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Mazloumi Z, Farahzadi R, Rafat A, Asl KD, Karimipour M, Montazer M, Movassaghpour AA, Dehnad A, Charoudeh HN. Effect of aberrant DNA methylation on cancer stem cell properties. Exp Mol Pathol 2022; 125:104757. [PMID: 35339454 DOI: 10.1016/j.yexmp.2022.104757] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 03/09/2022] [Accepted: 03/19/2022] [Indexed: 12/21/2022]
Abstract
DNA methylation, as an epigenetic mechanism, occurs by adding a methyl group of cytosines in position 5 by DNA methyltransferases and has essential roles in cellular function, especially in the transcriptional regulation of embryonic and adult stem cells. Hypomethylation and hypermethylation cause either the expression or inhibition of genes, and there is a tight balance between regulating the activation or repression of genes in normal cellular activity. Abnormal methylation is well-known hallmark of cancer development and progression and can switch normal stem cells into cancer stem cells. Cancer Stem Cells (CSCs) are minor populations of tumor cells that exhibit unique properties such as self-regeneration, resistance to chemotherapy, and high ability of metastasis. The purpose of this paper is to show how aberrant DNA methylation accumulation affects self-renewal, differentiation, multidrug-resistant, and metastasis processes in cancer stem cells.
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Affiliation(s)
- Zeinab Mazloumi
- Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Raheleh Farahzadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Rafat
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Anatomical Sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khadijeh Dizaji Asl
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Anatomical Sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Karimipour
- Department of Anatomical Sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Majid Montazer
- Department of Cardiovascular Surgery, Imam Reza Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Alireza Dehnad
- Department of Bacterial Disease Research, Razi Vaccine and Serum Research Institute, AREEO, Tabriz, Iran
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Marofi F, Choupani J, Solali S, Vahedi G, Hassanzadeh A, Gharibi T, Hagh MF. ATF4, DLX3, FRA1, MSX2, C/EBP-ζ, and C/EBP-α Shape the Molecular Basis of Therapeutic Effects of Zoledronic Acid in Bone Disorders. Anticancer Agents Med Chem 2021; 20:2274-2284. [PMID: 32698734 DOI: 10.2174/1871520620666200721101904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 01/30/2020] [Accepted: 02/10/2020] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Zoledronic Acid (ZA) is one of the common treatment choices used in various boneassociated conditions. Also, many studies have investigated the effect of ZA on Osteoblastic-Differentiation (OSD) of Mesenchymal Stem Cells (MSCs), but its clear molecular mechanism(s) has remained to be understood. It seems that the methylation of the promoter region of key genes might be an important factor involved in the regulation of genes responsible for OSD. The present study aimed to evaluate the changes in the mRNA expression and promoter methylation of central Transcription Factors (TFs) during OSD of MSCs under treatment with ZA. MATERIALS AND METHODS MSCs were induced to be differentiated into the osteoblastic cell lineage using routine protocols. MSCs received ZA during OSD and then the methylation and mRNA expression levels of target genes were measured by Methylation Specific-quantitative Polymerase Chain Reaction (MS-qPCR) and real-time PCR, respectively. The osteoblastic differentiation was confirmed by Alizarin Red Staining and the related markers to this stage. RESULTS Gene expression and promoter methylation level for DLX3, FRA1, ATF4, MSX2, C/EBPζ, and C/EBPa were up or down-regulated in both ZA-treated and untreated cells during the osteodifferentiation process on days 0 to 21. ATF4, DLX3, and FRA1 genes were significantly up-regulated during the OSD processes, while the result for MSX2, C/EBPζ, and C/EBPa was reverse. On the other hand, ATF4 and DLX3 methylation levels gradually reduced in both ZA-treated and untreated cells during the osteodifferentiation process on days 0 to 21, while the pattern was increasing for MSX2 and C/EBPa. The methylation pattern of C/EBPζ was upward in untreated groups while it had a downward pattern in ZA-treated groups at the same scheduled time. The result for FRA1 was not significant in both groups at the same scheduled time (days 0-21). CONCLUSION The results indicated that promoter-hypomethylation of ATF4, DLX3, and FRA1 genes might be one of the mechanism(s) controlling their gene expression. Moreover, we found that promoter-hypermethylation led to the down-regulation of MSX2, C/EBP-ζ and C/EBP-α. The results implicate that ATF4, DLX3 and FRA1 may act as inducers of OSD while MSX2, C/EBP-ζ and C/EBP-α could act as the inhibitor ones. We also determined that promoter-methylation is an important process in the regulation of OSD. However, yet there was no significant difference in the promoter-methylation level of selected TFs in ZA-treated and control cells, a methylation- independent pathway might be involved in the regulation of target genes during OSD of MSCs.
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Affiliation(s)
- Faroogh Marofi
- Department of Immunology, Division of Hematology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran,Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalal Choupani
- Department of Medical Genetic, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Solali
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ghasem Vahedi
- Department of Immunology, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Ali Hassanzadeh
- Department of Immunology, Division of Hematology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran,Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tohid Gharibi
- Department of Immunology, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Majid F Hagh
- Department of Immunology, Division of Hematology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran,Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Tansriratanawong K, Tabei I, Ishikawa H, Ohyama A, Toyomura J, Sato S. Characterization and comparative DNA methylation profiling of four adipogenic genes in adipose-derived stem cells and dedifferentiated fat cells from aging subjects. Hum Cell 2020; 33:974-989. [PMID: 32495194 PMCID: PMC7505878 DOI: 10.1007/s13577-020-00379-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/14/2020] [Indexed: 12/20/2022]
Abstract
Adipose-derived stem cells (ASCs) and dedifferentiated fat (DFAT) cells are alternative cell sources in tissue engineering and regeneration because they are easily obtained and exhibit multilineage differentiation. However, aging may attenuate their regenerative potential and metabolic functions. Reports characterizing DFAT cells derived from aging donors are rare, and comparisons of DNA methylation profiles between aging ASCs and DFAT cells are poorly understood. Therefore, this study aimed to characterize DFAT cells relative to ASCs derived from aging subjects and compare the DNA methylation profiles of four adipogenic genes in these cells. ASCs and DFAT cells from aging donors exhibited characteristics similar to those of stem cells, including colony formation, proliferation, and multilineage differentiation abilities. However, compared with ASCs, DFAT cells exhibited increased proliferation, smooth muscle actin alpha (SMA-α) expression and decreased cellular senescence. DNA methylation profiling of ASCs and DFAT cells by combined bisulfite restriction analysis (COBRA) demonstrated hypermethylation patterns in three potent adipogenic genes—peroxisome proliferator-activated receptor gamma 2 (PPARγ2), fatty acid-binding protein 4 (FABP4), and lipoprotein lipase (LPL)—but hypomethylation of CCAAT/enhancer binding protein alpha (C/EBPα) in the aging group. Statistically significant differences were observed between the aging group and the young group. Epigenetic regulation maintains the stability of ASCs and DFAT cells in an age-dependent manner. Our findings suggested that although the DNA methylation patterns of three adipogenic genes correlated with hypermethylation and aging, ASCs and DFAT cells exhibited cellular stability and several stem cell characteristics, offering further opportunities for personalized regeneration and energy maintenance by adipogenesis during aging.
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Affiliation(s)
- Kallapat Tansriratanawong
- Department of Oral Medicine and Periodontology, Faculty of Dentistry, Mahidol University, 6 Yothi Street Rajthevi, Bangkok, 10400, Thailand.
| | - Isao Tabei
- Department of Surgery, Jikei University School of Medicine, Tokyo, 105-0003, Japan
| | - Hiroshi Ishikawa
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Akihiro Ohyama
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Junko Toyomura
- Department of Neurosurgery, Faculty of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Soh Sato
- Department of Periodontology, Nippon Dental University, Niigata, 951-1500, Japan
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Histone Modifications Pattern Associated With a State of Mesenchymal Stem Cell Cultures Derived From Amniotic Fluid of Normal and Fetus‐Affected Gestations. J Cell Biochem 2017; 118:3744-3755. [DOI: 10.1002/jcb.26022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/30/2017] [Indexed: 12/17/2022]
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Jin W, Peng J, Jiang S. The epigenetic regulation of embryonic myogenesis and adult muscle regeneration by histone methylation modification. Biochem Biophys Rep 2016; 6:209-219. [PMID: 28955879 PMCID: PMC5600456 DOI: 10.1016/j.bbrep.2016.04.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 12/11/2022] Open
Abstract
Skeletal muscle formation in vertebrates is derived from the paraxial mesoderm, which develops into myogenic precursor cells and finally differentiates into mature myofibers. This myogenic program involves temporal-spatial molecular events performed by transcription regulators (such as members of the Pax, MRFs and Six families) and signaling pathways (such as Wnts, BMP and Shh signaling). Epigenetic regulation, including histone post-translational modifications is crucial for controlling gene expression through recruitment of various chromatin-modifying enzymes that alter chromatin dynamics during myogenesis. The chromatin modifying enzymes are also recruited at regions of muscle gene regulation, coordinating transcription regulators to influence gene expression. In particular, the reversible methylation status of histone N-terminal tails provides the important regulatory mechanisms in either activation or repression of muscle genes. In this report, we review the recent literatures to deduce mechanisms underlying the epigenetic regulation of gene expression with a focus on histone methylation modification during embryo myogenesis and adult muscle regeneration. Recent results from different histone methylation/demethylation modifications have increased our understanding about the highly intricate layers of epigenetic regulations involved in myogenesis and cross-talk of histone enzymes with the muscle-specific transcriptional machinery. Myogenesis is influenced by regulation of transcription factors, signal pathways and post-transcriptional modifications. Histone methylation modifications as “on/off” switches regulated myogenic lineage commitment and differentiation. The myogenic regulatory factors and histone methylation modifications established dynamic regulatory mechanism.
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Key Words
- BMP4, bone morphogenic protein 4
- ChIP, chromatin immunoprecipitation
- Epigenetic
- H3K27, methylation of histone H3 lysine 27
- H3K4, methylation of histone H3 lysine 4
- H3K9, methylation of histone H3 lysine 9
- Histone methylation/demethylation modification
- KDMs, lysine demethyltransferases
- LSD1, lysine specific demethyltransferase 1
- MEF2, myocyte enhancer factor 2
- MRFs, myogenic regulatory factors
- Muscle differentiation
- Muscle progenitor cells
- Muscle regeneration
- Myogenesis
- PRC2, polycomb repressive complex 2
- SCs, satellite cells
- Shh, sonic hedgehog
- TSS, transcription start sites
- UTX, ubiquitously transcribed tetratricopeptide repeat, X chromosome
- bHLH, basic helix-loop-helix
- p38 MAPK, p38 mitogen-activated protein kinase
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Affiliation(s)
- Wei Jin
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jian Peng
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - Siwen Jiang
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China.,Key Projects in the Cooperative Innovation Center for Sustainable Pig Production of Wuhan, PR China
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Veluscek G, Li Y, Yang SH, Sharrocks AD. Jun-Mediated Changes in Cell Adhesion Contribute to Mouse Embryonic Stem Cell Exit from Ground State Pluripotency. Stem Cells 2016; 34:1213-24. [PMID: 26850660 PMCID: PMC4864893 DOI: 10.1002/stem.2294] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/02/2015] [Indexed: 01/02/2023]
Abstract
Embryonic stem cells (ESC) are able to give rise to any somatic cell type. A lot is known about how ESC pluripotency is maintained, but comparatively less is known about how differentiation is promoted. Cell fate decisions are regulated by interactions between signaling and transcriptional networks. Recent studies have shown that the overexpression or downregulation of the transcription factor Jun can affect the ESC fate. Here we have focussed on the role of the Jun in the exit of mouse ESCs from ground state pluripotency and the onset of early differentiation. Transcriptomic analysis of differentiating ESCs reveals that Jun is required to upregulate a programme of genes associated with cell adhesion as ESCs exit the pluripotent ground state. Several of these Jun-regulated genes are shown to be required for efficient adhesion. Importantly this adhesion is required for the timely regulated exit of ESCs from ground state pluripotency and the onset of early differentiation events. Stem Cells 2016;34:1213-1224.
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Affiliation(s)
- Giulia Veluscek
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Yaoyong Li
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Shen-Hsi Yang
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Andrew D Sharrocks
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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Cadmium affects mitotically inherited histone modification pathways in mouse embryonic stem cells. Toxicol In Vitro 2015; 30:583-92. [PMID: 26562325 DOI: 10.1016/j.tiv.2015.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 10/19/2015] [Accepted: 11/02/2015] [Indexed: 11/21/2022]
Abstract
The fetal basis of adult disease (FeBAD) theorizes that embryonic challenges initiate pathologies in adult life through epigenetic modification of gene expression. In addition, inheritance of H3K27 methylation marks, especially in vitro, is still controversial. Metals, such as Cd, are known to affect differentiation, DNA repair and epigenetic status in mES cells. We tested the premise that Cd exerts differential toxicity in mouse embryonic stem (mES) cells by targeting total histone protein (THP) production early in stem cell development, while affecting H3K27-mono-methylation (H3K27me(1)) in latter stages of differentiation. The inability of mES cells to recover from Cd insult at concentrations greater than IC50 indicates that maximum cytotoxicity occurs during initial hours of exposure. Moreover, as a measure of chromatin stability, low dose acute Cd exposure lowers THP production. The heritable effects of Cd exposure on cell proliferation, chromatin stability and transcription observed through several cell population doublings were detected only during alternate passages on days 3, 7, and 11, presumably due to slower maturation of histone methylation marks. These findings demonstrate a selective disruption of chromatin structure following acute Cd exposure, an effect not seen in developmentally mature cells. Hence, we present that acute Cd toxicity is cumulative and disrupts DNA repair, while concurrently affecting cell cycle progression, chromatin stability and transcriptional state in mES cells.
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8
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Ha SW, Jang HL, Nam KT, Beck GR. Nano-hydroxyapatite modulates osteoblast lineage commitment by stimulation of DNA methylation and regulation of gene expression. Biomaterials 2015; 65:32-42. [PMID: 26141836 DOI: 10.1016/j.biomaterials.2015.06.039] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 12/26/2022]
Abstract
Hydroxyapatite (HA) is the primary structural component of the skeleton and dentition. Under biological conditions, HA does not occur spontaneously and therefore must be actively synthesized by mineralizing cells such as osteoblasts. The mechanism(s) by which HA is actively synthesized by cells and deposited to create a mineralized matrix are not fully understood and the consequences of mineralization on cell function are even less well understood. HA can be chemically synthesized (HAp) and is therefore currently being investigated as a promising therapeutic biomaterial for use as a functional scaffold and implant coating for skeletal repair and dental applications. Here we investigated the biological effects of nano-HAp (10 × 100 nm) on the lineage commitment and differentiation of bone forming osteoblasts. Exposure of early stage differentiating osteoblasts resulted in dramatic and sustained changes in gene expression, both increased and decreased, whereas later stage osteoblasts were much less responsive. Analysis of the promoter region one of the most responsive genes, alkaline phosphatase, identified the stimulation of DNA methylation following cell exposure to nano-HAp. Collectively, the results reveal the novel epigenetic regulation of cell function by nano-HAp which has significant implication on lineage determination as well as identifying a novel potential therapeutic use of nanomaterials.
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Affiliation(s)
- Shin-Woo Ha
- Department of Medicine, Division of Endocrinology Metabolism and Lipids, Emory University, Atlanta, GA 30322, United States
| | - Hae Lin Jang
- Department of Materials Science and Engineering, Seoul National University, Seoul 151-744, Republic of Korea
| | - Ki Tae Nam
- Department of Materials Science and Engineering, Seoul National University, Seoul 151-744, Republic of Korea
| | - George R Beck
- The Atlanta Department of Veterans Affairs Medical Center, Decatur, GA 30033, United States; Department of Medicine, Division of Endocrinology Metabolism and Lipids, Emory University, Atlanta, GA 30322, United States; The Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, United States.
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9
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Lu DF, Yao Y, Su ZZ, Zeng ZH, Xing XW, He ZY, Zhang C. Downregulation of HDAC1 is involved in the cardiomyocyte differentiation from mesenchymal stem cells in a myocardial microenvironment. PLoS One 2014; 9:e93222. [PMID: 24690943 PMCID: PMC3972222 DOI: 10.1371/journal.pone.0093222] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/28/2014] [Indexed: 02/06/2023] Open
Abstract
Under myocardial microenvironment, bone marrow-derived mesenchymal stem cells (MSCs) can transdifferentiate into cardiomyocytes (CMs). However, the role of histone deacetylase 1 (HDAC1) in this directed differentiation process remains unclear. The current study is to determine the acetylation regulatory mechanisms that may be involved in the directed CM differentiation from MSCs. MSCs isolated from male Sprague-Dawley (SD) rats were marked with Ad-EGFP and co-cultured with CMs. Flow cytometry was used to sort EGFP-positive (EGFP+) MSCs from the co-culture system. Then, the expression of cardiac troponin T (cTnT) in these MSCs was detected by immunofluorescence assay. In addition, HDAC1 levels at different co-culture times were measured by quantitative real-time polymerase chain reaction (QT-PCR) and Western blotting. At 4 days after co-culture with CMs, the MSCs began to expression detectable levels of cTnT. The expression of HDAC1 in CMs was much lower than that in MSCs. After co-culture with CMs, the expression of HDAC1 in MSCs was significantly decreased in a time dependent manner. In addition, our recent study has also identified that knockdown of the HDAC1 could promote the directed differentiation of MSCs into CMs. The results suggest that HDAC1 has a negative correlation with cardiac cell differentiation from MSCs under a myocardial microenvironment. HDAC1 might play an important role in the directed differentiation of MSCs into CMs in heart.
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Affiliation(s)
- Dong-feng Lu
- Department of Cardiology and Sino-US Cardiovascular Research Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- * E-mail: (CZ); (D-fL)
| | - Yan Yao
- Department of Cardiology and Sino-US Cardiovascular Research Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zi-zhuo Su
- Department of Cardiology and Sino-US Cardiovascular Research Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhao-hua Zeng
- Department of Cardiology and Sino-US Cardiovascular Research Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiao-wen Xing
- Department of Cardiology and Sino-US Cardiovascular Research Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhi-yu He
- Department of Cardiology and Sino-US Cardiovascular Research Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Chunxiang Zhang
- Department of Pharmacology and Cardiovascular Research Center, Rush Medical College, Rush University, Chicago, Illinois, United States of America
- * E-mail: (CZ); (D-fL)
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Lu DF, Wang Y, Su ZZ, Zeng ZH, Xing XW, He ZY, Zhang C. Knockdown of the HDAC1 promotes the directed differentiation of bone mesenchymal stem cells into cardiomyocytes. PLoS One 2014; 9:e92179. [PMID: 24686813 PMCID: PMC3970960 DOI: 10.1371/journal.pone.0092179] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 02/19/2014] [Indexed: 12/13/2022] Open
Abstract
Failure of the directed differentiation of the transplanted stem cells into cardiomyocytes is still a major challenge of cardiac regeneration therapy. Our recent study has demonstrated that the expression of histone deacetylase 1 (HDAC1) is decreased in bone mesenchymal stem cells (BMSCs) during their differentiation into cardiomyocytes. However, the potential roles of HDAC1 in cardiac cell differentiation of BMSCs, as well as the mechanisms involved are still unclear. In current study, the expression of HDAC1 in cultured rat BMSCs is knocked down by lentiviral vectors expressing HDAC1-RNAi. The directed differentiation of BMSCs into cardiomyocytes is evaluated by the expression levels of cardiomyocyte-related genes such as GATA-binding protein 4 (GATA-4), Nirenberg, Kim gene 2 homeobox 5 (Nkx2.5), cardiac troponin T (CTnT), myosin heavy chain (MHC), and connexin-43. Compared with that in control BMSCs, the expression of these cardiomyocyte-related genes is significantly increased in these HDAC1 deficient stem cells. The results suggest that HDAC1 is involved in the cardiomyocyte differentiation of BMSCs. Knockdown of the HDAC1 may promote the directed differentiation of BMSCs into cardiomyocytes.
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Affiliation(s)
- Dong-feng Lu
- Department of Cardiology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- * E-mail: (CZ); (DFL)
| | - Ying Wang
- Department of Cardiology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zi-zhuo Su
- Department of Cardiology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhao-hua Zeng
- Department of Cardiology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiao-wen Xing
- Department of Cardiology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhi-yu He
- Department of Cardiology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Chunxiang Zhang
- Department of Pharmacology and Cardiovascular Research Center, Rush Medical college of Rush University, Chicago, Illinois, United States of America
- * E-mail: (CZ); (DFL)
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11
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Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells. PLoS One 2014; 9:e92689. [PMID: 24658136 PMCID: PMC3962432 DOI: 10.1371/journal.pone.0092689] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/24/2014] [Indexed: 12/31/2022] Open
Abstract
Genome-wide distribution of the majority of H2A and H3 variants (H2A, H2AX, H2AZ, macroH2A, H3.1, H3.2 and H3.3) was simultaneously investigated in mouse embryonic stem cells by chromatin immunoprecipitation sequencing. Around the transcription start site, histone variant distribution differed between genes possessing promoters of high and low CpG density, regardless of their expression levels. In the intergenic regions, regulatory elements were enriched in H2A.Z and H3.3, whereas repeat elements were abundant in H2A and macroH2A, and H3.1, respectively. Analysis of H2A and H3 variant combinations composing nucleosomes revealed that the H2A.Z and H3.3 combinations were present at a higher frequency throughout the genome than the other combinations, suggesting that H2A.Z and H3.3 associate preferentially with each other to comprise the nucleosomes independently of genome region. Finally, we found that chromatin was unstable only in regions where it was enriched in both H2A.Z and H3.3, but strongly quantified stable in regions in which only H3.3 was abundant. Therefore, histone variant composition is an important determinant of chromatin structure, which is associated with specific genomic functions.
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12
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Kar S, Parbin S, Deb M, Shilpi A, Sengupta D, Rath SK, Rakshit M, Patra A, Patra SK. Epigenetic choreography of stem cells: the DNA demethylation episode of development. Cell Mol Life Sci 2014; 71:1017-32. [PMID: 24114325 PMCID: PMC11113617 DOI: 10.1007/s00018-013-1482-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/12/2013] [Accepted: 09/16/2013] [Indexed: 12/17/2022]
Abstract
Reversible DNA methylation is a fundamental epigenetic manipulator of the genomic information in eukaryotes. DNA demethylation plays a very significant role during embryonic development and stands out for its contribution in molecular reconfiguration during cellular differentiation for determining stem cell fate. DNA demethylation arbitrated extensive make-over of the genome via reprogramming in the early embryo results in stem cell plasticity followed by commitment to the principal cell lineages. This article attempts to highlight the sequential phases and hierarchical mode of DNA demethylation events during enactment of the molecular strategy for developmental transition. A comprehensive knowledge regarding the pattern of DNA demethylation during embryogenesis and organogenesis and study of the related lacunae will offer exciting avenues for future biomedical research and stem cell-based regenerative therapy.
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Affiliation(s)
- Swayamsiddha Kar
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Sabnam Parbin
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Moonmoon Deb
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Arunima Shilpi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Dipta Sengupta
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Sandip Kumar Rath
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Madhumita Rakshit
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Aditi Patra
- Additional Block Animal Health Centre, Veterinary Office, Oodlabari, Malbazar, Jalpaiguri, West Bengal India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
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13
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NARTPRAYUT KUNEERAT, U-PRATYA YAOWALAK, KHEOLAMAI PAKPOOM, MANOCHANTR SIRIKUL, CHAYOSUMRIT METHICHIT, ISSARAGRISIL SURAPOL, SUPOKAWEJ AUNGKURA. Cardiomyocyte differentiation of perinatally-derived mesenchymal stem cells. Mol Med Rep 2013; 7:1465-9. [DOI: 10.3892/mmr.2013.1356] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/20/2013] [Indexed: 11/06/2022] Open
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14
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Leu YW, Huang THM, Hsiao SH. Epigenetic reprogramming of mesenchymal stem cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 754:195-211. [PMID: 22956503 DOI: 10.1007/978-1-4419-9967-2_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mesenchymal stem cells (MSCs) are multipotent stem cells of mesodermal origin that can be isolated from various sources and induced into different cell types. Although MSCs possess immune privilege and are more easily obtained than embryonic stem cells, their propensity to tumorigenesis has not been fully explored. Epigenomic changes in DNA methylation and chromatin structure have been hypothesized to be critical in the determination of lineage-specific differentiation and tumorigenesis of MSCs, but this has not been formally proven. We applied a targeted DNA methylation method to methylate a Polycomb group protein-governed gene, Trip10, in MSCs, which accelerated the cell fate determination of MSCs. In addition, targeted methylation of HIC1 and RassF1A, both tumor suppressor genes, transformed MSCs into tumor stem cell-like cells. This new method will allow better control of the differentiation of MSCs and their use in downstream applications.
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Affiliation(s)
- Yu-Wei Leu
- Department of Life Science, National Chung Cheng University, Chia-Yi 621, Taiwan.
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15
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Steiner L, Hopp L, Wirth H, Galle J, Binder H, Prohaska SJ, Rohlf T. A global genome segmentation method for exploration of epigenetic patterns. PLoS One 2012; 7:e46811. [PMID: 23077526 PMCID: PMC3470578 DOI: 10.1371/journal.pone.0046811] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 09/05/2012] [Indexed: 11/18/2022] Open
Abstract
Current genome-wide ChIP-seq experiments on different epigenetic marks aim at unraveling the interplay between their regulation mechanisms. Published evaluation tools, however, allow testing for predefined hypotheses only. Here, we present a novel method for annotation-independent exploration of epigenetic data and their inter-correlation with other genome-wide features. Our method is based on a combinatorial genome segmentation solely using information on combinations of epigenetic marks. It does not require prior knowledge about the data (e.g. gene positions), but allows integrating the data in a straightforward manner. Thereby, it combines compression, clustering and visualization of the data in a single tool. Our method provides intuitive maps of epigenetic patterns across multiple levels of organization, e.g. of the co-occurrence of different epigenetic marks in different cell types. Thus, it facilitates the formulation of new hypotheses on the principles of epigenetic regulation. We apply our method to histone modification data on trimethylation of histone H3 at lysine 4, 9 and 27 in multi-potent and lineage-primed mouse cells, analyzing their combinatorial modification pattern as well as differentiation-related changes of single modifications. We demonstrate that our method is capable of reproducing recent findings of gene centered approaches, e.g. correlations between CpG-density and the analyzed histone modifications. Moreover, combining the clustered epigenetic data with information on the expression status of associated genes we classify differences in epigenetic status of e.g. house-keeping genes versus differentiation-related genes. Visualizing the distribution of modification states on the chromosomes, we discover strong patterns for chromosome X. For example, exclusively H3K9me3 marked segments are enriched, while poised and active states are rare. Hence, our method also provides new insights into chromosome-specific epigenetic patterns, opening up new questions how "epigenetic computation" is distributed over the genome in space and time.
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Affiliation(s)
- Lydia Steiner
- Junior Professorship for Computational EvoDevo, Institute of Computer Science, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Lydia Hopp
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Henry Wirth
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Jörg Galle
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Sonja J. Prohaska
- Junior Professorship for Computational EvoDevo, Institute of Computer Science, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Thimo Rohlf
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Max-Planck-Institute for Mathematics in the Sciences, Leipzig, Germany
- * E-mail:
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16
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Berdasco M, Melguizo C, Prados J, Gómez A, Alaminos M, Pujana MA, Lopez M, Setien F, Ortiz R, Zafra I, Aranega A, Esteller M. DNA methylation plasticity of human adipose-derived stem cells in lineage commitment. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 181:2079-93. [PMID: 23031258 DOI: 10.1016/j.ajpath.2012.08.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 08/17/2012] [Accepted: 08/23/2012] [Indexed: 01/28/2023]
Abstract
Adult stem cells have an enormous potential for clinical use in regenerative medicine that avoids many of the drawbacks characteristic of embryonic stem cells and induced pluripotent stem cells. In this context, easily obtainable human adipose-derived stem cells offer an interesting option for future strategies in regenerative medicine. However, little is known about their repertoire of differentiation capacities, how closely they resemble the target primary tissues, and the potential safety issues associated with their use. DNA methylation is one of the most widely recognized epigenetic factors involved in cellular identity, prompting us to consider how the analyses of 27,578 CpG sites in the genome of these cells under different conditions reflect their different natural history. We show that human adipose-derived stem cells generate myogenic and osteogenic lineages that share much of the DNA methylation landscape characteristic of primary myocytes and osteocytes. Most important, adult stem cells and in vitro-generated myocytes and osteocytes display a significantly different DNA methylome from that observed in transformed cells from these tissue types, such as rhabdomyosarcoma and osteosarcoma. These results suggest that the plasticity of the DNA methylation patterns plays an important role in lineage commitment of adult stem cells and that it could be used for clinical purposes as a biomarker of efficient and safely differentiated cells.
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Affiliation(s)
- María Berdasco
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Biomedical Research Institute, Barcelona, Spain
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17
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Siddiqi S, Matushansky I. Piwis and piwi-interacting RNAs in the epigenetics of cancer. J Cell Biochem 2012; 113:373-80. [PMID: 21928326 DOI: 10.1002/jcb.23363] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
An increasing body of evidence suggests that cancer cells acquire "stem-like" epigenetic and signaling characteristics during the tumorigenic process, including global DNA hypo-methylation, gene-specific DNA hyper-methylation, and small RNA deregulation. RNAs have been known to be epigenetic regulators, both in stem cells and in differentiated cells. A novel class of small RNAs, called piwi-interacting RNAs (piRNAs), maintains genome integrity by epigenetically silencing transposons via DNA methylation, especially in germline stem cells. piRNAs interact exclusively with the Piwi family of proteins. The human Piwi ortholog, Hiwi, has been found to be aberrantly expressed in a variety of human cancers and in some, its expression correlates with poor clinical prognosis. However, there has been little investigation into the potential role that Piwi and piRNAs might play in contributing to the "stem-like" epigenetic state of a cancer. This review will highlight the current evidence supporting the importance of Piwi and piRNAs in the epigenetics of cancer and provide a potential model for the role of Piwi and piRNAs in tumorigenesis.
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Affiliation(s)
- Sara Siddiqi
- Integrated Program, Graduate School of Arts and Sciences, Columbia University, New York, New York, USA
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18
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Kawaguchi N, Hayama E, Furutani Y, Nakanishi T. Prospective in vitro models of channelopathies and cardiomyopathies. Stem Cells Int 2012; 2012:439219. [PMID: 22969812 PMCID: PMC3437306 DOI: 10.1155/2012/439219] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 02/17/2012] [Accepted: 03/08/2012] [Indexed: 01/23/2023] Open
Abstract
An in vitro heart disease model is a promising model used for identifying the genes responsible for the disease, evaluating the effects of drugs, and regenerative medicine. We were interested in disease models using a patient-induced pluripotent stem (iPS) cell-derived cardiomyocytes because of their similarity to a patient's tissues. However, as these studies have just begun, we would like to review the literature in this and other related fields and discuss the path for future models of molecular biology that can help to diagnose and cure diseases, and its involvement in regenerative medicine. The heterogeneity of iPS cells and/or differentiated cardiomyocytes has been recognized as a problem. An in vitro heart disease model should be evaluated using molecular biological analyses, such as mRNA and micro-RNA expression profiles and proteomic analysis.
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Affiliation(s)
- Nanako Kawaguchi
- Department of Pediatric Cardiology, Tokyo Women's Medical University, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Emiko Hayama
- Department of Pediatric Cardiology, Tokyo Women's Medical University, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Yoshiyuki Furutani
- Department of Pediatric Cardiology, Tokyo Women's Medical University, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Toshio Nakanishi
- Department of Pediatric Cardiology, Tokyo Women's Medical University, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
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19
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Hupkes M, Jonsson MKB, Scheenen WJ, van Rotterdam W, Sotoca AM, van Someren EP, van der Heyden MAG, van Veen TA, van Ravestein-van Os RI, Bauerschmidt S, Piek E, Ypey DL, van Zoelen EJ, Dechering KJ. Epigenetics: DNA demethylation promotes skeletal myotube maturation. FASEB J 2011; 25:3861-72. [PMID: 21795504 DOI: 10.1096/fj.11-186122] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mesenchymal progenitor cells can be differentiated in vitro into myotubes that exhibit many characteristic features of primary mammalian skeletal muscle fibers. However, in general, they do not show the functional excitation-contraction coupling or the striated sarcomere arrangement typical of mature myofibers. Epigenetic modifications have been shown to play a key role in regulating the progressional changes in transcription necessary for muscle differentiation. In this study, we demonstrate that treatment of murine C2C12 mesenchymal progenitor cells with 10 μM of the DNA methylation inhibitor 5-azacytidine (5AC) promotes myogenesis, resulting in myotubes with enhanced maturity as compared to untreated myotubes. Specifically, 5AC treatment resulted in the up-regulation of muscle genes at the myoblast stage, while at later stages nearly 50% of the 5AC-treated myotubes displayed a mature, well-defined sarcomere organization, as well as spontaneous contractions that coincided with action potentials and intracellular calcium transients. Both the percentage of striated myotubes and their contractile activity could be inhibited by 20 nM TTX, 10 μM ryanodine, and 100 μM nifedipine, suggesting that action potential-induced calcium transients are responsible for these characteristics. Our data suggest that genomic demethylation induced by 5AC overcomes an epigenetic barrier that prevents untreated C2C12 myotubes from reaching full maturity.
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Affiliation(s)
- Marlinda Hupkes
- Department of Cell and Applied Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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20
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Abstract
ESCs (embryonic stem cells), derived from the blastocyst stage embryo, are characterized by an indefinite ability for self-renewal as well as pluripotency, enabling them to differentiate into all cell types of the three germ layers. In the undifferentiated state, ESCs display a global promiscuous transcriptional programme which is restricted gradually upon differentiation. Supporting transcriptional promiscuity, chromatin in pluripotent cells is more 'plastic' or 'open', with decondensed heterochromatin architecture, enrichment of active histone modifications, and a hyperdynamic association of chromatin proteins with chromatin. During ESC differentiation, nuclear architecture and chromatin undergo substantial changes. Heterochromatin foci appear smaller, more numerous and more condensed in the differentiated state, the nuclear lamina becomes more defined and chromatin protein dynamics becomes restricted. In the present chapter we discuss chromatin plasticity and epigenetics and the mechanisms that regulate the various chromatin states, which are currently a central theme in the studies of stem cell maintenance and differentiation, and which will no doubt assist in delineating the secrets of pluripotency and self-renewal.
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21
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Current world literature. Curr Opin Endocrinol Diabetes Obes 2010; 17:568-80. [PMID: 21030841 DOI: 10.1097/med.0b013e328341311d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Boeuf S, Richter W. Chondrogenesis of mesenchymal stem cells: role of tissue source and inducing factors. Stem Cell Res Ther 2010; 1:31. [PMID: 20959030 PMCID: PMC2983444 DOI: 10.1186/scrt31] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Multipotent mesenchymal stromal cells (MSCs) are an attractive cell source for cell therapy in cartilage. Although their therapeutic potential is clear, the requirements and conditions for effective induction of chondrogenesis in MSCs and for the production of a stable cartilaginous tissue by these cells are far from being understood. Different sources of MSCs have been considered for cartilage tissue engineering, mainly based on criteria of availability, as for adipose tissue, or of proximity to cartilage and the joint environment in vivo, as for bone marrow and synovial tissues. Focussing on human MSCs, this review will provide an overview of studies featuring comparative analysis of the chondrogenic differentiation of MSCs from different sources. In particular, it will examine the influence of the cells' origin on the requirements for the induction of chondrogenesis and on the phenotype achieved by the cells after differentiation.
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Affiliation(s)
- Stephane Boeuf
- Research Centre for Experimental Orthopaedics, Orthopaedic University Hospital Heidelberg, Schlierbacher Landstrasse 200a, 69118 Heidelberg, Germany.
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23
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Weishaupt H, Attema JL. A Method to Study the Epigenetic Chromatin States of Rare Hematopoietic Stem and Progenitor Cells; MiniChIP-Chip. Biol Proced Online 2010; 12:1-17. [PMID: 21406121 PMCID: PMC3396287 DOI: 10.1007/s12575-010-9031-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 04/21/2010] [Indexed: 12/18/2022] Open
Abstract
Dynamic chromatin structure is a fundamental property of gene transcriptional regulation, and has emerged as a critical modulator of physiological processes during cellular differentiation and development. Analysis of chromatin structure using molecular biology and biochemical assays in rare somatic stem and progenitor cells is key for understanding these processes but poses a great challenge because of their reliance on millions of cells. Through the development of a miniaturized genome-scale chromatin immunoprecipitation method (miniChIP–chip), we have documented the genome-wide chromatin states of low abundant populations that comprise hematopoietic stem cells and immediate progeny residing in murine bone marrow. In this report, we describe the miniChIP methodology that can be used for increasing an understanding of the epigenetic mechanisms underlying hematopoietic stem and progenitor cell function. Application of this method will reveal the contribution of dynamic chromatin structure in regulating the function of other somatic stem cell populations, and how this process becomes perturbed in pathological conditions.
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Affiliation(s)
- Holger Weishaupt
- Immunology Unit, Institute for Experimental Medical Science, BMC D14, Lund University, 221 84, Lund, Sweden.
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24
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Chromatin plasticity and genome organization in pluripotent embryonic stem cells. Curr Opin Cell Biol 2010; 22:334-41. [PMID: 20226651 DOI: 10.1016/j.ceb.2010.02.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 02/04/2010] [Accepted: 02/10/2010] [Indexed: 12/23/2022]
Abstract
In search of the mechanisms that govern pluripotency and embryonic stem cell (ESC) self-renewal, a growing list of evidence highlights chromatin as a leading factor, controlling ESC maintenance and differentiation. In-depth investigation of chromatin in ESCs revealed distinct features, including DNA methylation, histone modifications, chromatin protein composition and nuclear architecture. Here we review recent literature describing different aspects of chromatin and genome organization in ESCs. The emerging theme seems to support a mechanism maintaining chromatin plasticity in ESCs but without any dramatic changes in the organization and nuclear positioning of chromosomes and gene loci themselves. Plasticity thus seems to be supported more by different mechanisms maintaining an open chromatin state and less by regulating the location of genomic regions.
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25
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Munro SK, Farquhar CM, Mitchell MD, Ponnampalam AP. Epigenetic regulation of endometrium during the menstrual cycle. Mol Hum Reprod 2010; 16:297-310. [PMID: 20139117 DOI: 10.1093/molehr/gaq010] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The endometrium undergoes morphological and functional changes during the menstrual cycle which are essential for uterine receptivity. These changes are driven by estrogen and progesterone and involve the fine control of many different genes-several of which have been identified as being epigenetically regulated. Epigenetic modification may therefore influence the functional changes in the endometrium required for successful implantation. There is, however, only limited information on epigenetic regulation in endometrium. We review the potential role of epigenetic regulation of key processes during the menstrual cycle and present our own findings following a preliminary study into global acetylation levels in the human endometrium. A changing epigenetic state is associated with the differentiation of stem cells into different lineages and thus may be involved in endometrial regeneration. Histone acetylation is implicated in the vascular endothelial growth factor pathway during angiogenesis, and studies using histone deacetylase inhibitors suggest an involvement in endometrial proliferation and differentiation. The processes of decidualization and implantation are also associated with epigenetic change and epigenetic modulators show variable expression across the menstrual cycle. Our own studies found that endometrial global histone acetylation, as determined by western blotting, changed throughout the menstrual cycle and correlated well with expected transcription activity during the different phases. This suggests that epigenetics may be involved in the regulation of endometrial gene expression during the menstrual cycle and that abnormal epigenetic modifications may therefore be associated with implantation failure and early pregnancy loss as well as with other endometrial pathologies.
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Affiliation(s)
- S K Munro
- The Liggins Institute, The University of Auckland, Auckland 1142, New Zealand
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26
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Epigenetic chromatin states uniquely define the developmental plasticity of murine hematopoietic stem cells. Blood 2009; 115:247-56. [PMID: 19887676 DOI: 10.1182/blood-2009-07-235176] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Heritable epigenetic signatures are proposed to serve as an important regulatory mechanism in lineage fate determination. To investigate this, we profiled chromatin modifications in murine hematopoietic stem cells, lineage-restricted progenitors, and CD4(+) T cells using modified genome-scale mini-chromatin immunoprecipitation technology. We show that genes involved in mature hematopoietic cell function associate with distinct chromatin states in stem and progenitor cells, before their activation or silencing upon cellular maturation. Many lineage-restricted promoters are associated with bivalent histone methylation and highly combinatorial histone modification patterns, which may determine their selective priming of gene expression during lineage commitment. These bivalent chromatin states are conserved in mammalian evolution, with a particular overrepresentation of promoters encoding key regulators of hematopoiesis. After differentiation into progenitors and T cells, activating histone modifications persist at transcriptionally repressed promoters, suggesting that these transcriptional programs might be reactivated after lineage restriction. Collectively, our data reveal the epigenetic framework that underlies the cell fate options of hematopoietic stem cells.
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