydney, NSW, 2011, Australia
| | - Graham R S Ritchie
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Usher Institute of Population Health Sciences & Informatics, University of Edinburgh, Edinburgh, EH16 4UX, UK.,MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Theodoros I Roumeliotis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Raveen L Jayasuriya
- Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Matthew J Clark
- Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Roger A Brooks
- Division of Trauma & Orthopaedic Surgery, University of Cambridge, Box 180, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Abbie L A Binch
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Karan M Shah
- Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Rachael Coyle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Mercedes Pardo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Christine L Le Maitre
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Yolande F M Ramos
- Department of Medical Statistics and Bioinformatics, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, 2300RC, The Netherlands
| | - Rob G H H Nelissen
- Department of Orthopedics, Leiden University Medical Center, Leiden, 2300RC, The Netherlands
| | - Ingrid Meulenbelt
- Department of Medical Statistics and Bioinformatics, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, 2300RC, The Netherlands
| | - Andrew W McCaskie
- Division of Trauma & Orthopaedic Surgery, University of Cambridge, Box 180, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Jyoti S Choudhary
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - J Mark Wilkinson
- Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK.
| | - Eleftheria Zeggini
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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Marchev AS, Dimitrova PA, Burns AJ, Kostov RV, Dinkova-Kostova AT, Georgiev MI. Oxidative stress and chronic inflammation in osteoarthritis: can NRF2 counteract these partners in crime? Ann N Y Acad Sci 2017; 1401:114-135. [PMID: 28662306 DOI: 10.1111/nyas.13407] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/08/2017] [Accepted: 05/12/2017] [Indexed: 01/15/2023]
Abstract
Osteoarthritis (OA) is an age-related joint degenerative disease associated with pain, joint deformity, and disability. The disease starts with cartilage damage but then progressively involves subchondral bone, causing an imbalance between osteoclast-driven bone resorption and osteoblast-driven remodeling. Here, we summarize the data for the role of oxidative stress and inflammation in OA pathology and discuss how these two processes are integrated during OA progression, as well as their contribution to abnormalities in cartilage/bone metabolism and integrity. At the cellular level, oxidative stress and inflammation are counteracted by transcription factor nuclear factor erythroid p45-related factor 2 (NRF2), and we describe the regulation of NRF2, highlighting its role in OA pathology. We also discuss the beneficial effect of some phytonutrients, including the therapeutic potential of NRF2 activation, in OA.
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Affiliation(s)
- Andrey S Marchev
- Group of Plant Cell Biotechnology and Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Plovdiv, Bulgaria
| | - Petya A Dimitrova
- Department of Immunology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Andrew J Burns
- Jacqui Wood Cancer Centre, Division of Cancer Research, School of Medicine, University of Dundee, Dundee, UK
| | - Rumen V Kostov
- Jacqui Wood Cancer Centre, Division of Cancer Research, School of Medicine, University of Dundee, Dundee, UK
| | - Albena T Dinkova-Kostova
- Jacqui Wood Cancer Centre, Division of Cancer Research, School of Medicine, University of Dundee, Dundee, UK
- Departments of Medicine and Pharmacology and Molecular Sciences, Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Milen I Georgiev
- Group of Plant Cell Biotechnology and Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Plovdiv, Bulgaria
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20
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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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21
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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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22
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Smeeton J, Askary A, Crump JG. Building and maintaining joints by exquisite local control of cell fate. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2017; 6:10.1002/wdev.245. [PMID: 27581688 PMCID: PMC5877473 DOI: 10.1002/wdev.245] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/30/2016] [Accepted: 07/01/2016] [Indexed: 12/18/2022]
Abstract
We owe the flexibility of our bodies to sophisticated articulations between bones. Establishment of these joints requires the integration of multiple tissue types: permanent cartilage that cushions the articulating bones, synovial membranes that enclose a lubricating fluid-filled cavity, and a fibrous capsule and ligaments that provide structural support. Positioning the prospective joint region involves establishment of an "interzone" region of joint progenitor cells within a nascent cartilage condensation, which is achieved through the interplay of activators and inhibitors of multiple developmental signaling pathways. Within the interzone, tight regulation of BMP and TGFβ signaling prevents the hypertrophic maturation of joint chondrocytes, in part through downstream transcriptional repressors and epigenetic modulators. Synovial cells then acquire further specializations through expression of genes that promote lubrication, as well as the formation of complex structures such as cavities and entheses. Whereas genetic investigations in mice and humans have uncovered a number of regulators of joint development and homeostasis, recent work in zebrafish offers a complementary reductionist approach toward understanding joint positioning and the regulation of chondrocyte fate at joints. The complexity of building and maintaining joints may help explain why there are still few treatments for osteoarthritis, one of the most common diseases in the human population. A major challenge will be to understand how developmental abnormalities in joint structure, as well as postnatal roles for developmental genes in joint homeostasis, contribute to birth defects and degenerative diseases of joints. WIREs Dev Biol 2017, 6:e245. doi: 10.1002/wdev.245 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Joanna Smeeton
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - Amjad Askary
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - J. Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
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23
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Xu Y, Liu Z, Wang T, Chen X, Deng J, Chen M, Li Z. Identification of differentially methylated regions (DMRs) of neuronatin in mice. SPRINGERPLUS 2016; 5:2018. [PMID: 27994995 PMCID: PMC5125312 DOI: 10.1186/s40064-016-3721-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 11/21/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Neuronatin (NNAT) is a paternal-inherited imprinted gene, first discovered in the rat neonatal brain, where it plays vital roles for neuronal growth, brain development, and metabolic regulation. The maternal imprint of NNAT has been identified in mice; however, the differentially methylated regions (DMRs) involved in the monoallelic expression of NNAT have not yet been investigated. RESULTS In this study, we confirmed expression of two isoforms of the NNAT (α and β) in the mice brain via quantitative RT-PCR. Additionally, the methylation profile of the CpG island located in the NNAT gene locus was determined in the mice liver, brain, sperm, and the MII oocyte via bisulfite sequencing PCR. CONCLUSION In summary, we provide the first evidence for tissue- and gamete-specific methylation patterns of CpG3 that are located on exon 1, to be putative DMR of NNAT in mice.
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Affiliation(s)
- Yuxin Xu
- College of Animal Science, Jilin University, 5333#, Xi’an Road, Changchun, 130062 China
| | - Zhiquan Liu
- College of Animal Science, Jilin University, 5333#, Xi’an Road, Changchun, 130062 China
| | - Tiedong Wang
- College of Animal Science, Jilin University, 5333#, Xi’an Road, Changchun, 130062 China
| | - Xianju Chen
- College of Animal Science, Jilin University, 5333#, Xi’an Road, Changchun, 130062 China
| | - Jichao Deng
- College of Animal Science, Jilin University, 5333#, Xi’an Road, Changchun, 130062 China
| | - Mao Chen
- College of Animal Science, Jilin University, 5333#, Xi’an Road, Changchun, 130062 China
| | - Zhanjun Li
- College of Animal Science, Jilin University, 5333#, Xi’an Road, Changchun, 130062 China
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Lewallen EA, Bonin CA, Li X, Smith J, Karperien M, Larson AN, Lewallen DG, Cool SM, Westendorf JJ, Krych AJ, Leontovich AA, Im HJ, van Wijnen AJ. The synovial microenvironment of osteoarthritic joints alters RNA-seq expression profiles of human primary articular chondrocytes. Gene 2016; 591:456-64. [PMID: 27378743 PMCID: PMC5989726 DOI: 10.1016/j.gene.2016.06.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 11/20/2022]
Abstract
Osteoarthritis (OA) is a disabling degenerative joint disease that prompts pain and has limited treatment options. To permit early diagnosis and treatment of OA, a high resolution mechanistic understanding of human chondrocytes in normal and diseased states is necessary. In this study, we assessed the biological effects of OA-related changes in the synovial microenvironment on chondrocytes embedded within anatomically intact cartilage from joints with different pathological grades by next generation RNA-sequencing (RNA-seq). We determined the transcriptome of primary articular chondrocytes derived from anatomically unaffected knees and ankles, as well as from joints affected by OA. The GALAXY bioinformatics platform was used to facilitate biological interpretations. Comparisons of patient samples by k-means, hierarchical clustering and principal component analyses together reveal that primary chondrocytes exhibit OA grade-related differences in gene expression, including genes involved in cell-adhesion, ECM production and immune response. We conclude that diseased synovial microenvironments in joints with different histopathological OA grades directly alter gene expression in chondrocytes. One ramification of this finding is that anatomically intact cartilage from OA joints is not an ideal source of healthy chondrocytes, nor should these specimens be used to generate a normal baseline for the molecular characterization of diseased joints.
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Affiliation(s)
- Eric A Lewallen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States.
| | - Carolina A Bonin
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States.
| | - Xin Li
- Jesse Brown VA Medical Center, Chicago, IL, United States.
| | - Jay Smith
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, United States.
| | - Marcel Karperien
- Department of Developmental Bioengineering, University of Twente, Enschede, The Netherlands.
| | - A Noelle Larson
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States.
| | - David G Lewallen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States.
| | - Simon M Cool
- Department of Orthopedic Surgery, National University of Singapore, Singapore.
| | - Jennifer J Westendorf
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States; Department of Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, United States.
| | - Aaron J Krych
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States.
| | - Alexey A Leontovich
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States.
| | - Hee-Jeong Im
- Jesse Brown VA Medical Center, Chicago, IL, United States; Department of Biochemistry, Rush University, Chicago, IL, United States; Department of Orthopedic Surgery, Rush University, Chicago, IL, United States; Department of Internal Medicine, Rush University, Chicago, IL, United States.
| | - Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States; Department of Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, United States; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, United States.
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25
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Bradley EW, Carpio LR, McGee-Lawrence ME, Becerra CC, Amanatullah DF, Ta LE, Otero M, Goldring MB, Kakar S, Westendorf JJ. Phlpp1 facilitates post-traumatic osteoarthritis and is induced by inflammation and promoter demethylation in human osteoarthritis. Osteoarthritis Cartilage 2016; 24:1021-8. [PMID: 26746148 PMCID: PMC4875839 DOI: 10.1016/j.joca.2015.12.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/23/2015] [Accepted: 12/20/2015] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Osteoarthritis (OA) is the most common form of arthritis and a leading cause of disability. OA is characterized by articular chondrocyte deterioration, subchondral bone changes and debilitating pain. One strategy to promote cartilage regeneration and repair is to accelerate proliferation and matrix production of articular chondrocytes. We previously reported that the protein phosphatase Phlpp1 controls chondrocyte differentiation by regulating the activities of anabolic kinases. Here we examined the role of Phlpp1 in OA progression in a murine model. We also assessed PHLPP1 expression and promoter methylation. DESIGN Knee joints of WT and Phlpp1(-/-) mice were surgically destabilized by transection of the medial meniscal ligament (DMM). Mice were assessed for signs of OA progression via radiographic and histological analyses, and pain assessment for mechanical hypersensitivity using the von Frey assay. Methylation of the PHLPP1 promoter and PHLPP1 expression were evaluated in human articular cartilage and chondrocyte cell lines. RESULTS Following DMM surgeries, Phlpp1 deficient mice showed fewer signs of OA and cartilage degeneration. Mechanical allodynia associated with DMM surgeries was also attenuated in Phlpp1(-/-) mice. PHLPP1 was highly expressed in human articular cartilage from OA patients, but was undetectable in cartilage specimens from femoral neck fractures (FNFxs). Higher PHLPP1 levels correlated with less PHLPP1 promoter CpG methylation in cartilage from OA patients. Blocking cytosine methylation or treatment with inflammatory mediators enhanced PHLPP1 expression in human chondrocyte cell lines. CONCLUSION Phlpp1 deficiency protects against OA progression while CpG demethylation and inflammatory cytokines promote PHLPP1 expression.
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Affiliation(s)
| | | | - Meghan E. McGee-Lawrence
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN 55905,Department of Cellular Biology and Anatomy, Georgia Regents University, Augusta, GA, 30912
| | | | | | - Lauren E. Ta
- Department of Neurology, Mayo Clinic, Rochester, MN 55905
| | - Miguel Otero
- Research Division, Hospital for Special Surgery, Weill Cornell Medical College, New York, NY 10021
| | - Mary B. Goldring
- Research Division, Hospital for Special Surgery, Weill Cornell Medical College, New York, NY 10021
| | - Sanjeev Kakar
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN 55905
| | - Jennifer J. Westendorf
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN 55905,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905
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26
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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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