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Walewska A, Janucik A, Tynecka M, Moniuszko M, Eljaszewicz A. Mesenchymal stem cells under epigenetic control - the role of epigenetic machinery in fate decision and functional properties. Cell Death Dis 2023; 14:720. [PMID: 37932257 PMCID: PMC10628230 DOI: 10.1038/s41419-023-06239-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023]
Abstract
Mesenchymal stem cells (mesenchymal stromal cells, MSC) are multipotent stem cells that can differentiate into cells of at least three mesodermal lineages, namely adipocytes, osteoblasts, and chondrocytes, and have potent immunomodulatory properties. Epigenetic modifications are critical regulators of gene expression and cellular differentiation of mesenchymal stem cells (MSCs). Epigenetic machinery controls MSC differentiation through direct modifications to DNA and histones. Understanding the role of epigenetic machinery in MSC is crucial for the development of effective cell-based therapies for degenerative and inflammatory diseases. In this review, we summarize the current understanding of the role of epigenetic control of MSC differentiation and immunomodulatory properties.
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Affiliation(s)
- Alicja Walewska
- Centre of Regenerative Medicine, Medical University of Bialystok, ul. Waszyngtona 15B, 15-269, Bialystok, Poland
| | - Adrian Janucik
- Centre of Regenerative Medicine, Medical University of Bialystok, ul. Waszyngtona 15B, 15-269, Bialystok, Poland
| | - Marlena Tynecka
- Centre of Regenerative Medicine, Medical University of Bialystok, ul. Waszyngtona 15B, 15-269, Bialystok, Poland
| | - Marcin Moniuszko
- Centre of Regenerative Medicine, Medical University of Bialystok, ul. Waszyngtona 15B, 15-269, Bialystok, Poland
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, ul. Waszyngtona 13, 15-269, Bialystok, Poland
- Department of Allergology and Internal Medicine, Medical University of Bialystok, ul. M. Sklodowskiej-Curie 24A, 15-276, Bialystok, Poland
| | - Andrzej Eljaszewicz
- Centre of Regenerative Medicine, Medical University of Bialystok, ul. Waszyngtona 15B, 15-269, Bialystok, Poland.
- Tissue and Cell Bank, Medical University of Bialystok Clinical Hospital, ul. Waszyngtona 13, 15-069, Bialystok, Poland.
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2
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Bispo DSC, Jesus CSH, Romek K, Marques IMC, Oliveira MB, Mano JF, Gil AM. An Intracellular Metabolic Signature as a Potential Donor-Independent Marker of the Osteogenic Differentiation of Adipose Tissue Mesenchymal Stem Cells. Cells 2022; 11:cells11233745. [PMID: 36497004 PMCID: PMC9739047 DOI: 10.3390/cells11233745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022] Open
Abstract
This paper describes an untargeted NMR metabolomics study to identify potential intracellular donor-dependent and donor-independent metabolic markers of proliferation and osteogenic differentiation of human adipose mesenchymal stem cells (hAMSCs). The hAMSCs of two donors with distinct proliferating/osteogenic characteristics were fully characterized regarding their polar endometabolome during proliferation and osteogenesis. An 18-metabolites signature (including changes in alanine, aspartate, proline, tyrosine, ATP, and ADP, among others) was suggested to be potentially descriptive of cell proliferation, independently of the donor. In addition, a set of 11 metabolites was proposed to compose a possible donor-independent signature of osteogenesis, mostly involving changes in taurine, glutathione, methylguanidine, adenosine, inosine, uridine, and creatine/phosphocreatine, choline/phosphocholine and ethanolamine/phosphocholine ratios. The proposed signatures were validated for a third donor, although they require further validation in a larger donor cohort. We believe that this proof of concept paves the way to exploit metabolic markers to monitor (and potentially predict) cell proliferation and the osteogenic ability of different donors.
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3
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Gamma-glutamyltransferase of Helicobacter pylori alters the proliferation, migration, and pluripotency of mesenchymal stem cells by affecting metabolism and methylation status. J Microbiol 2022; 60:627-639. [DOI: 10.1007/s12275-022-1575-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 02/07/2023]
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4
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Rummukainen P, Tarkkonen K, Dudakovic A, Al-Majidi R, Nieminen-Pihala V, Valensisi C, Hawkins RD, van Wijnen AJ, Kiviranta R. Lysine-Specific Demethylase 1 (LSD1) epigenetically controls osteoblast differentiation. PLoS One 2022; 17:e0265027. [PMID: 35255108 PMCID: PMC8901060 DOI: 10.1371/journal.pone.0265027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/18/2022] [Indexed: 02/03/2023] Open
Abstract
Epigenetic mechanisms regulate osteogenic lineage differentiation of mesenchymal stromal cells. Histone methylation is controlled by multiple lysine demethylases and is an important step in controlling local chromatin structure and gene expression. Here, we show that the lysine-specific histone demethylase Kdm1A/Lsd1 is abundantly expressed in osteoblasts and that its suppression impairs osteoblast differentiation and bone nodule formation in vitro. Although Lsd1 knockdown did not affect global H3K4 methylation levels, genome-wide ChIP-Seq analysis revealed high levels of Lsd1 at gene promoters and its binding was associated with di- and tri-methylation of histone 3 at lysine 4 (H3K4me2 and H3K4me3). Lsd1 binding sites in osteoblastic cells were enriched for the Runx2 consensus motif suggesting a functional link between the two proteins. Importantly, inhibition of Lsd1 activity decreased osteoblast activity in vivo. In support, mesenchymal-targeted knockdown of Lsd1 led to decreased osteoblast activity and disrupted primary spongiosa ossification and reorganization in vivo. Together, our studies demonstrate that Lsd1 occupies Runx2-binding cites at H3K4me2 and H3K4me3 and its activity is required for proper bone formation.
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Affiliation(s)
| | - Kati Tarkkonen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States of America
- Department of Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, United States of America
| | - Rana Al-Majidi
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Cristina Valensisi
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - R. David Hawkins
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Andre J. van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States of America
- Department of Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, United States of America
- Department of Biochemistry, University of Vermont, Burlington, VT, United States of America
- * E-mail: (AJW); (RK)
| | - Riku Kiviranta
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Endocrinology, Turku University Hospital, Turku, Finland
- * E-mail: (AJW); (RK)
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5
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Karlsen TA, Sundaram AYM, Brinchmann JE. Single-Cell RNA Sequencing of In Vitro Expanded Chondrocytes: MSC-Like Cells With No Evidence of Distinct Subsets. Cartilage 2021; 13:774S-784S. [PMID: 31072202 PMCID: PMC8804791 DOI: 10.1177/1947603519847746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To investigate the heterogeneity of in vitro expanded chondrocytes used for autologous chondrocyte implantation. METHODS Human articular chondrocytes were expanded in vitro for 14 days, sorted into 86 single cells using fluorescence-activated cell sorting and subjected to single-cell RNA sequencing. Principal component, Cross R2 hierarchical clustering, and differential gene expression analyses were used for data evaluation. Flow cytometry and single-cell RT-qPCR (reverse transcriptase quantitative polymerase chain reaction) was used to validate the results of the RNA sequencing data Polyclonal chondrocyte populations from the same donor were differentiated in vitro toward the osteogenic and adipogenic lineages. RESULTS There was considerable variation in gene expression between individual cells, but we found no evidence for separate cell subpopulations based on principal component, hierarchical clustering, and differential gene expression analysis. Most of the cells expressed all the markers defining mesenchymal stem cells, and as polyclonal chondrocyte populations from the same donor were shown to differentiate into osteocytes and adipocytes in vitro, these cells formally qualify as mesenchymal stem cells. CONCLUSIONS In vitro expanded chondrocytes consist of one single population of cells with heterogeneity in gene expression between the cells. Dedifferentiated chondrocytes qualify as mesenchymal stem cells as they fulfill all the criteria suggested by the International Society for Cellular Therapy.
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Affiliation(s)
- Tommy A. Karlsen
- Norwegian Center for Stem Cell
Research, Department of Immunology, Oslo University Hospital Rikshospitalet,
Oslo, Norway,Tommy A. Karlsen, Department of
Immunology, Oslo University Hospital Rikshospitalet, PO Box 4950
Nydalen, Oslo 0424, Norway.
| | - Arvind Y. M. Sundaram
- Norwegian Sequencing Centre,
Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Jan E. Brinchmann
- Norwegian Center for Stem Cell
Research, Department of Immunology, Oslo University Hospital Rikshospitalet,
Oslo, Norway,Department of Molecular Medicine,
Faculty of Medicine, University of Oslo, Oslo, Norway
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6
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Rauch A, Mandrup S. Transcriptional networks controlling stromal cell differentiation. Nat Rev Mol Cell Biol 2021; 22:465-482. [PMID: 33837369 DOI: 10.1038/s41580-021-00357-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 02/02/2023]
Abstract
Stromal progenitors are found in many different tissues, where they play an important role in the maintenance of tissue homeostasis owing to their ability to differentiate into parenchymal cells. These progenitor cells are differentially pre-programmed by their tissue microenvironment but, when cultured and stimulated in vitro, these cells - commonly referred to as mesenchymal stromal cells (MSCs) - exhibit a marked plasticity to differentiate into many different cell lineages. Loss-of-function studies in vitro and in vivo have uncovered the involvement of specific signalling pathways and key transcriptional regulators that work in a sequential and coordinated fashion to activate lineage-selective gene programmes. Recent advances in omics and single-cell technologies have made it possible to obtain system-wide insights into the gene regulatory networks that drive lineage determination and cell differentiation. These insights have important implications for the understanding of cell differentiation, the contribution of stromal cells to human disease and for the development of cell-based therapeutic applications.
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Affiliation(s)
- Alexander Rauch
- Molecular Endocrinology & Stem Cell Research Unit (KMEB), Department of Endocrinology and Metabolism, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark. .,Steno Diabetes Center Odense, Odense University Hospital, Odense, Denmark.
| | - Susanne Mandrup
- Center for Functional Genomics and Tissue Plasticity, Functional Genomics & Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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7
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Wuelling M, Neu C, Thiesen AM, Kitanovski S, Cao Y, Lange A, Westendorf AM, Hoffmann D, Vortkamp A. Epigenetic Mechanisms Mediating Cell State Transitions in Chondrocytes. J Bone Miner Res 2021; 36:968-985. [PMID: 33534175 DOI: 10.1002/jbmr.4263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 01/06/2023]
Abstract
Epigenetic modifications play critical roles in regulating cell lineage differentiation, but the epigenetic mechanisms guiding specific differentiation steps within a cell lineage have rarely been investigated. To decipher such mechanisms, we used the defined transition from proliferating (PC) into hypertrophic chondrocytes (HC) during endochondral ossification as a model. We established a map of activating and repressive histone modifications for each cell type. ChromHMM state transition analysis and Pareto-based integration of differential levels of mRNA and epigenetic marks revealed that differentiation-associated gene repression is initiated by the addition of H3K27me3 to promoters still carrying substantial levels of activating marks. Moreover, the integrative analysis identified genes specifically expressed in cells undergoing the transition into hypertrophy. Investigation of enhancer profiles detected surprising differences in enhancer number, location, and transcription factor binding sites between the two closely related cell types. Furthermore, cell type-specific upregulation of gene expression was associated with increased numbers of H3K27ac peaks. Pathway analysis identified PC-specific enhancers associated with chondrogenic genes, whereas HC-specific enhancers mainly control metabolic pathways linking epigenetic signature to biological functions. Since HC-specific enhancers show a higher conservation in postnatal tissues, the switch to metabolic pathways seems to be a hallmark of differentiated tissues. Surprisingly, the analysis of H3K27ac levels at super-enhancers revealed a rapid adaption of H3K27ac occupancy to changes in gene expression, supporting the importance of enhancer modulation for acute alterations in gene expression. © 2021 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Manuela Wuelling
- Developmental Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Christoph Neu
- Developmental Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Andrea M Thiesen
- Developmental Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Simo Kitanovski
- Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Yingying Cao
- Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Anja Lange
- Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Astrid M Westendorf
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Andrea Vortkamp
- Developmental Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
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8
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Wan C, Zhang F, Yao H, Li H, Tuan RS. Histone Modifications and Chondrocyte Fate: Regulation and Therapeutic Implications. Front Cell Dev Biol 2021; 9:626708. [PMID: 33937229 PMCID: PMC8085601 DOI: 10.3389/fcell.2021.626708] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/17/2021] [Indexed: 12/12/2022] Open
Abstract
The involvement of histone modifications in cartilage development, pathology and regeneration is becoming increasingly evident. Understanding the molecular mechanisms and consequences of histone modification enzymes in cartilage development, homeostasis and pathology provides fundamental and precise perspectives to interpret the biological behavior of chondrocytes during skeletal development and the pathogenesis of various cartilage related diseases. Candidate molecules or drugs that target histone modifying proteins have shown promising therapeutic potential in the treatment of cartilage lesions associated with joint degeneration and other chondropathies. In this review, we summarized the advances in the understanding of histone modifications in the regulation of chondrocyte fate, cartilage development and pathology, particularly the molecular writers, erasers and readers involved. In addition, we have highlighted recent studies on the use of small molecules and drugs to manipulate histone signals to regulate chondrocyte functions or treat cartilage lesions, in particular osteoarthritis (OA), and discussed their potential therapeutic benefits and limitations in preventing articular cartilage degeneration or promoting its repair or regeneration.
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Affiliation(s)
- Chao Wan
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China.,MOE Key Laboratory for Regenerative Medicine (Shenzhen Base), School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Fengjie Zhang
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China.,MOE Key Laboratory for Regenerative Medicine (Shenzhen Base), School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Hanyu Yao
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China.,MOE Key Laboratory for Regenerative Medicine (Shenzhen Base), School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Rocky S Tuan
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, China.,MOE Key Laboratory for Regenerative Medicine (Shenzhen Base), School of Biomedical Sciences Core Laboratory, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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9
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Pouikli A, Tessarz P. Metabolism and chromatin: A dynamic duo that regulates development and ageing: Elucidating the metabolism-chromatin axis in bone-marrow mesenchymal stem cell fate decisions. Bioessays 2021; 43:e2000273. [PMID: 33629755 DOI: 10.1002/bies.202000273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022]
Abstract
Bone-marrow mesenchymal stem cell (BM-MSC) proliferation and lineage commitment are under the coordinated control of metabolism and epigenetics; the MSC niche contains low oxygen, which is an important determinant of the cellular metabolic state. In turn, metabolism drives stem cell fate decisions via alterations of the chromatin landscape. Due to the fundamental role of BM-MSCs in the development of adipose tissue, bones and cartilage, age-associated changes in metabolism and the epigenome perturb the balance between stem cell proliferation and differentiation leading to stem cell depletion, fat accumulation and bone-quality related diseases. Therefore, understanding the dynamics of the metabolism-chromatin interplay is crucial for maintaining the stem cell pool and delaying the development and progression of ageing. This review summarizes the current knowledge on the role of metabolism in stem cell identity and highlights the impact of the metabolic inputs on the epigenome, with regards to stemness and pluripotency.
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Affiliation(s)
- Andromachi Pouikli
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Peter Tessarz
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Excellence Cluster on Stress Responses in ageing-associated Diseases (CECAD), Cologne, Germany
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10
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Abstract
PURPOSE OF REVIEW Although many signalling pathways have been discovered to be essential in mesenchymal stem/stromal (MSC) differentiation, it has become increasingly clear in recent years that epigenetic regulation of gene transcription is a vital component of lineage determination, encompassing diet, lifestyle and parental influences on bone, fat and cartilage development. RECENT FINDINGS This review discusses how specific enzymes that modify histone methylation and acetylation or DNA methylation orchestrate the differentiation programs in lineage determination of MSC and the epigenetic changes that facilitate development of bone related diseases such as osteoporosis. The review also describes how environmental factors such as mechanical loading influence the epigenetic signatures of MSC, and how the use of chemical agents or small peptides can regulate epigenetic drift in MSC populations during ageing and disease. Epigenetic regulation of MSC lineage commitment is controlled through changes in enzyme activity, which modifies DNA and histone residues leading to alterations in chromatin structure. The co-ordinated epigenetic regulation of transcriptional activation and repression act to mediate skeletal tissue homeostasis, where deregulation of this process can lead to bone loss during ageing or osteoporosis.
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Affiliation(s)
- Dimitrios Cakouros
- Mesenchymal Stem Cell Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Stan Gronthos
- Mesenchymal Stem Cell Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia.
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
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11
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Barter MJ, Cheung K, Falk J, Panagiotopoulos AC, Cosimini C, O'Brien S, Teja-Putri K, Neill G, Deehan DJ, Young DA. Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation. Epigenetics 2020; 16:106-119. [PMID: 32741307 PMCID: PMC7889151 DOI: 10.1080/15592294.2020.1789266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Dynamic modifications of chromatin allow rapid access of the gene regulatory machinery to condensed genomic regions facilitating subsequent gene expression. Inflammatory cytokine stimulation of cells can cause rapid gene expression changes through direct signalling pathway-mediated transcription factor activation and regulatory element binding. Here we used the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to assess regions of the genome that are differentially accessible following treatment of cells with interleukin-1 (IL-1). We identified 126,483 open chromatin regions, with 241 regions significantly differentially accessible following stimulation, with 64 and 177 more or less accessible, respectively. These differentially accessible regions predominantly correspond to regions of the genome marked as enhancers. Motif searching identified an overrepresentation of a number of transcription factors, most notably RelA, in the regions becoming more accessible, with analysis of ChIP-seq data confirmed RelA binding to these regions. A significant correlation in differential chromatin accessibility and gene expression was also observed. Functionality in regulating gene expression was confirmed using CRISPR/Cas9 genome-editing to delete regions that became more accessible following stimulation in the genes MMP13, IKBKE and C1QTNF1. These same regions were also accessible for activation using a dCas9-transcriptional activator and showed enhancer activity in a cellular model. Together, these data describe and functionally validate a number of dynamically accessible chromatin regions involved in inflammatory signalling.
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Affiliation(s)
- Matt J Barter
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Kathleen Cheung
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK.,Faculty of Medical Sciences, Bioinformatics Support Unit, Newcastle University , Newcastle upon Tyne, UK
| | - Julia Falk
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Andreas C Panagiotopoulos
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Caitlin Cosimini
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Siobhan O'Brien
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Karina Teja-Putri
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Graham Neill
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - David J Deehan
- Department of Orthopaedics, Freeman Hospital, Orthopaedics , UK
| | - David A Young
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
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12
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Stegen S, Rinaldi G, Loopmans S, Stockmans I, Moermans K, Thienpont B, Fendt SM, Carmeliet P, Carmeliet G. Glutamine Metabolism Controls Chondrocyte Identity and Function. Dev Cell 2020; 53:530-544.e8. [DOI: 10.1016/j.devcel.2020.05.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 04/20/2020] [Accepted: 05/01/2020] [Indexed: 12/31/2022]
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13
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Epigenetics in Inflammatory Breast Cancer: Biological Features and Therapeutic Perspectives. Cells 2020; 9:cells9051164. [PMID: 32397183 PMCID: PMC7291154 DOI: 10.3390/cells9051164] [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] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/25/2020] [Accepted: 04/30/2020] [Indexed: 12/12/2022] Open
Abstract
Evidence has emerged implicating epigenetic alterations in inflammatory breast cancer (IBC) origin and progression. IBC is a rare and rapidly progressing disease, considered the most aggressive type of breast cancer (BC). At clinical presentation, IBC is characterized by diffuse erythema, skin ridging, dermal lymphatic invasion, and peau d'orange aspect. The widespread distribution of the tumor as emboli throughout the breast and intra- and intertumor heterogeneity is associated with its poor prognosis. In this review, we highlighted studies documenting the essential roles of epigenetic mechanisms in remodeling chromatin and modulating gene expression during mammary gland differentiation and the development of IBC. Compiling evidence has emerged implicating epigenetic changes as a common denominator linking the main risk factors (socioeconomic status, environmental exposure to endocrine disruptors, racial disparities, and obesity) with IBC development. DNA methylation changes and their impact on the diagnosis, prognosis, and treatment of IBC are also described. Recent studies are focusing on the use of histone deacetylase inhibitors as promising epigenetic drugs for treating IBC. All efforts must be undertaken to unravel the epigenetic marks that drive this disease and how this knowledge could impact strategies to reduce the risk of IBC development and progression.
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14
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Rice SJ, Beier F, Young DA, Loughlin J. Interplay between genetics and epigenetics in osteoarthritis. Nat Rev Rheumatol 2020; 16:268-281. [PMID: 32273577 DOI: 10.1038/s41584-020-0407-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2020] [Indexed: 12/15/2022]
Abstract
Research into the molecular genetics of osteoarthritis (OA) has been substantially bolstered in the past few years by the implementation of powerful genome-wide scans that have revealed a large number of novel risk loci associated with the disease. This refreshing wave of discovery has occurred concurrently with epigenetic studies of joint tissues that have examined DNA methylation, histone modifications and regulatory RNAs. These epigenetic analyses have involved investigations of joint development, homeostasis and disease and have used both human samples and animal models. What has become apparent from a comparison of these two complementary approaches is that many OA genetic risk signals interact with, map to or correlate with epigenetic mediators. This discovery implies that epigenetic mechanisms, and their effect on gene expression, are a major conduit through which OA genetic risk polymorphisms exert their functional effects. This observation is particularly exciting as it provides mechanistic insight into OA susceptibility. Furthermore, this knowledge reveals avenues for attenuating the negative effect of risk-conferring alleles by exposing the epigenome as an exploitable target for therapeutic intervention in OA.
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Affiliation(s)
- Sarah J Rice
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Frank Beier
- Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada.,Western Bone and Joint Institute, The University of Western Ontario, London, ON, Canada
| | - David A Young
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - John Loughlin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
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15
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González-Rico FJ, Vicente-García C, Fernández A, Muñoz-Santos D, Montoliu L, Morales-Hernández A, Merino JM, Román AC, Fernández-Salguero PM. Alu retrotransposons modulate Nanog expression through dynamic changes in regional chromatin conformation via aryl hydrocarbon receptor. Epigenetics Chromatin 2020; 13:15. [PMID: 32169107 PMCID: PMC7071633 DOI: 10.1186/s13072-020-00336-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 03/02/2020] [Indexed: 12/19/2022] Open
Abstract
Transcriptional repression of Nanog is an important hallmark of stem cell differentiation. Chromatin modifications have been linked to the epigenetic profile of the Nanog gene, but whether chromatin organization actually plays a causal role in Nanog regulation is still unclear. Here, we report that the formation of a chromatin loop in the Nanog locus is concomitant to its transcriptional downregulation during human NTERA-2 cell differentiation. We found that two Alu elements flanking the Nanog gene were bound by the aryl hydrocarbon receptor (AhR) and the insulator protein CTCF during cell differentiation. Such binding altered the profile of repressive histone modifications near Nanog likely leading to gene insulation through the formation of a chromatin loop between the two Alu elements. Using a dCAS9-guided proteomic screening, we found that interaction of the histone methyltransferase PRMT1 and the chromatin assembly factor CHAF1B with the Alu elements flanking Nanog was required for chromatin loop formation and Nanog repression. Therefore, our results uncover a chromatin-driven, retrotransposon-regulated mechanism for the control of Nanog expression during cell differentiation.
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Affiliation(s)
- Francisco J González-Rico
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Av. de Elvas s/n, 06071, Badajoz, Spain
| | - Cristina Vicente-García
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, C/Darwin 3, 28049, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Almudena Fernández
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, C/Darwin 3, 28049, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Diego Muñoz-Santos
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, C/Darwin 3, 28049, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Lluís Montoliu
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, C/Darwin 3, 28049, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Antonio Morales-Hernández
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Av. de Elvas s/n, 06071, Badajoz, Spain
| | - Jaime M Merino
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Av. de Elvas s/n, 06071, Badajoz, Spain
| | - Angel-Carlos Román
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Av. de Elvas s/n, 06071, Badajoz, Spain.
| | - Pedro M Fernández-Salguero
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Av. de Elvas s/n, 06071, Badajoz, Spain.
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16
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Cheung K, Barter MJ, Falk J, Proctor CJ, Reynard LN, Young DA. Histone ChIP-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity. FASEB J 2020; 34:5317-5331. [PMID: 32058623 PMCID: PMC7187454 DOI: 10.1096/fj.201902061rr] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/27/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022]
Abstract
Epigenetic mechanisms are known to regulate gene expression during chondrogenesis. In this study, we have characterized the epigenome during the in vitro differentiation of human mesenchymal stem cells (hMSCs) into chondrocytes. Chromatin immunoprecipitation followed by next‐generation sequencing (ChIP‐seq) was used to assess a range of N‐terminal posttranscriptional modifications (marks) to histone H3 lysines (H3K4me3, H3K4me1, H3K27ac, H3K27me3, and H3K36me3) in both hMSCs and differentiated chondrocytes. Chromatin states were characterized using histone ChIP‐seq and cis‐regulatory elements were identified in chondrocytes. Chondrocyte enhancers were associated with chondrogenesis‐related gene ontology (GO) terms. In silico analysis and integration of DNA methylation data with chondrogenesis chromatin states revealed that enhancers marked by histone marks H3K4me1 and H3K27ac were de‐methylated during in vitro chondrogenesis. Similarity analysis between hMSC and chondrocyte chromatin states defined in this study with epigenomes of cell‐types defined by the Roadmap Epigenomics project revealed that enhancers are more distinct between cell‐types compared to other chromatin states. Motif analysis revealed that the transcription factor SOX9 is enriched in chondrocyte enhancers. Luciferase reporter assays confirmed that chondrocyte enhancers characterized in this study exhibited enhancer activity which may be modulated by DNA methylation and SOX9 overexpression. Altogether, these integrated data illustrate the cross‐talk between different epigenetic mechanisms during chondrocyte differentiation.
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Affiliation(s)
- Kathleen Cheung
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK.,Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew J Barter
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Julia Falk
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Carole J Proctor
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - Louise N Reynard
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
| | - David A Young
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, UK
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17
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Ying J, Xu T, Wang C, Jin H, Tong P, Guan J, Abu-Amer Y, O’Keefe R, Shen J. Dnmt3b ablation impairs fracture repair through upregulation of Notch pathway. JCI Insight 2020; 5:131816. [PMID: 32051335 PMCID: PMC7098799 DOI: 10.1172/jci.insight.131816] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/26/2019] [Indexed: 12/13/2022] Open
Abstract
We previously established that DNA methyltransferase 3b (Dnmt3b) is the sole Dnmt responsive to fracture repair and that Dnmt3b expression is induced in progenitor cells during fracture repair. In the current study, we confirmed that Dnmt3b ablation in mesenchymal progenitor cells (MPCs) resulted in impaired endochondral ossification, delayed fracture repair, and reduced mechanical strength of the newly formed bone in Prx1-Cre;Dnmt3bf/f (Dnmt3bPrx1) mice. Mechanistically, deletion of Dnmt3b in MPCs led to reduced chondrogenic and osteogenic differentiation in vitro. We further identified Rbpjκ as a downstream target of Dnmt3b in MPCs. In fact, we located 2 Dnmt3b binding sites in the murine proximal Rbpjκ promoter and gene body and confirmed Dnmt3b interaction with the 2 binding sites by ChIP assays. Luciferase assays showed functional utilization of the Dnmt3b binding sites in murine C3H10T1/2 cells. Importantly, we showed that the MPC differentiation defect observed in Dnmt3b deficiency cells was due to the upregulation of Rbpjκ, evident by restored MPC differentiation upon Rbpjκ inhibition. Consistent with in vitro findings, Rbpjκ blockage via dual antiplatelet therapy reversed the differentiation defect and accelerated fracture repair in Dnmt3bPrx1 mice. Collectively, our data suggest that Dnmt3b suppresses Notch signaling during MPC differentiation and is necessary for normal fracture repair.
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Affiliation(s)
- Jun Ying
- Department of Orthopaedic Surgery, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Institute of Orthopaedics and Traumatology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Taotao Xu
- Department of Orthopaedic Surgery, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Institute of Orthopaedics and Traumatology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Cuicui Wang
- Department of Orthopaedic Surgery, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Hongting Jin
- Institute of Orthopaedics and Traumatology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Peijian Tong
- Institute of Orthopaedics and Traumatology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Jianjun Guan
- Department of Biomedical Engineering, School of Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yousef Abu-Amer
- Department of Orthopaedic Surgery, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Shriners Hospital for Children, St. Louis, Missouri, USA
| | - Regis O’Keefe
- Department of Orthopaedic Surgery, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jie Shen
- Department of Orthopaedic Surgery, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
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18
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Ren J, Huang D, Li R, Wang W, Zhou C. Control of mesenchymal stem cell biology by histone modifications. Cell Biosci 2020; 10:11. [PMID: 32025282 PMCID: PMC6996187 DOI: 10.1186/s13578-020-0378-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 01/24/2020] [Indexed: 12/13/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are considered the most promising seed cells for regenerative medicine because of their considerable therapeutic properties and accessibility. Fine-tuning of cell biological processes, including differentiation and senescence, is essential for achievement of the expected regenerative efficacy. Researchers have recently made great advances in understanding the spatiotemporal gene expression dynamics that occur during osteogenic, adipogenic and chondrogenic differentiation of MSCs and the intrinsic and environmental factors that affect these processes. In this context, histone modifications have been intensively studied in recent years and have already been indicated to play significant and universal roles in MSC fate determination and differentiation. In this review, we summarize recent discoveries regarding the effects of histone modifications on MSC biology. Moreover, we also provide our insights and perspectives for future applications.
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Affiliation(s)
- Jianhan Ren
- Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Lingyuanxi Road, Guangzhou, 510055 China
| | - Delan Huang
- Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Lingyuanxi Road, Guangzhou, 510055 China
| | - Runze Li
- Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Lingyuanxi Road, Guangzhou, 510055 China
| | - Weicai Wang
- Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Lingyuanxi Road, Guangzhou, 510055 China
| | - Chen Zhou
- Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, 56 Lingyuanxi Road, Guangzhou, 510055 China
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19
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Concise Review: The Regulatory Mechanism of Lysine Acetylation in Mesenchymal Stem Cell Differentiation. Stem Cells Int 2020; 2020:7618506. [PMID: 32399051 PMCID: PMC7204305 DOI: 10.1155/2020/7618506] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
Nowadays, the use of MSCs has attracted considerable attention in the global science and technology field, with the self-renewal and multidirectional differentiation potential for diabetes, obesity treatment, bone repair, nerve repair, myocardial repair, and so on. Epigenetics plays an important role in the regulation of mesenchymal stem cell differentiation, which has become a research hotspot in the medical field. This review focuses on the role of lysine acetylation modification on the determination of MSC differentiation direction. During this progress, the recruitment of lysine acetyltransferases (KATs) and lysine deacetylases (KDACs) is the crux of transcriptional mechanisms in the dynamic regulation of key genes controlling MSC multidirectional differentiation.
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20
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DNA hypomethylation during MSC chondrogenesis occurs predominantly at enhancer regions. Sci Rep 2020; 10:1169. [PMID: 31980739 PMCID: PMC6981252 DOI: 10.1038/s41598-020-58093-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/21/2019] [Indexed: 12/12/2022] Open
Abstract
Regulation of transcription occurs in a cell type specific manner orchestrated by epigenetic mechanisms including DNA methylation. Methylation changes may also play a key role in lineage specification during stem cell differentiation. To further our understanding of epigenetic regulation in chondrocytes we characterised the DNA methylation changes during chondrogenesis of mesenchymal stem cells (MSCs) by Infinium 450 K methylation array. Significant DNA hypomethylation was identified during chondrogenic differentiation including changes at many key cartilage gene loci. Integration with chondrogenesis gene expression data revealed an enrichment of significant CpGs in upregulated genes, while characterisation of significant CpG loci indicated their predominant localisation to enhancer regions. Comparison with methylation profiles of other tissues, including healthy and diseased adult cartilage, identified chondrocyte-specific regions of hypomethylation and the overlap with differentially methylated CpGs in osteoarthritis. Taken together we have associated DNA methylation levels with the chondrocyte phenotype. The consequences of which has potential to improve cartilage generation for tissue engineering purposes and also to provide context for observed methylation changes in cartilage diseases such as osteoarthritis.
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21
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Hernández R, Jiménez-Luna C, Perales-Adán J, Perazzoli G, Melguizo C, Prados J. Differentiation of Human Mesenchymal Stem Cells towards Neuronal Lineage: Clinical Trials in Nervous System Disorders. Biomol Ther (Seoul) 2020; 28:34-44. [PMID: 31649208 PMCID: PMC6939692 DOI: 10.4062/biomolther.2019.065] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/12/2019] [Accepted: 08/12/2019] [Indexed: 12/13/2022] Open
Abstract
Mesenchymal stem cells (MSCs) have been proposed as an alternative therapy to be applied into several pathologies of the nervous system. These cells can be obtained from adipose tissue, umbilical cord blood and bone marrow, among other tissues, and have remarkable therapeutic properties. MSCs can be isolated with high yield, which adds to their ability to differentiate into non-mesodermal cell types including neuronal lineage both in vivo and in vitro. They are able to restore damaged neural tissue, thus being suitable for the treatment of neural injuries, and possess immunosuppressive activity, which may be useful for the treatment of neurological disorders of inflammatory etiology. Although the long-term safety of MSC-based therapies remains unclear, a large amount of both pre-clinical and clinical trials have shown functional improvements in animal models of nervous system diseases following transplantation of MSCs. In fact, there are several ongoing clinical trials evaluating the possible benefits this cell-based therapy could provide to patients with neurological damage, as well as their clinical limitations. In this review we focus on the potential of MSCs as a therapeutic tool to treat neurological disorders, summarizing the state of the art of this topic and the most recent clinical studies.
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Affiliation(s)
- Rosa Hernández
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada 18100, Spain.,Department of Anatomy and Embryology, University of Granada, Granada 18016, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), Granada 18012, Spain
| | - Cristina Jiménez-Luna
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada 18100, Spain.,Department of Anatomy and Embryology, University of Granada, Granada 18016, Spain.,Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Epalinges 1066, Switzerland
| | - Jesús Perales-Adán
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada 18100, Spain
| | - Gloria Perazzoli
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada 18100, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), Granada 18012, Spain
| | - Consolación Melguizo
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada 18100, Spain.,Department of Anatomy and Embryology, University of Granada, Granada 18016, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), Granada 18012, Spain
| | - José Prados
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada 18100, Spain.,Department of Anatomy and Embryology, University of Granada, Granada 18016, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), Granada 18012, Spain
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22
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Nomura Y, Hara ES, Yoshioka Y, Nguyen HT, Nosho S, Komori T, Ishibashi K, Oohashi T, Ono M, Kuboki T. DNA Methylation-Based Regulation of Human Bone Marrow-Derived Mesenchymal Stem/Progenitor Cell Chondrogenic Differentiation. Cells Tissues Organs 2019; 207:115-126. [PMID: 31574516 DOI: 10.1159/000502885] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/22/2019] [Indexed: 11/19/2022] Open
Abstract
Stem cells have essential applications in in vitro tissue engineering or regenerative medicine. However, there is still a need to understand more deeply the mechanisms of stem cell differentiation and to optimize the methods to control stem cell function. In this study, we first investigated the activity of DNA methyltransferases (DNMTs) during chondrogenic differentiation of human bone marrow-derived mesenchymal stem/progenitor cells (hBMSCs) and found that DNMT3A and DNMT3B were markedly upregulated during hBMSC chondrogenic differentiation. In an attempt to understand the effect of DNMT3A and DNMT3B on the chondrogenic differentiation of hBMSCs, we transiently transfected the cells with expression vectors for the two enzymes. Interestingly, DNMT3A overexpression strongly enhanced the chondrogenesis of hBMSCs, by increasing the gene expression of the mature chondrocyte marker, collagen type II, more than 200-fold. Analysis of the methylation condition in the cells revealed that DNMT3A and DNMT3B methylated the promoter sequence of early stem cell markers, NANOG and POU5F1(OCT-4). Conversely, the suppression of chondrogenic differentiation and the increase in stem cell markers of hBMSCs were obtained by chemical stimulation with the demethylating agent, 5-azacitidine. Loss-of-function assays with siRNAs targeting DNMT3A also significantly suppressed the chondrogenic differentiation of hBMSCs. Together, these results not only show the critical roles of DNMTs in regulating the chondrogenic differentiation of hBMSCs, but also suggest that manipulation of DNMT activity can be important tools to enhance the differentiation of hBMSCs towards chondrogenesis for potential application in cartilage tissue engineering or cartilage regeneration.
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Affiliation(s)
- Yu Nomura
- Department of Oral Rehabilitation and Regenerative Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Emilio Satoshi Hara
- Department of Biomaterials, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan,
| | - Yuya Yoshioka
- Department of Oral Rehabilitation and Regenerative Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Há Thi Nguyen
- Department of Oral Rehabilitation and Regenerative Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Department of Molecular Biology and Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Shuji Nosho
- Department of Oral Rehabilitation and Regenerative Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Taishi Komori
- Department of Oral Rehabilitation and Regenerative Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kei Ishibashi
- Department of Oral Rehabilitation and Regenerative Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Department of Molecular Biology and Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Toshitaka Oohashi
- Department of Molecular Biology and Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Mitsuaki Ono
- Department of Molecular Biology and Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Takuo Kuboki
- Department of Oral Rehabilitation and Regenerative Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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23
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Govarthanan K, Gupta PK, Ramasamy D, Kumar P, Mahadevan S, Verma RS. DNA methylation microarray uncovers a permissive methylome for cardiomyocyte differentiation in human mesenchymal stem cells. Genomics 2019; 112:1384-1395. [PMID: 31415810 DOI: 10.1016/j.ygeno.2019.08.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/25/2019] [Accepted: 08/11/2019] [Indexed: 12/22/2022]
Abstract
Differentiation of Wharton's Jelly-Mesenchymal Stem cells (WJ-MSCs) into cardiomyocytes (CMs) in vitro has been reported widely although contradictions remain regarding the maturation of differentiated MSCs into fully functioning CMs. Studies suggest that use of epigenetic modifiers like 5'Azacytidine (5-AC) in MSCs de-methylates DNA and results in expression of cardiac-specific genes (CSGs). However, only partial expression of the CSG set leads to incomplete differentiation of WJ-MSCs to CMs. We used the Agilent 180 K human DNA methylation microarray on WJ-MSCs, 5-AC treated WJ-MSCs and human cardiac tissue (hCT) to analyze differential DNA methylation profiles which were then validated by bisulfite sequencing PCR (BSP). BSP confirmed that only a limited number of CSGs were de-methylated by 5-AC in WJ-MSCs. It also revealed that hCT displays a methylation profile similar to promoter regions of CSG in untreated WJ-MSCs. Thus, the presence of hypo-methylated CSGs indicates that WJ-MSCs are ideal cell types for cardiomyogenic differentiation.
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Affiliation(s)
- Kavitha Govarthanan
- Stem cells and Molecular Biology Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India
| | - Piyush Kumar Gupta
- Stem cells and Molecular Biology Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India
| | - Deepa Ramasamy
- Stem cells and Molecular Biology Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India
| | - Pavitra Kumar
- AU-KBC Research Centre, Madras Institute of Technology, Anna University, Chennai 600044, Tamilnadu, India
| | - Shobana Mahadevan
- Seethapathy Clinic and Hospital, Royapettah, Chennai 60014, Tamilnadu, India
| | - Rama Shanker Verma
- Stem cells and Molecular Biology Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India.
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24
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Klein JC, Keith A, Rice SJ, Shepherd C, Agarwal V, Loughlin J, Shendure J. Functional testing of thousands of osteoarthritis-associated variants for regulatory activity. Nat Commun 2019; 10:2434. [PMID: 31164647 PMCID: PMC6547687 DOI: 10.1038/s41467-019-10439-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 04/29/2019] [Indexed: 12/19/2022] Open
Abstract
To date, genome-wide association studies have implicated at least 35 loci in osteoarthritis but, due to linkage disequilibrium, the specific variants underlying these associations and the mechanisms by which they contribute to disease risk have yet to be pinpointed. Here, we functionally test 1,605 single nucleotide variants associated with osteoarthritis for regulatory activity using a massively parallel reporter assay. We identify six single nucleotide polymorphisms (SNPs) with differential regulatory activity between the major and minor alleles. We show that the most significant SNP, rs4730222, exhibits differential nuclear protein binding in electrophoretic mobility shift assays and drives increased expression of an alternative isoform of HBP1 in a heterozygote chondrosarcoma cell line, in a CRISPR-edited osteosarcoma cell line, and in chondrocytes derived from osteoarthritis patients. This study provides a framework for prioritization of GWAS variants and highlights a role of HBP1 and Wnt signaling in osteoarthritis pathogenesis.
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Affiliation(s)
- Jason C Klein
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Aidan Keith
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Sarah J Rice
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Colin Shepherd
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Vikram Agarwal
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - John Loughlin
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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25
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5-Azacytidine and Resveratrol Enhance Chondrogenic Differentiation of Metabolic Syndrome-Derived Mesenchymal Stem Cells by Modulating Autophagy. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:1523140. [PMID: 31214275 PMCID: PMC6535830 DOI: 10.1155/2019/1523140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 02/16/2019] [Accepted: 04/15/2019] [Indexed: 12/18/2022]
Abstract
Recently, metabolic syndrome (MS) has gained attention in human and animal metabolic medicine. Insulin resistance, inflammation, hyperleptinemia, and hyperinsulinemia are critical to its definition. MS is a complex cluster of metabolic risk factors that together exert a wide range of effects on multiple organs, tissues, and cells in the body. Adipose stem cells (ASCs) are multipotent stem cell population residing within the adipose tissue that is inflamed during MS. Studies have indicated that these cells lose their stemness and multipotency during MS, which strongly reduces their therapeutic potential. They suffer from oxidative stress, apoptosis, and mitochondrial deterioration. Thus, the aim of this study was to rejuvenate these cells in vitro in order to improve their chondrogenic differentiation effectiveness. Pharmacotherapy of ASCs was based on resveratrol and 5-azacytidine pretreatment. We evaluated whether those substances are able to reverse aged phenotype of metabolic syndrome-derived ASCs and improve their chondrogenic differentiation at its early stage using immunofluorescence, transmission and scanning electron microscopy, real-time PCR, and flow cytometry. Obtained results indicated that 5-azacytidine and resveratrol modulated mitochondrial dynamics, autophagy, and ER stress, leading to the enhancement of chondrogenesis in metabolically impaired ASCs. Therefore, pretreatment of these cells with 5-azacytidine and resveratrol may become a necessary intervention before clinical application of these cells in order to strengthen their multipotency and therapeutic potential.
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Zhou Y, Chen M, O’Keefe RJ, Shen J, Li Z, Zhou J, Zhou X, Mao JJ. Epigenetic and therapeutic implications of dnmt3b in temporomandibular joint osteoarthritis. Am J Transl Res 2019; 11:1736-1747. [PMID: 30972197 PMCID: PMC6456519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 01/15/2019] [Indexed: 06/09/2023]
Abstract
Temporomandibular joint (TMJ) arthritis causes severe debilitation and has few treatment options. Here, we found a small molecule, DNA methyltransferase 3B (Dnmt3b), as a putative therapeutic target, partially rescued osteoarthritic phenotype. Dnmt3b was detected differentially expressed in cell zones of mandibular condylar cartilage and the expression of Dnmt3b decreased in the progression of TMJ osteoarthritis. Dnmt3b deficiency using conditional knockout mice led to the onset of osteoarthritis-like conditions including cartilage clefts, cartilage matrix loss and premature chondrocyte hypertrophy, which suggested that Dnmt3b functioned as a osteoarthritis suppressor. Dnmt3b gain-of-function in TMJ stem/progenitor cells showed increases in collagen type II but decreases in collagen type X, whereas Dnmt3b knockdown had opposite effects with attenuated collagen type II but increased collagen type X. Dnmt3b acted via Wnt/β-catenin signaling and Dnmt3b regulated TMJ stem/progenitor cells differentiation by inducing their premature progression towards hypertrophic chondrocytes through β-catenin transnucleation and activation. Finally, local Dnmt3b delivery partially rescued cartilage degradation in experimentally induced osteoarthritis. Thus, novel molecules in articular cartilage, such as Dnmt3b, may have therapeutic effects for TMJ osteoarthritis.
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Affiliation(s)
- Yue Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, West China School of Stomatology, Sichuan UniversityChengdu 610041, China
- Center for Craniofacial Regeneration, Columbia University Medical CenterNew York, NY 10032, USA
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, School and Hospital of Stomatology, Tongji UniversityShanghai 200072, China
| | - Mo Chen
- Center for Craniofacial Regeneration, Columbia University Medical CenterNew York, NY 10032, USA
- Columbia University College of Dental MedicineNew York, NY 10032, USA
| | - Regis J O’Keefe
- Department of Orthopedic Surgery, Washington University School of MedicineSt. Louis, MO 63110, USA
| | - Jie Shen
- Department of Orthopedic Surgery, Washington University School of MedicineSt. Louis, MO 63110, USA
| | - Zhi Li
- Center for Craniofacial Regeneration, Columbia University Medical CenterNew York, NY 10032, USA
| | - Jian Zhou
- Center for Craniofacial Regeneration, Columbia University Medical CenterNew York, NY 10032, USA
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, West China School of Stomatology, Sichuan UniversityChengdu 610041, China
| | - Jeremy J Mao
- Center for Craniofacial Regeneration, Columbia University Medical CenterNew York, NY 10032, USA
- Columbia University College of Dental MedicineNew York, NY 10032, USA
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27
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Kimura T, Hino K, Kono T, Takano A, Nitta N, Ushio N, Hino S, Takase R, Kudo M, Daigo Y, Morita W, Nakao M, Nakatsukasa M, Tamagawa T, Rafiq AM, Matsumoto A, Otani H, Udagawa J. Maternal undernutrition during early pregnancy inhibits postnatal growth of the tibia in the female offspring of rats by alteration of chondrogenesis. Gen Comp Endocrinol 2018; 260:58-66. [PMID: 29277418 DOI: 10.1016/j.ygcen.2017.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 11/30/2017] [Accepted: 12/19/2017] [Indexed: 12/31/2022]
Abstract
Epidemiological research has suggested that birth weights are correlated with adult leg lengths. However, the relationship between prenatal undernutrition (UN) and postnatal leg growth remains controversial. We investigated the effects of UN during early pregnancy on postnatal hindlimb growth and determined whether early embryonic malnutrition affects the functions of postnatal chondrocytes in rats. Undernourished Wistar dams were fed 40% of the daily intake of rats in the control groups from gestational days 5.5-11.5, and femurs, tibias, and trunks or spinal columns were morphologically measured at birth and at 16 weeks of age in control and undernourished offspring of both sexes. We evaluated cell proliferation and differentiation of cultured chondrocytes derived from neonatal tibias of female offspring and determined chondrocyte-related gene expression levels in neonatal epiphysis and embryonic limb buds. Tibial lengths of undernourished female, but not male, offspring were longer at birth and shorter at 16 weeks of age (p < .05) compared with those of control rats. In chondrocyte culture studies, stimulating effects of IGF-1 on cell proliferation (p < .01) were significantly decreased and levels of type II collagen were lower in female undernourished offspring (p < .05). These phenomena were accompanied by decreased expression levels of Col2a1 and Igf1r and increased expression levels of Fgfr3 (p < .05), which might be attributable to the decreased expression of specificity protein 1 (p < .05), a key transactivator of Col2a1 and Igf1r. In conclusion, UN stress during early pregnancy reduces postnatal tibial growth in female offspring by altering the function of chondrocytes, likely reflecting altered expression of gene transactivators.
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Affiliation(s)
- Tomoko Kimura
- Department of Anatomy, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Kodai Hino
- Department of Anatomy, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Tadaaki Kono
- Department of Anatomy, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Atsushi Takano
- Department of Medical Oncology, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Norihisa Nitta
- Department of Radiology, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Noritoshi Ushio
- Department of Radiology, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-8555, Japan
| | - Ryuta Takase
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-8555, Japan
| | - Motoi Kudo
- Department of Anatomy, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Yataro Daigo
- Department of Medical Oncology, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Wataru Morita
- Department of Oral Functional Anatomy, Faculty of Dental Medicine, Hokkaido University, Hokkaido 060-8586, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-8555, Japan
| | - Masato Nakatsukasa
- Laboratory of Physical Anthropology, Kyoto University Graduate School of Science, Kyoto 606-8502, Japan
| | - Toshihiro Tamagawa
- Department of Anatomy, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Ashiq Mahmood Rafiq
- Department of Anatomy, Faculty of Medicine, Shimane University, Shimane 693-8501, Japan
| | - Akihiro Matsumoto
- Department of Anatomy, Faculty of Medicine, Shimane University, Shimane 693-8501, Japan
| | - Hiroki Otani
- Department of Anatomy, Faculty of Medicine, Shimane University, Shimane 693-8501, Japan
| | - Jun Udagawa
- Department of Anatomy, Shiga University of Medical Science, Shiga 520-2192, Japan.
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Wang C, Abu-Amer Y, O'Keefe RJ, Shen J. Loss of Dnmt3b in Chondrocytes Leads to Delayed Endochondral Ossification and Fracture Repair. J Bone Miner Res 2018; 33:283-297. [PMID: 29024060 PMCID: PMC5809267 DOI: 10.1002/jbmr.3305] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 09/27/2017] [Accepted: 10/07/2017] [Indexed: 12/12/2022]
Abstract
Despite advanced understanding of signaling mediated by local and systemic factors, the role of epigenetic factors in the regulation of bone regeneration remains vague. The DNA methyltransferases (Dnmts) Dnmt3a and Dnmt3b have tissue specific expression patterns and create unique methylation signatures to regulate gene expression. Using a stabilized murine tibia fracture model we find that Dnmt3b is induced early in fracture healing, peaks at 10 days post fracture (dpf), and declines to nearly undetectable levels by 28 dpf. Dnmt3b expression was cell-specific and stage-specific. High levels were observed in chondrogenic lineage cells within the fracture callus. To determine the role of Dnmt3b in fracture healing, Agc1CreERT2 ;Dnmt3bf/f (Dnmt3bAgc1ER ) mice were generated to delete Dnmt3b in chondrogenic cells. Dnmt3bAgc1ER fracture displayed chondrogenesis and chondrocyte maturation defect, and a delay in the later events of angiogenesis, ossification, and bone remodeling. Biomechanical studies demonstrated markedly reduced strength in Dnmt3bAgc1ER fractures and confirmed the delay in repair. The angiogenic response was reduced in both vessel number and volume at 10 and 14 dpf in Dnmt3bAgc1ER mice. Immunohistochemistry showed decreased CD31 expression, consistent with the reduced angiogenesis. Finally, in vitro angiogenesis assays with human umbilical vein endothelial cells (HUVECs) revealed that loss of Dnmt3b in chondrocytes significantly reduced tube formation and endothelial migration. To identify specific angiogenic factors involved in the decreased callus vascularization, a protein array was performed using conditioned media isolated from control and Dnmt3b loss-of-function chondrocytes. Several angiogenic factors, including CXCL12 and osteopontin (OPN) were reduced in chondrocytes following loss of Dnmt3b. DNA methylation analysis further identified hypomethylation in Cxcl12 promoter region. Importantly, the defects in tube formation and cell migration could be rescued by administration of CXCL12 and/or OPN. Altogether, our findings establish that Dnmt3b positively regulates chondrocyte maturation process, and its genetic ablation leads to delayed angiogenesis and fracture repair. © 2017 American Society for Bone and Mineral Research.
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Affiliation(s)
- Cuicui Wang
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, MO, USA
| | - Yousef Abu-Amer
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, MO, USA
| | - Regis J O'Keefe
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, MO, USA
| | - Jie Shen
- Department of Orthopaedic Surgery, School of Medicine, Washington University, St. Louis, MO, USA
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Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network. BMC Genomics 2017; 18:983. [PMID: 29262782 PMCID: PMC5738906 DOI: 10.1186/s12864-017-4378-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 12/11/2017] [Indexed: 01/05/2023] Open
Abstract
Background Chondrogenesis is the earliest stage of skeletal development and is a highly dynamic process, integrating the activities and functions of transcription factors, cell signaling molecules and extracellular matrix proteins. The molecular mechanisms underlying chondrogenesis have been extensively studied and multiple key regulators of this process have been identified. However, a genome-wide overview of the gene regulatory network in chondrogenesis has not been achieved. Results In this study, employing RNA sequencing, we identified 332 protein coding genes and 34 long non-coding RNA (lncRNA) genes that are highly selectively expressed in human fetal growth plate chondrocytes. Among the protein coding genes, 32 genes were associated with 62 distinct human skeletal disorders and 153 genes were associated with skeletal defects in knockout mice, confirming their essential roles in skeletal formation. These gene products formed a comprehensive physical interaction network and participated in multiple cellular processes regulating skeletal development. The data also revealed 34 transcription factors and 11,334 distal enhancers that were uniquely active in chondrocytes, functioning as transcriptional regulators for the cartilage-selective genes. Conclusions Our findings revealed a complex gene regulatory network controlling skeletal development whereby transcription factors, enhancers and lncRNAs participate in chondrogenesis by transcriptional regulation of key genes. Additionally, the cartilage-selective genes represent candidate genes for unsolved human skeletal disorders. Electronic supplementary material The online version of this article (10.1186/s12864-017-4378-y) contains supplementary material, which is available to authorized users.
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30
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Guo M, Liu Z, Willen J, Shaw CP, Richard D, Jagoda E, Doxey AC, Hirschhorn J, Capellini TD. Epigenetic profiling of growth plate chondrocytes sheds insight into regulatory genetic variation influencing height. eLife 2017; 6:29329. [PMID: 29205154 PMCID: PMC5716665 DOI: 10.7554/elife.29329] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/07/2017] [Indexed: 12/23/2022] Open
Abstract
GWAS have identified hundreds of height-associated loci. However, determining causal mechanisms is challenging, especially since height-relevant tissues (e.g. growth plates) are difficult to study. To uncover mechanisms by which height GWAS variants function, we performed epigenetic profiling of murine femoral growth plates. The profiled open chromatin regions recapitulate known chondrocyte and skeletal biology, are enriched at height GWAS loci, particularly near differentially expressed growth plate genes, and enriched for binding motifs of transcription factors with roles in chondrocyte biology. At specific loci, our analyses identified compelling mechanisms for GWAS variants. For example, at CHSY1, we identified a candidate causal variant (rs9920291) overlapping an open chromatin region. Reporter assays demonstrated that rs9920291 shows allelic regulatory activity, and CRISPR/Cas9 targeting of human chondrocytes demonstrates that the region regulates CHSY1 expression. Thus, integrating biologically relevant epigenetic information (here, from growth plates) with genetic association results can identify biological mechanisms important for human growth.
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Affiliation(s)
- Michael Guo
- Broad Institute of MIT and Harvard, Cambridge, United States.,Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States
| | - Zun Liu
- Department of Human Evolutionary Biology, Harvard University, Cambridge, United States
| | - Jessie Willen
- Department of Human Evolutionary Biology, Harvard University, Cambridge, United States
| | - Cameron P Shaw
- Department of Human Evolutionary Biology, Harvard University, Cambridge, United States
| | - Daniel Richard
- Department of Human Evolutionary Biology, Harvard University, Cambridge, United States.,Department of Biology, University of Waterloo, Waterloo, Canada
| | - Evelyn Jagoda
- Department of Human Evolutionary Biology, Harvard University, Cambridge, United States
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Joel Hirschhorn
- Broad Institute of MIT and Harvard, Cambridge, United States.,Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States
| | - Terence D Capellini
- Broad Institute of MIT and Harvard, Cambridge, United States.,Department of Human Evolutionary Biology, Harvard University, Cambridge, United States
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31
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Lim JE, Son Y. Endogenous Stem Cells in Homeostasis and Aging. Tissue Eng Regen Med 2017; 14:679-698. [PMID: 30603520 PMCID: PMC6171667 DOI: 10.1007/s13770-017-0097-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 12/22/2022] Open
Abstract
In almost all human tissues and organs, adult stem cells or tissue stem cells are present in a unique location, the so-called stem cell niche or its equivalent, continuously replenishing functional differentiated cells. Those endogenous stem cells can be expanded for cell therapeutics using ex vivo cell culture or recalled for tissue repair in situ through cell trafficking and homing. In the aging process, inefficiency in the endogenous stem cell-mediated healing mechanism can emerge from a variety of impairments that accumulate in the processes of stem cell self-renewal, function, differentiation capacity, and trafficking through cell autonomous intrinsic pathways (such as epigenetic alterations) or systemic extrinsic pathways. This review examines the homeostasis of endogenous stem cells, particularly bone marrow stem cells, and their dysregulation in disease and aging and discusses possible intervention strategies. Several systemic pro-aging and rejuvenating factors, recognized in heterochronic parabiosis or premature aging progeroid animal models, are reviewed as possible anti-aging pharmaceutical targets from the perspective of a healthy environment for endogenous stem cells. A variety of epigenetic modifications and chromosome architectures are reviewed as an intrinsic cellular pathway for aging and senescence. A gradual increase in inflammatory burden during aging is also reviewed. Finally, the tissue repair and anti-aging effects of Substance-P, a peptide stimulating stem cell trafficking from the bone marrow and modifying the inflammatory response, are discussed as a future anti-aging target.
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Affiliation(s)
- Ji Eun Lim
- Department of Genetic Engineering, College of Life Science and Graduate School of Biotechnology, Kyung Hee University, 1732 Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104 Republic of Korea
| | - Youngsook Son
- Department of Genetic Engineering, College of Life Science and Graduate School of Biotechnology, Kyung Hee University, 1732 Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104 Republic of Korea
- Kyung Hee Institute of Regenerative Medicine, Kyung Hee University Hospital, 24 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02453 Republic of Korea
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32
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Wang P, Li Y, Meng T, Zhang J, Wei Y, Meng Z, Lin Y, Liu D, Sui L. KDM6A promotes chondrogenic differentiation of periodontal ligament stem cells by demethylation of SOX9. Cell Prolif 2017; 51:e12413. [PMID: 29171124 DOI: 10.1111/cpr.12413] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/26/2017] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES KDM6A has been demonstrated critical in the regulation of cell fates. However, whether KDM6A is involved in cartilage formation remains unclear. In this study, we investigated the role of KDM6A in chondrogenic differentiation of PDLSCs, as well as the underlying epigenetic mechanisms. METHODS KDM6A shRNA was transfected into PDLSCs by lentivirus. The chondrogenic differentiation potential of PDLSCs was assessed by Alcian blue staining. Immunofluorescence was performed to demonstrate H3K27me3 and H3K4me3 levels during chondrogenesis. SOX9, Col2a1, ACAN and miRNAs (miR-29a, miR-204, miR-211) were detected by real-time RT-PCR. Western blot was performed to evaluate SOX9, H3K27me3 and H3K4me3. RESULTS The production of proteoglycans in PDLSCs was decreased after knockdown of KDM6A. Depletion of KDM6A inhibited the expression of SOX9, Col2a1, ACAN and resulted in increased H3K27me3 and decreased H3K4me3 levels. EZH2 inhibitor rescued the chondrogenic potential of PDLSCs after knockdown of KDM6A by regulating H3K27me3. Additionally, miR-29a, miR-204 and miR-211 were also involved in the process of PDLSCs chondrogenesis. CONCLUSIONS KDM6A is required in chondrogenic differentiation of PDLSCs by demethylation of H3K27me3, and EZH2 inhibitor could rescue chondrogenesis of PDLSCs after knockdown of KDM6A. It could be inferred that upregulation of KDM6A or application of EZH2 inhibitor might improve mesenchymal stem cell mediated cartilage regeneration in inflammatory tissue destruction such as osteoarthritis.
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Affiliation(s)
- Pingting Wang
- Department of Endodontics & Laboratory for Dental Stem Cells and Endocrine Immunology, Tianjin Medical University School of Stomatology, Tianjin, China
| | - Yanjing Li
- Department of Endodontics & Laboratory for Dental Stem Cells and Endocrine Immunology, Tianjin Medical University School of Stomatology, Tianjin, China.,Department of Prosthodontics, Tianjin Medical University School of Stomatology, Tianjin, China
| | - Tingting Meng
- Department of Endodontics & Laboratory for Dental Stem Cells and Endocrine Immunology, Tianjin Medical University School of Stomatology, Tianjin, China
| | - Junjiang Zhang
- Department of Prosthodontics, Tianjin Medical University School of Stomatology, Tianjin, China
| | - Yuanyuan Wei
- Department of Endodontics & Laboratory for Dental Stem Cells and Endocrine Immunology, Tianjin Medical University School of Stomatology, Tianjin, China
| | - Zhaosong Meng
- Department of Oral Maxillofacial Surgery, Tianjin Medical University School of Stomatology, Tianjin, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Dayong Liu
- Department of Endodontics & Laboratory for Dental Stem Cells and Endocrine Immunology, Tianjin Medical University School of Stomatology, Tianjin, China
| | - Lei Sui
- Department of Prosthodontics, Tianjin Medical University School of Stomatology, Tianjin, China
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Lorzadeh A, Bilenky M, Hammond C, Knapp DJHF, Li L, Miller PH, Carles A, Heravi-Moussavi A, Gakkhar S, Moksa M, Eaves CJ, Hirst M. Nucleosome Density ChIP-Seq Identifies Distinct Chromatin Modification Signatures Associated with MNase Accessibility. Cell Rep 2017; 17:2112-2124. [PMID: 27851972 DOI: 10.1016/j.celrep.2016.10.055] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 07/05/2016] [Accepted: 09/12/2016] [Indexed: 12/22/2022] Open
Abstract
Nucleosome position, density, and post-translational modification are widely accepted components of mechanisms regulating DNA transcription but still incompletely understood. We present a modified native ChIP-seq method combined with an analytical framework that allows MNase accessibility to be integrated with histone modification profiles. Application of this methodology to the primitive (CD34+) subset of normal human cord blood cells enabled genomic regions enriched in one versus two nucleosomes marked by histone 3 lysine 4 trimethylation (H3K4me3) and/or histone 3 lysine 27 trimethylation (H3K27me3) to be associated with their transcriptional and DNA methylation states. From this analysis, we defined four classes of promoter-specific profiles and demonstrated that a majority of bivalent marked promoters are heterogeneously marked at a single-cell level in this primitive cell type. Interestingly, extension of this approach to human embryonic stem cells revealed an altered relationship between chromatin modification state and nucleosome content at promoters, suggesting developmental stage-specific organization of histone methylation states.
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Affiliation(s)
- Alireza Lorzadeh
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Misha Bilenky
- Canada's Michael Smith Genome Science Center, BC Cancer Agency Vancouver, BC V5Z 4S6, Canada
| | - Colin Hammond
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - David J H F Knapp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Luolan Li
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Paul H Miller
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Annaick Carles
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Alireza Heravi-Moussavi
- Canada's Michael Smith Genome Science Center, BC Cancer Agency Vancouver, BC V5Z 4S6, Canada
| | - Sitanshu Gakkhar
- Canada's Michael Smith Genome Science Center, BC Cancer Agency Vancouver, BC V5Z 4S6, Canada
| | - Michelle Moksa
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Connie J Eaves
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Martin Hirst
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Canada's Michael Smith Genome Science Center, BC Cancer Agency Vancouver, BC V5Z 4S6, Canada.
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34
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Mortada I, Mortada R. Epigenetic changes in mesenchymal stem cells differentiation. Eur J Med Genet 2017; 61:114-118. [PMID: 29079547 DOI: 10.1016/j.ejmg.2017.10.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 08/30/2017] [Accepted: 10/22/2017] [Indexed: 01/09/2023]
Abstract
Epigenetic factors are known to play a major role in determining stem cell fate and differentiation. Mesenchymal stem cells are the most studied population of stem cells due to their important applications in experimental biology and regenerative medicine. After a brief overview on mesenchymal stem cells, this review aims to highlight the role of epigenetic changes on mesenchymal stem cells biology and differentiation protocols with a focus on osteocytic, chondrocytic and adipocytic differentiation. Chromatin remodeling, DNA methylation, histone modifications and miRNA expression will be investigated. The impact of epigenetics on transdifferentiation of mesenchymal stem cells will also be discussed. Indeed, epigenetic modulation appears to constitute a promising experimental target in stem cell basic and translational research.
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35
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Yao Y, Deng Q, Sun C, Song W, Liu H, Zhou Y. A genome-wide analysis of the gene expression profiles and alternative splicing events during the hypoxia-regulated osteogenic differentiation of human cartilage endplate-derived stem cells. Mol Med Rep 2017; 16:1991-2001. [PMID: 28656244 PMCID: PMC5562021 DOI: 10.3892/mmr.2017.6846] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 04/25/2017] [Indexed: 12/20/2022] Open
Abstract
It has been hypothesized that intervertebral disc degeneration is initiated by degeneration of the cartilage endplate (CEP), which is characterized by cartilage ossification. CEP‑derived stem cells (CESCs), with the potential for chondro‑osteogenic differentiation, may be responsible for the balance between chondrification and ossification in the CEP. The CEP remains in an avascular and hypoxic microenvironment; the present study observed that hypoxia was able to markedly inhibit the osteogenic differentiation of CESCs. This tissue‑specific CESC differentiation in response to a hypoxic microenvironment was physiologically important for the prevention of ossification in the CEP. In order to study the hypoxia‑regulated mechanisms underlying osteogenic differentiation of CESCs, a Human Transcriptome Array 2.0 was used to detect differentially expressed genes (DEGs) and alternatively spliced genes (ASGs) during the osteogenic differentiation of CESCs under hypoxia, compared with those induced under normoxia. High‑throughput analysis of DEGs and ASGs demonstrated that genes in the complement pathway were enriched, which may be a potential mechanism underlying hypoxia inhibition of CESCs osteogenesis. The results of the present study may provide a basis for future mechanistic studies regarding gene expression levels and alternative splicing events during the hypoxia‑regulated inhibition of osteogenesis, which may be helpful in identifying targets for CEP degeneration therapy.
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Affiliation(s)
- Yuan Yao
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Qiyue Deng
- Department of Neurobiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, P.R. China
| | - Chao Sun
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Weiling Song
- Department of Ophthalmology, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Huan Liu
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Yue Zhou
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
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Lee WYW, Wang B. Cartilage repair by mesenchymal stem cells: Clinical trial update and perspectives. J Orthop Translat 2017; 9:76-88. [PMID: 29662802 PMCID: PMC5822962 DOI: 10.1016/j.jot.2017.03.005] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/20/2017] [Accepted: 03/21/2017] [Indexed: 12/28/2022] Open
Abstract
Osteoarthritis is a degenerative disease of joints with destruction of articular cartilage associated with subchondral bone hypertrophy and inflammation. OA is the leading cause of joint pain resulting in significant worsening of the quality-of-life in the elderly. Numerous efforts have been spent to overcome the inherently poor healing ability of articular cartilage. Mesenchymal stem cells (MSCs) have been in the limelight of cell-based therapies to promote cartilage repair. Despite progressive advancements in MSC manipulation and the introduction of various bioactive scaffolds and growth factors in preclinical studies, current clinical trials are still at early stages with preliminary aims to evaluate safety, feasibility and efficacy. This review summarises recently reported MSC-based clinical trials and discusses new research directions with particular focus on the potential application of MSC-derived extracellular vehicles, miRNAs and advanced gene editing techniques which may shed light on the development of novel treatment strategies. The translational potential of this article: This review summarises recent MSC-related clinical research that focuses on cartilage repair. We also propose a novel possible translational direction for hyaline cartilage formation and a new paradigm making use of extra-cellular signalling and epigenetic regulation in the application of MSCs for cartilage repair.
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Affiliation(s)
- Wayne Yuk-wai Lee
- Department of Orthopaedics & Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, PR China
- Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, PR China
- SMART Program, Lui Che Woo Institute of Innovative Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, PR China
| | - Bin Wang
- Department of Orthopaedics & Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, PR China
- Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, PR China
- SMART Program, Lui Che Woo Institute of Innovative Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, PR China
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Dai J, Yu D, Wang Y, Chen Y, Sun H, Zhang X, Zhu S, Pan Z, Heng BC, Zhang S, Ouyang H. Kdm6b regulates cartilage development and homeostasis through anabolic metabolism. Ann Rheum Dis 2017; 76:1295-1303. [PMID: 28314754 DOI: 10.1136/annrheumdis-2016-210407] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 01/22/2017] [Accepted: 02/21/2017] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Epigenetic mechanisms have been reported to play key roles in chondrogenesis and osteoarthritis (OA) development. Here, we sought to identify specific histone demethylases that are involved and delineate the underlying mechanisms. METHODS We screened the expression of 17 distinct histone demethylases by quantitative real time PCR (qRT-PCR) during chondrogenic differentiation of C3H10T1/2 cells. The role of Kdm6b in cartilage development was then analysed with transgenic Col2a1-CreERT2;Kdm6bf/f . RNA-Seq was applied to explore the underlying changes in chondrocytes upon knockdown of Kdm6b. Experimental OA in mice was induced by destabilisation of the medial meniscus in C57BL/6J (wild type, Kdm6bf/f and Col2a1-CreERT2;Kdm6bf/f ) mice, either with intra-articular injection of shKdm6b lentivirus or after tamoxifen treatment. Mouse joints and human cartilage samples were used for histological analysis. RESULTS Kdm6b expression was significantly increased during cartilage development. Col2a1-CreERT2;Kdm6bf/f mice displayed obvious skeletal abnormalities at E16.5 and E18.5 with intraperitoneal injection of tamoxifen at E12.5. RNA-Seq and qRT-PCR analyses revealed decreased expression of chondrocyte anabolic genes in Col2a1-CreERT2;Kdm6bf/f chondrocytes. The histological OA score was significantly higher in mice injected with Kdm6b short hairpin RNA lentivirus. Col2a1-CreERT2;Kdm6bf/f mice exhibited accelerated OA development at 8 and 12 weeks following surgical induction. The number of Kdm6b-positive chondrocytes was lower in both mice and human OA cartilage samples. CONCLUSIONS These findings indicate that knockdown of Kdm6b in chondrocytes leads to abnormal cartilage development and accelerated OA progression via inhibition of the anabolic metabolism of chondrocytes. Understanding the epigenetic mechanism of joint cartilage development and homeostasis would be useful for development of new therapeutic modalities for OA.
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Affiliation(s)
- Jun Dai
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, School of Medicine, Zhejiang University, Zhejiang, China
| | - Dongsheng Yu
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, School of Medicine, Zhejiang University, Zhejiang, China.,Department of Sports Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yafei Wang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, School of Medicine, Zhejiang University, Zhejiang, China
| | - Yishan Chen
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, School of Medicine, Zhejiang University, Zhejiang, China
| | - Heng Sun
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, School of Medicine, Zhejiang University, Zhejiang, China
| | - Xiaolei Zhang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, School of Medicine, Zhejiang University, Zhejiang, China
| | - Shouan Zhu
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, School of Medicine, Zhejiang University, Zhejiang, China
| | - Zongyou Pan
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, School of Medicine, Zhejiang University, Zhejiang, China
| | - Boon Chin Heng
- Endodontology, Faculty of Dentistry, The University of Hong Kong, Pokfulam, Hong Kong
| | - Shufang Zhang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, School of Medicine, Zhejiang University, Zhejiang, China
| | - Hongwei Ouyang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, School of Medicine, Zhejiang University, Zhejiang, China.,Department of Sports Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,China Orthopedic Regenerative Medicine Group, Hangzhou, China
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38
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An Emerging Regulatory Landscape for Skeletal Development. Trends Genet 2016; 32:774-787. [PMID: 27814929 DOI: 10.1016/j.tig.2016.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/21/2016] [Accepted: 10/04/2016] [Indexed: 02/02/2023]
Abstract
Skeletal development creates the physical framework that shapes our body and its actions. In the past two decades, genetic studies have provided important insights into the molecular processes at play, including the roles of signaling pathways and transcriptional effectors that coordinate an orderly, progressive emergence and expansion of distinct cartilage and bone cell fates in an invariant temporal and spatial pattern for any given skeletal element within that specific vertebrate species. Genome-scale studies have provided additional layers of understanding, moving from individual genes to the gene regulatory landscape, integrating regulatory information through cis-regulatory modules into cell type-specific gene regulatory programs. This review discusses our current understanding of the transcriptional control of mammalian skeletal development, focusing on recent genome-scale studies.
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Yapp C, Carr AJ, Price A, Oppermann U, Snelling SJB. H3K27me3 demethylases regulate in vitro chondrogenesis and chondrocyte activity in osteoarthritis. Arthritis Res Ther 2016; 18:158. [PMID: 27388528 PMCID: PMC4936015 DOI: 10.1186/s13075-016-1053-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/20/2016] [Indexed: 11/10/2022] Open
Abstract
Background Epigenetic changes (i.e., chromatin modifications) occur during chondrogenesis and in osteoarthritis (OA). We investigated the effect of H3K27me3 demethylase inhibition on chondrogenesis and assessed its utility in cartilage tissue engineering and in understanding cartilage destruction in OA. Methods We used a high-content screen to assess the effect of epigenetic modifying compounds on collagen output during chondrogenesis of monolayer human mesenchymal stem cells (MSCs). The impact of GSK-J4 on gene expression, glycosaminoglycan output and collagen formation during differentiation of MSCs into cartilage discs was investigated. Expression of lysine (K)-specific demethylase 6A (UTX) and Jumonji domain-containing 3 (JMJD3), the HEK27Me3 demethylases targeted by GSK-J4, was measured in damaged and undamaged cartilage from patients with OA. The impact of GSK-J4 on ex vivo cartilage destruction and expression of OA-related genes in human articular chondrocytes (HACs) was assessed. H3K27Me3 demethylase regulation of transforming growth factor (TGF)-β-induced gene expression was measured in MSCs and HACs. Results Treatment of chondrogenic MSCs with the H3K27me3 demethylase inhibitor GSK-J4, which targets JMJD3 and UTX, inhibited collagen output; expression of chondrogenic genes, including SOX9 and COL2A1; and disrupted glycosaminoglycan and collagen synthesis. JMJD3 but not UTX expression was increased during chondrogenesis and in damaged OA cartilage, suggesting a predominant role of JMJD3 in chondrogenesis and OA. GSK-J4 prevented ex vivo cartilage destruction and expression of the OA-related genes MMP13 and PTGS2. TGF-β is a key regulator of chondrogenesis and articular cartilage homeostasis, and TGF-β-induced gene expression was inhibited by GSK-J4 treatment of both chondrogenic MSCs and HACs. Conclusions Overall, we show that H3K27me3 demethylases modulate chondrogenesis and that enhancing this activity may improve production of tissue-engineered cartilage. In contrast, targeted inhibition of H3K27me3 demethylases could provide a novel approach in OA therapeutics. Electronic supplementary material The online version of this article (doi:10.1186/s13075-016-1053-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clarence Yapp
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, OX3 7LD, Oxford, UK.,Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Andrew J Carr
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, OX3 7LD, Oxford, UK
| | - Andrew Price
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, OX3 7LD, Oxford, UK
| | - Udo Oppermann
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, OX3 7LD, Oxford, UK.,Structural Genomics Consortium, University of Oxford, Oxford, UK.,Oxford Stem Cell Institute, Oxford, UK
| | - Sarah J B Snelling
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, OX3 7LD, Oxford, UK.
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Human Pluripotent Stem Cells: Advances in Chondrogenic Differentiation and Articular Cartilage Regeneration. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s40610-016-0041-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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41
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Shang J, Wang H, Fan X, Shangguan L, Liu H. A genome wide analysis of alternative splicing events during the osteogenic differentiation of human cartilage endplate-derived stem cells. Mol Med Rep 2016; 14:1389-96. [PMID: 27278552 DOI: 10.3892/mmr.2016.5359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 05/12/2016] [Indexed: 11/06/2022] Open
Abstract
Low back pain is a prevalent disease, which leads to suffering and disabilities in a vast number of individuals. Degenerative disc diseases are usually the underlying causes of low back pain. However, the pathogenesis of degenerative disc diseases is highly complex and difficult to determine. Current therapies for degenerative disc diseases are various. In particular, cell-based therapies have proven to be effective and promising. Our research group has previously isolated and identified the cartilage endplate‑derived stem cells. In addition, alternative splicing is a sophisticated regulatory mechanism, which greatly increases cellular complexity and phenotypic diversity of eukaryotic organisms. The present study continued to investigate alternative splicing events in osteogenic differentiation of cartilage endplate‑derived stem cells. An Affymetrix Human Transcriptome Array 2.0 was used to detect splicing changes between the control and differentiated samples. Additionally, molecular function and pathway analysis were also performed. Following rigorous bioinformatics analysis of the data, 3,802 alternatively spliced genes were identified, and 10 of these were selected for validation by reverse transcription‑polymerase chain reaction. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analysis also revealed numerous enriched GO terms and signaling pathways. To the best of our knowledge, the present study is the first to investigate alternative splicing mechanisms in osteogenic differentiation of stem cells on a genome‑wide scale. The illumination of molecular mechanisms of stem cell osteogenic differentiation may assist the development novel bioengineered methods to treat degenerative disc diseases.
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Affiliation(s)
- Jin Shang
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Honggang Wang
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Xin Fan
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Lei Shangguan
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Huan Liu
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
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van den Dungen MW, Murk AJ, Kok DE, Steegenga WT. Comprehensive DNA Methylation and Gene Expression Profiling in Differentiating Human Adipocytes. J Cell Biochem 2016; 117:2707-2718. [PMID: 27061314 DOI: 10.1002/jcb.25568] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 04/05/2016] [Indexed: 01/09/2023]
Abstract
Insight into the processes controlling adipogenesis is important in the battle against the obesity epidemic and its related disorders. The transcriptional regulatory cascade involved in adipocyte differentiation has been extensively studied, however, the mechanisms driving the transcription activation are still poorly understood. In this study, we explored the involvement of DNA methylation in transcriptional regulation during adipocyte differentiation of primary human mesenchymal stem cells (hMSCs). Genome-wide changes in DNA methylation were measured using the Illumina 450K BeadChip. In addition, expression of 84 adipogenic genes was determined, of which 43 genes showed significant expression changes during the differentiation process. Among these 43 differentially expressed genes, differentially methylated regions (DMRs) were detected in only three genes. By comparing genome-wide DNA methylation profiles in undifferentiated and differentiated adipocytes 793 significant DMRs were detected. Pathway analysis revealed the adipogenesis pathway as the most statistically significant, although only a small number of genes were differentially methylated. Genome-wide DNA methylation changes for single probes were most often located in intergenic regions, and underrepresented close to the transcription start site. In conclusion, DNA methylation remained relatively stable during adipocyte differentiation, implying that changes in DNA methylation are not the underlying mechanism regulating gene expression during adipocyte differentiation. J. Cell. Biochem. 117: 2707-2718, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Myrthe W van den Dungen
- Sub-Department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands.,Division of Human Nutrition, Wageningen University, P.O. Box 8129, 6700 EV, Wageningen, The Netherlands
| | - Albertinka J Murk
- Sub-Department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands.,Marine Animal Ecology Group, Wageningen University, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Dieuwertje E Kok
- Sub-Department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands
| | - Wilma T Steegenga
- Sub-Department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands.
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43
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Ozkul Y, Galderisi U. The Impact of Epigenetics on Mesenchymal Stem Cell Biology. J Cell Physiol 2016; 231:2393-401. [PMID: 26960183 DOI: 10.1002/jcp.25371] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/07/2016] [Indexed: 02/06/2023]
Abstract
Changes in epigenetic marks are known to be important regulatory factors in stem cell fate determination and differentiation. In the past years, the investigation of the epigenetic regulation of stem cell biology has largely focused on embryonic stem cells (ESCs). Contrarily, less is known about the epigenetic control of gene expression during differentiation of adult stem cells (AdSCs). Among AdSCs, mesenchymal stem cells (MSCs) are the most investigated stem cell population because of their enormous potential for therapeutic applications in regenerative medicine and tissue engineering. In this review, we analyze the main studies addressing the epigenetic changes in MSC landscape during in vitro cultivation and replicative senescence, as well as follow osteocyte, chondrocyte, and adipocyte differentiation. In these studies, histone acetylation, DNA methylation, and miRNA expression are among the most investigated phenomena. We describe also epigenetic changes that are associated with in vitro MSC trans-differentiation. Although at the at initial stage, the epigenetics of MSCs promise to have profound implications for stem cell basic and applied research. J. Cell. Physiol. 231: 2393-2401, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yusuf Ozkul
- Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
| | - Umberto Galderisi
- Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
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Yao Y, Shang J, Song W, Deng Q, Liu H, Zhou Y. Global profiling of the gene expression and alternative splicing events during hypoxia-regulated chondrogenic differentiation in human cartilage endplate-derived stem cells. Genomics 2016; 107:170-7. [PMID: 26996146 DOI: 10.1016/j.ygeno.2016.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 03/09/2016] [Accepted: 03/16/2016] [Indexed: 01/08/2023]
Abstract
The intervertebral disc (IVD) degeneration is initiated by cartilage endplate (CEP) degeneration and is characterised by reduced chondrification. Cartilage endplate-derived stem cells (CESCs) with chondrogenic differentiation abilities are responsible for the restoration of cartilage. CEP remains in an avascular and hypoxic microenvironment. In this study, we observed that the physiological hypoxia greatly promotes the chondrogenic differentiation of CESCs. This tissue specificity of the differentiation fate of CESCs in response to the hypoxic microenvironment was physiologically significant for the CEP to maintain the chondrification status. To investigate the mechanisms underlying the hypoxia-regulated chondrogenic differentiation of CESCs, we adopted a high-throughput scanning technology to detect the global profiling of gene expression and alternative splicing (AS) event changes during chondrogenic differentiation under hypoxia in CESCs compared to those induced under normoxia. An Affymetrix Human Transcriptome Array 2.0 was used to identify the differentially expressed genes (DEGs) and alternatively spliced genes (ASGs). After RT-PCR validation, GO and KEGG pathway analyses of both the DEGs and ASGs were performed. The enrichment of the GO functional terms and signalling pathways provided referential direction of the mechanism to study the gene expression and AS in the hypoxia-regulated chondrogenesis promotion, which could be helpful in understanding this physiological phenomenon, and it could also be instrumental in finding targets for CEP degeneration therapy.
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Affiliation(s)
- Yuan Yao
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Jin Shang
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Weilin Song
- Department of Ophthalmology, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Qiyue Deng
- Department of Neurobiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Huan Liu
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
| | - Yue Zhou
- Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
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Lee HL, Yu B, Deng P, Wang CY, Hong C. Transforming Growth Factor-β-Induced KDM4B Promotes Chondrogenic Differentiation of Human Mesenchymal Stem Cells. Stem Cells 2015; 34:711-9. [PMID: 26485430 DOI: 10.1002/stem.2231] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/21/2015] [Accepted: 09/14/2015] [Indexed: 02/05/2023]
Abstract
The high prevalence of cartilage diseases and limited treatment options create a significant biomedical burden. Due to the inability of cartilage to regenerate itself, introducing chondrocyte progenitor cells to the affected site is of significant interest in cartilage regenerative therapies. Tissue engineering approaches using human mesenchymal stem cells (MSCs) are promising due to their chondrogenic potential, but a comprehensive understanding of the mechanisms governing the fate of MSCs is required for precise therapeutic applications in cartilage regeneration. TGF-β is known to induce chondrogenesis by activating SMAD signaling pathway and upregulating chondrogenic genes such as SOX9; however, the epigenetic regulation of TGF-β-mediated chondrogenesis is not understood. In this report, we found that TGF-β dramatically induced the expression of KDM4B in MSCs. When KDM4B was overexpressed, chondrogenic differentiation was significantly enhanced while KDM4B depletion by shRNA led to a significant reduction in chondrogenic potential. Mechanistically, upon TGF-β stimulation, KDM4B was recruited to the SOX9 promoter, removed the silencing H3K9me3 marks, and activated the transcription of SOX9. Furthermore, KDM4B depletion reduced the occupancy of SMAD3 in the SOX9 promoter, suggesting that KDM4B is required for SMAD-dependent coactivation of SOX9. Our results demonstrate the critical role of KDM4B in the epigenetic regulation of TGF-β-mediated chondrogenic differentiation of MSCs. Since histone demethylases are chemically modifiable, KDM4B may be a novel therapeutic target in cartilage regenerative therapy.
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Affiliation(s)
- Hye-Lim Lee
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry and Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, California, USA
| | - Bo Yu
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry and Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, California, USA
| | - Peng Deng
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry and Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, California, USA.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, SiChuan University, Chengdu, Sichuan Province, China
| | - Cun-Yu Wang
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry and Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, California, USA
| | - Christine Hong
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry and Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, California, USA.,Section of Orthodontics, School of Dentistry, University of California, Los Angeles, Los Angeles, California, USA
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Global Gene Expression Profiling and Alternative Splicing Events during the Chondrogenic Differentiation of Human Cartilage Endplate-Derived Stem Cells. BIOMED RESEARCH INTERNATIONAL 2015; 2015:604972. [PMID: 26649308 PMCID: PMC4662983 DOI: 10.1155/2015/604972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 01/07/2023]
Abstract
Low back pain (LBP) is a very prevalent disease and degenerative disc diseases (DDDs) usually account for the LBP. However, the pathogenesis of DDDs is complicated and difficult to elucidate. Alternative splicing is a sophisticated regulatory process which greatly increases cellular complexity and phenotypic diversity of eukaryotic organisms. In addition, the cartilage endplate-derived stem cells have been discovered and identified by our research group. In this paper, we continue to investigate gene expression profiling and alternative splicing events during chondrogenic differentiation of cartilage endplate-derived stem cells. We adopted Affymetrix Human Transcriptome Array 2.0 (HTA 2.0) to compare the transcriptional and splicing changes between the control and differentiated samples. RT-PCR and quantitative PCR are used to validate the microarray results. The GO and KEGG pathway analysis was also performed. After bioinformatics analysis of the data, we detected 1953 differentially expressed genes. In terms of alternative splicing, the Splicing Index algorithm was used to select alternatively spliced genes. We detected 4411 alternatively spliced genes. GO and KEGG pathway analysis also revealed several functionally involved biological processes and signaling pathways. To our knowledge, this is the first study to investigate the alternative splicing mechanisms in chondrogenic differentiation of stem cells on a genome-wide scale.
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48
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Stoddart MJ, Bara J, Alini M. Cells and secretome--towards endogenous cell re-activation for cartilage repair. Adv Drug Deliv Rev 2015; 84:135-45. [PMID: 25174306 DOI: 10.1016/j.addr.2014.08.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 06/26/2014] [Accepted: 08/20/2014] [Indexed: 01/01/2023]
Abstract
Regenerative medicine approaches to cartilage tissue repair have mainly been concerned with the implantation of a scaffold material containing monolayer expanded cells into the defect, with the aim to differentiate the cells into chondrocytes. While this may be a valid approach, the secretome of the implanted cells and its effects on the endogenous resident cells, is gaining in interest. This review aims to summarize the knowledge on the secretome of mesenchymal stem cells, including knowledge from other tissues, in order to indicate how these mechanisms may be of value in repairing articular cartilage defects. Potential therapies and their effects on the repair of articular cartilage defects will be discussed, with a focus on the transition from classical cell therapy to the implantation of cell free matrices releasing specific cytokines.
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Huang B, Li G, Jiang XH. Fate determination in mesenchymal stem cells: a perspective from histone-modifying enzymes. Stem Cell Res Ther 2015; 6:35. [PMID: 25890062 PMCID: PMC4365520 DOI: 10.1186/s13287-015-0018-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mesenchymal stem cells (MSCs) hold great promise for therapeutic use in regenerative medicine and tissue engineering. A detailed understanding of the molecular processes governing MSC fate determination will be instrumental in the application of MSCs. Much progress has been made in recent years in defining the epigenetic events that control the differentiation of MSCs into different lineages. A complex network of transcription factors and histone modifiers, in concert with specific transcriptional co-activators and co-repressors, activates or represses MSC differentiation. In this review, we summarize recent progress in determining the effects of histone-modifying enzymes on the multilineage differentiation of MSCs. In addition, we propose that the manipulation of histone signatures associated with lineage-specific differentiation by small molecules has immense potential for the advancement of MSC-based regenerative medicine.
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Affiliation(s)
- Biao Huang
- Key Laboratory for Regenerative Medicine, Ministry of Education, Epithelial Cell Biology Research Centre, School of Biomedical Sciences, Lo Kwee-Seong Integrated Biomedical Sciences Building, Shatin, New Territories, Hong Kong, PR China.
| | - Gang Li
- Department of Orthopaedics & Traumatology, Li Ka Shing Institute of Health Science, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, New Territories, Hong Kong, PR China. .,Lui Che Woo Institute of Innovative Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China. .,School of Biomedical Sciences Core Laboratory, The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China.
| | - Xiao Hua Jiang
- Key Laboratory for Regenerative Medicine, Ministry of Education, Epithelial Cell Biology Research Centre, School of Biomedical Sciences, Lo Kwee-Seong Integrated Biomedical Sciences Building, Shatin, New Territories, Hong Kong, PR China. .,Lui Che Woo Institute of Innovative Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China. .,School of Biomedical Sciences Core Laboratory, The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China.
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Herlofsen SR, Høiby T, Cacchiarelli D, Zhang X, Mikkelsen TS, Brinchmann JE. Brief report: importance of SOX8 for in vitro chondrogenic differentiation of human mesenchymal stromal cells. Stem Cells 2015; 32:1629-35. [PMID: 24449344 DOI: 10.1002/stem.1642] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 12/11/2013] [Indexed: 01/05/2023]
Abstract
The transcription factor SOX9 is believed to be the master regulator of chondrogenesis. SOX8 is another SOX group E transcription factor with a high degree of homology to SOX9. Here, we demonstrate that SOX8 mRNA levels decrease during in vitro dedifferentiation of human articular chondrocytes and increase during chondrogenic differentiation of mesenchymal stromal cells. Knockdown of SOX9 reduced the expression of SOX8, COL2A1, and a range of other chondrogenic molecules. SOX8 knockdown reduced the expression of a large number of overlapping chondrogenic molecules, but not SOX9. Neither siSOX9 nor siSOX8 altered expression of the hypertrophic marker gene COL10A1. siSOX9, but not siSOX8 led to upregulation of hypertrophy associated genes MMP13 and ALPL. Transfection of synthetic SOX5, 6, and 9 mRNA trio upregulated SOX8, COL2A1, and ACAN, but not COL10A1 mRNA. Replacement of synthetic SOX9 by SOX8 in the SOX trio showed similar but lower chondrogenic effect. We conclude that SOX8 expression is regulated by SOX9, and that both together with SOX5 and SOX6 are required as a SOX quartet for transcription of COL2A1 and a large number of other chondrogenic molecules. Neither SOX8 nor SOX9 affect COL10A1 expression, but SOX9 inhibits chondrocyte hypertrophy through inhibition of MMP13 and ALPL expression.
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Affiliation(s)
- Sarah R Herlofsen
- Norwegian Center for Stem Cell Research and Institute of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
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