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Chen C, Lee S, Zyner KG, Fernando M, Nemeruck V, Wong E, Marshall LL, Wark JR, Aryamanesh N, Tam PPL, Graham ME, Gonzalez-Cordero A, Yang P. Trans-omic profiling uncovers molecular controls of early human cerebral organoid formation. Cell Rep 2024; 43:114219. [PMID: 38748874 DOI: 10.1016/j.celrep.2024.114219] [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: 01/03/2024] [Revised: 04/01/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
Defining the molecular networks orchestrating human brain formation is crucial for understanding neurodevelopment and neurological disorders. Challenges in acquiring early brain tissue have incentivized the use of three-dimensional human pluripotent stem cell (hPSC)-derived neural organoids to recapitulate neurodevelopment. To elucidate the molecular programs that drive this highly dynamic process, here, we generate a comprehensive trans-omic map of the phosphoproteome, proteome, and transcriptome of the exit of pluripotency and neural differentiation toward human cerebral organoids (hCOs). These data reveal key phospho-signaling events and their convergence on transcriptional factors to regulate hCO formation. Comparative analysis with developing human and mouse embryos demonstrates the fidelity of our hCOs in modeling embryonic brain development. Finally, we demonstrate that biochemical modulation of AKT signaling can control hCO differentiation. Together, our data provide a comprehensive resource to study molecular controls in human embryonic brain development and provide a guide for the future development of hCO differentiation protocols.
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Affiliation(s)
- Carissa Chen
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Scott Lee
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Katherine G Zyner
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Milan Fernando
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Victoria Nemeruck
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Emilie Wong
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Lee L Marshall
- Bioinformatics Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Jesse R Wark
- Synapse Proteomics, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Nader Aryamanesh
- Bioinformatics Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Patrick P L Tam
- Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Mark E Graham
- Synapse Proteomics, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
| | - Anai Gonzalez-Cordero
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
| | - Pengyi Yang
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia.
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Ghosh K, Zhou JJ, Shao JY, Chen SR, Pan HL. DNA demethylation in the hypothalamus promotes transcription of Agtr1a and Slc12a2 and hypertension development. J Biol Chem 2024; 300:105597. [PMID: 38160798 PMCID: PMC10830874 DOI: 10.1016/j.jbc.2023.105597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/09/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024] Open
Abstract
Increased expression of angiotensin II AT1A receptor (encoded by Agtr1a) and Na+-K+-Cl- cotransporter-1 (NKCC1, encoded by Slc12a2) in the hypothalamic paraventricular nucleus (PVN) contributes to hypertension development. However, little is known about their transcriptional control in the PVN in hypertension. DNA methylation is a critical epigenetic mechanism that regulates gene expression. Here, we determined whether transcriptional activation of Agtr1a and Slc12a2 results from altered DNA methylation in spontaneously hypertensive rats (SHR). Methylated DNA immunoprecipitation and bisulfite sequencing-PCR showed that CpG methylation at Agtr1a and Slc12a2 promoters in the PVN was progressively diminished in SHR compared with normotensive Wistar-Kyoto rats (WKY). Chromatin immunoprecipitation-quantitative PCR revealed that enrichment of DNA methyltransferases (DNMT1 and DNMT3A) and methyl-CpG binding protein 2, a DNA methylation reader protein, at Agtr1a and Slc12a2 promoters in the PVN was profoundly reduced in SHR compared with WKY. By contrast, the abundance of ten-eleven translocation enzymes (TET1-3) at Agtr1a and Slc12a2 promoters in the PVN was much greater in SHR than in WKY. Furthermore, microinjecting of RG108, a selective DNMT inhibitor, into the PVN of WKY increased arterial blood pressure and correspondingly potentiated Agtr1a and Slc12a2 mRNA levels in the PVN. Conversely, microinjection of C35, a specific TET inhibitor, into the PVN of SHR markedly reduced arterial blood pressure, accompanied by a decrease in Agtr1a and Slc12a2 mRNA levels in the PVN. Collectively, our findings suggest that DNA hypomethylation resulting from the DNMT/TET switch at gene promoters in the PVN promotes transcription of Agtr1a and Slc12a2 and hypertension development.
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Affiliation(s)
- Krishna Ghosh
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jing-Jing Zhou
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jian-Ying Shao
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shao-Rui Chen
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hui-Lin Pan
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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Moazeny M, Dehbashi M, Hojati Z, Esmaeili F. Investigating neural differentiation of mouse P19 embryonic stem cells in a time-dependent manner by bioinformatic, microscopic and transcriptional analyses. Mol Biol Rep 2023; 50:2183-2194. [PMID: 36565416 DOI: 10.1007/s11033-022-08166-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/23/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND As an available cell line, mouse pluripotent P19 has been widely employed for neuronal differentiation studies. In this research, by applying the in vitro differentiation of this cell line into neuron-like cells through retinoic acid (RA) treatment, the roles of some genes including DNMT3B, ICAM1, IRX3, JAK2, LHX1, SOX9, TBX3 and THY1 in neural differentiation was investigated. METHODS AND RESULTS Bioinformatics, microscopic, and transcriptional studies were conducted in a time-dependent manner after RA-induced neural differentiation. According to bioinformatics studies, we determined the engagement of the metabolic and developmental super-pathways and pathways in neural cell differentiation, particularly focusing on the considered genes. According to our qRT-PCR analyses, JAK2, SOX9, TBX3, LHX1 and IRX3 genes were found to be significantly overexpressed in a time-dependent manner (p < 0.05). In addition, the significant downregulation of THY1, DNMT3B and ICAM1 genes was observed during the experiment (p < 0.05). The optical microscopic investigation showed that the specialized extensions of the neuron-like cells were revealed on day 8 after RA treatment. CONCLUSION Accordingly, the neural differentiation of P19 cell line and the role of the considered genes during the differentiation were proved. However, our results warrant further in vivo studies.
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Affiliation(s)
- Marzieh Moazeny
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, 81746-73441, Isfahan, Iran
| | - Moein Dehbashi
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, 81746-73441, Isfahan, Iran
| | - Zohreh Hojati
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, 81746-73441, Isfahan, Iran.
| | - Fariba Esmaeili
- Division of Animal Sciences, Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, 81746-73441, Isfahan, Iran
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Iannone C, Kainov Y, Zhuravskaya A, Hamid F, Nojima T, Makeyev EV. PTBP1-activated co-transcriptional splicing controls epigenetic status of pluripotent stem cells. Mol Cell 2023; 83:203-218.e9. [PMID: 36626906 DOI: 10.1016/j.molcel.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 11/15/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023]
Abstract
Many spliceosomal introns are excised from nascent transcripts emerging from RNA polymerase II (RNA Pol II). The extent of cell-type-specific regulation and possible functions of such co-transcriptional events remain poorly understood. We examined the role of the RNA-binding protein PTBP1 in this process using an acute depletion approach followed by the analysis of chromatin- and RNA Pol II-associated transcripts. We show that PTBP1 activates the co-transcriptional excision of hundreds of introns, a surprising effect given that this protein is known to promote intron retention. Importantly, some co-transcriptionally activated introns fail to complete their splicing without PTBP1. In a striking example, retention of a PTBP1-dependent intron triggers nonsense-mediated decay of transcripts encoding DNA methyltransferase DNMT3B. We provide evidence that this regulation facilitates the natural decline in DNMT3B levels in developing neurons and protects differentiation-specific genes from ectopic methylation. Thus, PTBP1-activated co-transcriptional splicing is a widespread phenomenon mediating epigenetic control of cellular identity.
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Affiliation(s)
- Camilla Iannone
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Yaroslav Kainov
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Fursham Hamid
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Takayuki Nojima
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK.
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Sae-Lee C, Barrow TM, Colicino E, Choi SH, Rabanal-Ruiz Y, Green D, Korolchuk VI, Mathers JC, Byun HM. Genomic targets and selective inhibition of DNA methyltransferase isoforms. Clin Epigenetics 2022; 14:103. [PMID: 35987848 PMCID: PMC9392947 DOI: 10.1186/s13148-022-01325-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background DNA methylation in the human genome is established and maintained by DNA methyltransferases (DNMTs). DNMT isoforms show differential expression by cell lineage and during development, but much remains to be elucidated about their shared and unique genomic targets. Results We examined changes in the epigenome following overexpression of 13 DNMT isoforms in HEK293T cells. We observed increased methylation (Δβ > 0.2) at 43,405 CpG sites, with expression of DNMT3A2, DNMTΔ3B4 and DNMTΔ3B2 associated with the greatest impact. De novo methylation occurred primarily within open sea regions and at loci with intermediate methylation levels (β: 0.2–0.6). 53% of differentially methylated loci showed specificity towards a single DNMT subfamily, primarily DNMTΔ3B and DNMT3A and 39% towards a single isoform. These loci were significantly enriched for pathways related to neuronal development (DNMTΔ3B4), calcium homeostasis (DNMTΔ3B3) and ion transport (DNMT3L). Repetitive elements did not display differential sensitivity to overexpressed DNMTs, but hypermethylation of Alu elements was associated with their evolutionary age following overexpression of DNMT3A2, DNMT3B1, DNMT3B2 and DNMT3L. Differential methylation (Δβ > 0.1) was observed at 121 of the 353 loci associated with the Horvath ‘epigenetic clock’ model of ageing, with 51 showing isoform specificity, and was associated with reduction of epigenetic age by 5–15 years following overexpression of seven isoforms. Finally, we demonstrate the potential for dietary constituents to modify epigenetic marks through isoform-specific inhibition of methylation activity. Conclusions Our results provide insight into regions of the genome methylated uniquely by specific DNMT isoforms and demonstrate the potential for dietary intervention to modify the epigenome. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01325-4.
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Asada M, Hayashi H, Takagi N. Possible Involvement of DNA Methylation and Protective Effect of Zebularine on Neuronal Cell Death after Glutamate Excitotoxity. Biol Pharm Bull 2022; 45:770-779. [PMID: 35650104 DOI: 10.1248/bpb.b22-00147] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Neuronal cell death after cerebral ischemia consists various steps including glutamate excitotoxity. Excessive Ca2+ influx through the N-methyl-D-aspartate (NMDA) receptor, which is one of the ionotropic glutamate receptors, plays a central role in neuronal cell death after cerebral ischemia. We previously reported that DNA methylation is transiently increased in neurons during ischemic injury and that this aberrant DNA methylation is accompanied by neuronal cell death. Therefore, we performed the present experiments on glutamate excitotoxicity to gain further insight into DNA methylation involvement in the neuronal cell death. We demonstrated that knockdown of DNA methyltransferase (DNMT)1, DNMT3a, or DNMT3b gene in Neuro2a cells was performed to examine which DNMTs were more important for neuronal cell death after glutamate excitotoxicity. Although we confirmed a decrease in the levels of the target DNMT protein after small interfering RNA (siRNA) transfection, the Neuro2a cells were not protected from injury by transfection with siRNA for each DNMT. We next revealed that the pharmacological inhibitor of DNMTs protected against glutamate excitotoxicity in Neuro2a cells and also in primary cultured cortical neurons. This protective effect was associated with a decrease in the number of 5-methylcytosine (5 mC)-positive cells under glutamate excitotoxicity. In addition, the increased level of cleaved caspase-3 was also reduced by a DNMT inhibitor. Our results suggest the possibility that at least 2 or all DNMTs functionally would cooperate to activate DNA methylation after glutamate excitotoxicity and that inhibition of DNA methylation in neurons after cerebral ischemia might become a strategy to reduce the neuronal injury.
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Affiliation(s)
- Mayumi Asada
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences
| | - Hideki Hayashi
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences
| | - Norio Takagi
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences
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Implications of Extended Inhibitory Neuron Development. Int J Mol Sci 2021; 22:ijms22105113. [PMID: 34066025 PMCID: PMC8150951 DOI: 10.3390/ijms22105113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/23/2022] Open
Abstract
A prolonged developmental timeline for GABA (γ-aminobutyric acid)-expressing inhibitory neurons (GABAergic interneurons) is an amplified trait in larger, gyrencephalic animals. In several species, the generation, migration, and maturation of interneurons take place over several months, in some cases persisting after birth. The late integration of GABAergic interneurons occurs in a region-specific pattern, especially during the early postnatal period. These changes can contribute to the formation of functional connectivity and plasticity, especially in the cortical regions responsible for higher cognitive tasks. In this review, we discuss GABAergic interneuron development in the late gestational and postnatal forebrain. We propose the protracted development of interneurons at each stage (neurogenesis, neuronal migration, and network integration), as a mechanism for increased complexity and cognitive flexibility in larger, gyrencephalic brains. This developmental feature of interneurons also provides an avenue for environmental influences to shape neural circuit formation.
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Ou-Yang L, Cai D, Zhang XF, Yan H. WDNE: an integrative graphical model for inferring differential networks from multi-platform gene expression data with missing values. Brief Bioinform 2021; 22:6272792. [PMID: 33975339 DOI: 10.1093/bib/bbab086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/14/2021] [Accepted: 02/23/2021] [Indexed: 11/14/2022] Open
Abstract
The mechanisms controlling biological process, such as the development of disease or cell differentiation, can be investigated by examining changes in the networks of gene dependencies between states in the process. High-throughput experimental methods, like microarray and RNA sequencing, have been widely used to gather gene expression data, which paves the way to infer gene dependencies based on computational methods. However, most differential network analysis methods are designed to deal with fully observed data, but missing values, such as the dropout events in single-cell RNA-sequencing data, are frequent. New methods are needed to take account of these missing values. Moreover, since the changes of gene dependencies may be driven by certain perturbed genes, considering the changes in gene expression levels may promote the identification of gene network rewiring. In this study, a novel weighted differential network estimation (WDNE) model is proposed to handle multi-platform gene expression data with missing values and take account of changes in gene expression levels. Simulation studies demonstrate that WDNE outperforms state-of-the-art differential network estimation methods. When applied WDNE to infer differential gene networks associated with drug resistance in ovarian tumors, cell differentiation and breast tumor heterogeneity, the hub genes in the estimated differential gene networks can provide important insights into the underlying mechanisms. Furthermore, a Matlab toolbox, differential network analysis toolbox, was developed to implement the WDNE model and visualize the estimated differential networks.
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Affiliation(s)
- Le Ou-Yang
- Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen Key Laboratory of Media Security, and Guangdong Laboratory of Artificial Intelligence and Digital Economy(SZ), College of Electronics and Information Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Dehan Cai
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Xiao-Fei Zhang
- School of Mathematics and Statistics & Hubei Key Laboratory of Mathematical Sciences, Central China Normal University, Wuhan, 430079, China
| | - Hong Yan
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong, 999077, China
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Raghuram N, Khan S, Mumal I, Bouffet E, Huang A. Embryonal tumors with multi-layered rosettes: a disease of dysregulated miRNAs. J Neurooncol 2020; 150:63-73. [PMID: 33090313 DOI: 10.1007/s11060-020-03633-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/23/2020] [Indexed: 01/01/2023]
Abstract
INTRODUCTION ETMRs are highly lethal, pediatric embryonal brain tumors, previously classified as various histologic diagnoses including supratentorial primitive neuroectodermal tumors (sPNET) and CNS PNET. With recognition that these tumors harbor recurrent amplification of a novel oncogenic miRNA cluster on chr19, C19MC, ETMRs were designated as a distinct biological and molecular entity with a spectrum of histologic and clinical manifestations. METHODS We reviewed published literature describing clinical presentation, the genetic and epigenetic drivers of oncogenesis, and recent therapeutic strategies adopted to combat these aggressive tumors. RESULTS As a consequence of C19MC amplification, ETMRs upregulate several oncogenic and pluripotency proteins, including LIN28A, DNMT3B and MYCN, that confer a unique epigenetic signature reminiscent of nascent embryonic stem cells. In this review, we focus on the dysregulation of miRNAs in ETMR, the major pathogenic mechanism identified in this disease. CONCLUSION Despite the use of multi-modal therapeutic regimens, ETMR patients have dismal survival. Understanding the unique biology of these tumors has provided new insights towards novel therapeutic targets.
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Affiliation(s)
- Nikhil Raghuram
- Division of Hematology-Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, 555 University Ave, Toronto, ON, M5G1X8, Canada
| | - Sara Khan
- Monash Children's Cancer Centre, Monash Children's Hospital. Monash Health. Center for Cancer Research, Hudson Institute of Medical Research, and Department of Molecular and Translational Science, School of Medicine, Nursing and Health Science, Monash University, Clayton, VIC, 3168, Australia.,Division of Hematology/Oncology, Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, Toronto, ON, M5G0A4, Canada
| | - Iqra Mumal
- Division of Hematology/Oncology, Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, Toronto, ON, M5G0A4, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Eric Bouffet
- Division of Hematology-Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, 555 University Ave, Toronto, ON, M5G1X8, Canada
| | - Annie Huang
- Division of Hematology-Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, 555 University Ave, Toronto, ON, M5G1X8, Canada. .,Division of Hematology/Oncology, Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, Toronto, ON, M5G0A4, Canada. .,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1A8, Canada. .,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, M5G1L7, Canada.
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Asada M, Hayashi H, Murakami K, Kikuiri K, Kaneko R, Yuan B, Takagi N. Investigating the Relationship Between Neuronal Cell Death and Early DNA Methylation After Ischemic Injury. Front Neurosci 2020; 14:581915. [PMID: 33177984 PMCID: PMC7591788 DOI: 10.3389/fnins.2020.581915] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/11/2020] [Indexed: 12/18/2022] Open
Abstract
Cerebral ischemia induces neuronal cell death and causes various kinds of brain dysfunction. Therefore, prevention of neuronal cell death is most essential for protection of the brain. On the other hand, it has been reported that epigenetics including DNA methylation plays a pivotal role in pathogenesis of some diseases such as cancer. Accumulating evidences indicate that aberrant DNA methylation is related to cell death. However, DNA methylation after cerebral ischemia has not been fully understood yet. The aim of this present study was to investigate the relationships between DNA methylation and neuronal cell death after cerebral ischemia. We examined DNA methylation under the ischemic condition by using transient middle cerebral artery occlusion and reperfusion (MCAO/R) model rats and N-methyl-D-aspartate (NMDA)–treated cortical neurons in primary culture. In this study, we demonstrated that DNA methylation increased in these neurons 24 h after MCAO/R and that DNA methylation, possibly through activation of DNA methyltransferases (DNMT) 3a, increased in such neurons immediately after NMDA treatment. Furthermore, NMDA-treated neurons were protected by treatment with a DNMT inhibitor that were accompanied by inhibition of DNA methylation. Our results showed that DNA methylation would be an initiation factor of neuronal cell death and that inhibition of such methylation could become an effective therapeutic strategy for stroke.
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Affiliation(s)
- Mayumi Asada
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Hideki Hayashi
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Kenjiro Murakami
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Kento Kikuiri
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Ryotaro Kaneko
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Bo Yuan
- Laboratory of Pharmacology, Faculty of Pharmacy and Pharmaceutical Sciences, School of Pharmacy, Josai University, Sakado, Japan
| | - Norio Takagi
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
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11
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Fu W, Yue Y, Miao K, Xi G, Zhang C, Wang W, An L, Tian J. Repression of FGF signaling is responsible for Dnmt3b inhibition and impaired de novo DNA methylation during early development of in vitro fertilized embryos. Int J Biol Sci 2020; 16:3085-3099. [PMID: 33061820 PMCID: PMC7545699 DOI: 10.7150/ijbs.51607] [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: 08/06/2020] [Accepted: 09/12/2020] [Indexed: 12/30/2022] Open
Abstract
Well-orchestrated epigenetic modifications during early development are essential for embryonic survival and postnatal growth. Erroneous epigenetic modifications due to environmental perturbations such as manipulation and culture of embryos during in vitro fertilization (IVF) are linked to various short- or long-term consequences. Among these, DNA methylation defects are of great concern. Despite the critical role of DNA methylation in determining embryonic development potential, the mechanisms underlying IVF-associated DNA methylation defects, however, remains largely elusive. We reported herein that repression of fibroblast growth factor (FGF) signaling as the main reason for IVF-associated DNA methylation defects. Comparative methylome analysis by postimplantation stage suggested that IVF mouse embryos undergo impaired de novo DNA methylation during implantation stage. Further analyses indicated that Dnmt3b, the main de novo DNA methyltransferase, was consistently inhibited during the transition from the blastocyst to postimplantation stage (Embryonic day 7.5, E7.5). Using blastocysts and embryonic stem cells (ESCs) as the model, we showed repression of FGF signaling is responsible for Dnmt3b inhibition and global hypomethylation during early development, and MEK/ERK-SP1 pathway plays an essential mediating role in FGF signaling-induced transcriptional activation of Dnmt3b. Supplementation of FGF2, which was exclusively produced in the maternal oviduct, into embryo culture medium significantly rescued Dnmt3b inhibition. Our study, using mouse embryos as the model, not only identifies FGF signaling as the main target for correcting IVF-associated epigenetic errors, but also highlights the importance of oviductal paracrine factors in supporting early embryonic development and improving in vitro culture system.
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Affiliation(s)
- Wei Fu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing 100193, P. R. China
| | - Yuan Yue
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing 100193, P. R. China
| | - Kai Miao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing 100193, P. R. China
| | - Guangyin Xi
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing 100193, P. R. China
| | - Chao Zhang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing 100193, P. R. China
| | - Wenjuan Wang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing 100193, P. R. China
| | - Lei An
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing 100193, P. R. China
| | - Jianhui Tian
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan West Road, Beijing 100193, P. R. China
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12
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Gordon A, Geschwind DH. Human in vitro models for understanding mechanisms of autism spectrum disorder. Mol Autism 2020; 11:26. [PMID: 32299488 PMCID: PMC7164291 DOI: 10.1186/s13229-020-00332-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/01/2020] [Indexed: 02/06/2023] Open
Abstract
Early brain development is a critical epoch for the development of autism spectrum disorder (ASD). In vivo animal models have, until recently, been the principal tool used to study early brain development and the changes occurring in neurodevelopmental disorders such as ASD. In vitro models of brain development represent a significant advance in the field. Here, we review the main methods available to study human brain development in vitro and the applications of these models for studying ASD and other psychiatric disorders. We discuss the main findings from stem cell models to date focusing on cell cycle and proliferation, cell death, cell differentiation and maturation, and neuronal signaling and synaptic stimuli. To be able to generalize the results from these studies, we propose a framework of experimental design and power considerations for using in vitro models to study ASD. These include both technical issues such as reproducibility and power analysis and conceptual issues such as the brain region and cell types being modeled.
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Affiliation(s)
- Aaron Gordon
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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13
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Radhakrishnan S, Trentz OA, Reddy MS, Rela M, Kandasamy M, Sellathamby S. In vitro transdifferentiation of human adipose tissue-derived stem cells to neural lineage cells - a stage-specific incidence. Adipocyte 2019; 8:164-177. [PMID: 31033391 PMCID: PMC6768268 DOI: 10.1080/21623945.2019.1607424] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The present Study investigated the intrinsic ability of adipose tissue-derived stem cells (ADSCs) and their neural transdifferentiation in a stage-specific manner. Woodbury’s Chemical induction was implemented with modifications to achieve neural transdifferentiation. In Group I, ADSCs were preinduced with β-mercaptoethanol (β-ME) and later, with neural induction medium (NIM). In Group II, ADSCs were directly treated with NIM. In Group III, a DNA methyltransferase (DNMT) inhibitor 5-azacytidine was applied to understand whether transdifferentiation is controlled by epigenetic marks. Irrespective of the presence of (β-ME), the differentiation protocol resulted in glial-lineage cells. Group III produced poorly -differentiated neural cells with neuron-specific enolase positivity. A neuroprogenitor stage (NPC) was identified at d 11 after induction only in Group I. In other groups, this stage was not morphologically distinct. We explored the stage-specific incidence NPC, by alternatively treating them with basic fibroblast growth factor (bFGF), and antioxidants to validate if different signalling could cause varied outcomes (Group IV). They differentiated into neurons, as defined by cell polarity and expression of specific proteins. Meanwhile, neuroprogenitors exposed to NIM (Group I) produced glial-lineage cells. Further refinement and study of the occurrence and terminal differentiation of neuroprogenitors would identify a promising source for neural tissue replacement.
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Affiliation(s)
- Subathra Radhakrishnan
- National Foundation for Liver Research (NFLR), Gleneagles Global Health City, Chennai, India
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, India
| | - Omana Anna Trentz
- MIOT Institute of Research (MIR), MIOT International, Chennai, India
| | - Mettu Srinivas Reddy
- National Foundation for Liver Research (NFLR), Gleneagles Global Health City, Chennai, India
- Institute of Liver Disease and Transplantation, Gleneagles Global Health City, Chennai, India
| | - Mohamed Rela
- National Foundation for Liver Research (NFLR), Gleneagles Global Health City, Chennai, India
- Institute of Liver Disease and Transplantation, Gleneagles Global Health City, Chennai, India
| | - Mahesh Kandasamy
- Department of Animal Science, Bharathidasan University, Tiruchirappalli, India
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14
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Wang H, Kuang Y, Li J, Shen R, Sun R, Huang D, Sheng Z, Shi J, Zhang M, Huang F, Yang H, Fei J. Dnmt3a is required for the tumor stemness of B16 melanoma cells. Acta Biochim Biophys Sin (Shanghai) 2019; 51:945-952. [PMID: 31435645 DOI: 10.1093/abbs/gmz081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Indexed: 11/14/2022] Open
Abstract
The relationship of carcinogenesis and DNA methyltransferases has attracted extensive attention in tumor research. We reported previously that inhibition of de novo DNA methyltransferase 3a (Dnmt3a) in murine B16 melanoma cells significantly suppressed tumor growth and metastasis in xenografted mouse model. Here, we further demonstrated that knockdown of Dnmt3a enhanced the proliferation in anchor-independent conditions of B16 cells, but severely disrupted its multipotent differentiation capacity in vitro. Furthermore, transforming growth factor β1, a key trigger in stem cell differentiation and tumor cell epithelial-mesenchymal transition (EMT), mainly induced apoptosis, but not EMT in Dnmt3a-deficient B16 cells. These data suggested that Dnmt3a is required for maintaining the tumor stemness of B16 cells and it assists B16 cells to escape from death during cell differentiation. Thus it is hypothesized that not only extraordinary self-renewal ability, but also the capacity of multipotent differentiation is necessary for the melanoma tumorigenesis. Inhibition of multipotent differentiation of tumor cells may shed light on the tumor treatment.
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Affiliation(s)
- Haoyue Wang
- School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Ying Kuang
- Shanghai Engineering Research Center for Model Organisms, Shanghai Research Center for Model Organisms/Shanghai Model Organisms Center, Inc., Shanghai 201203, China
| | - Jun Li
- Shanghai Engineering Research Center for Model Organisms, Shanghai Research Center for Model Organisms/Shanghai Model Organisms Center, Inc., Shanghai 201203, China
| | - Ruling Shen
- Shanghai Engineering Research Center for Model Organisms, Shanghai Research Center for Model Organisms/Shanghai Model Organisms Center, Inc., Shanghai 201203, China
| | - Ruilin Sun
- Shanghai Engineering Research Center for Model Organisms, Shanghai Research Center for Model Organisms/Shanghai Model Organisms Center, Inc., Shanghai 201203, China
| | - Danyi Huang
- Shanghai Engineering Research Center for Model Organisms, Shanghai Research Center for Model Organisms/Shanghai Model Organisms Center, Inc., Shanghai 201203, China
| | - Zhejin Sheng
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Jiahao Shi
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Mengjie Zhang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Fang Huang
- The State Key Laboratory of Medical Neurobiology, The Institutes of Brain Science and The Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hua Yang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Jian Fei
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Engineering Research Center for Model Organisms, Shanghai Research Center for Model Organisms/Shanghai Model Organisms Center, Inc., Shanghai 201203, China
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15
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de Nijs L, Choe K, Steinbusch H, Schijns OEMG, Dings J, van den Hove DLA, Rutten BPF, Hoogland G. DNA methyltransferase isoforms expression in the temporal lobe of epilepsy patients with a history of febrile seizures. Clin Epigenetics 2019; 11:118. [PMID: 31426844 PMCID: PMC6701147 DOI: 10.1186/s13148-019-0721-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 08/02/2019] [Indexed: 11/10/2022] Open
Abstract
Background Temporal lobe epilepsy (TLE) with hippocampal sclerosis (HS) is a common pharmaco-resistant epilepsy referred for adult epilepsy surgery. Though associated with prolonged febrile seizures (FS) in childhood, the neurobiological basis for this relationship is not fully understood and currently no preventive or curative therapies are available. DNA methylation, an epigenetic mechanism catalyzed by DNA methyltransferases (DNMTs), potentially plays a pivotal role in epileptogenesis associated with FS. In an attempt to start exploring this notion, the present cross-sectional pilot study investigated whether global DNA methylation levels (5-mC and 5-hmC markers) and DNMT isoforms (DNMT1, DNMT3a1, and DNMT3a2) expression would be different in hippocampal and neocortical tissues between controls and TLE patients with or without a history of FS. Results We found that global DNA methylation levels and DNMT3a2 isoform expression were lower in the hippocampus for all TLE groups when compared to control patients, with a more significant decrease amongst the TLE groups with a history of FS. Interestingly, we showed that DNMT3a1 expression was severely diminished in the hippocampus of TLE patients with a history of FS in comparison with control and other TLE groups. In the neocortex, we found a higher expression of DNMT1 and DNMT3a1 as well as increased levels of global DNA methylation for all TLE patients compared to controls. Conclusion Together, the findings of this descriptive cross-sectional pilot study demonstrated brain region-specific changes in DNMT1 and DNMT3a isoform expression as well as global DNA methylation levels in human TLE with or without a history of FS. They highlighted a specific implication of DNMT3a isoforms in TLE after FS. Therefore, longitudinal studies that aim at targeting DNMT3a isoforms to evaluate the potential causal relationship between FS and TLE or treatment of FS-induced epileptogenesis seem warranted. Electronic supplementary material The online version of this article (10.1186/s13148-019-0721-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laurence de Nijs
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands. .,GIGA-Neurosciences, University of Liège, Liège, Belgium.
| | - Kyonghwan Choe
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands
| | - Hellen Steinbusch
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands
| | - Olaf E M G Schijns
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands.,Department of Neurosurgery, Maastricht University Medical Center, Maastricht, The Netherlands.,Academic Center for Epileptology (ACE), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jim Dings
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands.,Department of Neurosurgery, Maastricht University Medical Center, Maastricht, The Netherlands.,Academic Center for Epileptology (ACE), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Daniel L A van den Hove
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands.,Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Bart P F Rutten
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands
| | - Govert Hoogland
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands.,Department of Neurosurgery, Maastricht University Medical Center, Maastricht, The Netherlands.,Academic Center for Epileptology (ACE), Maastricht University Medical Center, Maastricht, The Netherlands
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16
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Khalid M, Abdollahi M. Epigenetic modifications associated with pathophysiological effects of lead exposure. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2019; 37:235-287. [PMID: 31402779 DOI: 10.1080/10590501.2019.1640581] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lead (Pb) exposure during different stages of development has demonstrated dose, duration, sex, and tissue-specific pathophysiological outcomes due to altered epigenetic regulation via (a) DNA methylation, (b) histone modifications, (c) miRNAs, and (d) chromatin accessibility. Pb-induced alteration of epigenetic regulation causes neurotoxic and extra-neurotoxic pathophysiological outcomes. Neurotoxic effects of Pb include dysfunction of memory and learning, behavioral disorder, attention deficit hyperactivity disorder, autism spectrum disorder, aging, Alzheimer's disease, tauopathy, and neurodegeneration. Extra-neurotoxic effects of Pb include altered body weight, metabolic disorder, cardiovascular disorders, hematopoietic disorder, and reproductive impairment. Pb exposure either early in life or at any stage of development results in undesirable pathophysiological outcomes that tends to sustain and maintain for a lifetime.
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Affiliation(s)
- Madiha Khalid
- Toxicology and Diseases Group, Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Mohammad Abdollahi
- Toxicology and Diseases Group, Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences (TUMS), Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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17
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Seelan RS, Pisano M, Greene RM. Nucleic acid methylation and orofacial morphogenesis. Birth Defects Res 2019; 111:1593-1610. [PMID: 31385455 DOI: 10.1002/bdr2.1564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022]
Abstract
In this review, we highlight the current state of knowledge of the diverse roles nucleic acid methylation plays in the embryonic development of the orofacial region and how aberrant methylation may contribute to orofacial clefts. We also consider the role of methylation in the regulation of neural crest cell function as it pertains to orofacial ontogeny. Changes in DNA methylation, as a consequence of environmental effects, have been observed in the regulatory regions of several genes, potentially identifying new candidate genes for orofacial clefting and opening promising new avenues for further research. While the focus of this review is primarily on the nonsyndromic forms of orofacial clefting, syndromic forms are briefly discussed in the context of aberrant nucleic acid methylation.
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Affiliation(s)
- Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
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18
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Amberg N, Laukoter S, Hippenmeyer S. Epigenetic cues modulating the generation of cell-type diversity in the cerebral cortex. J Neurochem 2019; 149:12-26. [PMID: 30276807 PMCID: PMC6587822 DOI: 10.1111/jnc.14601] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 09/13/2018] [Accepted: 09/26/2018] [Indexed: 12/29/2022]
Abstract
The cerebral cortex is composed of a large variety of distinct cell-types including projection neurons, interneurons, and glial cells which emerge from distinct neural stem cell lineages. The vast majority of cortical projection neurons and certain classes of glial cells are generated by radial glial progenitor cells in a highly orchestrated manner. Recent studies employing single cell analysis and clonal lineage tracing suggest that neural stem cell and radial glial progenitor lineage progression are regulated in a profound deterministic manner. In this review we focus on recent advances based mainly on correlative phenotypic data emerging from functional genetic studies in mice. We establish hypotheses to test in future research and outline a conceptual framework how epigenetic cues modulate the generation of cell-type diversity during cortical development.
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Affiliation(s)
- Nicole Amberg
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Susanne Laukoter
- Institute of Science and Technology AustriaKlosterneuburgAustria
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19
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Gasiūnienė M, Zentelytė A, Treigytė G, Baronaitė S, Savickienė J, Utkus A, Navakauskienė R. Epigenetic alterations in amniotic fluid mesenchymal stem cells derived from normal and fetus-affected gestations: A focus on myogenic and neural differentiations. Cell Biol Int 2019; 43:299-312. [PMID: 30635962 DOI: 10.1002/cbin.11099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/05/2019] [Indexed: 12/21/2022]
Abstract
Amniotic fluid-derived mesenchymal stem cells (AF-MSCs) are autologous to the fetus and represent a potential alternative source for the regenerative medicine and treatment of perinatal disorders. To date, AF-MSCs differentiation capacity to non-mesodermal lineages and epigenetic regulation are still poorly characterized. The present study investigated the differentiation potential of AF-MSCs toward neural-like cells in comparison to the mesodermal myogenic lineage and assessed epigenetic factors involved in tissue-specific differentiation. Myogenic and neural differentiation assays were performed by the incubation with specific induction media. Typical MSCs markers were determined by flow cytometry, the expression of lineage-specific genes, microRNAs and chromatin modifying proteins were examined by RT-qPCR and Western blot, respectively. AF-MSCs of normal and fetus-affected gestations had similar stem cells characteristics and two-lineage potential, as characterized by cell morphology and the expression of myogenic and neural markers. Two-lineage differentiation process was associated with the down-regulation of miR-17 and miR-21, the up-regulation of miR-34a, miR-146a and DNMT3a/DNMT3b along with the gradual decrease in the levels of DNMT1, HDAC1, active marks of chromatin (H4hyperAc, H3K9ac, H3K4me3) and the repressive H3K9me3 mark. Differentiation was accompanied by the down-regulation of PRC1/2 proteins (BMI1/SUZ12, EZH2) and the retention of the repressive H3K27me3 mark. We report that both AF-MSCs of normal and fetus-affected gestations possess differentiation capacity toward myogenic and neural lineages through rather similar epigenetic mechanisms that may provide potential applications for further investigation of the molecular basis of prenatal diseases and for the future autologous therapy.
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Affiliation(s)
- Monika Gasiūnienė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, Vilnius, LT-10257, Lithuania
| | - Aistė Zentelytė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, Vilnius, LT-10257, Lithuania
| | - Gražina Treigytė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, Vilnius, LT-10257, Lithuania
| | - Sandra Baronaitė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, Vilnius, LT-10257, Lithuania
| | - Jūratė Savickienė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, Vilnius, LT-10257, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, M. K. Ciurlionio st. 21, Vilnius, LT-03101, Lithuania
| | - Rūta Navakauskienė
- Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, Vilnius, LT-10257, Lithuania
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20
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Ramírez Martínez L, Vargas Mejía M, Espadamala J, Gomez N, Lizcano JM, López-Bayghen E. Neuronal Growth Factor regulates Brain Specific Kinase 1 expression by inhibiting promoter methylation and promoting Sp1 recruitment. Neurochem Int 2018; 120:213-223. [PMID: 30196145 DOI: 10.1016/j.neuint.2018.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/28/2018] [Accepted: 08/31/2018] [Indexed: 11/16/2022]
Abstract
Brain specific kinases (BRSKs) are serine/threonine kinases, preferentially expressed in the brain after Embryonic Day 12. Although BRSKs are crucial neuronal development factors and regulation of their enzymatic activity has been widely explored, little is known of their transcriptional regulation. In this work, we show that Neuronal Growth Factor (NGF) increased the expression of Brsk1 in PC12 cells. Furthermore, during neuronal differentiation, Brsk1 mRNA increased through a MAPK-dependent Sp1 activation. To gain further insight into this regulation, we analyzed the transcriptional activity of the Brsk1 promoter in PC12 cells treated with NGF. Initially, we defined the minimal promoter region (-342 to +125 bp) responsive to NGF treatment. This region had multiple Sp1 binding sites, one of which was within a CpG island. In vitro binding assays showed that NGF-induced differentiation increased Sp1 binding to this site and that DNA methylation inhibited Sp1 binding. In vitro methylation of the Brsk1 promoter reduced its transcriptional activity and impaired the NGF effect. To evaluate the participation of DNA methyltransferases in Brsk1 gene regulation, the 5'Aza-dC inhibitor was used. 5'Aza-dC acted synergistically with NGF to promote Brsk1 promoter activity. Accordingly, DNMT3B overexpression abolished the response of the Brsk1 promoter to NGF. Surprisingly, we found Dnmt3b to be a direct target of NGF regulation, via the MAPK pathway. In conclusion, our results provide evidence of a novel mechanism of Brsk1 transcriptional regulation changing the promoter's methylation status, which was incited by the NGF-induced neuronal differentiation process.
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Affiliation(s)
- Leticia Ramírez Martínez
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México, 07360, Mexico; Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México, 07360, Mexico
| | - Miguel Vargas Mejía
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México, 07360, Mexico
| | - Josep Espadamala
- Institut de Neurociencies i Departament de Bioquímica i Biología Molecular, Facultat de Medicina, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Néstor Gomez
- Institut de Neurociencies i Departament de Bioquímica i Biología Molecular, Facultat de Medicina, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - José M Lizcano
- Institut de Neurociencies i Departament de Bioquímica i Biología Molecular, Facultat de Medicina, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Esther López-Bayghen
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 14-740, Ciudad de México, 07360, Mexico.
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21
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Lu YL, Yoo AS. Mechanistic Insights Into MicroRNA-Induced Neuronal Reprogramming of Human Adult Fibroblasts. Front Neurosci 2018; 12:522. [PMID: 30116172 PMCID: PMC6083049 DOI: 10.3389/fnins.2018.00522] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/12/2018] [Indexed: 12/16/2022] Open
Abstract
The use of transcriptional factors as cell fate regulators are often the primary focus in the direct reprogramming of somatic cells into neurons. However, in human adult fibroblasts, deriving functionally mature neurons with high efficiency requires additional neurogenic factors such as microRNAs (miRNAs) to evoke a neuronal state permissive to transcription factors to exert their reprogramming activities. As such, increasing evidence suggests brain-enriched miRNAs, miR-9/9∗ and miR-124, as potent neurogenic molecules through simultaneously targeting of anti-neurogenic effectors while allowing additional transcription factors to generate specific subtypes of human neurons. In this review, we will focus on methods that utilize neuronal miRNAs and provide mechanistic insights by which neuronal miRNAs, in synergism with brain-region specific transcription factors, drive the conversion of human fibroblasts into clinically relevant subtypes of neurons. Furthermore, we will provide insights into the age signature of directly converted neurons and how the converted human neurons can be utilized to model late-onset neurodegenerative disorders.
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Affiliation(s)
- Ya-Lin Lu
- Department of Developmental Biology, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States.,Program in Developmental, Regenerative and Stem Cell Biology, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Andrew S Yoo
- Department of Developmental Biology, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States
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22
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Grayson DR, Guidotti A. DNA Methylation in Animal Models of Psychosis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:105-132. [PMID: 29933947 DOI: 10.1016/bs.pmbts.2017.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Schizophrenia (SZ) is a debilitating disease that impacts 1% of the population worldwide. Association studies have shown that inherited genetic mutations account for a portion of disease risk. However, environmental factors play an important role in the pathophysiology of the disease by altering cellular epigenetic marks at the level of chromatin. Postmortem brain studies of SZ subjects suggest that the dynamic equilibrium between DNA methylation and demethylation network components is disrupted at the level of individual SZ target genes. Herein, we review the role of DNA methylation and demethylation in the context of what is currently known regarding SZ. Furthermore, we describe the deficits that accompany two mouse models of SZ. The chronic methionine mouse model of SZ is predicated on the administration of methionine to SZ patients and controls in the context of clinical studies that were carried out during the 1960s and 1970s. The prenatal restraint stress model of SZ is based on a prolonged stress paradigm administered to pregnant dams during gestation days 7-21. The adult offspring of these dams show various behavioral and biochemical deficits in adulthood. Both models are epigenetic in origin and mimic the positive and negative symptoms, as well as the cognitive endophenotypes commonly observed in SZ patients. We also discuss the utility of typical and atypical antipsychotic drugs in alleviating these symptoms in each model.
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Affiliation(s)
- Dennis R Grayson
- Center for Alcohol Research in Epigenetics, University of Illinois, Chicago, IL, United States.
| | - Alessandro Guidotti
- Center for Alcohol Research in Epigenetics, University of Illinois, Chicago, IL, United States
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23
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Ji S, Ding X, Ji J, Wu H, Sun R, Li X, Zhang L, Tian Y. Cranial irradiation inhibits hippocampal neurogenesis via DNMT1 and DNMT3A. Oncol Lett 2018; 15:2899-2904. [PMID: 29435016 PMCID: PMC5778827 DOI: 10.3892/ol.2017.7643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 11/16/2017] [Indexed: 02/07/2023] Open
Abstract
Impairment of neurogenesis in the hippocampus following whole-brain irradiation is the most important mechanism of radiation-induced cognitive dysfunction. However, the underlying mechanism remains obscure, meaning an ideal therapeutic target has not been identified. Evidence indicates that DNA methylation in neurons regulates synaptic plasticity and neuronal network activity. In the present study, the expression of DNA methyltransferases (DNMTs) in the hippocampus was analyzed to investigate their potential function in radiation-induced neurogenesis impairment. Sprague-Dawley rats were used throughout the present study, apportioned to the following groups: Control, radiation only, zebularine (a DNMT inhibitor) only, and radiation and zebularine together. Immunofluorescence staining revealed that radiation inhibited cellular proliferation and dendritic growth within new neurons of the hippocampus. In addition, western blot analysis demonstrated lower expression levels of DNMT1 and DNMT3A protein following radiation treatment compared with that in the non-irradiated control. Furthermore, compared with the radiation-only group, the radiation and zebularine group had significantly lower cell proliferative abilities, dendritic growth, and DNMT1 and DNMT3A protein levels. The results of the present study indicated that DNMT1 and DNMT3A may be involved in the pathogenesis of whole-brain radiation-induced neurogenesis impairment.
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Affiliation(s)
- Shengjun Ji
- Cancer Center, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu 215001, P.R. China
| | - Xin Ding
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Jiang Ji
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Haohao Wu
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Rui Sun
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Xiaoyang Li
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Liyuan Zhang
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
| | - Ye Tian
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China
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24
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Nagalakshmi B., Sagarkar S, Sakharkar AJ. Epigenetic Mechanisms of Traumatic Brain Injuries. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:263-298. [DOI: 10.1016/bs.pmbts.2017.12.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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25
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Gao J, Cahill CM, Huang X, Roffman JL, Lamon-Fava S, Fava M, Mischoulon D, Rogers JT. S-Adenosyl Methionine and Transmethylation Pathways in Neuropsychiatric Diseases Throughout Life. Neurotherapeutics 2018; 15:156-175. [PMID: 29340929 PMCID: PMC5794704 DOI: 10.1007/s13311-017-0593-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
S-Adenosyl methionine (SAMe), as a major methyl donor, exerts its influence on central nervous system function through cellular transmethylation pathways, including the methylation of DNA, histones, protein phosphatase 2A, and several catecholamine moieties. Based on available evidence, this review focuses on the lifelong range of severe neuropsychiatric and neurodegenerative diseases and their associated neuropathologies, which have been linked to the deficiency/load of SAMe production or/and the disturbance in transmethylation pathways. Also included in this review are the present-day applications of SAMe in the treatment in these diseases in each age group.
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Affiliation(s)
- Jin Gao
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Clinical Psychology, Qilu Hospital of Shandong University, Qingdao, Shandong Province, China
| | - Catherine M Cahill
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Xudong Huang
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Joshua L Roffman
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stefania Lamon-Fava
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| | - Maurizio Fava
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David Mischoulon
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jack T Rogers
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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26
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Torroglosa A, Villalba-Benito L, Fernández RM, Moya-Jiménez MJ, Antiñolo G, Borrego S. Dnmt3b knock-down in enteric precursors reveals a possible mechanism by which this de novo methyltransferase is involved in the enteric nervous system development and the onset of Hirschsprung disease. Oncotarget 2017; 8:106443-106453. [PMID: 29290961 PMCID: PMC5739746 DOI: 10.18632/oncotarget.22473] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/27/2017] [Indexed: 12/30/2022] Open
Abstract
Hirschsprung disease (HSCR, OMIM 142623) is a pathology that shows a lack of enteric ganglia along of the distal gastrointestinal tract. This aganglionosis is attributed to an abnormal proliferation, migration, differentiation and/or survival of enteric precursor cells (EPCs) derived from neural crest cells (NCCs) during the enteric nervous system (ENS) embryogenesis. DNMT3b de novo methyltransferase is associated with NCCs development and has been shown to be implicated in ENS formation as well as in HSCR. In this study we have aimed to elucidate the specific mechanism underlying the DNMT3b role in such processes. We have performed the knockdown of Dnmt3b expression (Dnmt3b-KD) in enteric precursor cells (EPCs) to clarify its role on these cells in vitro. Moreover, we have analyzed several signaling pathways to determine the mechanisms responsible for the effect caused by Dnmt3b-KD in EPCs. Our results seem to support that Dnmt3b-KD promotes an increase EPCs proliferation that may be mediated by P53 and P21 activity, since both proteins were observed to be down-regulated in our Dnmt3b-KD cultures. Moreover, we observed a down-regulation of P53 and P21 in HSCR patients. These results lead us to propose that DNMT3b could be involved in HSCR through P53 and P21 activity.
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Affiliation(s)
- Ana Torroglosa
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío, CSIC, University of Seville, Seville 41013, Spain.,Center for Biomedical Network Research on Rare Diseases, Seville 41013, Spain
| | - Leticia Villalba-Benito
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío, CSIC, University of Seville, Seville 41013, Spain.,Center for Biomedical Network Research on Rare Diseases, Seville 41013, Spain
| | - Raquel María Fernández
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío, CSIC, University of Seville, Seville 41013, Spain.,Center for Biomedical Network Research on Rare Diseases, Seville 41013, Spain
| | | | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío, CSIC, University of Seville, Seville 41013, Spain.,Center for Biomedical Network Research on Rare Diseases, Seville 41013, Spain
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío, CSIC, University of Seville, Seville 41013, Spain.,Center for Biomedical Network Research on Rare Diseases, Seville 41013, Spain
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27
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Mateen BA, Hill CS, Biddie SC, Menon DK. DNA Methylation: Basic Biology and Application to Traumatic Brain Injury. J Neurotrauma 2017; 34:2379-2388. [DOI: 10.1089/neu.2017.5007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Bilal A. Mateen
- Division of Medicine, University College London, London, United Kingdom
| | - Ciaran S. Hill
- John van Geest Centre for Brain Repair, School of Clinical Medicine, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Simon C. Biddie
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - David K. Menon
- John van Geest Centre for Brain Repair, School of Clinical Medicine, Addenbrookes Hospital, Cambridge, United Kingdom
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
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28
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Ludwig AK, Zhang P, Hastert FD, Meyer S, Rausch C, Herce HD, Müller U, Lehmkuhl A, Hellmann I, Trummer C, Storm C, Leonhardt H, Cardoso MC. Binding of MBD proteins to DNA blocks Tet1 function thereby modulating transcriptional noise. Nucleic Acids Res 2017; 45:2438-2457. [PMID: 27923996 PMCID: PMC5389475 DOI: 10.1093/nar/gkw1197] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/20/2016] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is a hallmark of various human disorders, indicating that the spatial and temporal regulation of methylation readers and modifiers is imperative for development and differentiation. In particular, the cross-regulation between 5-methylcytosine binders (MBD) and modifiers (Tet) has not been investigated. Here, we show that binding of Mecp2 and Mbd2 to DNA protects 5-methylcytosine from Tet1-mediated oxidation. The mechanism is not based on competition for 5-methylcytosine binding but on Mecp2 and Mbd2 directly restricting Tet1 access to DNA. We demonstrate that the efficiency of this process depends on the number of bound MBDs per DNA molecule. Accordingly, we find 5-hydroxymethylcytosine enriched at heterochromatin of Mecp2-deficient neurons of a mouse model for Rett syndrome and Tet1-induced reexpression of silenced major satellite repeats. These data unveil fundamental regulatory mechanisms of Tet enzymes and their potential pathophysiological role in Rett syndrome. Importantly, it suggests that Mecp2 and Mbd2 have an essential physiological role as guardians of the epigenome.
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Affiliation(s)
- Anne K Ludwig
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Florian D Hastert
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Stephanie Meyer
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Henry D Herce
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Udo Müller
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Carina Trummer
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Christian Storm
- Chemical Plant Ecology, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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29
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Villalba-Benito L, Torroglosa A, Fernández RM, Ruíz-Ferrer M, Moya-Jiménez MJ, Antiñolo G, Borrego S. Overexpression of DNMT3b target genes during Enteric Nervous System development contribute to the onset of Hirschsprung disease. Sci Rep 2017; 7:6221. [PMID: 28740121 PMCID: PMC5524929 DOI: 10.1038/s41598-017-06539-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/09/2017] [Indexed: 12/27/2022] Open
Abstract
Hirschsprung disease (HSCR) is attributed to a failure of neural crest cells (NCCs) to migrate, proliferate, differentiate and/or survive in the bowel wall during embryonic Enteric Nervous System (ENS) development. ENS formation is the result from a specific gene expression pattern regulated by epigenetic events, such DNA methylation by the DNA methyltransferases (DNMTs), among other mechanisms. Specifically, DNMT3b de novo methyltransferase is associated with NCCs development and has been shown to be implicated in ENS formation and in HSCR. Aiming to elucidate the specific mechanism underlying the DNMT3b role in such processes, we have performed a chromatin immunoprecipitation coupled with massively parallel sequencing analysis to identify the DNMT3B target genes in enteric precursor cells (EPCs) from mice. Moreover, the expression patterns of those target genes have been analyzed in human EPCs from HSCR patients in comparison with controls. Additionally, we have carried out a search of rare variants in those genes in a HSCR series. Through this approach we found 9 genes showing a significantly different expression level in both groups. Therefore, those genes may have a role in the proper human ENS formation and a failure in their expression pattern might contribute to this pathology.
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Affiliation(s)
- Leticia Villalba-Benito
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - Ana Torroglosa
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - Raquel María Fernández
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - Macarena Ruíz-Ferrer
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - María José Moya-Jiménez
- Department of Pediatric Surgery, University Hospital Virgen del Rocío, Seville, 41013, Spain
| | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain.
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain.
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30
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Singh RK, Mallela RK, Hayes A, Dunham NR, Hedden ME, Enke RA, Fariss RN, Sternberg H, West MD, Nasonkin IO. Dnmt1, Dnmt3a and Dnmt3b cooperate in photoreceptor and outer plexiform layer development in the mammalian retina. Exp Eye Res 2017; 159:132-146. [PMID: 27865785 DOI: 10.1016/j.exer.2016.11.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 10/21/2016] [Accepted: 11/14/2016] [Indexed: 11/18/2022]
Abstract
Characterizing the role of epigenetic regulation in the mammalian retina is critical for understanding fundamental mechanisms of retinal development and disease. DNA methylation, an epigenetic modifier of genomic DNA, plays an important role in modulating networks of tissue and cell-specific gene expression. However, the impact of DNA methylation on retinal development and homeostasis of retinal neurons remains unclear. Here, we have created a tissue-specific DNA methyltransferase (Dnmt) triple mutant mouse in an effort to characterize the impact of DNA methylation on retinal development and homeostasis. An Rx-Cre transgene was used to drive targeted mutation of all three murine Dnmt genes in the mouse retina encoding major DNA methylation enzymes DNMT1, DNMT3A and DNMT3B. The triple mutant mice represent a hypomorph model since Dnmt1 catalytic activity was still present and excision of Dnmt3a and Dnmt3b had only about 90% efficiency. Mutation of all three Dnmts resulted in global genomic hypomethylation and dramatic reorganization of the photoreceptor and synaptic layers within retina. Transcriptome and proteomic analyses demonstrated enrichment of dysregulated phototransduction and synaptic genes. The 5 mC signal in triple mutant retina was confined to the central heterochromatin but reduced in the peripheral heterochromatin region of photoreceptor nuclei. In addition, we found a reduction of the 5 mC signal in ganglion cell nuclei. Collectively, this data suggests cooperation of all three Dnmts in the formation and homeostasis of photoreceptors and other retinal neurons within the mammalian retina, and highlight the relevance of epigenetic regulation to sensory retinal disorders and vision loss.
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Affiliation(s)
- Ratnesh K Singh
- Department of Ophthalmology, University of Pittsburgh Medical School, USA.
| | - Ramya K Mallela
- Department of Ophthalmology, University of Pittsburgh Medical School, USA
| | - Abigail Hayes
- Department of Ophthalmology, West Virginia University, USA
| | | | | | - Raymond A Enke
- Department of Biology, James Madison University, USA; Center for Genome and Metagenome Studies, James Madison University, USA
| | - Robert N Fariss
- Biological Imaging Core, National Eye Institute, Bethesda, MD 20892, USA
| | - Hal Sternberg
- BioTime, 1010 Atlantic Avenue, Alameda, CA 94501, USA
| | | | - Igor O Nasonkin
- Department of Ophthalmology, University of Pittsburgh Medical School, USA.
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31
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Bayraktar G, Kreutz MR. Neuronal DNA Methyltransferases: Epigenetic Mediators between Synaptic Activity and Gene Expression? Neuroscientist 2017; 24:171-185. [PMID: 28513272 PMCID: PMC5846851 DOI: 10.1177/1073858417707457] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
DNMT3A and 3B are the main de novo DNA methyltransferases (DNMTs) in the brain that introduce new methylation marks to non-methylated DNA in postmitotic neurons. DNA methylation is a key epigenetic mark that is known to regulate important cellular processes in neuronal development and brain plasticity. Accumulating evidence disclosed rapid and dynamic changes in DNA methylation of plasticity-relevant genes that are important for learning and memory formation. To understand how DNMTs contribute to brain function and how they are regulated by neuronal activity is a prerequisite for a deeper appreciation of activity-dependent gene expression in health and disease. This review discusses the functional role of de novo methyltransferases and in particular DNMT3A1 in the adult brain with special emphasis on synaptic plasticity, memory formation, and brain disorders.
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Affiliation(s)
- Gonca Bayraktar
- 1 RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Michael R Kreutz
- 1 RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,2 Leibniz Group "Dendritic Organelles and Synaptic Function", ZMNH, Magdeburg, Germany
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32
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Tarusawa E, Sanbo M, Okayama A, Miyashita T, Kitsukawa T, Hirayama T, Hirabayashi T, Hasegawa S, Kaneko R, Toyoda S, Kobayashi T, Kato-Itoh M, Nakauchi H, Hirabayashi M, Yagi T, Yoshimura Y. Establishment of high reciprocal connectivity between clonal cortical neurons is regulated by the Dnmt3b DNA methyltransferase and clustered protocadherins. BMC Biol 2016; 14:103. [PMID: 27912755 PMCID: PMC5133762 DOI: 10.1186/s12915-016-0326-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/09/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The specificity of synaptic connections is fundamental for proper neural circuit function. Specific neuronal connections that underlie information processing in the sensory cortex are initially established without sensory experiences to a considerable extent, and then the connections are individually refined through sensory experiences. Excitatory neurons arising from the same single progenitor cell are preferentially connected in the postnatal cortex, suggesting that cell lineage contributes to the initial wiring of neurons. However, the postnatal developmental process of lineage-dependent connection specificity is not known, nor how clonal neurons, which are derived from the same neural stem cell, are stamped with the identity of their common neural stem cell and guided to form synaptic connections. RESULTS We show that cortical excitatory neurons that arise from the same neural stem cell and reside within the same layer preferentially establish reciprocal synaptic connections in the mouse barrel cortex. We observed a transient increase in synaptic connections between clonal but not nonclonal neuron pairs during postnatal development, followed by selective stabilization of the reciprocal connections between clonal neuron pairs. Furthermore, we demonstrate that selective stabilization of the reciprocal connections between clonal neuron pairs is impaired by the deficiency of DNA methyltransferase 3b (Dnmt3b), which determines DNA-methylation patterns of genes in stem cells during early corticogenesis. Dnmt3b regulates the postnatal expression of clustered protocadherin (cPcdh) isoforms, a family of adhesion molecules. We found that cPcdh deficiency in clonal neuron pairs impairs the whole process of the formation and stabilization of connections to establish lineage-specific connection reciprocity. CONCLUSIONS Our results demonstrate that local, reciprocal neural connections are selectively formed and retained between clonal neurons in layer 4 of the barrel cortex during postnatal development, and that Dnmt3b and cPcdhs are required for the establishment of lineage-specific reciprocal connections. These findings indicate that lineage-specific connection reciprocity is predetermined by Dnmt3b during embryonic development, and that the cPcdhs contribute to postnatal cortical neuron identification to guide lineage-dependent synaptic connections in the neocortex.
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Affiliation(s)
- Etsuko Tarusawa
- Section of Visual Information Processing, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585 Japan
- AMED-CREST, AMED, 1-3 Yamadaoka, Suita, 565-0871 Osaka Japan
| | - Makoto Sanbo
- National Institute for Physiological Sciences, Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, Okazaki, Aichi 444-8787 Japan
| | - Atsushi Okayama
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Toshio Miyashita
- Section of Visual Information Processing, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585 Japan
| | - Takashi Kitsukawa
- AMED-CREST, AMED, 1-3 Yamadaoka, Suita, 565-0871 Osaka Japan
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Teruyoshi Hirayama
- AMED-CREST, AMED, 1-3 Yamadaoka, Suita, 565-0871 Osaka Japan
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Takahiro Hirabayashi
- AMED-CREST, AMED, 1-3 Yamadaoka, Suita, 565-0871 Osaka Japan
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Sonoko Hasegawa
- AMED-CREST, AMED, 1-3 Yamadaoka, Suita, 565-0871 Osaka Japan
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Ryosuke Kaneko
- Bioresource Center, Gunma University Graduate School of Medicine, Maebashi, 371-8511 Japan
| | - Shunsuke Toyoda
- AMED-CREST, AMED, 1-3 Yamadaoka, Suita, 565-0871 Osaka Japan
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Toshihiro Kobayashi
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639 Japan
| | - Megumi Kato-Itoh
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639 Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639 Japan
- Department of Genetics, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, 291 Campus Drive, Li Ka Shing Building, Stanford, CA 94305-5101 USA
| | - Masumi Hirabayashi
- AMED-CREST, AMED, 1-3 Yamadaoka, Suita, 565-0871 Osaka Japan
- National Institute for Physiological Sciences, Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, Okazaki, Aichi 444-8787 Japan
- Department of Physiological Sciences, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8585 Japan
| | - Takeshi Yagi
- AMED-CREST, AMED, 1-3 Yamadaoka, Suita, 565-0871 Osaka Japan
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Yumiko Yoshimura
- Section of Visual Information Processing, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585 Japan
- Department of Physiological Sciences, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8585 Japan
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33
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Zhang YY, Tang LL, Zheng B, Ge RS, Zhu DY. Protein profiles of cardiomyocyte differentiation in murine embryonic stem cells exposed to perfluorooctane sulfonate. J Appl Toxicol 2016; 36:726-40. [PMID: 26178269 DOI: 10.1002/jat.3207] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 06/03/2015] [Accepted: 06/03/2015] [Indexed: 12/30/2022]
Abstract
Perfluorooctane sulfonate (PFOS) is a persistent organic contaminant that may affect diverse systems in animals and humans, including the cardiovascular system. However, little is known about the mechanism by which it affects the biological systems. Herein, we used embryonic stem cell test procedure as a tool to assess the developmental cardiotoxicity of PFOS. The differentially expressed proteins were identified by quantitative proteomics that combines the stable isotope labeling of amino acids with high-performance liquid chromatography-electrospray ionization tandem mass spectrometry. Results of the embryonic stem cell test procedure suggested that PFOS was a weak embryotoxic chemical. Nevertheless, a few marker proteins related to cardiovascular development (Brachyury, GATA4, MEF2C, α-actinin) were significantly reduced by exposure to PFOS. In total, 176 differential proteins were identified by proteomics analysis, of which 67 were upregulated and 109 were downregulated. Gene ontology annotation classified these proteins into 13 groups by molecular functions, 12 groups by cellular locations and 10 groups by biological processes. Most proteins were mainly relevant to either catalytic activity (25.6%), nucleus localization (28.9%) or to cellular component organization (19.8%). Pathway analysis revealed that 32 signaling pathways were affected, particularly these involved in metabolism. Changes in five proteins, including L-threonine dehydrogenase, X-ray repair cross-complementing 5, superoxide dismutase 2, and DNA methyltransferase 3b and 3a were confirmed by Western blotting, suggesting the reliability of the technique. These results revealed potential new targets of PFOS on the developmental cardiovascular system.
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Affiliation(s)
- Ying-Ying Zhang
- Institute of Pharmacology, Toxicology, and Biochemical Pharmaceutics, Zhejiang University, Hangzhou, China
| | - Lei-Lei Tang
- Institute of Pharmacology, Toxicology, and Biochemical Pharmaceutics, Zhejiang University, Hangzhou, China
| | - Bei Zheng
- Institute of Pharmacology, Toxicology, and Biochemical Pharmaceutics, Zhejiang University, Hangzhou, China
| | - Ren-Shan Ge
- Institute of Reproductive Biomedicine and the 2nd Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dan-Yan Zhu
- Institute of Pharmacology, Toxicology, and Biochemical Pharmaceutics, Zhejiang University, Hangzhou, China
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Kennedy BE, Hundert AS, Goguen D, Weaver ICG, Karten B. Presymptomatic Alterations in Amino Acid Metabolism and DNA Methylation in the Cerebellum of a Murine Model of Niemann-Pick Type C Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:1582-97. [PMID: 27083515 DOI: 10.1016/j.ajpath.2016.02.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 02/08/2016] [Accepted: 02/16/2016] [Indexed: 10/21/2022]
Abstract
The fatal neurodegenerative disorder Niemann-Pick type C (NPC) is caused in most cases by mutations in NPC1, which encodes the late endosomal NPC1 protein. Loss of NPC1 disrupts cholesterol trafficking from late endosomes to the endoplasmic reticulum and plasma membrane, causing cholesterol accumulation in late endosomes/lysosomes. Neurons are particularly vulnerable to this cholesterol trafficking defect, but the pathogenic mechanisms through which NPC1 deficiency causes neuronal dysfunction remain largely unknown. Herein, we have investigated amino acid metabolism in cerebella of NPC1-deficient mice at different stages of NPC disease. Imbalances in amino acid metabolism were evident from increased branched chain amino acid and asparagine levels and altered expression of key enzymes of glutamine/glutamate metabolism in presymptomatic and early symptomatic NPC1-deficient cerebellum. Increased levels of several amino acid intermediates of one-carbon metabolism indicated disturbances in folate and methylation pathways. Alterations in DNA methylation were apparent in decreased expression of DNA methyltransferase 3a and methyl-5'-cytosine-phosphodiester-guanine-domain binding proteins, reduced 5-methylcytosine immunoreactivity in the molecular and Purkinje cell layers, demethylation of genome-wide repetitive LINE-1 elements, and hypermethylation in specific promoter regions of single-copy genes in NPC1-deficient cerebellum at early stages of the disease. Alterations in amino acid metabolism and epigenetic changes in the cerebellum at presymptomatic stages of NPC disease represent previously unrecognized mechanisms of NPC pathogenesis.
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Affiliation(s)
- Barry E Kennedy
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Amos S Hundert
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Donna Goguen
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ian C G Weaver
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Barbara Karten
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
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Bailey ZS, Grinter MB, De La Torre Campos D, VandeVord PJ. Blast induced neurotrauma causes overpressure dependent changes to the DNA methylation equilibrium. Neurosci Lett 2015; 604:119-23. [PMID: 26232681 DOI: 10.1016/j.neulet.2015.07.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/14/2015] [Accepted: 07/26/2015] [Indexed: 01/01/2023]
Abstract
Traumatic brain injury (TBI) has a high prevalence in our society and often leads to morbidity and mortality. TBI also occurs frequently in a military setting where exposure to blast waves is common. Abnormal gene expression involved with oxidative stress, inflammation and neuronal apoptosis has been well documented following blast induced neurotrauma (BINT). Altered epigenetic transcriptional regulation through DNA methylation has been implicated in the pathology of the injury. Imbalance between DNA methylation and DNA demethylation may lead to altered methylation patterns and subsequent changes in gene transcription. DNA methyltransferase enzymes (DNMT1, DNMT3a, and DNMT3b) are responsible for the addition of methyl groups to DNA, DNA methylation. Whereas the combined function of ten-eleven translocation enzymes (TET1, TET2, and TET3) and thymine-DNA glycosylase (TDG) result in the removal of methyl groups from DNA, DNA demethylation. We used an established rodent model of BINT to assess changes in DNA methylation and demethylation enzymes following injury. Three different blast overpressures were investigated (10, 17 and 23psi). Gene expression was investigated in the prefrontal cortex and hippocampus two weeks following injury. We observed DNMT, TET and TDG expression changes between pressure groups and brain regions. The hippocampus was more vulnerable to enzyme expression changes than the prefrontal cortex, which correlated with aberrant DNA methylation. A significant negative correlation was found between global DNA methylation and the magnitude of blast overpressure exposure. Through transcriptional regulation, altered DNA methylation patterns may offer insight into the characteristic outcomes associated with the injury pathology including inflammation, oxidative stress and apoptosis. As such, these enzymes may be important targets to future therapeutic intervention strategies.
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Affiliation(s)
- Zachary S Bailey
- Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24060, USA
| | - Michael B Grinter
- Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24060, USA
| | | | - Pamela J VandeVord
- Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24060, USA; Salem Veterans Affairs Medical Center, Salem, VA 24153, USA.
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36
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Abstract
Histone modifications and DNA methylation represent central dynamic and reversible processes that regulate gene expression and contribute to cellular phenotypes. These epigenetic marks have been shown to play fundamental roles in a diverse set of signaling and behavioral outcomes. Serotonin is a monoamine that regulates numerous physiological responses including those in the central nervous system. The cardinal signal transduction mechanisms via serotonin and its receptors are well established, but fundamental questions regarding complex interactions between the serotonin system and heritable epigenetic modifications that exert control on gene function remain a topic of intense research and debate. This review focuses on recent advances and contributions to our understanding of epigenetic mechanisms of serotonin receptor-dependent signaling, with focus on psychiatric disorders such as schizophrenia and depression.
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Affiliation(s)
- Terrell Holloway
- Department of Psychiatry, ‡Department of Neurology, and §Friedman Brain Institute, Icahn School of Medicine at Mount Sinai New York, New York 10029, United States
| | - Javier González-Maeso
- Department of Psychiatry, ‡Department of Neurology, and §Friedman Brain Institute, Icahn School of Medicine at Mount Sinai New York, New York 10029, United States
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Aluru N, Kuo E, Helfrich LW, Karchner SI, Linney EA, Pais JE, Franks DG. Developmental exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin alters DNA methyltransferase (dnmt) expression in zebrafish (Danio rerio). Toxicol Appl Pharmacol 2015; 284:142-51. [PMID: 25732252 DOI: 10.1016/j.taap.2015.02.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 02/09/2015] [Accepted: 02/13/2015] [Indexed: 01/14/2023]
Abstract
DNA methylation is one of the most important epigenetic modifications involved in the regulation of gene expression. The DNA methylation reaction is catalyzed by DNA methyltransferases (DNMTs). Recent studies have demonstrated that toxicants can affect normal development by altering DNA methylation patterns, but the mechanisms of action are poorly understood. Hence, we tested the hypothesis that developmental exposure to TCDD affects dnmt gene expression patterns. Zebrafish embryos were exposed to 5nM TCDD for 1h from 4 to 5h post-fertilization (hpf) and sampled at 12, 24, 48, 72, and 96 hpf to determine dnmt gene expression and DNA methylation patterns. We performed a detailed analysis of zebrafish dnmt gene expression during development and in adult tissues. Our results demonstrate that dnmt3b genes are highly expressed in early stages of development, and dnmt3a genes are more abundant in later stages. TCDD exposure upregulated dnmt1 and dnmt3b2 expression, whereas dnmt3a1, 3b1, and 3b4 are downregulated following exposure. We did not observe any TCDD-induced differences in global methylation or hydroxymethylation levels, but the promoter methylation of aryl hydrocarbon receptor (AHR) target genes was altered. In TCDD-exposed embryos, AHR repressor a (ahrra) and c-fos promoters were differentially methylated. To characterize the TCDD effects on DNMTs, we cloned the dnmt promoters with xenobiotic response elements and conducted AHR transactivation assays using a luciferase reporter system. Our results suggest that ahr2 can regulate dnmt3a1, dnmt3a2, and dnmt3b2 expression. Overall, we demonstrate that developmental exposure to TCDD alters dnmt expression and DNA methylation patterns.
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Affiliation(s)
- Neelakanteswar Aluru
- Biology Department and Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
| | - Elaine Kuo
- Biology Department and Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Stanford University, 450 Serra Mall, Stanford, CA 94305, USA
| | - Lily W Helfrich
- Biology Department and Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Northwestern University, 633 Clark St, Evanston, IL 60208, USA
| | - Sibel I Karchner
- Biology Department and Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Elwood A Linney
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Box 3020, Durham, NC 27710, USA
| | - June E Pais
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Diana G Franks
- Biology Department and Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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Torroglosa A, Enguix-Riego MV, Fernández RM, Román-Rodriguez FJ, Moya-Jiménez MJ, de Agustín JC, Antiñolo G, Borrego S. Involvement of DNMT3B in the pathogenesis of Hirschsprung disease and its possible role as a regulator of neurogenesis in the human enteric nervous system. Genet Med 2014; 16:703-10. [PMID: 24577265 DOI: 10.1038/gim.2014.17] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/28/2014] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Hirschsprung disease (OMIM 142623) is a neurocristopathy attributed to a failure of cell proliferation or migration and/or failure of the enteric precursors along the gut to differentiate during embryonic development. Although some genes involved in this pathology are well characterized, many aspects remain poorly understood. In this study, we aimed to identify novel genes implicated in the pathogenesis of Hirschsprung disease. METHODS We compared the expression patterns of genes involved in human stem cell pluripotency between enteric precursors from controls and Hirschsprung disease patients. We further evaluated the role of DNMT3B in the context of Hirschsprung disease by inmunocytochemistry, global DNA methylation assays, and mutational screening. RESULTS Seven differentially expressed genes were identified. We focused on DNMT3B, which encodes a DNA methyltransferase that performs de novo DNA methylation during embryonic development. DNMT3B mutational analysis in our Hirschsprung disease series revealed the presence of potentially pathogenic mutations (p.Gly25Arg, p.Arg190Cys, and p.Gly198Trp). CONCLUSION DNMT3B may be regulating enteric nervous system development through DNA methylation in the neural crest cells, suggesting that aberrant methylation patterns could have a relevant role in Hirschsprung disease. Moreover, the synergistic effect of mutations in both DNMT3B and other Hirschsprung disease-related genes may be contributing to a more severe phenotype in our Hirschsprung disease patients.
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Affiliation(s)
- Ana Torroglosa
- 1] Department of Genetics, Reproduction, and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain [2] Centre for Biomedical Network Research on Rare Diseases, Seville, Spain
| | - María Valle Enguix-Riego
- 1] Department of Genetics, Reproduction, and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain [2] Centre for Biomedical Network Research on Rare Diseases, Seville, Spain
| | - Raquel María Fernández
- 1] Department of Genetics, Reproduction, and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain [2] Centre for Biomedical Network Research on Rare Diseases, Seville, Spain
| | - Francisco José Román-Rodriguez
- 1] Department of Genetics, Reproduction, and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain [2] Centre for Biomedical Network Research on Rare Diseases, Seville, Spain
| | | | | | - Guillermo Antiñolo
- 1] Department of Genetics, Reproduction, and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain [2] Centre for Biomedical Network Research on Rare Diseases, Seville, Spain
| | - Salud Borrego
- 1] Department of Genetics, Reproduction, and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain [2] Centre for Biomedical Network Research on Rare Diseases, Seville, Spain
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Rinaldi L, Benitah SA. Epigenetic regulation of adult stem cell function. FEBS J 2014; 282:1589-604. [PMID: 25060320 DOI: 10.1111/febs.12946] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/17/2014] [Accepted: 07/22/2014] [Indexed: 01/09/2023]
Abstract
Understanding the cellular and molecular mechanisms that specify cell lineages throughout development, and that maintain tissue homeostasis during adulthood, is paramount towards our understanding of why we age or develop pathologies such as cancer. Epigenetic mechanisms ensure that genetically identical cells acquire different fates during embryonic development and are therefore essential for the proper progression of development. How they do so is still a matter of intense investigation, but there is sufficient evidence indicating that they act in a concerted manner with inductive signals and tissue-specific transcription factors to promote and stabilize fate changes along the three germ layers during development. In consequence, it is generally hypothesized that epigenetic mechanisms are also required for the continuous maintenance of cell fate during adulthood. However, in vivo models in which different epigenetic factors have been depleted in different tissues do not show overt changes in cell lineage, thus not strongly supporting this view. Instead, the function of some of these factors appears to be primarily associated with tissue functionality, and a strong causal relationship has been established between their misregulation and a diseased state. In this review, we summarize our current knowledge of the role of epigenetic factors in adult stem cell function and tissue homeostasis.
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Affiliation(s)
- Lorenzo Rinaldi
- Centre for Genomic Regulation, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain
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40
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Dnmt3a regulates global gene expression in olfactory sensory neurons and enables odorant-induced transcription. Neuron 2014; 83:823-38. [PMID: 25123312 DOI: 10.1016/j.neuron.2014.07.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2014] [Indexed: 12/11/2022]
Abstract
During differentiation, neurons exhibit a reorganization of DNA modification patterns across their genomes. The de novo DNA methyltransferase Dnmt3a is implicated in this process, but the effects of its absence have not been fully characterized in a purified neuronal population. To better understand how DNA modifications contribute to neuronal function, we performed a comprehensive analysis of the epigenetic and transcriptional landscapes of Dnmt3a-deficient mature olfactory sensory neurons (mOSNs), the primary sensory neurons of the olfactory epithelium. Dnmt3a is required for both 5-methylcytosine and 5-hydroxymethylcytosine patterning within accessible genomic regions, including hundreds of neurodevelopmental genes and neural enhancers. Loss of Dnmt3a results in the global disruption of gene expression via activation of silent genes and reduction of mOSN-expressed transcripts. Importantly, the DNA modification state and inducibility of odorant-activated genes are markedly impaired in Dnmt3a knockouts, suggesting a crucial role for this enzyme in establishing an epigenetic landscape compatible with neuronal plasticity.
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41
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He F, Lupu DS, Niculescu MD. Perinatal α-linolenic acid availability alters the expression of genes related to memory and to epigenetic machinery, and the Mecp2 DNA methylation in the whole brain of mouse offspring. Int J Dev Neurosci 2014; 36:38-44. [PMID: 24866706 DOI: 10.1016/j.ijdevneu.2014.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/15/2014] [Accepted: 05/15/2014] [Indexed: 01/07/2023] Open
Abstract
Many animal and human studies indicated that dietary ω-3 fatty acids could have beneficial roles on brain development, memory, and learning. However, the exact mechanisms involved are far from being clearly understood, especially for α-linolenic acid (ALA), which is the precursor for the ω-3 elongation and desaturation pathways. This study investigated the alterations induced by different intakes of flaxseed oil (containing 50% ALA), during gestation and lactation, upon the expression of genes involved in neurogenesis, memory-related molecular processes, and DNA methylation, in the brains of mouse offspring at the end of lactation (postnatal day 19, P19). In addition, DNA methylation status for the same genes was investigated. Maternal flaxseed oil supplementation during lactation increased the expression of Mecp2, Ppp1cc, and Reelin, while decreasing the expression of Ppp1cb and Dnmt3a. Dnmt1 expression was decreased by postnatal flaxseed oil supplementation but this effect was offset by ALA deficiency during gestation. Mecp2 DNA methylation was decreased by maternal ALA deficiency during gestation, with a more robust effect in the lactation-deficient group. In addition, linear regression analysis revealed positive correlations between Mecp2, Reelin, and Ppp1cc, between Gadd45b, Bdnf, and Creb1, and between Egr1 and Dnmt1, respectively. However, there were no correlations, in any gene, between DNA methylation and gene expression. In summary, the interplay between ALA availability during gestation and lactation differentially altered the expression of genes involved in neurogenesis and memory, in the whole brain of the offspring at the end of lactation. The Mecp2 epigenetic status was correlated with ALA availability during gestation. However, the epigenetic status of the genes investigated was not associated with transcript levels, suggesting that either the regulation of these genes is not necessarily under epigenetic control, or that the whole brain model is not adequate for the exploration of epigenetic regulation in the context of this study.
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Affiliation(s)
- Fuli He
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC 28081, USA
| | - Daniel S Lupu
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC 28081, USA
| | - Mihai D Niculescu
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC 28081, USA.
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Yan B, Yao J, Tao ZF, Jiang Q. Epigenetics and ocular diseases: from basic biology to clinical study. J Cell Physiol 2014; 229:825-33. [PMID: 24318407 DOI: 10.1002/jcp.24522] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/02/2013] [Indexed: 12/23/2022]
Abstract
Epigenetics is an emerging field in ophthalmology and has opened a new avenue for understanding ocular development and ocular diseases related to aging and environment. Epigenetic mechanisms, including DNA methylation, histone modifications, chromatin remodeling, and deployment of non-coding RNAs, result in the heritable silencing of gene expression without any change in DNA sequence. Accumulating evidence suggests a potential link between gene expression, chromatin structure, non-coding RNAs, and cellular differentiation during ocular development. Disruption of the balance of epigenetic networks could become the etiology of several ocular diseases. Here, we summarized the current knowledge about epigenetic regulatory mechanisms in ocular development and diseases.
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Affiliation(s)
- Biao Yan
- Eye Hospital, Nanjing Medical University, Nanjing, China
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43
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Roessler R, Smallwood SA, Veenvliet JV, Pechlivanoglou P, Peng SP, Chakrabarty K, Groot-Koerkamp MJA, Pasterkamp RJ, Wesseling E, Kelsey G, Boddeke E, Smidt MP, Copray S. Detailed analysis of the genetic and epigenetic signatures of iPSC-derived mesodiencephalic dopaminergic neurons. Stem Cell Reports 2014; 2:520-33. [PMID: 24749075 PMCID: PMC3986662 DOI: 10.1016/j.stemcr.2014.03.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 03/04/2014] [Accepted: 03/05/2014] [Indexed: 12/15/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) hold great promise for in vitro generation of disease-relevant cell types, such as mesodiencephalic dopaminergic (mdDA) neurons involved in Parkinson’s disease. Although iPSC-derived midbrain DA neurons have been generated, detailed genetic and epigenetic characterizations of such neurons are lacking. The goal of this study was to examine the authenticity of iPSC-derived DA neurons obtained by established protocols. We FACS purified mdDA (Pitx3Gfp/+) neurons derived from mouse iPSCs and primary mdDA (Pitx3Gfp/+) neurons to analyze and compare their genetic and epigenetic features. Although iPSC-derived DA neurons largely adopted characteristics of their in vivo counterparts, relevant deviations in global gene expression and DNA methylation were found. Hypermethylated genes, mainly involved in neurodevelopment and basic neuronal functions, consequently showed reduced expression levels. Such abnormalities should be addressed because they might affect unambiguous long-term functionality and hamper the potential of iPSC-derived DA neurons for in vitro disease modeling or cell-based therapy. Purification of iPSC-derived mdDA neurons and primary embryonic mdDA neurons Comparative gene-expression profiling and DNA methylation mapping of mdDA neurons High similarity but also differences between primary and iPSC-derived mdDA neurons Differences mainly in genes involved in neuron differentiation and development
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Affiliation(s)
- Reinhard Roessler
- Department of Neuroscience, Section Medical Physiology, University Medical Center Groningen, 9713AV Groningen, the Netherlands
| | | | - Jesse V Veenvliet
- Center for Neuroscience, Swammerdam Institute for Life Science, Science Park Amsterdam, 1098XH Amsterdam, the Netherlands
| | - Petros Pechlivanoglou
- Unit of Pharmacoepidemiology and Pharmacoeconomics, Department of Pharmacy, University of Groningen, 9713AV Groningen, the Netherlands
| | - Su-Ping Peng
- Department of Neuroscience, Section Medical Physiology, University Medical Center Groningen, 9713AV Groningen, the Netherlands
| | - Koushik Chakrabarty
- Department of Neuroscience and Pharmacology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Marian J A Groot-Koerkamp
- Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - R Jeroen Pasterkamp
- Department of Neuroscience and Pharmacology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Evelyn Wesseling
- Department of Neuroscience, Section Medical Physiology, University Medical Center Groningen, 9713AV Groningen, the Netherlands
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Erik Boddeke
- Department of Neuroscience, Section Medical Physiology, University Medical Center Groningen, 9713AV Groningen, the Netherlands
| | - Marten P Smidt
- Center for Neuroscience, Swammerdam Institute for Life Science, Science Park Amsterdam, 1098XH Amsterdam, the Netherlands
| | - Sjef Copray
- Department of Neuroscience, Section Medical Physiology, University Medical Center Groningen, 9713AV Groningen, the Netherlands
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Toyoda S, Kawaguchi M, Kobayashi T, Tarusawa E, Toyama T, Okano M, Oda M, Nakauchi H, Yoshimura Y, Sanbo M, Hirabayashi M, Hirayama T, Hirabayashi T, Yagi T. Developmental epigenetic modification regulates stochastic expression of clustered protocadherin genes, generating single neuron diversity. Neuron 2014; 82:94-108. [PMID: 24698270 DOI: 10.1016/j.neuron.2014.02.005] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2014] [Indexed: 01/08/2023]
Abstract
In the brain, enormous numbers of neurons have functional individuality and distinct circuit specificities. Clustered Protocadherins (Pcdhs), diversified cell-surface proteins, are stochastically expressed by alternative promoter choice and affect dendritic arborization in individual neurons. Here we found that the Pcdh promoters are differentially methylated by the de novo DNA methyltransferase Dnmt3b during early embryogenesis. To determine this methylation's role in neurons, we produced chimeric mice from Dnmt3b-deficient induced pluripotent stem cells (iPSCs). Single-cell expression analysis revealed that individual Dnmt3b-deficient Purkinje cells expressed increased numbers of Pcdh isoforms; in vivo, they exhibited abnormal dendritic arborization. These results indicate that DNA methylation by Dnmt3b at early embryonic stages regulates the probability of expression for the stochastically expressed Pcdh isoforms. They also suggest a mechanism for a rare human recessive disease, the ICF (Immunodeficiency, Centromere instability, and Facial anomalies) syndrome, which is caused by Dnmt3b mutations.
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Affiliation(s)
- Shunsuke Toyoda
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Japan Science and Technology Agency-Core Research for Evolutional Science and Technology, CREST, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahumi Kawaguchi
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshihiro Kobayashi
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Japan Science Technology Agency, ERATO, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Etsuko Tarusawa
- Japan Science and Technology Agency-Core Research for Evolutional Science and Technology, CREST, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Division of Developmental Neurophysiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Tomoko Toyama
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masaki Okano
- Laboratory for Mammalian Epigenetic Studies, RIKEN Center for Developmental Biology, Minatojima-minamimachi 2-2-3, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Masaaki Oda
- Laboratory for Mammalian Epigenetic Studies, RIKEN Center for Developmental Biology, Minatojima-minamimachi 2-2-3, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Japan Science Technology Agency, ERATO, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yumiko Yoshimura
- Division of Developmental Neurophysiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Department of Physiological Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Makoto Sanbo
- Japan Science and Technology Agency-Core Research for Evolutional Science and Technology, CREST, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Masumi Hirabayashi
- Japan Science and Technology Agency-Core Research for Evolutional Science and Technology, CREST, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Physiological Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan; Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Teruyoshi Hirayama
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Japan Science and Technology Agency-Core Research for Evolutional Science and Technology, CREST, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takahiro Hirabayashi
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Japan Science and Technology Agency-Core Research for Evolutional Science and Technology, CREST, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Japan Science and Technology Agency-Core Research for Evolutional Science and Technology, CREST, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Expression patterns of dnmt3aa, dnmt3ab, and dnmt4 during development and fin regeneration in zebrafish. Gene Expr Patterns 2014; 14:105-10. [DOI: 10.1016/j.gep.2014.01.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 01/06/2014] [Accepted: 01/25/2014] [Indexed: 11/21/2022]
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Kleinman CL, Gerges N, Papillon-Cavanagh S, Sin-Chan P, Pramatarova A, Quang DAK, Adoue V, Busche S, Caron M, Djambazian H, Bemmo A, Fontebasso AM, Spence T, Schwartzentruber J, Albrecht S, Hauser P, Garami M, Klekner A, Bognar L, Montes JL, Staffa A, Montpetit A, Berube P, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel PM, Duchaine T, Perotti C, Fleming A, Faury D, Remke M, Gallo M, Dirks P, Taylor MD, Sladek R, Pastinen T, Chan JA, Huang A, Majewski J, Jabado N. Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR. Nat Genet 2014; 46:39-44. [PMID: 24316981 DOI: 10.1038/ng.2849] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 11/13/2013] [Indexed: 12/20/2022]
Abstract
Embryonal tumors with multilayered rosettes (ETMRs) are rare, deadly pediatric brain tumors characterized by high-level amplification of the microRNA cluster C19MC. We performed integrated genetic and epigenetic analyses of 12 ETMR samples and identified, in all cases, C19MC fusions to TTYH1 driving expression of the microRNAs. ETMR tumors, cell lines and xenografts showed a specific DNA methylation pattern distinct from those of other tumors and normal tissues. We detected extreme overexpression of a previously uncharacterized isoform of DNMT3B originating at an alternative promoter that is active only in the first weeks of neural tube development. Transcriptional and immunohistochemical analyses suggest that C19MC-dependent DNMT3B deregulation is mediated by RBL2, a known repressor of DNMT3B. Transfection with individual C19MC microRNAs resulted in DNMT3B upregulation and RBL2 downregulation in cultured cells. Our data suggest a potential oncogenic re-engagement of an early developmental program in ETMR via epigenetic alteration mediated by an embryonic, brain-specific DNMT3B isoform.
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Affiliation(s)
- Claudia L Kleinman
- 1] McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada. [2] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [3]
| | - Noha Gerges
- 1] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [2]
| | | | - Patrick Sin-Chan
- Division of Hematology-Oncology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Albena Pramatarova
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | | | - Véronique Adoue
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Stephan Busche
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Maxime Caron
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Haig Djambazian
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Amandine Bemmo
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Adam M Fontebasso
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Tara Spence
- Division of Hematology-Oncology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Steffen Albrecht
- Department of Pathology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Peter Hauser
- Second Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Miklos Garami
- Second Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Almos Klekner
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Laszlo Bognar
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Jose-Luis Montes
- Division of Neurosurgery, Department of Surgery, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - Alfredo Staffa
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Alexandre Montpetit
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Pierre Berube
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Magdalena Zakrzewska
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Krzysztof Zakrzewski
- Department of Neurosurgery, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Pawel P Liberski
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Zhifeng Dong
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Peter M Siegel
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Thomas Duchaine
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Christian Perotti
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Adam Fleming
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, McGill University and the McGill University Health Centre Research Institute, Montreal, Quebec, Canada
| | - Damien Faury
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, McGill University and the McGill University Health Centre Research Institute, Montreal, Quebec, Canada
| | - Marc Remke
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Marco Gallo
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Dirks
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Robert Sladek
- 1] McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada. [2] Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Tomi Pastinen
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Jennifer A Chan
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Annie Huang
- 1] Division of Hematology-Oncology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada. [2] Program in Cell Biology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada. [3]
| | - Jacek Majewski
- 1] McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada. [2] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [3]
| | - Nada Jabado
- 1] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [2] Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada. [3]
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CRL4B promotes tumorigenesis by coordinating with SUV39H1/HP1/DNMT3A in DNA methylation-based epigenetic silencing. Oncogene 2013; 34:104-18. [PMID: 24292684 DOI: 10.1038/onc.2013.522] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 10/16/2013] [Accepted: 10/18/2013] [Indexed: 12/16/2022]
Abstract
Cullin 4B (CUL4B) is a component of the Cullin4B-Ring E3 ligase complex (CRL4B) that functions in proteolysis and is implicated in tumorigenesis. Here, we report that CRL4B is associated with histone methyltransferase SUV39H1, heterochromatin protein 1 (HP1) and DNA methyltransferases 3A (DNMT3A). We showed that CRL4B, through catalyzing H2AK119 monoubiquitination, facilitates H3K9 tri-methylation and DNA methylation, two key epigenetic modifications involved in DNA methylation-based gene silencing. Depletion of CUL4B resulted in loss of not only H2AK119 monoubiquitination but also H3K9 trimethylation and DNA methylation, leading to derepression of a collection of genes, including the tumor suppressor IGFBP3. We demonstrated that CUL4B promotes cell proliferation and invasion, which are consistent with a tumorigenic phenotype, at least partially by repressing IGFBP3. We found that the expression of CUL4B is markedly upregulated in samples of human cervical carcinoma and is negatively correlated with the expression of IGFBP3. Our experiments unveiled a coordinated action between histone ubiquitination/methylation and DNA methylation in transcription repression, providing a mechanism for CUL4B in tumorigenesis.
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48
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Cain JT, Berosik MA, Snyder SD, Crawford NF, Nour SI, Schaubhut GJ, Darland DC. Shifts in the vascular endothelial growth factor isoforms result in transcriptome changes correlated with early neural stem cell proliferation and differentiation in mouse forebrain. Dev Neurobiol 2013; 74:63-81. [PMID: 24124161 DOI: 10.1002/dneu.22130] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/21/2013] [Accepted: 09/04/2013] [Indexed: 12/12/2022]
Abstract
Regulation of neural stem cell (NSC) fate decisions is critical during the transition from a multicellular mammalian forebrain neuroepithelium to the multilayered neocortex. Forebrain development requires coordinated vascular investment alongside NSC differentiation. Vascular endothelial growth factor A (Vegf) has proven to be a pleiotrophic gene whose multiple protein isoforms regulate a broad range of effects in neurovascular systems. To test the hypothesis that the Vegf isoforms (120, 164, and 188) are required for normal forebrain development, we analyzed the forebrain transcriptome of mice expressing specific Vegf isoforms, Vegf120, VegfF188, or a combination of Vegf120/188. Transcriptome analysis identified differentially expressed genes in embryonic day (E) 9.5 forebrain, a time point preceding dramatic neuroepithelial expansion and vascular investment in the telencephalon. Meta-analysis identified gene pathways linked to chromosome-level modifications, cell fate regulation, and neurogenesis that were altered in Vegf isoform mice. Based on these gene network shifts, we predicted that NSC populations would be affected in later stages of forebrain development. In the E11.5 telencephalon, we quantified mitotic cells [Phospho-Histone H3 (pHH3)-positive] and intermediate progenitor cells (Tbr2/Eomes-positive), observing quantitative and qualitative shifts in these populations. We observed qualitative shifts in cortical layering at P0, particularly with Ctip2-positive cells in layer V. The results identify a suite of genes and functional gene networks that can be used to further dissect the role of Vegf in regulating NSC differentiation and downstream consequences for NSC fate decisions.
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Affiliation(s)
- Jacob T Cain
- Department of Biology, University of North Dakota, Grand Forks, North Dakota
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49
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Lindner R, Puttagunta R, Di Giovanni S. Epigenetic regulation of axon outgrowth and regeneration in CNS injury: the first steps forward. Neurotherapeutics 2013; 10:771-81. [PMID: 23881454 PMCID: PMC3805867 DOI: 10.1007/s13311-013-0203-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Inadequate axonal sprouting and lack of regeneration limit functional recovery following neurologic injury, such as stroke, brain, and traumatic spinal cord injury. Recently, the enhancement of the neuronal regenerative program has led to promising improvements in axonal sprouting and regeneration in animal models of axonal injury. However, precise knowledge of the essential molecular determinants of this regenerative program remains elusive, thus limiting the choice of fully effective therapeutic strategies. Given that molecular regulation of axonal outgrowth and regeneration requires carefully orchestrated waves of gene expression, both temporally and spatially, epigenetic changes may be an ideal regulatory mechanism to address this unique need. While recent evidence suggests that epigenetic modifications could contribute to the regulation of axonal outgrowth and regeneration following axonal injury in models of stroke, and spinal cord and optic nerve injury, a number of unanswered questions remain. Such questions require systematic investigation of the epigenetic landscape between regenerative and non-regenerative conditions for the potential translation of this knowledge into regenerative strategies in human spinal and brain injury, as well as stroke.
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Affiliation(s)
- Ricco Lindner
- Laboratory for NeuroRegeneration and Repair, Center for Neurology, Hertie Institute for Clinical Brain Research, University of Tuebingen, Otfried-Mueller Strasse 27, 72076 Tuebingen, Germany
| | - Radhika Puttagunta
- Laboratory for NeuroRegeneration and Repair, Center for Neurology, Hertie Institute for Clinical Brain Research, University of Tuebingen, Otfried-Mueller Strasse 27, 72076 Tuebingen, Germany
| | - Simone Di Giovanni
- Laboratory for NeuroRegeneration and Repair, Center for Neurology, Hertie Institute for Clinical Brain Research, University of Tuebingen, Otfried-Mueller Strasse 27, 72076 Tuebingen, Germany
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50
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Jiang JX, Aitken KJ, Sotiropolous C, Kirwan T, Panchal T, Zhang N, Pu S, Wodak S, Tolg C, Bägli DJ. Phenotypic switching induced by damaged matrix is associated with DNA methyltransferase 3A (DNMT3A) activity and nuclear localization in smooth muscle cells (SMC). PLoS One 2013; 8:e69089. [PMID: 24282625 PMCID: PMC3735580 DOI: 10.1371/journal.pone.0069089] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 06/09/2013] [Indexed: 12/27/2022] Open
Abstract
Extracellular matrix changes are often crucial inciting events for fibroproliferative disease. Epigenetic changes, specifically DNA methylation, are critical factors underlying differentiated phenotypes. We examined the dependency of matrix-induced fibroproliferation and SMC phenotype on DNA methyltransferases. The cooperativity of matrix with growth factors, cell density and hypoxia was also examined. Primary rat visceral SMC of early passage (0–2) were plated on native collagen or damaged/heat-denatured collagen. Hypoxia was induced with 3% O2 (balanced 5% CO2 and 95% N2) over 48 hours. Inhibitors were applied 2–3 hours after cells were plated on matrix, or immediately before hypoxia. Cells were fixed and stained for DNMT3A and smooth muscle actin (SMA) or smooth muscle myosin heavy chain. Illumina 450 K array of CpG sites was performed on bisulfite-converted DNA from smooth muscle cells on damaged matrix vs native collagen. Matrix exquisitely regulates DNMT3A localization and expression, and influences differentiation in SMCs exposed to denatured matrix +/− hypoxia. Analysis of DNA methylation signatures showed that Matrix caused significant DNA methylation alterations in a discrete number of CpG sites proximal to genes related to SMC differentiation. Matrix has a profound effect on the regulation of SMC phenotype, which is associated with altered expression, localization of DNMTs and discrete changes DNA methylation.
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Affiliation(s)
- Jia-Xin Jiang
- Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Urology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Karen J. Aitken
- Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Urology, Hospital for Sick Children, Toronto, Ontario, Canada
- * E-mail:
| | - Chris Sotiropolous
- Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Urology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Tyler Kirwan
- Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Urology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Trupti Panchal
- Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Zhang
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Shuye Pu
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shoshana Wodak
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Cornelia Tolg
- Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Urology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Darius J. Bägli
- Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Urology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Sciences, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
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