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Kawarai Y, Nakamura J, Hagiwara S, Suzuki-Narita M, Inage K, Ohtori S. Alterations in DNA methylation machinery in a rat model of osteoarthritis of the hip. J Orthop Surg Res 2024; 19:357. [PMID: 38880910 PMCID: PMC11181635 DOI: 10.1186/s13018-024-04847-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024] Open
Abstract
BACKGROUND This study aimed to validate alterations in the gene expression of DNA methylation-related enzymes and global methylation in the peripheral blood mononuclear cell (PBMC) and synovial tissues of animal hip osteoarthritis (OA) models. METHODS Animals were assigned to the control (no treatment), sham (25 µL of sterile saline), and OA (25 µL of sterile saline and 2 mg of monoiodoacetate) groups. Microcomputed tomography scan, histopathological assessment and pain threshold measurement were performed after induction. The mRNA expression of the DNA methylation machinery genes and global DNA methylation in the PBMC and hip synovial tissue were evaluated. RESULTS The OA group presented with hip joint OA histopathologically and radiologically and decreased pain threshold. The mRNA expression of DNA methyltransferase (Dnmt 3a), ten-eleven translocation (Tet) 1 and Tet 3 in the synovial tissue of the OA group was significantly upregulated. Global DNA methylation in the synovial tissue of the OA group was significantly higher than that of the control and sham groups. CONCLUSIONS The intra-articular administration of monoiodoacetate induced hip joint OA and decreased pain threshold. The DNA methylation machinery in the synovial tissues of hip OA was altered.
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Affiliation(s)
- Yuya Kawarai
- Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, 1- 8-1 Inohana, Chuo-ku, Chiba City, Chiba, 260-8677, Japan.
| | - Junichi Nakamura
- Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, 1- 8-1 Inohana, Chuo-ku, Chiba City, Chiba, 260-8677, Japan
| | - Shigeo Hagiwara
- Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, 1- 8-1 Inohana, Chuo-ku, Chiba City, Chiba, 260-8677, Japan
| | - Miyako Suzuki-Narita
- Department of Bioenvironmental Medicine, Graduate School of Medicine, Chiba University, 1- 8-1 Inohana, Chuo-ku, Chiba City, Chiba, 260-8677, Japan
| | - Kazuhide Inage
- Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, 1- 8-1 Inohana, Chuo-ku, Chiba City, Chiba, 260-8677, Japan
| | - Seiji Ohtori
- Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, 1- 8-1 Inohana, Chuo-ku, Chiba City, Chiba, 260-8677, Japan
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Núñez-Carro C, Blanco-Blanco M, Villagrán-Andrade KM, Blanco FJ, de Andrés MC. Epigenetics as a Therapeutic Target in Osteoarthritis. Pharmaceuticals (Basel) 2023; 16:156. [PMID: 37259307 PMCID: PMC9964205 DOI: 10.3390/ph16020156] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 08/15/2023] Open
Abstract
Osteoarthritis (OA) is a heterogenous, complex disease affecting the integrity of diarthrodial joints that, despite its high prevalence worldwide, lacks effective treatment. In recent years it has been discovered that epigenetics may play an important role in OA. Our objective is to review the current knowledge of the three classical epigenetic mechanisms-DNA methylation, histone post-translational modifications (PTMs), and non-coding RNA (ncRNA) modifications, including microRNAs (miRNAs), circular RNAs (circRNAs), and long non-coding RNAs (lncRNAs)-in relation to the pathogenesis of OA and focusing on articular cartilage. The search for updated literature was carried out in the PubMed database. Evidence shows that dysregulation of numerous essential cartilage molecules is caused by aberrant epigenetic regulatory mechanisms, and it contributes to the development and progression of OA. This offers the opportunity to consider new candidates as therapeutic targets with the potential to attenuate OA or to be used as novel biomarkers of the disease.
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Affiliation(s)
- Carmen Núñez-Carro
- Unidad de Epigenética, Grupo de Investigación en Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario, de A Coruña (CHUAC), Sergas, 15006 A Coruña, Spain
| | - Margarita Blanco-Blanco
- Unidad de Epigenética, Grupo de Investigación en Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario, de A Coruña (CHUAC), Sergas, 15006 A Coruña, Spain
| | - Karla Mariuxi Villagrán-Andrade
- Unidad de Epigenética, Grupo de Investigación en Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario, de A Coruña (CHUAC), Sergas, 15006 A Coruña, Spain
| | - Francisco J. Blanco
- Unidad de Epigenética, Grupo de Investigación en Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario, de A Coruña (CHUAC), Sergas, 15006 A Coruña, Spain
- Grupo de Investigación en Reumatología y Salud, Departamento de Fisioterapia, Medicina y Ciencias Biomédicas, Facultad de Fisioterapia, Campus de Oza, Universidade da Coruña (UDC), 15008 A Coruña, Spain
| | - María C. de Andrés
- Unidad de Epigenética, Grupo de Investigación en Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario, de A Coruña (CHUAC), Sergas, 15006 A Coruña, Spain
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Hernaiz A, Sentre S, Betancor M, López-Pérez Ó, Salinas-Pena M, Zaragoza P, Badiola JJ, Toivonen JM, Bolea R, Martín-Burriel I. 5-Methylcytosine and 5-Hydroxymethylcytosine in Scrapie-Infected Sheep and Mouse Brain Tissues. Int J Mol Sci 2023; 24:ijms24021621. [PMID: 36675131 PMCID: PMC9864596 DOI: 10.3390/ijms24021621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Scrapie is a neurodegenerative disorder belonging to the group of transmissible spongiform encephalopathies or prion diseases, which are caused by an infectious isoform of the innocuous cellular prion protein (PrPC) known as PrPSc. DNA methylation, one of the most studied epigenetic mechanisms, is essential for the proper functioning of the central nervous system. Recent findings point to possible involvement of DNA methylation in the pathogenesis of prion diseases, but there is still a lack of knowledge about the behavior of this epigenetic mechanism in such neurodegenerative disorders. Here, we evaluated by immunohistochemistry the 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) levels in sheep and mouse brain tissues infected with scrapie. Expression analysis of different gene coding for epigenetic regulatory enzymes (DNMT1, DNMT3A, DNMT3B, HDAC1, HDAC2, TET1, and TET2) was also carried out. A decrease in 5mC levels was observed in scrapie-affected sheep and mice compared to healthy animals, whereas 5hmC displayed opposite patterns between the two models, demonstrating a decrease in 5hmC in scrapie-infected sheep and an increase in preclinical mice. 5mC correlated with prion-related lesions in mice and sheep, but 5hmC was associated with prion lesions only in sheep. Differences in the expression changes of epigenetic regulatory genes were found between both disease models, being differentially expressed Dnmt3b, Hdac1, and Tet1 in mice and HDAC2 in sheep. Our results support the evidence that DNA methylation in both forms, 5mC and 5hmC, and its associated epigenetic enzymes, take part in the neurodegenerative course of prion diseases.
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Affiliation(s)
- Adelaida Hernaiz
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Sara Sentre
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Marina Betancor
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Óscar López-Pérez
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Mónica Salinas-Pena
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Pilar Zaragoza
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, 28029 Madrid, Spain
| | - Juan José Badiola
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Janne Markus Toivonen
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, 28029 Madrid, Spain
| | - Rosa Bolea
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Inmaculada Martín-Burriel
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-976-761662
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Sahu N, Grandi FC, Bhutani N. A single-cell mass cytometry platform to map the effects of preclinical drugs on cartilage homeostasis. JCI Insight 2022; 7:160702. [PMID: 36194485 PMCID: PMC9744259 DOI: 10.1172/jci.insight.160702] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/12/2022] [Indexed: 02/04/2023] Open
Abstract
No disease-modifying drug exists for osteoarthritis (OA). Despite success in animal models, candidate drugs continue to fail in clinical trials owing to the unmapped interpatient heterogeneity and disease complexity. We used a single-cell platform based on cytometry by time-of-flight (cyTOF) to precisely outline the effects of candidate drugs on human OA chondrocytes. OA chondrocytes harvested from patients undergoing total knee arthroplasty were treated with 2 drugs, an NF-κB pathway inhibitor, BMS-345541, and a chondroinductive small molecule, kartogenin, that showed preclinical success in animal models for OA. cyTOF conducted with 30 metal isotope-labeled antibodies parsed the effects of the drugs on inflammatory, senescent, and chondroprogenitor cell populations. The NF-κB pathway inhibition decreased the expression of p-NF-κB, HIF2A, and inducible NOS in multiple chondrocyte clusters and significantly depleted 4 p16ink4a-expressing senescent populations, including NOTCH1+STRO1+ chondroprogenitor cells. While kartogenin also affected select p16ink4a-expressing senescent clusters, there was a less discernible effect on chondroprogenitor cell populations. Overall, BMS-345541 elicited a uniform drug response in all patients, while only a few responded to kartogenin. These studies demonstrate that a single-cell cyTOF-based drug screening platform can provide insights into patient response assessment and patient stratification.
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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: 4] [Impact Index Per Article: 2.0] [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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6
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Singh P, Wang M, Mukherjee P, Lessard SG, Pannellini T, Carballo CB, Rodeo SA, Goldring MB, Otero M. Transcriptomic and epigenomic analyses uncovered Lrrc15 as a contributing factor to cartilage damage in osteoarthritis. Sci Rep 2021; 11:21107. [PMID: 34702854 PMCID: PMC8548547 DOI: 10.1038/s41598-021-00269-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/05/2021] [Indexed: 01/03/2023] Open
Abstract
In osteoarthritis (OA), articular chondrocytes display phenotypic and functional changes associated with epigenomic alterations. These changes contribute to the disease progression, which is characterized by dysregulated reparative processes and abnormal extracellular matrix remodeling leading to cartilage degradation. Recent studies using a murine model of posttraumatic OA highlighted the contribution of changes in DNA hydroxymethylation (5hmC) to OA progression. Here, we integrated transcriptomic and epigenomic analyses in cartilage after induction of OA to show that the structural progression of OA is accompanied by early transcriptomic and pronounced DNA methylation (5mC) changes in chondrocytes. These changes accumulate over time and are associated with recapitulation of developmental processes, including cartilage development, chondrocyte hypertrophy, and ossification. Our integrative analyses also uncovered that Lrrc15 is differentially methylated and expressed in OA cartilage, and that it may contribute to the functional and phenotypic alterations of chondrocytes, likely coordinating stress responses and dysregulated extracellular matrix remodeling.
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Affiliation(s)
- Purva Singh
- Hospital for Special Surgery, HSS Research Institute, New York, NY, 10021, USA
| | - Mengying Wang
- Hospital for Special Surgery, HSS Research Institute, New York, NY, 10021, USA.,School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | | | - Samantha G Lessard
- Hospital for Special Surgery, HSS Research Institute, New York, NY, 10021, USA
| | - Tania Pannellini
- Hospital for Special Surgery, HSS Research Institute, New York, NY, 10021, USA
| | - Camila B Carballo
- Hospital for Special Surgery, HSS Research Institute, New York, NY, 10021, USA
| | - Scott A Rodeo
- Hospital for Special Surgery, HSS Research Institute, New York, NY, 10021, USA.,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Mary B Goldring
- Hospital for Special Surgery, HSS Research Institute, New York, NY, 10021, USA.,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Miguel Otero
- Hospital for Special Surgery, HSS Research Institute, New York, NY, 10021, USA. .,Weill Cornell Medicine, New York, NY, 10021, USA. .,Hospital for Special Surgery, Orthopedic Soft Tissue Research Program, HSS Research Institute, Room 603, 535 East 70th Street, New York, NY, 10021, USA.
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7
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Deshpande SSS, Nemani H, Balasinor NH. High fat diet-induced- and genetically inherited- obesity differential alters DNA demethylation pathways in the germline of adult male rats. Reprod Biol 2021; 21:100532. [PMID: 34246869 DOI: 10.1016/j.repbio.2021.100532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/11/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022]
Abstract
Obesity is a multifactorial condition with predominantly genetic and environmental causes and is an emerging risk factor for male infertility/subfertility. Epigenetic mechanisms are vulnerable to genetic and environmental changes. Our earlier studies have shown differential effects of genetically inherited (GIO) - and diet-induced- obesity (DIO) on DNA methylation in male germline. Contrary to DNA methylation is DNA demethylation, which also regulates the gene expression by activating transcription. The present study aimed to delineate the effects of obesity on the DNA demethylation pathway using two rat models: GIO (WNIN/Ob) and DIO (high-fat diet). We observed differential alterations in enzymes involved in DNA demethylation by oxidation (Tet1-3) pathway in testis in both groups. An increase in Tets in DIO group and a decrease in GIO group were noted. Analysis of oxidation pathway intermediates (5-hmC, 5-fC, and 5-caC) did not show any effect on testis in DIO group but an increase in 5-hmC and decrease in 5-caC levels in GIO group was observed. Analysis of transcript levels of enzymes related to deamination pathway in testis showed an increase (Gadd45a, Aicda, and Tdg) in DIO group and a decrease (Gadd45a, Aicda, and Tdg) in GIO group. Also, 5-hmC levels were differentially altered in the spermatozoa of both groups without any changes in Tet enzyme levels. These findings highlight differences in effects of GIO and DIO on DNA demethylation mechanisms in male germline, which could be due to differences in endocrine and metabolic profile as well as white fat distribution observed earlier in two groups.
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Affiliation(s)
- Sharvari S S Deshpande
- Department of Neuroendocrinology, ICMR-National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Harishankar Nemani
- National Institute of Nutrition Animal Facility, ICMR-National Institute of Nutrition, Jamai-Osmania PO, Hyderabad, 500 007, India
| | - Nafisa H Balasinor
- Department of Neuroendocrinology, ICMR-National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India.
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Ratneswaran A, Kapoor M. Osteoarthritis year in review: genetics, genomics, epigenetics. Osteoarthritis Cartilage 2021; 29:151-160. [PMID: 33227439 DOI: 10.1016/j.joca.2020.11.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/23/2020] [Accepted: 11/13/2020] [Indexed: 02/02/2023]
Abstract
OBJECTIVE In this review, we have highlighted advances in genetics, genomics and epigenetics in the field of osteoarthritis (OA) over the past year. METHODS A literature search was performed using PubMed and the criteria: "osteoarthritis" and one of the following terms "genetic(s), genomic(s), epigenetic(s), epigenomic(s), noncoding RNA, microRNA, long noncoding RNA, lncRNA, circular RNA, RNA sequencing, single cell sequencing, or DNA methylation between April 1, 2019 and April 30, 2020. RESULTS We identified 653 unique publications, many studies spanned multiple search terms. We summarized advances relating to evolutionary genetics, pain, ethnicity specific risk factors, functional studies of gene variants, and interactions between coding and non-coding RNAs in OA pathogenesis. CONCLUSIONS Studies have identified variants contributing to OA susceptibility, candidate biomarkers for diagnosis and prognosis, as well as promising therapeutic candidates. Validation in multiple cohorts, multi-omics strategies, and machine learning aided computational analyses have all contributed to the strength of published literature. Open access data-sets, greater sample sizes to capture broader populations and understanding disease mechanisms by investigating the interactions between multiple tissue types will further aid in progress towards understanding and curing OA.
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Affiliation(s)
- A Ratneswaran
- Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada; Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - M Kapoor
- Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada; Krembil Research Institute, University Health Network, Toronto, ON, Canada; Department of Surgery, Faculty of Medicine, University of Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
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9
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Cai W, Hu X. Genome-wide methylation analysis of pre-pregnancy women in hypothyroidism. J Matern Fetal Neonatal Med 2021; 35:5035-5042. [PMID: 33455507 DOI: 10.1080/14767058.2021.1874907] [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: 10/22/2022]
Abstract
BACKGROUND Hypothyroidism is a systemic metabolic deficiency syndrome caused by a deficiency in thyroid hormone or a decrease in the action of thyroid hormones. It has a high incidence among women of child-bearing age, and pregnant women with hypothyroidism may have a higher risk of birth defects. OBJECTIVE To explore the specific biological mechanism affecting the occurrence of hypothyroidism. METHODS This study determined key molecules by comparing and analyzing the difference in methylation levels between pre-pregnancy women and normal controls using the Illumina Infinium MethylationEPIC BeadChip. RESULTS 3493 Differential methylation positions (DMPs) related genes and 47 differentially methylated regions (DMRs) related genes were found between the Hypothyroidism group and the control group. Among them, miR-21 has been found to be closely related to thyroid hormone regulation. The results of enrichment analysis showed that the DMPs or DMRs-related genes are both significantly enriched in human T-cell leukemia virus 1 infection, osteoclast differentiation and sphingolipid signaling pathway, which were also closely related to the occurrence and development of hypothyroidism. In addition, the combined analysis of CNVs and DMRs showed that significant differences occurred near the regions of 16 M bp in chromosome 1 between the two groups, and the genes involved in these regions included NDUFS2, FCER1G and SHC1. CONCLUSION This work screened molecular markers and key signaling pathways that are involved in the development of hypothyroidism in pre-pregnancy women, which may provide new targets for the research and diagnosis of hypothyroidism in the future.
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Affiliation(s)
- Wenqian Cai
- Eugenic Genetics Laboratory, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei Province, People's Republic of China
| | - Xijiang Hu
- Eugenic Genetics Laboratory, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei Province, People's Republic of China
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Grandi FC, Bhutani N. Mapping 5-Hydroxymethylcytosine (5hmC) Modifications in Skeletal Tissues Using High-Throughput Sequencing. Methods Mol Biol 2021; 2221:101-108. [PMID: 32979201 DOI: 10.1007/978-1-0716-0989-7_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cytosine modifications can alter the epigenetic landscape of a cell, affecting the binding of transcription factors, chromatin organizing complexes, and ultimately affecting gene expression and cell fate. 5-Hydroxymethylcytosine (5hmC) modifications are generated by the Ten-eleven-translocation (TET) family of enzymes, TET 1, 2, and 3, through the oxidation of methylated cytosines (5mC). The TET family is capable of further oxidizing 5hmC to 5fC and 5caC, leading to eventual DNA demethylation. However, 5hmC marks can also exist stably in DNA. Stable 5hmC is enriched in the gene bodies of activated genes in multiple tissues, as well as associated with regulatory regions such as enhancers. Alterations to 5hmC patterns have now been found in multiple diseases including osteoarthritis. Here, we describe a method to map 5hmC modifications by next-generation sequencing using a technique based on the selective modification and enrichment of the 5hmC mark. We additionally provide a bioinformatic analysis pipeline to interpret the resulting data.
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Affiliation(s)
| | - Nidhi Bhutani
- Department of Orthopaedic Surgery, Stanford University, Stanford, CA, USA.
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11
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Smeriglio P, Grandi FC, Taylor SEB, Zalc A, Bhutani N. TET1 Directs Chondrogenic Differentiation by Regulating SOX9 Dependent Activation of Col2a1 and Acan In Vitro. JBMR Plus 2020; 4:e10383. [PMID: 33134768 PMCID: PMC7587462 DOI: 10.1002/jbm4.10383] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/26/2020] [Accepted: 06/02/2020] [Indexed: 12/17/2022] Open
Abstract
Skeletal development is a tightly orchestrated process in which cartilage and bone differentiation are intricately intertwined. Recent studies have highlighted the contribution of epigenetic modifications and their writers to skeletal development. Methylated cytosine (5mC) can be oxidized to 5-hydroxymethylcytosine (5hmC) by the Ten-eleven-translocation (TET) enzymes leading to demethylation. We have previously demonstrated that 5hmC is stably accumulated on lineage-specific genes that are activated during in vitro chondrogenesis in the ATDC5 chondroprogenitors. Knockdown (KD) of Tet1 via short-hairpin RNAs blocked ATDC5 chondrogenic differentiation. Here, we aimed to provide the mechanistic basis for TET1 function during ATDC5 differentiation. Transcriptomic analysis of Tet1 KD cells demonstrated that 54% of downregulated genes were SOX9 targets, suggesting a role for TET1 in mediating activation of a subset of the SOX9 target genes. Using genome-wide mapping of 5hmC during ATDC5 differentiation, we found that 5hmC is preferentially accumulated at chondrocyte-specific class II binding sites for SOX9, as compared with the tissue-agnostic class I sites. Specifically, we find that SOX9 is unable to bind to Col2a1 and Acan after Tet1 KD, despite no changes in SOX9 levels. Finally, we compared this KD scenario with the genetic loss of TET1 in the growth plate using Tet1 -/- embryos, which are approximately 10% smaller than their WT counterparts. In E17.5 Tet1 -/- embryos, loss of SOX9 target gene expression is more modest than upon Tet1 KD in vitro. Overall, our data suggest a role for TET1-mediated 5hmC deposition in partly shaping an epigenome conducive for SOX9 function. © 2020 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Piera Smeriglio
- Department of Orthopaedic Surgery Stanford University School of Medicine Stanford CA USA
| | - Fiorella Carla Grandi
- Department of Orthopaedic Surgery Stanford University School of Medicine Stanford CA USA.,Cancer Biology Program Stanford University School of Medicine Stanford CA USA
| | | | - Antoine Zalc
- Department of Chemical and Systems Biology Stanford University School of Medicine Stanford CA USA
| | - Nidhi Bhutani
- Department of Orthopaedic Surgery Stanford University School of Medicine Stanford CA USA
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12
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Zhang Q, Wu Y, Xu Q, Ma F, Zhang CY. Recent advances in biosensors for in vitro detection and in vivo imaging of DNA methylation. Biosens Bioelectron 2020; 171:112712. [PMID: 33045657 DOI: 10.1016/j.bios.2020.112712] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/25/2020] [Accepted: 10/07/2020] [Indexed: 02/08/2023]
Abstract
DNA methylation is the predominant epigenetic modification that participates in many fundamental cellular processes through posttranscriptional regulation of gene expression. Aberrant DNA methylation is closely associated with a variety of human diseases including cancers. Therefore, accurate and sensitive detection of DNA methylation may greatly facilitate the epigenetic biological researches and disease diagnosis. In recent years, a series of novel biosensors have been developed for highly sensitive detection of DNA methylation, but an overview of recent advances in biosensors for in vitro detection and especially live-cell imaging of DNA methylation is absent. In this review, we summarize the emerging biosensors for in vitro and in vivo DNA methylation assays in the past five years (2015-2020). Based on the signal types, the biosensors for in vitro DNA methylation assay are classified into five categories including fluorescent, electrochemical, colorimetric, surface enhanced Raman spectroscopy, mass spectrometry, and surface plasmon resonance biosensors, while the biosensors for in vivo DNA methylation assay mainly rely on fluorescent imaging. We review the strategies, features and applications of these biosensors, and provide a new insight into the challenges and future directions in this area.
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Affiliation(s)
- Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Yanxia Wu
- Department of Pathology and Pathological Diagnosis & Research Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Fei Ma
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China.
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13
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Grandi FC, Bhutani N. Epigenetic Therapies for Osteoarthritis. Trends Pharmacol Sci 2020; 41:557-569. [PMID: 32586653 PMCID: PMC10621997 DOI: 10.1016/j.tips.2020.05.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/31/2022]
Abstract
Osteoarthritis (OA) is an age-associated disease characterized by chronic joint pain resulting from degradation of articular cartilage, inflammation of the synovial lining, and changes to the subchondral bone. Despite the wide prevalence, no FDA-approved disease-modifying drugs exist. Recent evidence has demonstrated that epigenetic dysregulation of multiple molecular pathways underlies OA pathogenesis, providing a new mechanistic and therapeutic axis with the advantage of targeting multiple deregulated pathways simultaneously. In this review, we focus on the epigenetic regulators that have been implicated in OA, their individual roles, and potential crosstalk. Finally, we discuss the pharmacological molecules that can modulate their activities and discuss the potential advantages and challenges associated with epigenome-based therapeutics for OA.
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Affiliation(s)
| | - Nidhi Bhutani
- Department of Orthopedic Surgery, Stanford University, Stanford, CA 94305, USA.
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14
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Smeriglio P, Grandi FC, Davala S, Masarapu V, Indelli PF, Goodman SB, Bhutani N. Inhibition of TET1 prevents the development of osteoarthritis and reveals the 5hmC landscape that orchestrates pathogenesis. Sci Transl Med 2020; 12:12/539/eaax2332. [DOI: 10.1126/scitranslmed.aax2332] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 11/20/2019] [Accepted: 03/23/2020] [Indexed: 12/13/2022]
Abstract
Osteoarthritis (OA) is a degenerative disease of the joint, which results in pain, loss of mobility, and, eventually, joint replacement. Currently, no disease-modifying drugs exist, partly because of the multiple levels at which cartilage homeostasis is disrupted. Recent studies have highlighted the importance of epigenetic dysregulation in OA, sparking interest in the epigenetic modulation for this disease. In our previous work, we characterized a fivefold increase in cytosine hydroxymethylation (5hmC), an oxidized derivative of cytosine methylation (5mC) associated with gene activation, accumulating at OA-associated genes. To test the role of 5hmC in OA, here, we used a mouse model of surgically induced OA and found that OA onset was accompanied by a gain of ~40,000 differentially hydroxymethylated sites before the notable histological appearance of disease. We demonstrated that ten-eleven-translocation enzyme 1 (TET1) mediates the 5hmC deposition because 98% of sites enriched for 5hmC in OA were lost in Tet1−/− mice. Loss of TET1-mediated 5hmC protected the Tet1−/− mice from OA development, including degeneration of the cartilage surface and osteophyte formation, by directly preventing the activation of multiple OA pathways. Loss of TET1 in human OA chondrocytes reduced the expression of the matrix metalloproteinases MMP3 and MMP13 and multiple inflammatory cytokines. Intra-articular injections of a dioxygenases inhibitor, 2-hydroxyglutarate, on mice after surgical induction of OA stalled disease progression. Treatment of human OA chondrocytes with the same inhibitor also phenocopied TET1 loss. Collectively, these data demonstrate that TET1-mediated 5hmC deposition regulates multiple OA pathways and can be modulated for therapeutic intervention.
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Affiliation(s)
- Piera Smeriglio
- Department of Orthopaedic Surgery, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Fiorella C. Grandi
- Department of Orthopaedic Surgery, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Venkata Masarapu
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Pier Francesco Indelli
- Department of Orthopaedic Surgery, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Stuart B. Goodman
- Department of Orthopaedic Surgery, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Nidhi Bhutani
- Department of Orthopaedic Surgery, School of Medicine, Stanford University, Stanford, CA 94305, USA
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15
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Rice SJ, Beier F, Young DA, Loughlin J. Interplay between genetics and epigenetics in osteoarthritis. Nat Rev Rheumatol 2020; 16:268-281. [PMID: 32273577 DOI: 10.1038/s41584-020-0407-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2020] [Indexed: 12/15/2022]
Abstract
Research into the molecular genetics of osteoarthritis (OA) has been substantially bolstered in the past few years by the implementation of powerful genome-wide scans that have revealed a large number of novel risk loci associated with the disease. This refreshing wave of discovery has occurred concurrently with epigenetic studies of joint tissues that have examined DNA methylation, histone modifications and regulatory RNAs. These epigenetic analyses have involved investigations of joint development, homeostasis and disease and have used both human samples and animal models. What has become apparent from a comparison of these two complementary approaches is that many OA genetic risk signals interact with, map to or correlate with epigenetic mediators. This discovery implies that epigenetic mechanisms, and their effect on gene expression, are a major conduit through which OA genetic risk polymorphisms exert their functional effects. This observation is particularly exciting as it provides mechanistic insight into OA susceptibility. Furthermore, this knowledge reveals avenues for attenuating the negative effect of risk-conferring alleles by exposing the epigenome as an exploitable target for therapeutic intervention in OA.
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Affiliation(s)
- Sarah J Rice
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Frank Beier
- Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada.,Western Bone and Joint Institute, The University of Western Ontario, London, ON, Canada
| | - David A Young
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - John Loughlin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
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16
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Grandi FC, Baskar R, Smeriglio P, Murkherjee S, Indelli PF, Amanatullah DF, Goodman S, Chu C, Bendall S, Bhutani N. Single-cell mass cytometry reveals cross-talk between inflammation-dampening and inflammation-amplifying cells in osteoarthritic cartilage. SCIENCE ADVANCES 2020; 6:eaay5352. [PMID: 32201724 PMCID: PMC7069698 DOI: 10.1126/sciadv.aay5352] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/17/2019] [Indexed: 05/06/2023]
Abstract
Aging or injury leads to degradation of the cartilage matrix and the development of osteoarthritis (OA). Because of a paucity of single-cell studies of OA cartilage, little is known about the interpatient variability in its cellular composition and, more importantly, about the cell subpopulations that drive the disease. Here, we profiled healthy and OA cartilage samples using mass cytometry to establish a single-cell atlas, revealing distinct chondrocyte progenitor and inflammation-modulating subpopulations. These rare populations include an inflammation-amplifying (Inf-A) population, marked by interleukin-1 receptor 1 and tumor necrosis factor receptor II, whose inhibition decreased inflammation, and an inflammation-dampening (Inf-D) population, marked by CD24, which is resistant to inflammation. We devised a pharmacological strategy targeting Inf-A and Inf-D cells that significantly decreased inflammation in OA chondrocytes. Using our atlas, we stratified patients with OA in three groups that are distinguished by the relative proportions of inflammatory to regenerative cells, making it possible to devise precision therapeutic approaches.
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Affiliation(s)
- Fiorella Carla Grandi
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | - Reema Baskar
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | - Piera Smeriglio
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | - Shravani Murkherjee
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | | | - Derek F. Amanatullah
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | - Stuart Goodman
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | - Constance Chu
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
- Palo Alto Veterans Administration Health Care System, Palo Alto, CA 94304, USA
| | - Sean Bendall
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | - Nidhi Bhutani
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
- Corresponding author.
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17
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Mahmood AM, Dunwell JM. Evidence for novel epigenetic marks within plants. AIMS GENETICS 2019; 6:70-87. [PMID: 31922011 PMCID: PMC6949463 DOI: 10.3934/genet.2019.4.70] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 12/07/2019] [Indexed: 12/21/2022]
Abstract
Variation in patterns of gene expression can result from modifications in the genome that occur without a change in the sequence of the DNA; such modifications include methylation of cytosine to generate 5-methylcytosine (5mC) resulting in the generation of heritable epimutation and novel epialleles. This type of non-sequence variation is called epigenetics. The enzymes responsible for generation of such DNA modifications in mammals are named DNA methyltransferases (DNMT) including DNMT1, DNMT2 and DNMT3. The later stages of oxidations to these modifications are catalyzed by Ten Eleven Translocation (TET) proteins, which contain catalytic domains belonging to the 2-oxoglutarate dependent dioxygenase family. In various mammalian cells/tissues including embryonic stem cells, cancer cells and brain tissues, it has been confirmed that these proteins are able to induce the stepwise oxidization of 5-methyl cytosine to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and finally 5-carboxylcytosine (5caC). Each stage from initial methylation until the end of the DNA demethylation process is considered as a specific epigenetic mark that may regulate gene expression. This review discusses controversial evidence for the presence of such oxidative products, particularly 5hmC, in various plant species. Whereas some reports suggest no evidence for enzymatic DNA demethylation, other reports suggest that the presence of oxidative products is followed by the active demethylation and indicate the contribution of possible TET-like proteins in the regulation of gene expression in plants. The review also summarizes the results obtained by expressing the human TET conserved catalytic domain in transgenic plants.
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Affiliation(s)
- Asaad M Mahmood
- Department of Biology, College of Education, University of Garmian, Kalar, KRG/Iraq
| | - Jim M Dunwell
- School of School of Agriculture, Policy and Development, University of Reading, Reading, Berkshire, UK
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18
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Lindsey RC, Cheng S, Mohan S. Vitamin C effects on 5-hydroxymethylcytosine and gene expression in osteoblasts and chondrocytes: Potential involvement of PHD2. PLoS One 2019; 14:e0220653. [PMID: 31390373 PMCID: PMC6685624 DOI: 10.1371/journal.pone.0220653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/20/2019] [Indexed: 12/02/2022] Open
Abstract
Vitamin C (ascorbic acid, AA) is a well-known regulator of bone and cartilage metabolism. However, the mechanisms of AA’s action in these tissues are only partly understood. In this study, we confirmed that AA contributes to bone and cartilage metabolism by showing decreased articular cartilage and trabecular bone in AA-deficient spontaneous fracture (sfx) mutant mice. In vitro, we found that AA exerts differential effects on chondrocyte and osteoblast differentiation. Since AA is known to increase levels of 5-hydroxymethylcytosine (5-hmC) and induce DNA demethylation via the ten-eleven translocases (TETs), and since prolyl hydroxylase domain-containing protein 2 (PHD2), a known mediator of AA’s effects in these tissues, is part of the same enzyme family as the TETs, we next investigated whether increases in 5-hmC might mediate some of these effects. All TETs and PHDs are expressed in chondrocytes and osteoblasts, and PHD2 is localized in both the cytoplasm and nucleus of the cell, lending plausibility to the hypothesis of altered 5-hmC content in these cells. We found that AA treatment increased levels of 5-hmC in both cell types globally, notably including promoter regions of osteoblast differentiation genes. Furthermore, inhibition of PHD2 decreased 5-hmC levels in chondrocyte differentiation gene promoters, and knockdown of Phd2 in chondrocytes reduced global 5-hmC levels, suggesting for the first time that PHD2 may itself directly mediate increases in 5-hmC in chondrocyte and osteoblast genes. Further investigation of this mechanism could lead to novel therapeutic approaches to treat debilitating diseases such as osteoarthritis and osteoporosis.
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Affiliation(s)
- Richard C. Lindsey
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, Loma Linda, CA, United States of America
- Center for Health Disparities and Molecular Medicine, School of Medicine, Loma Linda University, Loma Linda, CA, United States of America
- Division of Biochemistry, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, United States of America
| | - Shaohong Cheng
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, Loma Linda, CA, United States of America
| | - Subburaman Mohan
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, Loma Linda, CA, United States of America
- Center for Health Disparities and Molecular Medicine, School of Medicine, Loma Linda University, Loma Linda, CA, United States of America
- Division of Biochemistry, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, United States of America
- Department of Medicine, School of Medicine, Loma Linda University, Loma Linda, CA, United States of America
- Department of Orthopedics, School of Medicine, Loma Linda University, Loma Linda, CA, United States of America
- * E-mail:
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19
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Wijnen AJ, Westendorf JJ. Epigenetics as a New Frontier in Orthopedic Regenerative Medicine and Oncology. J Orthop Res 2019; 37:1465-1474. [PMID: 30977555 PMCID: PMC6588446 DOI: 10.1002/jor.24305] [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: 01/30/2019] [Revised: 03/24/2019] [Accepted: 03/27/2019] [Indexed: 02/04/2023]
Abstract
Skeletal regenerative medicine aims to repair or regenerate skeletal tissues using pharmacotherapies, cell-based treatments, and/or surgical interventions. The field is guided by biological principles active during development, wound healing, aging, and carcinogenesis. Skeletal development and tissue maintenance in adults represent highly intricate biological processes that require continuous adjustments in the expression of cell type-specific genes that generate, remodel, and repair the skeletal extracellular matrix. Errors in these processes can facilitate musculoskeletal disease including cancers or injury. The fundamental molecular mechanisms by which cell type-specific patterns in gene expression are established and retained during successive mitotic divisions require epigenetic control, which we review here. We focus on epigenetic regulatory proteins that control the mammalian epigenome at the level of chromatin with emphasis on proteins that are amenable to drug intervention to mitigate skeletal tissue degeneration (e.g., osteoarthritis and osteoporosis). We highlight recent findings on a number of druggable epigenetic regulators, including DNA methyltransferases (e.g., DNMT1, DNMT3A, and DNMT3B) and hydroxylases (e.g., TET1, TET2, and TET3), histone methyltransferases (e.g., EZH1, EZH2, and DOT1L) as well as histone deacetylases (e.g., HDAC3, HDAC4, and HDAC7) and histone acetyl readers (e.g., BRD4) in relation to the development of bone or cartilage regenerative drug therapies. We also review how histone mutations lead to epigenomic catastrophe and cause musculoskeletal tumors. The combined body of molecular and genetic studies focusing on epigenetic regulators indicates that these proteins are critical for normal skeletogenesis and viable candidate drug targets for short-term local pharmacological strategies to mitigate musculoskeletal tissue degeneration. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 37:1465-1474, 2019.
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Affiliation(s)
- Andre J. Wijnen
- Department of Orthopedic SurgeryMayo Clinic200 First Street SW Rochester Minnesota
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20
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Fang Y, Wang P, Xia L, Bai S, Shen Y, Li Q, Wang Y, Zhu J, Du J, Shen B. Aberrantly hydroxymethylated differentially expressed genes and the associated protein pathways in osteoarthritis. PeerJ 2019; 7:e6425. [PMID: 30828485 PMCID: PMC6394344 DOI: 10.7717/peerj.6425] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/10/2019] [Indexed: 12/15/2022] Open
Abstract
Background The elderly population is at risk of osteoarthritis (OA), a common, multifactorial, degenerative joint disease. Environmental, genetic, and epigenetic (such as DNA hydroxymethylation) factors may be involved in the etiology, development, and pathogenesis of OA. Here, comprehensive bioinformatic analyses were used to identify aberrantly hydroxymethylated differentially expressed genes and pathways in osteoarthritis to determine the underlying molecular mechanisms of osteoarthritis and susceptibility-related genes for osteoarthritis inheritance. Methods Gene expression microarray data, mRNA expression profile data, and a whole genome 5hmC dataset were obtained from the Gene Expression Omnibus repository. Differentially expressed genes with abnormal hydroxymethylation were identified by MATCH function. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the genes differentially expressed in OA were performed using Metascape and the KOBAS online tool, respectively. The protein–protein interaction network was built using STRING and visualized in Cytoscape, and the modular analysis of the network was performed using the Molecular Complex Detection app. Results In total, 104 hyperhydroxymethylated highly expressed genes and 14 hypohydroxymethylated genes with low expression were identified. Gene ontology analyses indicated that the biological functions of hyperhydroxymethylated highly expressed genes included skeletal system development, ossification, and bone development; KEGG pathway analysis showed enrichment in protein digestion and absorption, extracellular matrix–receptor interaction, and focal adhesion. The top 10 hub genes in the protein–protein interaction network were COL1A1, COL1A2, COL2A1, COL3A1, COL5A1, COL5A2, COL6A1, COL8A1, COL11A1, and COL24A1. All the aforementioned results are consistent with changes observed in OA. Conclusion After comprehensive bioinformatics analysis, we found aberrantly hydroxymethylated differentially expressed genes and pathways in OA. The top 10 hub genes may be useful hydroxymethylation analysis biomarkers to provide more accurate OA diagnoses and target genes for treatment of OA.
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Affiliation(s)
- Yang Fang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Pingping Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Lin Xia
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Suwen Bai
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Yonggang Shen
- Nursing Faculty, Anhui Health College, Chizhou, Anhui, China
| | - Qing Li
- Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Hefei, Anhui, China
| | - Yang Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Jinhang Zhu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Juan Du
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Bing Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
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21
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Wernig-Zorc S, Yadav MP, Kopparapu PK, Bemark M, Kristjansdottir HL, Andersson PO, Kanduri C, Kanduri M. Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia. Epigenetics Chromatin 2019; 12:4. [PMID: 30616658 PMCID: PMC6322269 DOI: 10.1186/s13072-018-0252-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/23/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot of attention as a regulatory epigenetic modification with prognostic and diagnostic implications for several cancers. However, there is no global study exploring the role of 5-hydroxymethylcytosine (5-hmC) levels in CLL. Herein, using mass spectrometry and hMeDIP-sequencing, we analysed the dynamics of 5-hmC during B cell maturation and CLL pathogenesis. RESULTS We show that naïve B-cells had higher levels of 5-hmC and 5-mC compared to non-class switched and class-switched memory B-cells. We found a significant decrease in global 5-mC levels in CLL patients (n = 15) compared to naïve and memory B cells, with no changes detected between the CLL prognostic groups. On the other hand, global 5-hmC levels of CLL patients were similar to memory B cells and reduced compared to naïve B cells. Interestingly, 5-hmC levels were increased at regulatory regions such as gene-body, CpG island shores and shelves and 5-hmC distribution over the gene-body positively correlated with degree of transcriptional activity. Importantly, CLL samples showed aberrant 5-hmC and 5-mC pattern over gene-body compared to well-defined patterns in normal B-cells. Integrated analysis of 5-hmC and RNA-sequencing from CLL datasets identified three novel oncogenic drivers that could have potential roles in CLL development and progression. CONCLUSIONS Thus, our study suggests that the global loss of 5-hmC, accompanied by its significant increase at the gene regulatory regions, constitute a novel hallmark of CLL pathogenesis. Our combined analysis of 5-mC and 5-hmC sequencing provided insights into the potential role of 5-hmC in modulating gene expression changes during CLL pathogenesis.
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Affiliation(s)
- Sara Wernig-Zorc
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Mukesh Pratap Yadav
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Pradeep Kumar Kopparapu
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Hallgerdur Lind Kristjansdottir
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg University, Gothenburg, Sweden
| | - Per-Ola Andersson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg University, Gothenburg, Sweden.,Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden.
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22
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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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23
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Miranda-Duarte A. DNA Methylation in Osteoarthritis: Current Status and Therapeutic Implications. Open Rheumatol J 2018; 12:37-49. [PMID: 29682093 PMCID: PMC5885469 DOI: 10.2174/1874312901812010037] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/24/2018] [Accepted: 03/05/2018] [Indexed: 01/25/2023] Open
Abstract
Background: Primary Osteoarthritis (OA) is a multifactorial disease in which genetic factors are strongly associated with its development; however, recently it has been observed that epigenetic modifications are also involved in the pathogenesis of OA. DNA methylation is related to gene silencing, and several studies have investigated its role in the loci of different pathways or molecules associated to OA. Objective: This review is focused on the current status of DNA methylation studies related to OA pathogenesis. Method: A review of the literature was conducted on searching in PUBMED for original papers on DNA methylation in OA. Conclusion: The DNA methylation research of loci related to OA pathogenesis has shown a correlation between methylation and gene repression; however, there are some exceptions to this rule. Recently, the development of genome-wide methylation and genome-wide hydroxymethylation profiles has demonstrated that several genes previously associated with OA can have changes in their methylation status, favoring the development of the disease, and these have even shown the role of other epigenetic markers.
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Affiliation(s)
- Antonio Miranda-Duarte
- Department of Genetics, Instituto Nacional de Rehabilitación "Luis Guillermo Ibarra Ibarra", Tlalpan, Mexico
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Alvarez-Garcia O, Fisch KM, Wineinger NE, Akagi R, Saito M, Sasho T, Su AI, Lotz MK. Increased DNA Methylation and Reduced Expression of Transcription Factors in Human Osteoarthritis Cartilage. Arthritis Rheumatol 2017; 68:1876-86. [PMID: 26881698 DOI: 10.1002/art.39643] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 02/11/2016] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To analyze the methylome of normal and osteoarthritic (OA) knee articular cartilage and to determine the role of DNA methylation in the regulation of gene expression in vitro. METHODS DNA was isolated from human normal (n = 11) and OA (n = 12) knee articular cartilage and analyzed using the Infinium HumanMethylation450 BeadChip array. To integrate methylation and transcription, RNA sequencing was performed on normal and OA cartilage and validated by quantitative polymerase chain reaction. Functional validation was performed in the human TC28 cell line and primary chondrocytes that were treated with the DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-aza-dC). RESULTS DNA methylation profiling revealed 929 differentially methylated sites between normal and OA cartilage, comprising a total of 500 individual genes. Among these, 45 transcription factors that harbored differentially methylated sites were identified. Integrative analysis and subsequent validation showed a subset of 6 transcription factors that were significantly hypermethylated and down-regulated in OA cartilage (ATOH8, MAFF, NCOR2, TBX4, ZBTB16, and ZHX2). Upon 5-aza-dC treatment, TC28 cells showed a significant increase in gene expression for all 6 transcription factors. In primary chondrocytes, ATOH8 and TBX4 were increased after 5-aza-dC treatment. CONCLUSION Our findings reveal that normal and OA knee articular cartilage have significantly different methylomes. The identification of a subset of epigenetically regulated transcription factors with reduced expression in OA may represent an important mechanism to explain changes in the chondrocyte transcriptome and function during OA pathogenesis.
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Affiliation(s)
| | | | | | - Ryuichiro Akagi
- The Scripps Research Institute, La Jolla, California, and Chiba University, Chiba, Japan
| | | | | | - Andrew I Su
- The Scripps Research Institute, La Jolla, California
| | - Martin K Lotz
- The Scripps Research Institute, La Jolla, California
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25
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DNA Hydroxymethylation by Ten-eleven Translocation Methylcytosine Dioxygenase 1 and 3 Regulates Nociceptive Sensitization in a Chronic Inflammatory Pain Model. Anesthesiology 2017; 127:147-163. [DOI: 10.1097/aln.0000000000001632] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Background
Ten-eleven translocation methylcytosine dioxygenase converts 5-methylcytosine in DNA to 5-hydroxymethylcytosine, which plays an important role in gene transcription. Although 5-hydroxymethylcytosine is enriched in mammalian neurons, its regulatory function in nociceptive information processing is unknown.
Methods
The global levels of 5-hydroxymethylcytosine and ten-eleven translocation methylcytosine dioxygenase were measured in spinal cords in mice treated with complete Freund’s adjuvant. Immunoblotting, immunohistochemistry, and behavioral tests were used to explore the downstream ten-eleven translocation methylcytosine dioxygenase-dependent signaling pathway.
Results
Complete Freund’s adjuvant-induced nociception increased the mean levels (± SD) of spinal 5-hydroxymethylcytosine (178 ± 34 vs. 100 ± 21; P = 0.0019), ten-eleven translocation methylcytosine dioxygenase-1 (0.52 ± 0.11 vs. 0.36 ± 0.064; P = 0.0088), and ten-eleven translocation methylcytosine dioxygenase-3 (0.61 ± 0.13 vs. 0.39 ± 0.08; P = 0.0083) compared with levels in control mice (n = 6/group). The knockdown of ten-eleven translocation methylcytosine dioxygenase-1 or ten-eleven translocation methylcytosine dioxygenase-3 alleviated thermal hyperalgesia and mechanical allodynia, whereas overexpression cytosinethem in naïve mice (n = 6/group). Down-regulation of spinal ten-eleven translocation methylcytosine dioxygenase-1 and ten-eleven translocation methylcytosine dioxygenase-3 also reversed the increases in Fos expression (123 ± 26 vs. 294 ± 6; P = 0.0031; and 140 ± 21 vs. 294 ± 60; P = 0.0043, respectively; n = 6/group), 5-hydroxymethylcytosine levels in the Stat3 promoter (75 ± 16.1 vs. 156 ± 28.9; P = 0.0043; and 91 ± 19.1 vs. 156 ± 28.9; P = 0.0066, respectively; n = 5/group), and consequent Stat3 expression (93 ± 19.6 vs. 137 ± 27.5; P = 0.035; and 72 ± 15.2 vs. 137 ± 27.5; P = 0.0028, respectively; n = 5/group) in complete Freund’s adjuvant-treated mice.
Conclusions
This study reveals a novel epigenetic mechanism for ten-eleven translocation methylcytosine dioxygenase-1 and ten-eleven translocation methylcytosine dioxygenase-3 in the modulation of spinal nociceptive information via targeting of Stat3.
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Shen J, Wang C, Li D, Xu T, Myers J, Ashton JM, Wang T, Zuscik MJ, McAlinden A, O'Keefe RJ. DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism. JCI Insight 2017; 2:93612. [PMID: 28614801 DOI: 10.1172/jci.insight.93612] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/10/2017] [Indexed: 01/05/2023] Open
Abstract
Osteoarthritis (OA) is the most common form of arthritis worldwide. It is a complex disease affecting the whole joint but is generally characterized by progressive degradation of articular cartilage. Recent genome-wide association screens have implicated distinct DNA methylation signatures in OA patients. We show that the de novo DNA methyltransferase (Dnmt) 3b, but not Dnmt3a, is present in healthy murine and human articular chondrocytes and its expression decreases in OA mouse models and in chondrocytes from human OA patients. Targeted deletion of Dnmt3b in murine articular chondrocytes results in an early-onset and progressive postnatal OA-like pathology. RNA-Seq and methylC-Seq analyses of Dnmt3b loss-of-function chondrocytes show that cellular metabolic processes are affected. Specifically, TCA metabolites and mitochondrial respiration are elevated. Importantly, a chondroprotective effect was found following Dnmt3b gain of function in murine articular chondrocytes in vitro and in vivo. This study shows that Dnmt3b plays a significant role in regulating postnatal articular cartilage homeostasis. Cellular pathways regulated by Dnmt3b in chondrocytes may provide novel targets for therapeutic approaches to treat OA.
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Affiliation(s)
- Jie Shen
- Department of Orthopaedic Surgery and
| | | | - Daofeng Li
- Department of Genetics, Center for Genome Sciences and Systems Biology, School of Medicine, Washington University, St. Louis, Missouri, USA
| | - Taotao Xu
- Department of Orthopaedic Surgery and.,Institute of Orthopaedics and Traumatology, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Jason Myers
- Genomics Research Center, School of Medicine and Dentistry, and
| | - John M Ashton
- Genomics Research Center, School of Medicine and Dentistry, and.,Department of Microbiology and Immunology, School of Medicine and Dentistry, and
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, School of Medicine, Washington University, St. Louis, Missouri, USA
| | - Michael J Zuscik
- Department of Orthopaedics, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
| | - Audrey McAlinden
- Department of Orthopaedic Surgery and.,Department of Cell Biology & Physiology, School of Medicine, Washington University, St. Louis, Missouri, USA
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Liu T, Sun J, Wang Z, Yang W, Zhang H, Fan C, Shan Z, Teng W. Changes in the DNA Methylation and Hydroxymethylation Status of the Intercellular Adhesion Molecule 1 Gene Promoter in Thyrocytes from Autoimmune Thyroiditis Patients. Thyroid 2017; 27:838-845. [PMID: 28388873 DOI: 10.1089/thy.2016.0576] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND The intercellular adhesion molecule 1 (ICAM1) gene is not expressed in normal thyroid tissue but was shown to be expressed in the thyroid tissue of autoimmune thyroiditis (AIT) patients. METHODS This study aimed to explore whether the DNA methylation and hydroxymethylation status of the ICAM1 promoter are aberrantly altered in the thyroid cells of AIT patients and whether this change is associated with dysfunctional expression of ICAM1. A total of 35 AIT patients and 35 sex- and age-matched controls were studied. After the isolation of thyrocytes via density-gradient centrifugation, ICAM1 mRNA expression was measured using real-time PCR. The DNA methylation and hydroxymethylation status were assessed using quantitative PCR following T4 β-glucosyltransferase treatment and MspI/HpaII cleavage at -937 bp, -701 bp, -226 bp, and -65 bp upstream of the transcription start site (TSS). The DNA methylation level was verified via pyrosequencing. RESULTS The AIT group showed increased DNA hydroxymethylation at -937 bp and -226 bp and decreased methylation at -937 bp, -701 bp, and -226 bp upstream of the TSS. Pyrosequencing also revealed DNA hypomethylation at -708 bp, -692 bp, -690 bp, and -688 bp upstream of the TSS. The DNA methylation status at -708 bp, -692 bp, and -226 bp upstream of the TSS was negatively associated with ICAM1 mRNA expression. CONCLUSION In summary, we identified aberrant DNA methylation and hydroxymethylation of the ICAM1 gene promoter in the thyrocytes of AIT patients. This aberrant epigenetic modification is associated with increased expression of the ICAM1 gene.
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Affiliation(s)
- Tingting Liu
- 1 Department of Endocrinology and Metabolism, Institute of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, First Affiliated Hospital of China Medical University , Shenyang, Liaoning Province, People's Republic of China
| | - Jie Sun
- 1 Department of Endocrinology and Metabolism, Institute of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, First Affiliated Hospital of China Medical University , Shenyang, Liaoning Province, People's Republic of China
| | - Zhaojun Wang
- 1 Department of Endocrinology and Metabolism, Institute of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, First Affiliated Hospital of China Medical University , Shenyang, Liaoning Province, People's Republic of China
| | - Wenqing Yang
- 1 Department of Endocrinology and Metabolism, Institute of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, First Affiliated Hospital of China Medical University , Shenyang, Liaoning Province, People's Republic of China
| | - Hao Zhang
- 2 Department of Thyroid Surgery, Institute of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, First Affiliated Hospital of China Medical University , Shenyang, Liaoning Province, People's Republic of China
| | - Chenling Fan
- 1 Department of Endocrinology and Metabolism, Institute of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, First Affiliated Hospital of China Medical University , Shenyang, Liaoning Province, People's Republic of China
| | - Zhongyan Shan
- 1 Department of Endocrinology and Metabolism, Institute of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, First Affiliated Hospital of China Medical University , Shenyang, Liaoning Province, People's Republic of China
| | - Weiping Teng
- 1 Department of Endocrinology and Metabolism, Institute of Endocrinology, Liaoning Provincial Key Laboratory of Endocrine Diseases, First Affiliated Hospital of China Medical University , Shenyang, Liaoning Province, People's Republic of China
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A comparative study of effect of autograft compared with allograft anterior cruciate ligament reconstruction on expressions of LOXs and MMPs. Biosci Rep 2017; 37:BSR20160533. [PMID: 28275205 PMCID: PMC5408659 DOI: 10.1042/bsr20160533] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 02/21/2017] [Accepted: 03/08/2017] [Indexed: 02/07/2023] Open
Abstract
The present study aimed to compare the effect of autograft or allograft anterior cruciate ligament (ACL) reconstruction on the expressions of lipoxygenases (LOXs) and matrix metalloproteinases (MMPs) in a New Zealand white rabbit model. New Zealand white rabbits were divided randomly into control, sham, autograft and allograft groups. At the 4th and 8th week after operation, biomechanical testing was performed to measure the primary length, cross-sectional area, maximum tensile load and stiffness of ACL, and HE staining was used to observe cell morphology and fibre alignment of ACL. At the 2nd, 4th and 8th week after operation, quantitative real-time PCR (qRT-PCR), Western blotting and immunohistochemistry were applied to detect LOXs and MMPs expressions, and expressions of adenomatous polyposis coli (APC)/Wnt signalling pathway-related proteins. At the 4th and 8th week after operation, the maximum tensile load and stiffness were higher in the autograft group than in the allograft group, and the values at the 8th week were higher than those at the 4th week after operation. The fibroblast proliferation in the allograft group was more significant than that in the autograft group. Compared with the control group, LOXs and MMPs expressions and the positive expression rates of LOXs and MMPs proteins were elevated, and the values in the allograft group were higher than those in the autograft group at all time points. At 8th week after operation, compared with the autograft group, Wnt expression was higher and APC expression was lower in the allograft group. Autograft and allograft ACL reconstruction can promote LOXs and MMPs expressions by activating the APC/Wnt signalling pathway.
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29
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Hasei J, Teramura T, Takehara T, Onodera Y, Horii T, Olmer M, Hatada I, Fukuda K, Ozaki T, Lotz MK, Asahara H. 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] [MESH Headings] [Grants] [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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Affiliation(s)
- Joe Hasei
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Takeshi Teramura
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University, Faculty of Medicine, Osaka, Japan
| | - Toshiyuki Takehara
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University, Faculty of Medicine, Osaka, Japan
| | - Yuta Onodera
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University, Faculty of Medicine, Osaka, Japan
| | - Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, Japan
| | - Merissa Olmer
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, Japan
| | - Kanji Fukuda
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University, Faculty of Medicine, Osaka, Japan
- Department of Rehabilitation Medicine, Kindai University, Faculty of Medicine, Osaka, Japan
| | - Toshifumi Ozaki
- Science of Functional Recovery and Reconstruction, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Martin K. Lotz
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Hiroshi Asahara
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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Chen D, Shen J, Zhao W, Wang T, Han L, Hamilton JL, Im HJ. Osteoarthritis: toward a comprehensive understanding of pathological mechanism. Bone Res 2017; 5:16044. [PMID: 28149655 PMCID: PMC5240031 DOI: 10.1038/boneres.2016.44] [Citation(s) in RCA: 683] [Impact Index Per Article: 97.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/02/2016] [Accepted: 09/08/2016] [Indexed: 12/14/2022] Open
Abstract
Osteoarthritis (OA) is the most common degenerative joint disease and a major cause of pain and disability in adult individuals. The etiology of OA includes joint injury, obesity, aging, and heredity. However, the detailed molecular mechanisms of OA initiation and progression remain poorly understood and, currently, there are no interventions available to restore degraded cartilage or decelerate disease progression. The diathrodial joint is a complicated organ and its function is to bear weight, perform physical activity and exhibit a joint-specific range of motion during movement. During OA development, the entire joint organ is affected, including articular cartilage, subchondral bone, synovial tissue and meniscus. A full understanding of the pathological mechanism of OA development relies on the discovery of the interplaying mechanisms among different OA symptoms, including articular cartilage degradation, osteophyte formation, subchondral sclerosis and synovial hyperplasia, and the signaling pathway(s) controlling these pathological processes.
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Affiliation(s)
- Di Chen
- Department of Biochemistry, Rush University Medical Center, Chicago, IL, USA
| | - Jie Shen
- Department of Orthopaedic Surgery, Washington University, St Louis, MO, USA
| | - Weiwei Zhao
- Department of Biochemistry, Rush University Medical Center, Chicago, IL, USA
- Department of Orthopaedics & Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tingyu Wang
- Department of Pharmacy, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Lin Han
- School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA, USA
| | - John L Hamilton
- Department of Biochemistry, Rush University Medical Center, Chicago, IL, USA
| | - Hee-Jeong Im
- Department of Biochemistry, Rush University Medical Center, Chicago, IL, USA
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Meulenbelt IM, Bhutani N, den Hollander W, Gay S, Oppermann U, Reynard LN, Skelton AJ, Young DA, Beier F, Loughlin J. The first international workshop on the epigenetics of osteoarthritis. Connect Tissue Res 2017; 58:37-48. [PMID: 27028588 DOI: 10.3109/03008207.2016.1168409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Osteoarthritis (OA) is a major clinical problem across the world, in part due to the lack of disease-modifying drugs resulting, to a significant degree, from our incomplete understanding of the underlying molecular mechanisms of the disease. Emerging evidence points to a role of epigenetics in the pathogenesis of OA, but research in this area is still in its early stages. In order to summarize current knowledge and to facilitate the potential coordination of future research activities, the first international workshop on the epigenetics of OA was held in Amsterdam in October 2015. Recent findings on DNA methylation and hydroxymethylation, histone modifications, noncoding RNAs, and other epigenetic mechanisms were presented and discussed. The workshop demonstrated the advantage of bringing together those working in this nascent field and highlights from the event are summarized in this report in the form of summaries from invited speakers and organizers.
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Affiliation(s)
- Ingrid M Meulenbelt
- a Department of Medical Statistics and Bioinformatics, Section of Molecular Epidemiology , Leiden University Medical Center , Leiden , The Netherlands
| | - Nidhi Bhutani
- b Department of Orthopaedic Surgery , Stanford University School of Medicine , Stanford , CA , USA
| | - Wouter den Hollander
- a Department of Medical Statistics and Bioinformatics, Section of Molecular Epidemiology , Leiden University Medical Center , Leiden , The Netherlands
| | - Steffen Gay
- c Department of Rheumatology , Center of Experimental Rheumatology, University Hospital Zurich , Zurich , Switzerland
| | - Udo Oppermann
- d Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics , Rheumatology and Musculoskeletal Sciences, University of Oxford , Oxford , UK.,e Structural Genomics Consortium , University of Oxford , Oxford , UK
| | - Louise N Reynard
- f Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University , Newcastle-upon-Tyne , UK
| | - Andrew J Skelton
- f Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University , Newcastle-upon-Tyne , UK.,g Faculty of Medical Sciences, Bioinformatics Support Unit , Newcastle University , Newcastle-upon-Tyne , UK
| | - David A Young
- f Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University , Newcastle-upon-Tyne , UK
| | - Frank Beier
- h Department of Physiology and Pharmacology , Schulich School of Medicine and Dentistry, University of Western Ontario , London , ON , Canada
| | - John Loughlin
- f Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University , Newcastle-upon-Tyne , UK
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Huynh NPT, Anderson BA, Guilak F, McAlinden A. Emerging roles for long noncoding RNAs in skeletal biology and disease. Connect Tissue Res 2017; 58:116-141. [PMID: 27254479 PMCID: PMC5301950 DOI: 10.1080/03008207.2016.1194406] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Normal skeletal development requires tight coordination of transcriptional networks, signaling pathways, and biomechanical cues, and many of these pathways are dysregulated in pathological conditions affecting cartilage and bone. Recently, a significant role has been identified for long noncoding RNAs (lncRNAs) in developing and maintaining cellular phenotypes, and improvements in sequencing technologies have led to the identification of thousands of lncRNAs across diverse cell types, including the cells within cartilage and bone. It is clear that lncRNAs play critical roles in regulating gene expression. For example, they can function as epigenetic regulators in the nucleus via chromatin modulation to control gene transcription, or in the cytoplasm, where they can function as scaffolds for protein-binding partners or modulate the activity of other coding and noncoding RNAs. In this review, we discuss the growing list of lncRNAs involved in normal development and/or homeostasis of the skeletal system, the potential mechanisms by which these lncRNAs might function, and recent improvements in the methodologies available to study lncRNA functions in vitro and in vivo. Finally, we address the likely utility of lncRNAs as biomarkers and therapeutic targets for diseases of the skeletal system, including osteoarthritis, osteoporosis, and in cancers of the skeletal system.
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Affiliation(s)
- Nguyen P. T. Huynh
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Shriners Hospitals for Children – St. Louis, St. Louis, MO, USA,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Britta A. Anderson
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Shriners Hospitals for Children – St. Louis, St. Louis, MO, USA,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, USA,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Audrey McAlinden
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, USA
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Abstract
Osteoarthritis (OA) was once defined as a non-inflammatory arthropathy, but it is now well-recognized that there is a major inflammatory component to this disease. In addition to synovial cells, articular chondrocytes and other cells of diarthrodial joints are also known to express inflammatory mediators. It has been proposed that targeting inflammation pathways could be a promising strategy to treat OA. There have been many reports of cross-talk between inflammation and epigenetic factors in cartilage. Specifically, inflammatory mediators have been shown to regulate levels of enzymes that catalyze changes in DNA methylation and histone structure, as well as alter levels of non-coding RNAs. In addition, expression levels of a number of these epigenetic factors have been shown to be altered in OA, thereby suggesting potential interplay between inflammation and epigenetics in this disease. This review provides information on inflammatory pathways in arthritis and summarizes published research on how epigenetic regulators are affected by inflammation in chondrocytes. Furthermore, we discuss data showing how altered expression of some of these epigenetic factors can induce either catabolic or anti-catabolic effects in response to inflammatory signals. A better understanding of how inflammation affects epigenetic factors in OA may provide us with novel therapeutic strategies to treat this condition.
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Affiliation(s)
- Jie Shen
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Yousef Abu-Amer
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, USA,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Regis J. O'Keefe
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Audrey McAlinden
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, USA,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA
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Abstract
UNLABELLED DNA 5-hydroxylmethylcytosine (5hmC) catalyzed by ten-eleven translocation methylcytosine dioxygenase (TET) occurs abundantly in neurons of mammals. However, the in vivo causal link between TET dysregulation and nociceptive modulation has not been established. Here, we found that spinal TET1 and TET3 were significantly increased in the model of formalin-induced acute inflammatory pain, which was accompanied with the augment of genome-wide 5hmC content in spinal cord. Knockdown of spinal TET1 or TET3 alleviated the formalin-induced nociceptive behavior and overexpression of spinal TET1 or TET3 in naive mice produced pain-like behavior as evidenced by decreased thermal pain threshold. Furthermore, we found that TET1 or TET3 regulated the nociceptive behavior by targeting microRNA-365-3p (miR-365-3p). Formalin increased 5hmC in the miR-365-3p promoter, which was inhibited by knockdown of TET1 or TET3 and mimicked by overexpression of TET1 or TET3 in naive mice. Nociceptive behavior induced by formalin or overexpression of spinal TET1 or TET3 could be prevented by downregulation of miR-365-3p, and mimicked by overexpression of spinal miR-365-3p. Finally, we demonstrated that a potassium channel, voltage-gated eag-related subfamily H member 2 (Kcnh2), validated as a target of miR-365-3p, played a critical role in nociceptive modulation by spinal TET or miR-365-3p. Together, we concluded that TET-mediated hydroxymethylation of miR-365-3p regulates nociceptive behavior via Kcnh2. SIGNIFICANCE STATEMENT Mounting evidence indicates that epigenetic modifications in the nociceptive pathway contribute to pain processes and analgesia response. Here, we found that the increase of 5hmC content mediated by TET1 or TET3 in miR-365-3p promoter in the spinal cord is involved in nociceptive modulation through targeting a potassium channel, Kcnh2. Our study reveals a new epigenetic mechanism underlying nociceptive information processing, which may be a novel target for development of antinociceptive drugs.
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Steinberg J, Zeggini E. Functional genomics in osteoarthritis: Past, present, and future. J Orthop Res 2016; 34:1105-10. [PMID: 27176659 PMCID: PMC4980743 DOI: 10.1002/jor.23296] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/10/2016] [Indexed: 02/04/2023]
Abstract
Osteoarthritis (OA) is a common complex disease of high public health burden. OA is characterized by the degeneration of affected joints leading to pain and reduced mobility. Over the last few years, several studies have focused on the genomic changes underpinning OA. Here, we provide a comprehensive overview of genome-wide, non-hypothesis-driven functional genomics (methylation, gene, and protein expression) studies of knee and hip OA in humans. Individual studies have generally been limited in sample size and hence power, and have differed in their approaches; nonetheless, some common themes have started to emerge, notably the role played by biological processes related to the extracellular matrix, immune response, the WNT pathway, angiogenesis, and skeletal development. Larger-scale studies and streamlined, robust methodologies will be needed to further elucidate the biological etiology of OA going forward. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1105-1110, 2016.
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Affiliation(s)
- Julia Steinberg
- Wellcome Trust Sanger InstituteHinxtonCambridgeCB10 1HHUnited Kingdom
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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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Mitochondrial DNA haplogroups modify the risk of osteoarthritis by altering mitochondrial function and intracellular mitochondrial signals. Biochim Biophys Acta Mol Basis Dis 2016; 1862:829-836. [DOI: 10.1016/j.bbadis.2015.12.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/10/2015] [Accepted: 12/11/2015] [Indexed: 12/15/2022]
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Taylor SEB, Lee J, Smeriglio P, Razzaque A, Smith RL, Dragoo JL, Maloney WJ, Bhutani N. Identification of Human Juvenile Chondrocyte-Specific Factors that Stimulate Stem Cell Growth. Tissue Eng Part A 2016; 22:645-53. [PMID: 26955889 DOI: 10.1089/ten.tea.2015.0366] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although regeneration of human cartilage is inherently inefficient, age is an important risk factor for osteoarthritis. Recent reports have provided compelling evidence that juvenile chondrocytes (from donors below 13 years of age) are more efficient at generating articular cartilage as compared to adult chondrocytes. However, the molecular basis for such a superior regenerative capability is not understood. To identify the cell-intrinsic differences between juvenile and adult cartilage, we have systematically profiled global gene expression changes between a small cohort of human neonatal/juvenile and adult chondrocytes. No such study is available for human chondrocytes although young and old bovine and equine cartilage have been recently profiled. Our studies have identified and validated new factors enriched in juvenile chondrocytes as compared to adult chondrocytes including secreted extracellular matrix factors chordin-like 1 (CHRDL1) and microfibrillar-associated protein 4 (MFAP4). Network analyses identified cartilage development pathways, epithelial-mesenchymal transition, and innate immunity pathways to be overrepresented in juvenile-enriched genes. Finally, CHRDL1 was observed to aid the proliferation and survival of bone marrow-derived human mesenchymal stem cells (hMSC) while maintaining their stem cell potential. These studies, therefore, provide a mechanism for how young cartilage factors can potentially enhance stem cell function in cartilage repair.
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Affiliation(s)
- Sarah E B Taylor
- Department of Orthopedic Surgery, Stanford University School of Medicine , Stanford, California
| | - Jieun Lee
- Department of Orthopedic Surgery, Stanford University School of Medicine , Stanford, California
| | - Piera Smeriglio
- Department of Orthopedic Surgery, Stanford University School of Medicine , Stanford, California
| | - Adnan Razzaque
- Department of Orthopedic Surgery, Stanford University School of Medicine , Stanford, California
| | - Robert L Smith
- Department of Orthopedic Surgery, Stanford University School of Medicine , Stanford, California
| | - Jason L Dragoo
- Department of Orthopedic Surgery, Stanford University School of Medicine , Stanford, California
| | - William J Maloney
- Department of Orthopedic Surgery, Stanford University School of Medicine , Stanford, California
| | - Nidhi Bhutani
- Department of Orthopedic Surgery, Stanford University School of Medicine , Stanford, California
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Taylor SEB, Li YH, Smeriglio P, Rath M, Wong WH, Bhutani N. Stable 5-Hydroxymethylcytosine (5hmC) Acquisition Marks Gene Activation During Chondrogenic Differentiation. J Bone Miner Res 2016; 31:524-34. [PMID: 26363184 PMCID: PMC4860191 DOI: 10.1002/jbmr.2711] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 09/05/2015] [Accepted: 09/10/2015] [Indexed: 12/21/2022]
Abstract
Regulation of gene expression changes during chondrogenic differentiation by DNA methylation and demethylation is little understood. Methylated cytosines (5mC) are oxidized by the ten-eleven-translocation (TET) proteins to 5-hydroxymethylcytosines (5hmC), 5-formylcytosines (5fC), and 5-carboxylcytosines (5caC), eventually leading to a replacement by unmethylated cytosines (C), ie, DNA demethylation. Additionally, 5hmC is stable and acts as an epigenetic mark by itself. Here, we report that global changes in 5hmC mark chondrogenic differentiation in vivo and in vitro. Tibia anlagen and growth plate analyses during limb development at mouse embryonic days E 11.5, 13.5, and 17.5 showed dynamic changes in 5hmC levels in the differentiating chondrocytes. A similar increase in 5hmC levels was observed in the ATDC5 chondroprogenitor cell line accompanied by increased expression of the TET proteins during in vitro differentiation. Loss of TET1 in ATDC5 decreased 5hmC levels and impaired differentiation, demonstrating a functional role for TET1-mediated 5hmC dynamics in chondrogenic differentiation. Global analyses of the 5hmC-enriched sequences during early and late chondrogenic differentiation identified 5hmC distribution to be enriched in the regulatory regions of genes preceding the transcription start site (TSS), as well as in the gene bodies. Stable gains in 5hmC were observed in specific subsets of genes, including genes associated with cartilage development and in chondrogenic lineage-specific genes. 5hmC gains in regulatory promoter and enhancer regions as well as in gene bodies were strongly associated with activated but not repressed genes, indicating a potential regulatory role for DNA hydroxymethylation in chondrogenic gene expression.
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Affiliation(s)
- Sarah E. B. Taylor
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ye Henry Li
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Piera Smeriglio
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Madhusikta Rath
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wing H. Wong
- Department of Statistics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nidhi Bhutani
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
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40
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Wang XL, Song SH, Wu YS, Li YL, Chen TT, Huang ZY, Liu S, Dunwell TL, Pfeifer GP, Dunwell JM, Wamaedeesa R, Ullah I, Wang Y, Hu SN. Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6651-63. [PMID: 26272901 PMCID: PMC4715260 DOI: 10.1093/jxb/erv372] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
5-Hydroxymethylcytosine (5hmC), a modified form of cytosine that is considered the sixth nucleobase in DNA, has been detected in mammals and is believed to play an important role in gene regulation. In this study, 5hmC modification was detected in rice by employing a dot-blot assay, and its levels was further quantified in DNA from different rice tissues using liquid chromatography-multistage mass spectrometry (LC-MS/MS/MS). The results showed large intertissue variation in 5hmC levels. The genome-wide profiles of 5hmC modification in three different rice cultivars were also obtained using a sensitive chemical labelling followed by a next-generation sequencing method. Thousands of 5hmC peaks were identified, and a comparison of the distributions of 5hmC among different rice cultivars revealed the specificity and conservation of 5hmC modification. The identified 5hmC peaks were significantly enriched in heterochromatin regions, and mainly located in transposable elements (TEs), especially around retrotransposons. The correlation analysis of 5hmC and gene expression data revealed a close association between 5hmC and silent TEs. These findings provide a resource for plant DNA 5hmC epigenetic studies and expand our knowledge of 5hmC modification.
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Affiliation(s)
- Xi-liang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Graduate University of Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China
| | - Shu-hui Song
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong-Sheng Wu
- Mudanjiang Youbo Pharmaceutical Co., Ltd, Heilongjiang 157011, China
| | - Yu-Li Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Graduate University of Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China
| | - Ting-ting Chen
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-yuan Huang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Shuo Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
| | | | - Gerd P Pfeifer
- Beckman Research Institute, City of Hope Medical Centre, Duarte, CA 91010, USA
| | - Jim M Dunwell
- School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading RG6 6AR, UK
| | - Raheema Wamaedeesa
- School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading RG6 6AR, UK
| | - Ihsan Ullah
- School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading RG6 6AR, UK Agricultural Biotechnology Research Institute, Faisalabad 38000, Pakistan
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Song-nian Hu
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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Taylor SEB, Li YH, Wong WH, Bhutani N. Genome-wide mapping of DNA hydroxymethylation in osteoarthritic chondrocytes. Arthritis Rheumatol 2015; 67:2129-40. [PMID: 25940674 DOI: 10.1002/art.39179] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/28/2015] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To examine the genome-wide distribution of hydroxymethylated cytosine (5hmC) in osteoarthritic (OA) and normal chondrocytes in order to investigate the effect on OA-specific gene expression. METHODS Cartilage was obtained from OA patients undergoing total knee arthroplasty or from control patients undergoing anterior cruciate ligament reconstruction. Genome-wide sequencing of 5hmC-enriched DNA was performed in a small cohort of normal and OA chondrocytes to identify differentially hydroxymethylated regions (DhMRs) in OA chondrocytes. Data from the genome-wide sequencing of 5hmC-enriched DNA were intersected with global OA gene expression data to define subsets of genes and pathways potentially affected by increased 5hmC levels in OA chondrocytes. RESULTS A total of 70,591 DhMRs were identified in OA chondrocytes as compared to normal chondrocytes, 44,288 (63%) of which were increased in OA chondrocytes. The majority of DhMRs (66%) were gained in gene bodies. Increased DhMRs were observed in ∼50% of genes previously implicated in OA pathology including MMP3, LRP5, GDF5, and COL11A1. Furthermore, analyses of gene expression data revealed gene body gain of 5hmC appears to be preferentially associated with activated, but not repressed, genes in OA chondrocytes. CONCLUSION This study provides the first genome-wide profiling of 5hmC distribution in OA chondrocytes. We had previously reported a global increase in 5hmC levels in OA chondrocytes. Gain of 5hmC in the gene body is found to be characteristic of activated genes in OA chondrocytes, highlighting the influence of 5hmC as an epigenetic mark in OA. In addition, this study identifies multiple OA-associated genes that are potentially regulated either singularly by gain of DNA hydroxymethylation or in combination with loss of DNA methylation.
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Affiliation(s)
| | - Ye Henry Li
- Stanford University School of Medicine, Stanford, California
| | - Wing H Wong
- Stanford University School of Medicine, Stanford, California
| | - Nidhi Bhutani
- Stanford University School of Medicine, Stanford, California
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42
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Lee J, Taylor SEB, Smeriglio P, Lai J, Maloney WJ, Yang F, Bhutani N. Early induction of a prechondrogenic population allows efficient generation of stable chondrocytes from human induced pluripotent stem cells. FASEB J 2015; 29:3399-410. [PMID: 25911615 DOI: 10.1096/fj.14-269720] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/16/2015] [Indexed: 12/14/2022]
Abstract
Regeneration of human cartilage is inherently inefficient; an abundant autologous source, such as human induced pluripotent stem cells (hiPSCs), is therefore attractive for engineering cartilage. We report a growth factor-based protocol for differentiating hiPSCs into articular-like chondrocytes (hiChondrocytes) within 2 weeks, with an overall efficiency >90%. The hiChondrocytes are stable and comparable to adult articular chondrocytes in global gene expression, extracellular matrix production, and ability to generate cartilage tissue in vitro and in immune-deficient mice. Molecular characterization identified an early SRY (sex-determining region Y) box (Sox)9(low) cluster of differentiation (CD)44(low)CD140(low) prechondrogenic population during hiPSC differentiation. In addition, 2 distinct Sox9-regulated gene networks were identified in the Sox9(low) and Sox9(high) populations providing novel molecular insights into chondrogenic fate commitment and differentiation. Our findings present a favorable method for generating hiPSC-derived articular-like chondrocytes. The hiChondrocytes are an attractive cell source for cartilage engineering because of their abundance, autologous nature, and potential to generate articular-like cartilage rather than fibrocartilage. In addition, hiChondrocytes can be excellent tools for modeling human musculoskeletal diseases in a dish and for rapid drug screening.
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Affiliation(s)
- Jieun Lee
- *Department of Orthopaedic Surgery, Department of Mechanical Engineering, and Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Sarah E B Taylor
- *Department of Orthopaedic Surgery, Department of Mechanical Engineering, and Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Piera Smeriglio
- *Department of Orthopaedic Surgery, Department of Mechanical Engineering, and Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Janice Lai
- *Department of Orthopaedic Surgery, Department of Mechanical Engineering, and Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - William J Maloney
- *Department of Orthopaedic Surgery, Department of Mechanical Engineering, and Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Fan Yang
- *Department of Orthopaedic Surgery, Department of Mechanical Engineering, and Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Nidhi Bhutani
- *Department of Orthopaedic Surgery, Department of Mechanical Engineering, and Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
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Abstract
Osteoarthritis (OA) is a common degenerative joint disease, the pathological mechanism of which is currently unknown. Genetic alteration is one of the key contributing factors for OA pathology. Recent evidence suggests that epigenetic and microRNA regulation of critical genes may contribute to OA development. In this article, we review the epigenetic and microRNA regulations of genes related to OA development. Potential therapeutic strategies may be developed on the basis of novel findings.
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Affiliation(s)
- Di Chen
- Department of Biochemistry, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Jie Shen
- Department of Orthopedic Surgery, Washington University, St. Louis, MO, 63110, USA
| | - Tianqian Hui
- Department of Biochemistry, Rush University Medical Center, Chicago, IL, 60612, USA
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44
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Tsezou A. Osteoarthritis year in review 2014: genetics and genomics. Osteoarthritis Cartilage 2014; 22:2017-24. [PMID: 25456297 DOI: 10.1016/j.joca.2014.07.024] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/24/2014] [Accepted: 07/29/2014] [Indexed: 02/02/2023]
Abstract
Recent developments in genetics/genomics of osteoarthritis (OA) are discussed to improve our understanding of OA pathophysiology. The discovery of a novel variant near the NCOA3 (nuclear receptor coactivator 3) gene associated with hip OA and the regulation of GDF5 gene by four transcription factors via the OA susceptibility locus rs143383 are among important findings in OA genetics. Several microarray-based gene expression studies were published for different tissues of the joint. In OA synovium elevation of collagens and cross-linking enzymes (COL1A1, COL5A1, PLOD2, LOX and TIMP1) responsive to TGF-β was found as well as differential expression pattern between different areas of the osteoarthritic synovial membrane. In OA peripheral blood the role of apoptotic genes was highlighted, while whole genome expression profiling in OA subchondral bone and cartilage revealed common genes in cartilage and bone to be involved in OA development. In epigenetics, several microRNAs (miRNAs) were found to regulate genes' expression in chondrocytes, among which miR-125, miR-127b miR-21, miR-148a and their use as potential drug targets was highlighted. Future studies must focus on the integration of genetics, genomics and epigenetics for the identification of signaling pathways and regulatory networks responsible for OA development.
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Affiliation(s)
- A Tsezou
- University of Thessaly, Faculty of Medicine, Dept. Biology, 41110 Larissa, Greece
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45
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Blanco FJ, Rego-Pérez I. Editorial: Is it time for epigenetics in osteoarthritis? Arthritis Rheumatol 2014; 66:2324-7. [PMID: 24838530 DOI: 10.1002/art.38710] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 05/13/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Francisco J Blanco
- Instituto de Investigación Biomédica de A Coruña, Complexo Hospitalario Universitario de A Coruña, SERGAS, and Universidade da Coruña, A Coruña, Spain
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Ciccone NA, Mwangi W, Ruzov A, Smith LP, Butter C, Nair V. A B-cell targeting virus disrupts potentially protective genomic methylation patterns in lymphoid tissue by increasing global 5-hydroxymethylcytosine levels. Vet Res 2014; 45:108. [PMID: 25338704 PMCID: PMC4258027 DOI: 10.1186/s13567-014-0108-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/07/2014] [Indexed: 11/10/2022] Open
Abstract
The mechanisms by which viruses modulate the immune system include changes in host genomic methylation. 5-hydroxymethylcytosine (5hmC) is the catalytic product of the Tet (Ten-11 translocation) family of enzymes and may serve as an intermediate of DNA demethylation. Recent reports suggest that 5hmC may confer consequences on cellular events including the pathogenesis of disease; in order to explore this possibility further we investigated both 5-methylcytosine (5mC) and 5hmC levels in healthy and diseased chicken bursas of Fabricius. We discovered that embryonic B-cells have high 5mC content while 5hmC decreases during bursa development. We propose that a high 5mC level protects from the mutagenic activity of the B-cell antibody diversifying enzyme activation induced deaminase (AID). In support of this view, AID mRNA increases significantly within the developing bursa from embryonic to post hatch stages while mRNAs that encode Tet family members 1 and 2 reduce over the same period. Moreover, our data revealed that infectious bursal disease virus (IBDV) disrupts this genomic methylation pattern causing a global increase in 5hmC levels in a mechanism that may involve increased Tet 1 and 2 mRNAs. To our knowledge this is the first time that a viral infection has been observed to cause global increases in genomic 5hmC within infected host tissues, underlining a mechanism that may involve the induction of B-cell genomic instability and cell death to facilitate viral egress.
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Affiliation(s)
- Nick A Ciccone
- Avian Viral Diseases (AVD), Compton Laboratory, The Pirbright Institute, Compton, Berkshire, RG20 7NN, UK.
| | - William Mwangi
- Avian Viral Diseases (AVD), Compton Laboratory, The Pirbright Institute, Compton, Berkshire, RG20 7NN, UK.
| | - Alexey Ruzov
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), Division of Cancer and Stem Cells, School of Medicine, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Lorraine P Smith
- Avian Viral Diseases (AVD), Compton Laboratory, The Pirbright Institute, Compton, Berkshire, RG20 7NN, UK.
| | - Colin Butter
- Avian Viral Diseases (AVD), Compton Laboratory, The Pirbright Institute, Compton, Berkshire, RG20 7NN, UK.
| | - Venugopal Nair
- Avian Viral Diseases (AVD), Compton Laboratory, The Pirbright Institute, Compton, Berkshire, RG20 7NN, UK.
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Epigenetically modified nucleotides in chronic heroin and cocaine treated mice. Toxicol Lett 2014; 229:451-7. [PMID: 25064621 DOI: 10.1016/j.toxlet.2014.07.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 12/19/2022]
Abstract
Epigenetic changes include the addition of a methyl group to the 5' carbon of the cytosine ring, known as DNA methylation, which results in the generation of the fifth DNA base, namely 5-methylcytosine. During active or passive demethylation, an intermediate modified base is formed, 5-hydroxymethylcytosine. We have currently quantified 5-methylcytosine and 5-hydroxymethylcytosine in the liver and brain of mice treated with cocaine or heroin, using liquid chromatography/tandem mass spectrometry (LC-MS/MS). Our results show that global 5-methylcytosine levels are not affected by heroin or cocaine administration, neither in the liver nor in the brain. However, 5-hydroxymethylcytosine levels are reduced in the liver following cocaine administration, while they are not affected by cocaine in the brain or by heroin administration in the liver and the brain. Elucidation of the epigenetic phenomena that takes place with respect to drug abuse and addiction, via quantitative analysis of different modified bases, may enable a better understanding of the underlying mechanisms and may lead to more personalized and effective treatment options.
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