1
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Gao K, Xie Y, Xu F, Peng Q, Fu L, Wang G, Qiu J. Silk fibroin promotes H3K9me3 expression and chromatin reorganization to regulate endothelial cell proliferation. APL Bioeng 2024; 8:026115. [PMID: 38827498 PMCID: PMC11143938 DOI: 10.1063/5.0203858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 05/07/2024] [Indexed: 06/04/2024] Open
Abstract
Silk fibroin (SF), which is extensively utilized in tissue engineering and vascular grafts for enhancing vascular regeneration, has not been thoroughly investigated for its epigenetic effects on endothelial cells (EC). This study employed RNA sequencing analysis to evaluate the activation of histone modification regulatory genes in EC treated with SF. Subsequent investigations revealed elevated H3K9me3 levels in SF-treated EC, as evidenced by immunofluorescence and western blot analysis. The study utilized H2B-eGFP endothelial cells to demonstrate that SF treatment results in the accumulation of H2B-marked chromatin in the nuclear inner cavities of EC. Inhibition of H3K9me3 levels by a histone deacetylase inhibitor TSA decreased cell proliferation. Furthermore, the activation of the MAPK signaling pathway using chromium picolinate decreased the proliferative activity and H3K9me3 level in SF-treated EC. SF also appeared to enhance cell growth and proliferation by modulating the H3K9me3 level and reorganizing chromatin, particularly after oxidative stress induced by H2O2 treatment. In summary, these findings indicate that SF promotes EC proliferation by increasing the H3K9me3 level even under stress conditions.
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Affiliation(s)
- Kaixiang Gao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400030, China
| | - Yafan Xie
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400030, China
| | - Fangning Xu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400030, China
| | - Qin Peng
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Li Fu
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Guixue Wang
- Authors to whom correspondence should be addressed:; ; and . Tel.: 023-65102507
| | - Juhui Qiu
- Authors to whom correspondence should be addressed:; ; and . Tel.: 023-65102507
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2
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Kho J, Polak U, Jiang MM, Odom JD, Hunter JV, Ali SM, Burrage LC, Nagamani SC, Pautler RG, Thompson HP, Urayama A, Jin Z, Lee B. Argininosuccinate lyase deficiency causes blood-brain barrier disruption via nitric oxide-mediated dysregulation of claudin expression. JCI Insight 2023; 8:e168475. [PMID: 37490345 PMCID: PMC10544197 DOI: 10.1172/jci.insight.168475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023] Open
Abstract
Nitric oxide (NO) is a critical signaling molecule that has been implicated in the pathogenesis of neurocognitive diseases. Both excessive and insufficient NO production have been linked to pathology. Previously, we have shown that argininosuccinate lyase deficiency (ASLD) is a novel model system to investigate cell-autonomous, nitric oxide synthase-dependent NO deficiency. Humans with ASLD are at increased risk for developing hyperammonemia due to a block in ureagenesis. However, natural history studies have shown that individuals with ASLD have multisystem disease including neurocognitive deficits that can be independent of ammonia. Here, using ASLD as a model of NO deficiency, we investigated the effects of NO on brain endothelial cells in vitro and the blood-brain barrier (BBB) in vivo. Knockdown of ASL in human brain microvascular endothelial cells (HBMECs) led to decreased transendothelial electrical resistance, indicative of increased cell permeability. Mechanistically, treatment with an NO donor or inhibition of Claudin-1 improved barrier integrity in ASL-deficient HBMECs. Furthermore, in vivo assessment of a hypomorphic mouse model of ASLD showed increased BBB leakage, which was partially rescued by NO supplementation. Our results suggest that ASL-mediated NO synthesis is required for proper maintenance of brain microvascular endothelial cell functions as well as BBB integrity.
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Affiliation(s)
- Jordan Kho
- Department of Molecular and Human Genetics and
| | | | | | | | - Jill V. Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
| | | | - Lindsay C. Burrage
- Department of Molecular and Human Genetics and
- Texas Children’s Hospital, Houston, Texas, USA
| | - Sandesh C.S. Nagamani
- Department of Molecular and Human Genetics and
- Texas Children’s Hospital, Houston, Texas, USA
| | - Robia G. Pautler
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
| | - Hannah P. Thompson
- Department of Neurology, University of Texas Health Science Center, Houston, Texas, USA
| | - Akihiko Urayama
- Department of Neurology, University of Texas Health Science Center, Houston, Texas, USA
| | - Zixue Jin
- Department of Molecular and Human Genetics and
| | - Brendan Lee
- Department of Molecular and Human Genetics and
- Texas Children’s Hospital, Houston, Texas, USA
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3
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Kim JP, Kim BH, Bice PJ, Seo SW, Bennett DA, Saykin AJ, Nho K. Integrative Co-methylation Network Analysis Identifies Novel DNA Methylation Signatures and Their Target Genes in Alzheimer's Disease. Biol Psychiatry 2023; 93:842-851. [PMID: 36150909 PMCID: PMC9789210 DOI: 10.1016/j.biopsych.2022.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 06/16/2022] [Accepted: 06/16/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND DNA methylation is a key epigenetic marker, and its alternations may be involved in Alzheimer's disease (AD). CpGs sharing similar biological functions or pathways tend to be co-methylated. METHODS We performed an integrative network-based DNA methylation analysis on 2 independent cohorts (N = 941) using brain DNA methylation profiles and RNA-sequencing as well as AD pathology data. RESULTS Weighted co-methylation network analysis identified 6 modules as significantly associated with neuritic plaque burden. In total, 15 hub CpGs including 3 novel CpGs were identified and replicated as being significantly associated with AD pathology. Furthermore, we identified and replicated 4 target genes (ATP6V1G2, VCP, RAD52, and LST1) as significantly regulated by DNA methylation at hub CpGs. In particular, VCP gene expression was also associated with AD pathology in both cohorts. CONCLUSIONS This integrative network-based multiomics study provides compelling evidence for a potential role of DNA methylation alternations and their target genes in AD.
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Affiliation(s)
- Jun Pyo Kim
- Center for Neuroimaging, Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana; Medical Research Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Bo-Hyun Kim
- Department of Biomedical Engineering, Hanyang University, Seoul, Korea
| | - Paula J Bice
- Center for Neuroimaging, Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana; Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, Indiana
| | - Sang Won Seo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
| | - Andrew J Saykin
- Center for Neuroimaging, Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana; Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, Indiana; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kwangsik Nho
- Center for Neuroimaging, Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana; Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, Indiana; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana.
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4
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Boulasiki P, Tan XW, Spinelli M, Riccio A. The NuRD Complex in Neurodevelopment and Disease: A Case of Sliding Doors. Cells 2023; 12:cells12081179. [PMID: 37190088 DOI: 10.3390/cells12081179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
The Nucleosome Remodelling and Deacetylase (NuRD) complex represents one of the major chromatin remodelling complexes in mammalian cells, uniquely coupling the ability to "open" the chromatin by inducing nucleosome sliding with histone deacetylase activity. At the core of the NuRD complex are a family of ATPases named CHDs that utilise the energy produced by the hydrolysis of the ATP to induce chromatin structural changes. Recent studies have highlighted the prominent role played by the NuRD in regulating gene expression during brain development and in maintaining neuronal circuitry in the adult cerebellum. Importantly, components of the NuRD complex have been found to carry mutations that profoundly affect neurological and cognitive development in humans. Here, we discuss recent literature concerning the molecular structure of NuRD complexes and how the subunit composition and numerous permutations greatly determine their functions in the nervous system. We will also discuss the role of the CHD family members in an array of neurodevelopmental disorders. Special emphasis will be given to the mechanisms that regulate the NuRD complex composition and assembly in the cortex and how subtle mutations may result in profound defects of brain development and the adult nervous system.
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Affiliation(s)
- Paraskevi Boulasiki
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Xiao Wei Tan
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Matteo Spinelli
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
- Neuroscience Department, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Antonella Riccio
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
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5
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Akaba Y, Takahashi S, Suzuki K, Kosaki K, Tsujimura K. miR-514a promotes neuronal development in human iPSC-derived neurons. Front Cell Dev Biol 2023; 11:1096463. [PMID: 36824367 PMCID: PMC9941156 DOI: 10.3389/fcell.2023.1096463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Proper development and function of the central nervous system require precise regulation of gene expression. MicroRNAs (miRNAs), a group of small non-coding RNAs that can negatively regulate gene expression at the post-transcriptional level, are critical regulators of neuronal development, and dysregulation of microRNAs has been implicated in various neurological disorders. Changes in microRNA expression and repertoire are related to the emergence of social and behavioral variations in closely related primates, including humans, during evolution. MicroRNA-514a (miR-514a) is an X-linked miRNA that is conserved in species with higher social and cognitive functions, and frequent tandem duplications of miR-514a have been found in primate genomes. Here, we demonstrate that miR-514a plays a crucial role in neuronal development in neurons derived from human induced pluripotent stem cells (iPSCs). Overexpression of miR-514a increased dendritic length, soma size, and activity levels of mammalian target of rapamycin (mTOR) signaling in induced pluripotent stem cell-derived neurons, whereas blocking of endogenous miR-514a inhibited neuronal development. Furthermore, we performed a functional analysis of the miR-514a variation found during primate evolution, to investigate the impact of miR-514a sequence variation and associated changes in expression on brain development during evolution. We found that mutation in miR-514a significantly reduced the expression of the mature form and abolished the effects observed when native miR-514a was expressed. Our findings provide new insights into the functional role of miR-514a in the regulation of neuronal development and evolution of primate brain development.
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Affiliation(s)
- Yuichi Akaba
- Group of Brain Function and Development, Neuroscience Institute of the Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan,Research Unit for Developmental Disorders, Institute for Advanced Research, Nagoya University, Nagoya, Aichi, Japan,Department of Pediatrics, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Satoru Takahashi
- Department of Pediatrics, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Keiichiro Suzuki
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan,Graduate School of Engineering Science, Osaka University, Osaka, Japan,Graduate School of Frontier Bioscience, Osaka University, Osaka, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Keita Tsujimura
- Group of Brain Function and Development, Neuroscience Institute of the Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan,Research Unit for Developmental Disorders, Institute for Advanced Research, Nagoya University, Nagoya, Aichi, Japan,*Correspondence: Keita Tsujimura,
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6
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Mishra S, Raval M, Kachhawaha AS, Tiwari BS, Tiwari AK. Aging: Epigenetic modifications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:171-209. [PMID: 37019592 DOI: 10.1016/bs.pmbts.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Aging is one of the most complex and irreversible health conditions characterized by continuous decline in physical/mental activities that eventually poses an increased risk of several diseases and ultimately death. These conditions cannot be ignored by anyone but there are evidences that suggest that exercise, healthy diet and good routines may delay the Aging process significantly. Several studies have demonstrated that Epigenetics plays a key role in Aging and Aging-associated diseases through methylation of DNA, histone modification and non-coding RNA (ncRNA). Comprehension and relevant alterations in these epigenetic modifications can lead to new therapeutic avenues of age-delaying contrivances. These processes affect gene transcription, DNA replication and DNA repair, comprehending epigenetics as a key factor in understanding Aging and developing new avenues for delaying Aging, clinical advancements in ameliorating aging-related diseases and rejuvenating health. In the present article, we have described and advocated the epigenetic role in Aging and associated diseases.
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7
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Micale V, Di Bartolomeo M, Di Martino S, Stark T, Dell'Osso B, Drago F, D'Addario C. Are the epigenetic changes predictive of therapeutic efficacy for psychiatric disorders? A translational approach towards novel drug targets. Pharmacol Ther 2023; 241:108279. [PMID: 36103902 DOI: 10.1016/j.pharmthera.2022.108279] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 02/06/2023]
Abstract
The etiopathogenesis of mental disorders is not fully understood and accumulating evidence support that clinical symptomatology cannot be assigned to a single gene mutation, but it involves several genetic factors. More specifically, a tight association between genes and environmental risk factors, which could be mediated by epigenetic mechanisms, may play a role in the development of mental disorders. Several data suggest that epigenetic modifications such as DNA methylation, post-translational histone modification and interference of microRNA (miRNA) or long non-coding RNA (lncRNA) may modify the severity of the disease and the outcome of the therapy. Indeed, the study of these mechanisms may help to identify patients particularly vulnerable to mental disorders and may have potential utility as biomarkers to facilitate diagnosis and treatment of psychiatric disorders. This article summarizes the most relevant preclinical and human data showing how epigenetic modifications can be central to the therapeutic efficacy of antidepressant and/or antipsychotic agents, as possible predictor of drugs response.
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Affiliation(s)
- Vincenzo Micale
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy.
| | - Martina Di Bartolomeo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Serena Di Martino
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy
| | - Tibor Stark
- Department of Pharmacology, Faculty of Medicine, Masaryk University, Brno, Czech Republic; Scientific Core Unit Neuroimaging, Max Planck Institute of Psychiatry, Munich, Germany
| | - Bernardo Dell'Osso
- Department of Biomedical and Clinical Sciences 'Luigi Sacco', University of Milan, Milan, Italy, Department of Mental Health, ASST Fatebenefratelli-Sacco, Milan, Italy; "Aldo Ravelli" Research Center for Neurotechnology and Experimental Brain Therapeutics, Department of Health Sciences, University of Milan Medical School, Milan, Italy; Department of Psychiatry and Behavioral Sciences, Stanford University, CA, USA
| | - Filippo Drago
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy.
| | - Claudio D'Addario
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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8
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Hong JY, Kim H, Jeon WJ, Lee J, Yeo C, Lee YJ, Ha IH. Epigenetic Changes within the Annulus Fibrosus by DNA Methylation in Rat Intervertebral Disc Degeneration Model. Cells 2022; 11:cells11223547. [PMID: 36428977 PMCID: PMC9688069 DOI: 10.3390/cells11223547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/28/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022] Open
Abstract
Intervertebral disc degeneration (IDD) is an age-dependent progressive spinal disease that causes chronic back or neck pain. Although aging has long been presented as the main risk factor, the exact cause is not fully known. DNA methylation is associated with chronic pain, suggesting that epigenetic modulation may ameliorate disc degeneration. We examined histological changes in the DNA methylation within the discs and their association with pain-related transient receptor potential vanilloid subtype 1 (TrpV1) expression in rats subjected to IDD. Epigenetic markers (5-hydroxymethylcytosine (5hmC), 5-methylcytosine (5Mc)), DNA methyltransferases (DNMTs), and Ten-eleven translocations (Tets) were analyzed using immunohistochemistry, real-time PCR, and DNA dot-blot following IDD. Results revealed high 5mC levels in the annulus fibrosus (AF) region within the disc after IDD and an association with TrpV1 expression. DNMT1 is mainly involved in 5mC conversion in degenerated discs. However, 5hmC levels did not differ between groups. A degenerated disc can lead to locomotor defects as assessed by ladder and tail suspension tests, no pain signals in the von Frey test, upregulated matrix metalloproteinase-3, and downregulated aggrecan levels within the disc. Thus, we found that the DNA methylation status in the AF region of the disc was mainly changed after IDD and associated with aberrant TrpV1 expression in degenerated discs.
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9
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Hsu CC, Serio A, Gopal S, Gelmi A, Chiappini C, Desai RA, Stevens MM. Biophysical Regulations of Epigenetic State and Notch Signaling in Neural Development Using Microgroove Substrates. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32773-32787. [PMID: 35830496 PMCID: PMC9335410 DOI: 10.1021/acsami.2c01996] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A number of studies have recently shown how surface topography can alter the behavior and differentiation patterns of different types of stem cells. Although the exact mechanisms and molecular pathways involved remain unclear, a consistent portion of the literature points to epigenetic changes induced by nuclear remodeling. In this study, we investigate the behavior of clinically relevant neural populations derived from human pluripotent stem cells when cultured on polydimethylsiloxane microgrooves (3 and 10 μm depth grooves) to investigate what mechanisms are responsible for their differentiation capacity and functional behavior. Our results show that microgrooves enhance cell alignment, modify nuclear geometry, and significantly increase cellular stiffness, which we were able to measure at high resolution with a combination of light and electron microscopy, scanning ion conductance microscopy (SICM), and atomic force microscopy (AFM) coupled with quantitative image analysis. The microgrooves promoted significant changes in the epigenetic landscape, as revealed by the expression of key histone modification markers. The main behavioral change of neural stem cells on microgrooves was an increase of neuronal differentiation under basal conditions on the microgrooves. Through measurements of cleaved Notch1 levels, we found that microgrooves downregulate Notch signaling. We in fact propose that microgroove topography affects the differentiation potential of neural stem cells by indirectly altering Notch signaling through geometric segregation and that this mechanism in parallel with topography-dependent epigenetic modulations acts in concert to enhance stem cell neuronal differentiation.
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Affiliation(s)
- Chia-Chen Hsu
- Department
of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Department
of Bioengineering, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Institute
of Biomedical Engineering, Imperial College
London, Exhibition Road, London SW7 2AZ, U.K.
| | - Andrea Serio
- Department
of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Department
of Bioengineering, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Institute
of Biomedical Engineering, Imperial College
London, Exhibition Road, London SW7 2AZ, U.K.
| | - Sahana Gopal
- Department
of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Department
of Bioengineering, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Institute
of Biomedical Engineering, Imperial College
London, Exhibition Road, London SW7 2AZ, U.K.
| | - Amy Gelmi
- Department
of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Department
of Bioengineering, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Institute
of Biomedical Engineering, Imperial College
London, Exhibition Road, London SW7 2AZ, U.K.
| | - Ciro Chiappini
- Department
of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Department
of Bioengineering, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Institute
of Biomedical Engineering, Imperial College
London, Exhibition Road, London SW7 2AZ, U.K.
| | - Ravi A. Desai
- Department
of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Department
of Bioengineering, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Institute
of Biomedical Engineering, Imperial College
London, Exhibition Road, London SW7 2AZ, U.K.
| | - Molly M. Stevens
- Department
of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Department
of Bioengineering, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- Institute
of Biomedical Engineering, Imperial College
London, Exhibition Road, London SW7 2AZ, U.K.
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10
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Wang X, Wu J, Wang W, Zhang Y, He D, Xiao B, Zhang H, Song A, Xing Y, Li B. Reprogramming of Rat Fibroblasts into Induced Neurons by Small-Molecule Compounds In Vitro and In Vivo. ACS Chem Neurosci 2022; 13:2099-2109. [PMID: 35723446 DOI: 10.1021/acschemneuro.2c00078] [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: 11/29/2022] Open
Abstract
Cell replacement is a promising approach for neurodegenerative disease treatment. Somatic cells such as fibroblasts can be induced to differentiate into neurons by specific transcription factors; however, the potential of viral vectors used for reprogramming to integrate into the genome raises concerns about the potential clinical applications of this approach. Here, we directly reprogrammed rat embryonic skin fibroblasts into induced neurons (iNs) via six small-molecule compounds (SMs) (VPA, CHIR99021, forskolin, Y-27632, Repsox, and P7C3-A20). iNs exhibit typical neuronal morphology, and immunofluorescence showed that more than 96% of the iNs expressed the early neuronal marker class III beta-tubulin (TUJ1) and that more than 91% of iNs expressed the mature neuronal marker neuron-specific enolase (NSE) after 10 days of reprogramming. Quantitative real-time polymerase chain reaction also showed that most iNs expressed the dopaminergic neuron marker tyrosine hydroxylase, the neural marker Nur correlation factor 1, the (γ-aminobutyric acid, GABA) GABAergic neuronal marker GABA, and the cholinergic neuron marker choline acetyltransferase. In addition, we found that cell proliferation decreased during reprogramming and that protein synthesis increased initially and then decreased. SMs were mixed with hydrogels, and the hydrogels were implanted subcutaneously into the backs of rats. After 7 days, the TUJ1 and NSE proteins were expressed in surrounding tissues, indicating that SMs caused reprogramming in vivo. In summary, rat skin fibroblasts can be efficiently reprogrammed into iNs by SMs in vitro and in vivo.
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Affiliation(s)
- Xueyun Wang
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, P.R. China
| | - Jing Wu
- Department of Paediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001 Henan, P.R. China
| | - Wang Wang
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, P.R. China
| | - Yuanwang Zhang
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, P.R. China
| | - Dixin He
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, P.R. China
| | - Boying Xiao
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, P.R. China
| | - Haohao Zhang
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, P.R. China
| | - Anqi Song
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, P.R. China
| | - Ying Xing
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, P.R. China
| | - Bo Li
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000 Henan, P.R. China
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11
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Ghosh K, Zhang GF, Chen H, Chen SR, Pan HL. Cannabinoid CB2 receptors are upregulated via bivalent histone modifications and control primary afferent input to the spinal cord in neuropathic pain. J Biol Chem 2022; 298:101999. [PMID: 35500651 PMCID: PMC9168157 DOI: 10.1016/j.jbc.2022.101999] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/24/2022] Open
Abstract
Type-2 cannabinoid receptors (CB2, encoded by the Cnr2 gene) are mainly expressed in immune cells, and CB2 agonists normally have no analgesic effect. However, nerve injury upregulates CB2 in the dorsal root ganglion (DRG), following which CB2 stimulation reduces neuropathic pain. It is unclear how nerve injury increases CB2 expression or how CB2 activity is transformed in neuropathic pain. In this study, immunoblotting showed that spinal nerve ligation (SNL) induced a delayed and sustained increase in CB2 expression in the DRG and dorsal spinal cord synaptosomes. RNAscope in situ hybridization also showed that SNL substantially increased CB2 mRNA levels, mostly in medium and large DRG neurons. Furthermore, we found that the specific CB2 agonist JWH-133 significantly inhibits the amplitude of dorsal root-evoked glutamatergic excitatory postsynaptic currents in spinal dorsal horn neurons in SNL rats, but not in sham control rats; intrathecal injection of JWH-133 reversed pain hypersensitivity in SNL rats, but had no effect in sham control rats. In addition, chromatin immunoprecipitation-qPCR analysis showed that SNL increased enrichment of two activating histone marks (H3K4me3 and H3K9ac) and diminished occupancy of two repressive histone marks (H3K9me2 and H3K27me3) at the Cnr2 promoter in the DRG. In contrast, SNL had no effect on DNA methylation levels around the Cnr2 promoter. Our findings suggest that peripheral nerve injury promotes CB2 expression in primary sensory neurons via epigenetic bivalent histone modifications and that CB2 activation reduces neuropathic pain by attenuating nociceptive transmission from primary afferent nerves to the spinal cord.
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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
| | - Guang-Fen Zhang
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hong Chen
- 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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12
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Histone methylation-mediated microRNA-32-5p down-regulation in sensory neurons regulates pain behaviors via targeting Cav3.2 channels. Proc Natl Acad Sci U S A 2022; 119:e2117209119. [PMID: 35353623 PMCID: PMC9168926 DOI: 10.1073/pnas.2117209119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In this study, we identify microRNA-32-5p (miR-32-5p) as a key functional noncoding RNA in trigeminal-mediated neuropathic pain. We report that injury-induced histone methylation attenuates the binding of glucocorticoid receptor to the promoter region of the miR-32-5p gene and decreases the expression of miR-32-5p, in turn promoting the development of neuropathic pain through regulation of Cav3.2 channels. miRNA-mediated gene regulation has been proposed as a therapeutic approach in neuropathic pain. Our findings identify miR-32-5p replenishment as a therapeutic strategy for treating chronic neuropathic pain. microRNA (miRNA)–mediated gene regulation has been studied as a therapeutic approach, but its functional regulatory mechanism in neuropathic pain is not well understood. Here, we identify that miRNA-32-5p (miR-32-5p) is a functional RNA in regulating trigeminal-mediated neuropathic pain. High-throughput sequencing and qPCR analysis showed that miR-32-5p was the most down-regulated miRNA in the injured trigeminal ganglion (TG) of rats. Intra-TG injection of miR-32-5p agomir or overexpression of miR-32-5p by lentiviral delivery in neurons of the injured TG attenuated established trigeminal neuropathic pain. miR-32-5p overexpression did not affect acute physiological pain, while miR-32-5p down-regulation in intact rats was sufficient to cause pain-related behaviors. Nerve injury increased the methylated histone occupancy of binding sites for the transcription factor glucocorticoid receptor in the miR-32-5p promoter region. Inhibition of the enzymes that catalyze H3K9me2 and H3K27me3 restored the expression of miR-32-5p and markedly attenuated pain behaviors. Further, miR-32-5p–targeted Cav3.2 T-type Ca2+ channels and decreased miR-32-5p associated with neuropathic pain caused an increase in Cav3.2 protein expression and T-type channel currents. Conversely, miR-32-5p overexpression in injured TG suppressed the increased expression of Cav3.2 and reversed mechanical allodynia. Together, we conclude that histone methylation-mediated miR-32-5p down-regulation in TG neurons regulates trigeminal neuropathic pain by targeting Cav3.2 channels.
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13
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Sheehy RN, Quintanilla LJ, Song J. Epigenetic regulation in the neurogenic niche of the adult dentate gyrus. Neurosci Lett 2022; 766:136343. [PMID: 34774980 PMCID: PMC8691367 DOI: 10.1016/j.neulet.2021.136343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/06/2021] [Accepted: 11/08/2021] [Indexed: 01/03/2023]
Abstract
The adult dentate gyrus (DG) of the hippocampal formation is a specialized region of the brain that creates new adult-born neurons from a pool of resident adult neural stem and progenitor cells (aNSPCs) throughout life. These aNSPCs undergo epigenetic and epitranscriptomic regulation, including 3D genome interactions, histone modifications, DNA modifications, noncoding RNA mechanisms, and RNA modifications, to precisely control the neurogenic process. Furthermore, the specialized neurogenic niche also uses epigenetic mechanisms in mature neurons and glial cells to communicate signals to direct the behavior of the aNSPCs. Here, we review recent advances of epigenetic regulation in aNSPCs and their surrounding niche cells within the adult DG.
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Affiliation(s)
- Ryan N. Sheehy
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Pharmacology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Luis J. Quintanilla
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Neuroscience Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Juan Song
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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14
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Seelbinder B, Ghosh S, Schneider SE, Scott AK, Berman AG, Goergen CJ, Margulies KB, Bedi K, Casas E, Swearingen AR, Brumbaugh J, Calve S, Neu CP. Nuclear deformation guides chromatin reorganization in cardiac development and disease. Nat Biomed Eng 2021; 5:1500-1516. [PMID: 34857921 PMCID: PMC9300284 DOI: 10.1038/s41551-021-00823-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 10/20/2021] [Indexed: 01/31/2023]
Abstract
In cardiovascular tissues, changes in the mechanical properties of the extracellular matrix are associated with cellular de-differentiation and with subsequent functional declines. However, the underlying mechanoreceptive mechanisms are largely unclear. Here, by generating high-resolution, full-field strain maps of cardiomyocyte nuclei during contraction in vitro, complemented with evidence from tissues from patients with cardiomyopathy and from mice with reduced cardiac performance, we show that cardiomyocytes establish a distinct nuclear organization during maturation, characterized by the reorganization of H3K9me3-marked chromatin towards the nuclear border. Specifically, we show that intranuclear tension is spatially correlated with H3K9me3-marked chromatin, that reductions in nuclear deformation (through environmental stiffening or through the disruption of complexes of the linker of nucleoskeleton and cytoskeleton) abrogate chromatin reorganization and lead to the dissociation of H3K9me3-marked chromatin from the nuclear periphery, and that the suppression of H3K9 methylation induces chromatin reorganization and reduces the expression of cardiac developmental genes. Overall, our findings indicate that, by integrating environmental mechanical cues, the nuclei of cardiomyocytes guide and stabilize the fate of cells through the reorganization of epigenetically marked chromatin.
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Affiliation(s)
- Benjamin Seelbinder
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO)
| | - Soham Ghosh
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO)
| | | | - Adrienne K. Scott
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO)
| | - Alycia G. Berman
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette (IN)
| | - Craig J. Goergen
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette (IN)
| | | | - Kenneth Bedi
- Cardiovascular Institute, University of Pennsylvania, Philadelphia (PA)
| | - Eduard Casas
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder (CO)
| | - Alison R. Swearingen
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder (CO)
| | - Justin Brumbaugh
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder (CO)
| | - Sarah Calve
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO),Weldon School of Biomedical Engineering, Purdue University, West Lafayette (IN)
| | - Corey P. Neu
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO),Corresponding Author
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15
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Zhang Y, Li F, Fu K, Liu X, Lien IC, Li H. Potential Role of S-Palmitoylation in Cancer Stem Cells of Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:734897. [PMID: 34621750 PMCID: PMC8490697 DOI: 10.3389/fcell.2021.734897] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
S-palmitoylation, catalyzed by a family of 23 zinc finger Asp-His-His-Cys (DHHC) domain-containing (ZDHHC) protein acyltransferases localized on the cell membrane. However, stemness genes modulated by ZDHHCs in lung adenocarcinoma (LUAD) remain to be defined. Previously, we have constructed a network of cancer stem cell genes, including INCENP, based on mRNA stemness indices (mRNAsi) of LUAD. INCENP has the function of a chromosomal passenger complex locating to centromeres, which is performed by the conserved region of its N-terminal domain. INCENP protein with a deletion of the first non-conserved 26 amino acid sequence failed to target centromeres. However, the exact function of the deleted sequence has not been elucidated. To identify novel cancer stem cell-relevant palmitoylated proteins and responsible ZDHHC enzymes in LUAD, we analyzed multi-omics data obtained from the database of The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Clinical Proteomic Tumor Analysis Consortium (CPTAC), and the Human Protein Atlas (HPA). ZDHHC5 is distinguished from the ZDHHC family for being up-regulated in mRNA and protein levels and associated with malignant prognosis. ZDHHC5 was positively associated with INCENP, and the correlation score increased with LUAD stages. CSS-Palm results showed Cys15 was the S-palmitoylation site of INCENP. Interestingly, Cys15 locates in the 1-26 aa sequence of INCENP, and is a conserved site across species. As INCENP is a nuclear protein, we predicted that the nuclear localization signal of ZDHHC5 was specific to the importin αβ pathway, and the result of immunofluorescence proves that ZDHHC5 is located in the nucleoplasm, in addition to the plasma membrane. Therefore, our study indicates the S-palmitoylation of INCENP mediated by ZDHHC5 as a potential mechanism of S-palmitoylation to modulate CSCs in LUAD.
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Affiliation(s)
- Yitong Zhang
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Fenglan Li
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Kexin Fu
- Department of Gastrointestinal, The First Hospital of Jilin University, Changchun, China
| | - Xiqing Liu
- The State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, China
| | - I-Chia Lien
- Insight Genomics Inc., National Cheng Kung University, Tainan, Taiwan
| | - Hui Li
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
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16
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Abstract
Neuroepigenetics, a new branch of epigenetics, plays an important role in the regulation of gene expression. Neuroepigenetics is associated with holistic neuronal function and helps in formation and maintenance of memory and learning processes. This includes neurodevelopment and neurodegenerative defects in which histone modification enzymes appear to play a crucial role. These modifications, carried out by acetyltransferases and deacetylases, regulate biologic and cellular processes such as apoptosis and autophagy, inflammatory response, mitochondrial dysfunction, cell-cycle progression and oxidative stress. Alterations in acetylation status of histone as well as non-histone substrates lead to transcriptional deregulation. Histone deacetylase decreases acetylation status and causes transcriptional repression of regulatory genes involved in neural plasticity, synaptogenesis, synaptic and neural plasticity, cognition and memory, and neural differentiation. Transcriptional deactivation in the brain results in development of neurodevelopmental and neurodegenerative disorders. Mounting evidence implicates histone deacetylase inhibitors as potential therapeutic targets to combat neurologic disorders. Recent studies have targeted naturally-occurring biomolecules and micro-RNAs to improve cognitive defects and memory. Multi-target drug ligands targeting HDAC have been developed and used in cell-culture and animal-models of neurologic disorders to ameliorate synaptic and cognitive dysfunction. Herein, we focus on the implications of histone deacetylase enzymes in neuropathology, their regulation of brain function and plausible involvement in the pathogenesis of neurologic defects.
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17
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Peter M, Aschauer DF, Rose R, Sinning A, Grössl F, Kargl D, Kraitsy K, Burkard TR, Luhmann HJ, Haubensak W, Rumpel S. Rapid nucleus-scale reorganization of chromatin in neurons enables transcriptional adaptation for memory consolidation. PLoS One 2021; 16:e0244038. [PMID: 33951054 PMCID: PMC8099114 DOI: 10.1371/journal.pone.0244038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/05/2021] [Indexed: 12/27/2022] Open
Abstract
The interphase nucleus is functionally organized in active and repressed territories defining the transcriptional status of the cell. However, it remains poorly understood how the nuclear architecture of neurons adapts in response to behaviorally relevant stimuli that trigger fast alterations in gene expression patterns. Imaging of fluorescently tagged nucleosomes revealed that pharmacological manipulation of neuronal activity in vitro and auditory cued fear conditioning in vivo induce nucleus-scale restructuring of chromatin within minutes. Furthermore, the acquisition of auditory fear memory is impaired after infusion of a drug into auditory cortex which blocks chromatin reorganization in vitro. We propose that active chromatin movements at the nucleus scale act together with local gene-specific modifications to enable transcriptional adaptations at fast time scales. Introducing a transgenic mouse line for photolabeling of histones, we extend the realm of systems available for imaging of chromatin dynamics to living animals.
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Affiliation(s)
- Manuel Peter
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Dominik F. Aschauer
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Renata Rose
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Anne Sinning
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Florian Grössl
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Dominic Kargl
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Klaus Kraitsy
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Preclinical Phenotyping, Vienna Biocenter Core Facilities, Vienna, Austria
| | - Thomas R. Burkard
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Heiko J. Luhmann
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Wulf Haubensak
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Simon Rumpel
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
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18
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Neural Stem Cell-Derived Exosomes Revert HFD-Dependent Memory Impairment via CREB-BDNF Signalling. Int J Mol Sci 2020; 21:ijms21238994. [PMID: 33256199 PMCID: PMC7729830 DOI: 10.3390/ijms21238994] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 11/17/2022] Open
Abstract
Overnutrition and metabolic disorders impair cognitive functions through molecular mechanisms still poorly understood. In mice fed with a high fat diet (HFD) we analysed the expression of synaptic plasticity-related genes and the activation of cAMP response element-binding protein (CREB)-brain-derived neurotrophic factor (BDNF)-tropomyosin receptor kinase B (TrkB) signalling. We found that a HFD inhibited both CREB phosphorylation and the expression of a set of CREB target genes in the hippocampus. The intranasal administration of neural stem cell (NSC)-derived exosomes (exo-NSC) epigenetically restored the transcription of Bdnf, nNOS, Sirt1, Egr3, and RelA genes by inducing the recruitment of CREB on their regulatory sequences. Finally, exo-NSC administration rescued both BDNF signalling and memory in HFD mice. Collectively, our findings highlight novel mechanisms underlying HFD-related memory impairment and provide evidence of the potential therapeutic effect of exo-NSC against metabolic disease-related cognitive decline.
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19
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Lloyd S, Larivée A. Time, trauma, and the brain: How suicide came to have no significant precipitating event. SCIENCE IN CONTEXT 2020; 33:299-327. [PMID: 34096495 DOI: 10.1017/s0269889721000065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In this article, we trace shifting narratives of trauma within psychiatric, neuroscience, and environmental epigenetics research. We argue that two contemporary narratives of trauma - each of which concerns questions of time and psychopathology, of the past invading the present - had to be stabilized in order for environmental epigenetics models of suicide risk to be posited. Through an examination of these narratives, we consider how early trauma came to be understood as playing an etiologically significant role in the development of suicide risk. Suicide, in these models, has come to be seen as a behavior that has no significant precipitating event, but rather an exceptional precipitating neurochemical state, whose origins are identified in experiences of early traumatic events. We suggest that this is a part of a broader move within contemporary neurosciences and biopsychiatry to see life as post: seeing life as specific form of post-traumatic subjectivity.
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20
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Bianchetti G, Di Giacinto F, De Spirito M, Maulucci G. Machine-learning assisted confocal imaging of intracellular sites of triglycerides and cholesteryl esters formation and storage. Anal Chim Acta 2020; 1121:57-66. [PMID: 32493590 DOI: 10.1016/j.aca.2020.04.076] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/30/2020] [Accepted: 04/28/2020] [Indexed: 11/30/2022]
Abstract
All living systems are maintained by a constant flux of metabolic energy and, among the different reactions, the process of lipids storage and lipolysis is of fundamental importance. Current research has focused on the investigation of lipid droplets (LD) as a powerful biomarker for the early detection of metabolic and neurological disorders. Efforts in this field aim at increasing selectivity for LD detection by exploiting existing or newly synthesized probes. However, LD constitute only the final product of a complex series of reactions during which fatty acids are transformed into triglycerides and cholesterol is transformed in cholesteryl esters. These final products can be accumulated in intracellular organelles or deposits other than LD. A complete spatial mapping of the intracellular sites of triglycerides and cholesteryl esters formation and storage is, therefore, crucial to highlight any potential metabolic imbalance, thus predicting and counteracting its progression. Here, we present a machine learning assisted, polarity-driven segmentation which enables to localize and quantify triglycerides and cholesteryl esters biosynthesis sites in all intracellular organelles, thus allowing to monitor in real-time the overall process of the turnover of these non-polar lipids in living cells. This technique is applied to normal and differentiated PC12 cells to test how the level of activation of biosynthetic pathways changes in response to the differentiation process.
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Affiliation(s)
- Giada Bianchetti
- Fondazione Policlinico Universitario A. Gemelli IRCSS, Rome, Italy; Dipartimento di Neuroscienze, Università Cattolica Del Sacro Cuore, Rome, Italy
| | - Flavio Di Giacinto
- Fondazione Policlinico Universitario A. Gemelli IRCSS, Rome, Italy; Dipartimento di Neuroscienze, Università Cattolica Del Sacro Cuore, Rome, Italy
| | - Marco De Spirito
- Fondazione Policlinico Universitario A. Gemelli IRCSS, Rome, Italy; Dipartimento di Neuroscienze, Università Cattolica Del Sacro Cuore, Rome, Italy
| | - Giuseppe Maulucci
- Fondazione Policlinico Universitario A. Gemelli IRCSS, Rome, Italy; Dipartimento di Neuroscienze, Università Cattolica Del Sacro Cuore, Rome, Italy.
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21
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Barra R, Morgan C, Sáez-Briones P, Reyes-Parada M, Burgos H, Morales B, Hernández A. Facts and hypotheses about the programming of neuroplastic deficits by prenatal malnutrition. Nutr Rev 2020; 77:65-80. [PMID: 30445479 DOI: 10.1093/nutrit/nuy047] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Studies in rats have shown that a decrease in either protein content or total dietary calories results in molecular, structural, and functional changes in the cerebral cortex and hippocampus, among other brain regions, which lead to behavioral disturbances, including learning and memory deficits. The neurobiological bases underlying those effects depend at least in part on fetal programming of the developing brain, which in turn relies on epigenetic regulation of specific genes via stable and heritable modifications of chromatin. Prenatal malnutrition also leads to epigenetic programming of obesity, and obesity on its own can lead to poor cognitive performance in humans and experimental animals, complicating understanding of the factors involved in the fetal programming of neuroplasticity deficits. This review focuses on the role of epigenetic mechanisms involved in prenatal malnutrition-induced brain disturbances, which are apparent at a later postnatal age, through either a direct effect of fetal programming on brain plasticity or an indirect effect on the brain mediated by the postnatal development of obesity.
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Affiliation(s)
- Rafael Barra
- School of Medicine, Faculty of Medical Sciences, University of Santiago de Chile, Santiago, Chile
| | - Carlos Morgan
- Laboratory of Nutrition and Metabolic Regulation, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Patricio Sáez-Briones
- School of Medicine, Faculty of Medical Sciences, University of Santiago de Chile, Santiago, Chile
| | - Miguel Reyes-Parada
- School of Medicine, Faculty of Medical Sciences, University of Santiago de Chile, Santiago, Chile.,Facultad de Ciencias de la Salud Universidad Autónoma de Chile, Talca, Chile
| | - Héctor Burgos
- Núcleo Disciplinar Psicología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.,Center of Innovation on Information Technologies for Social Applications (CITIAPS), University of Santiago de Chile, Santiago, Chile
| | - Bernardo Morales
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago de Chile, Santiago, Chile
| | - Alejandro Hernández
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago de Chile, Santiago, Chile
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22
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Latusz J, Maćkowiak M. Early-life blockade of NMDA receptors induces epigenetic abnormalities in the adult medial prefrontal cortex: possible involvement in memory impairment in trace fear conditioning. Psychopharmacology (Berl) 2020; 237:231-248. [PMID: 31654083 PMCID: PMC6952333 DOI: 10.1007/s00213-019-05362-5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/11/2019] [Indexed: 12/20/2022]
Abstract
RATIONALE Several findings indicate that early-life dysfunction of N-methyl-D-aspartate (NMDA) receptors might cause schizophrenia-like abnormalities in adulthood that might be induced by impairments in epigenetic regulation. OBJECTIVES In the present study, we investigated whether postnatal blockade of NMDA receptors (within the first 3 weeks of life) by the competitive antagonist CGP 37849 (CGP) might affect some epigenetic markers in the adult medial prefrontal cortex (mPFC). METHODS Histone H3 phosphorylation at serine 10 (H3S10ph), histone H3 acetylation at lysine 9 or 14 (H3K9ac or H3K14ac, respectively), or expression of histone deacetylase (HDAC) 2, HDAC5, myocyte enhancer factor (MEF) 2D and activity-regulated cytoskeleton-associated protein (Arc) were analysed. Moreover, we also evaluated whether the deacetylase inhibitor sodium butyrate (SB; 1.2 mg/kg, ip) could prevent behavioural and neurochemical changes in the mPFC induced by CGP during memory retrieval in the trace fear conditioning paradigm. RESULTS The results showed that CGP administration increased the number of H3S10ph nuclei but did not affect H3K9ac and H3K14ac or HDAC2 protein levels. However, CGP administration altered the HDAC5 mRNA and protein levels and increased the mRNA and protein levels of MEF2D. CGP also increased Arc mRNA, which was correlated with an increase in the amount of Arc DNA bound to MEF2D. SB given 2 h after training prevented impairment of the freezing response and disruption of epigenetic markers (H3S10ph, HDAC5, MEF2D) and Arc expression during memory retrieval induced by CGP administration. CONCLUSIONS The early-life blockade of NMDA receptors impairs some epigenetic regulatory processes in the mPFC that are involved in fear memory formation.
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Affiliation(s)
- Joachim Latusz
- grid.413454.30000 0001 1958 0162Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Pharmacology, Laboratory of Pharmacology and Brain Biostructure, Smętna Str. 12, 31-343 Kraków, Poland
| | - Marzena Maćkowiak
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Pharmacology, Laboratory of Pharmacology and Brain Biostructure, Smętna Str. 12, 31-343, Kraków, Poland.
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24
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Abstract
Permanent disabilities following CNS injuries result from the failure of injured axons to regenerate and rebuild functional connections with their original targets. By contrast, injury to peripheral nerves is followed by robust regeneration, which can lead to recovery of sensory and motor functions. This regenerative response requires the induction of widespread transcriptional and epigenetic changes in injured neurons. Considerable progress has been made in recent years in understanding how peripheral axon injury elicits these widespread changes through the coordinated actions of transcription factors, epigenetic modifiers and, to a lesser extent, microRNAs. Although many questions remain about the interplay between these mechanisms, these new findings provide important insights into the pivotal role of coordinated gene expression and chromatin remodelling in the neuronal response to injury.
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Affiliation(s)
- Marcus Mahar
- Department of Neuroscience, Hope Center for Neurological Disorders and Center of Regenerative Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Valeria Cavalli
- Department of Neuroscience, Hope Center for Neurological Disorders and Center of Regenerative Medicine, Washington University School of Medicine, St Louis, MO, USA.
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25
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Martínez-Juárez A, Moreno-Mendoza N. Mechanisms related to sexual determination by temperature in reptiles. J Therm Biol 2019; 85:102400. [PMID: 31657741 DOI: 10.1016/j.jtherbio.2019.102400] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 08/12/2019] [Accepted: 08/21/2019] [Indexed: 01/08/2023]
Abstract
A number of strategies have emerged that appear to relate to the evolution of mechanisms for sexual determination in vertebrates, among which are genetic sex determination caused by sex chromosomes and environmental sex determination, where environmental factors influence the phenotype of the sex of an individual. Within the reptile group, some orders such as: Chelonia, Crocodylia, Squamata and Rhynchocephalia, manifest one of the most intriguing and exciting environmental sexual determination mechanisms that exists, comprising temperature-dependent sex determination (TSD), where the temperature of incubation that the embryo experiences during its development is fundamental to establishing the sex of the individual. This makes them an excellent model for the study of sexual determination at the molecular, cellular and physiological level, as well as in terms of their implications at an evolutionary and ecological level. There are different hypotheses concerning how this process is triggered and this review aims to describe any new contributions to particular TSD hypotheses, analyzing them from the "eco-evo-devo" perspective.
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Affiliation(s)
- Adriana Martínez-Juárez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228 México, D.F. 04510, Mexico
| | - Norma Moreno-Mendoza
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228 México, D.F. 04510, Mexico.
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26
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Li KN, Zhang YY, Yu YN, Wu HL, Wang Z. Met-Controlled Allosteric Module of Neural Generation as A New Therapeutic Target in Rodent Brain Ischemia. Chin J Integr Med 2019; 27:896-904. [PMID: 31418133 DOI: 10.1007/s11655-019-3182-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2019] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To investigate a Met-controlled allosteric module (AM) of neural generation as a potential therapeutic target for brain ischemia. METHODS We selected Markov clustering algorithm (MCL) to mine functional modules in the related target networks. According to the topological similarity, one functional module was predicted in the modules of baicalin (BA), jasminoidin (JA), cholic acid (CA), compared with I/R model modules. This functional module included three genes: Inppl1, Met and Dapk3 (IMD). By gene ontology enrichment analysis, biological process related to this functional module was obtained. This functional module participated in generation of neurons. Western blotting was applied to present the compound-dependent regulation of IMD. Co-immunoprecipitation was used to reveal the relationship among the three members. We used IF to determine the number of newborn neurons between compound treatment group and ischemia/reperfusion group. The expressions of vascular endothelial growth factor (VEGF) and matrix metalloproteinase 9 (MMP-9) were supposed to show the changing circumstances for neural generation under cerebral ischemia. RESULTS Significant reduction in infarction volume and pathological changes were shown in the compound treatment groups compared with the I/R model group (P<0.05). Three nodes in one novel module of IMD were found to exert diverse compound-dependent ischemic-specific excitatory regulatory activities. An anti-ischemic excitatory allosteric module (AME) of generation of neurons (AME-GN) was validated successfully in vivo. Newborn neurons increased in BJC treatment group (P<0.05). The expression of VEGF and MMP-9 decreased in the compound treatment groups compared with the I/R model group (P<0.05). CONCLUSIONS AME demonstrates effectiveness of our pioneering approach to the discovery of therapeutic target. The novel approach for AM discovery in an effort to identify therapeutic targets holds the promise of accelerating elucidation of underlying pharmacological mechanisms in cerebral ischemia.
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Affiliation(s)
- Kang-Ning Li
- Department of Traditional Chinese Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Ying-Ying Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ya-Nan Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Hong-Li Wu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Colbran LL, Chen L, Capra JA. Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity. Genetics 2019; 211:1205-1217. [PMID: 30696717 PMCID: PMC6456323 DOI: 10.1534/genetics.118.301895] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 01/27/2019] [Indexed: 01/08/2023] Open
Abstract
Enhancers and promoters both regulate gene expression by recruiting transcription factors (TFs); however, the degree to which enhancer vs. promoter activity is due to differences in their sequences or to genomic context is the subject of ongoing debate. We examined this question by analyzing the sequences of thousands of transcribed enhancers and promoters from hundreds of cellular contexts previously identified by cap analysis of gene expression. Support vector machine classifiers trained on counts of all possible 6-bp-long sequences (6-mers) were able to accurately distinguish promoters from enhancers and distinguish their breadth of activity across tissues. Classifiers trained to predict enhancer activity also performed well when applied to promoter prediction tasks, but promoter-trained classifiers performed poorly on enhancers. This suggests that the learned sequence patterns predictive of enhancer activity generalize to promoters, but not vice versa. Our classifiers also indicate that there are functionally relevant differences in enhancer and promoter GC content beyond the influence of CpG islands. Furthermore, sequences characteristic of broad promoter or broad enhancer activity matched different TFs, with predicted ETS- and RFX-binding sites indicative of promoters, and AP-1 sites indicative of enhancers. Finally, we evaluated the ability of our models to distinguish enhancers and promoters defined by histone modifications. Separating these classes was substantially more difficult, and this difference may contribute to ongoing debates about the similarity of enhancers and promoters. In summary, our results suggest that high-confidence transcribed enhancers and promoters can largely be distinguished based on biologically relevant sequence properties.
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Affiliation(s)
- Laura L Colbran
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee 37235
| | - Ling Chen
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
| | - John A Capra
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee 37235
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
- Center for Structural Biology, Departments of Biomedical Informatics and Computer Science, Vanderbilt University, Nashville, Tennessee 37235
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28
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Spinelli M, Fusco S, Grassi C. Nutrient-Dependent Changes of Protein Palmitoylation: Impact on Nuclear Enzymes and Regulation of Gene Expression. Int J Mol Sci 2018; 19:ijms19123820. [PMID: 30513609 PMCID: PMC6320809 DOI: 10.3390/ijms19123820] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/22/2018] [Accepted: 11/27/2018] [Indexed: 12/13/2022] Open
Abstract
Diet is the main environmental stimulus chronically impinging on the organism throughout the entire life. Nutrients impact cells via a plethora of mechanisms including the regulation of both protein post-translational modifications and gene expression. Palmitoylation is the most-studied protein lipidation, which consists of the attachment of a molecule of palmitic acid to residues of proteins. S-palmitoylation is a reversible cysteine modification finely regulated by palmitoyl-transferases and acyl-thioesterases that is involved in the regulation of protein trafficking and activity. Recently, several studies have demonstrated that diet-dependent molecules such as insulin and fatty acids may affect protein palmitoylation. Here, we examine the role of protein palmitoylation on the regulation of gene expression focusing on the impact of this modification on the activity of chromatin remodeler enzymes, transcription factors, and nuclear proteins. We also discuss how this physiological phenomenon may represent a pivotal mechanism underlying the impact of diet and nutrient-dependent signals on human diseases.
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Affiliation(s)
- Matteo Spinelli
- Institute of Human Physiology, Università Cattolica del Sacro Cuore, Rome 00168, Italy.
| | - Salvatore Fusco
- Institute of Human Physiology, Università Cattolica del Sacro Cuore, Rome 00168, Italy.
- Fondazione Policlinico Universitario A. Gemelli IRCSS, Rome 00168, Italy.
| | - Claudio Grassi
- Institute of Human Physiology, Università Cattolica del Sacro Cuore, Rome 00168, Italy.
- Fondazione Policlinico Universitario A. Gemelli IRCSS, Rome 00168, Italy.
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29
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Chatterjee B, Lin MH, Chen CC, Peng KL, Wu MS, Tseng MC, Chen YJ, Shen CKJ. DNA Demethylation by DNMT3A and DNMT3B in vitro and of Methylated Episomal DNA in Transiently Transfected Cells. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:1048-1061. [PMID: 30300721 DOI: 10.1016/j.bbagrm.2018.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/03/2018] [Accepted: 09/25/2018] [Indexed: 12/24/2022]
Abstract
The DNA methylation program in vertebrates is an essential part of the epigenetic regulatory cascade of development, cell differentiation, and progression of diseases including cancer. While the DNA methyltransferases (DNMTs) are responsible for the in vivo conversion of cytosine (C) to methylated cytosine (5mC), demethylation of 5mC on cellular DNA could be accomplished by the combined action of the ten-eleven translocation (TET) enzymes and DNA repair. Surprisingly, the mammalian DNMTs also possess active DNA demethylation activity in vitro in a Ca2+- and redox conditions-dependent manner, although little is known about its molecular mechanisms and occurrence in a cellular context. In this study, we have used LC-MS/MS to track down the fate of the methyl group removed from 5mC on DNA by mouse DNMT3B in vitro and found that it becomes covalently linked to the DNA methylation catalytic cysteine of the enzyme. We also show that Ca2+ homeostasis-dependent but TET1/TET2/TET3/TDG-independent demethylation of methylated episomal DNA by mouse DNMT3A or DNMT3B can occur in transfected human HEK 293 and mouse embryonic stem (ES) cells. Based on these results, we present a tentative working model of Ca2+ and redox conditions-dependent active DNA demethylation by DNMTs. Our study substantiates the potential roles of the vertebrate DNMTs as double-edged swords in DNA methylation-demethylation during Ca2+-dependent physiological processes.
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Affiliation(s)
| | - Miao-Hsia Lin
- Institute of Chemistry, Academia Sinica, Taipei City 115, Taiwan
| | - Chun-Chang Chen
- Institute of Molecular Biology, Academia Sinica, Taipei City 115, Taiwan
| | - Kai-Lin Peng
- Genomics Research Center, Academia Sinica, Taipei City 115, Taiwan
| | - Mu-Sheng Wu
- Genomics Research Center, Academia Sinica, Taipei City 115, Taiwan; Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei City 112, Taiwan
| | - Mei-Chun Tseng
- Institute of Chemistry, Academia Sinica, Taipei City 115, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei City 115, Taiwan.
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Taipei City 115, Taiwan.
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30
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Abstract
The temporal coding of action potential activity is fundamental to nervous system function. Here we consider how gene expression in neurons is regulated by specific patterns of action potential firing, with an emphasis on new information on epigenetic regulation of gene expression. Patterned action potential activity activates intracellular signaling networks selectively in accordance with the kinetics of activation and inactivation of second messengers, phosphorylation and dephosphorylation of protein kinases, and cytoplasmic and nuclear calcium dynamics, which differentially activate specific transcription factors. Increasing evidence also implicates activity-dependent regulation of epigenetic mechanisms to alter chromatin architecture. Changes in three-dimensional chromatin structure, including chromatin compaction, looping, double-stranded DNA breaks, histone and DNA modification, are altered by action potential activity to selectively inhibit or promote transcription of specific genes. These mechanisms of activity-dependent regulation of gene expression are important in neural development, plasticity, and in neurological and psychological disorders.
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Affiliation(s)
- Jillian Belgrad
- Nervous System Development and Plasticity Section, The
Eunice Kennedy Shriver National Institute of Child Health and Human Development
(NICHD), Bethesda, MD, USA
| | - R. Douglas Fields
- Nervous System Development and Plasticity Section, The
Eunice Kennedy Shriver National Institute of Child Health and Human Development
(NICHD), Bethesda, MD, USA
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31
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Sellers KJ, Watson IA, Gresz RE, Raval P, Srivastava DP. Cyto-nuclear shuttling of afadin is required for rapid estradiol-mediated modifications of histone H3. Neuropharmacology 2018; 143:153-162. [PMID: 30268521 PMCID: PMC6277849 DOI: 10.1016/j.neuropharm.2018.09.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/18/2018] [Accepted: 09/25/2018] [Indexed: 12/19/2022]
Abstract
Estrogens have been shown to rapidly regulate local signalling at synapses and within the nucleus. The result of these signalling events is to rapidly modulate synapse structure and function, as well as epigenetic mechanisms including histone modifications. Ultimately these mechanisms are thought to contribute to long-lasting changes in neural circuitry, and thus influence cognitive functions such as learning and memory. However, the mechanisms by which estrogen-mediated local synaptic and nuclear signalling events are coordinated are not well understood. In this study we have found that the scaffold protein afadin, (also known as AF-6), undergoes a bi-directional trafficking to both synaptic and nuclear compartment in response to acute 17β-estradiol (estradiol) treatment, in mixed sex neuronal cultures derived from fetal cortex. Interestingly, nuclear accumulation of afadin was coincidental with an increase in the phosphorylation of histone H3 at serine 10 (H3S10p). This epigenetic modification is associated with the remodeling of chromatin into an open euchromatin state, allowing for transcriptional activation and related learning and memory processes. Critically, the cyto-nuclear trafficking of afadin was required for estradiol-dependent H3S10p. We further determined that nuclear accumulation of afadin is sufficient to induce phosphorylation of the mitogentic kinases ERK1/2 (pERK1/2) within the nucleus. Moreover, nuclear pERK1/2 was required for estradiol-dependent H3S10p. Taken together, we propose a model whereby estradiol induces the bi-directional trafficking of afadin to synaptic and nuclear sub-compartments. Within the nucleus, afadin is required for increased pERK1/2 which in turn is required for H3S10p. Therefore this represents a mechanism through which estrogens may be able to coordinate both synaptic and nucleosomal events within the same neuronal population. 17β-estradiol targets afadin to membrane and nuclear subcompartments. Histone H3 is rapidly phosphorylated by 17β-estradiol. Histone H3 phosphorylation by 17β-estradiol requires afadin nuclear accumulation. 17β-estradiol-mediated ERK1/2 activation is required for histone H3 phosphorylation.
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Affiliation(s)
- Katherine J Sellers
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, SE5 9RT, UK
| | - Iain A Watson
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, SE5 9RT, UK
| | - Rahel E Gresz
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, SE5 9RT, UK
| | - Pooja Raval
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, SE5 9RT, UK
| | - Deepak P Srivastava
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, SE5 9RT, UK.
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32
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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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33
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Role of Nitric Oxide and Hydrogen Sulfide in Ischemic Stroke and the Emergent Epigenetic Underpinnings. Mol Neurobiol 2018; 56:1749-1769. [PMID: 29926377 DOI: 10.1007/s12035-018-1141-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 05/22/2018] [Indexed: 02/06/2023]
Abstract
Nitric oxide (NO) and hydrogen sulfide (H2S) are the key gasotransmitters with an imperious role in the maintenance of cerebrovascular homeostasis. A decline in their levels contributes to endothelial dysfunction that portends ischemic stroke (IS) or cerebral ischemia/reperfusion (CI/R). Nevertheless, their exorbitant production during CI/R is associated with exacerbation of cerebrovascular injury in the post-stroke epoch. NO-producing nitric oxide synthases are implicated in IS pathology and their activity is regulated, inter alia, by various post-translational modifications and chromatin-based mechanisms. These account for heterogeneous alterations in NO production in a disease setting like IS. Interestingly, NO per se has been posited as an endogenous epigenetic modulator. Further, there is compelling evidence for an ingenious crosstalk between NO and H2S in effecting the canonical (direct) and non-canonical (off-target collateral) functions. In this regard, NO-mediated S-nitrosylation and H2S-mediated S-sulfhydration of specific reactive thiols in an expanding array of target proteins are the principal modalities mediating the all-pervasive influence of NO and H2S on cell fate in an ischemic brain. An integrated stress response subsuming unfolded protein response and autophagy to cellular stressors like endoplasmic reticulum stress, in part, is entrenched in such signaling modalities that substantiate the role of NO and H2S in priming the cells for stress response. The precis presented here provides a comprehension on the multifarious actions of NO and H2S and their epigenetic underpinnings, their crosstalk in maintenance of cerebrovascular homeostasis, and their "Janus bifrons" effect in IS milieu together with plausible therapeutic implications.
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34
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Lamar KMJ, Carvill GL. Chromatin Remodeling Proteins in Epilepsy: Lessons From CHD2-Associated Epilepsy. Front Mol Neurosci 2018; 11:208. [PMID: 29962935 PMCID: PMC6013553 DOI: 10.3389/fnmol.2018.00208] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/25/2018] [Indexed: 12/24/2022] Open
Abstract
The chromodomain helicase DNA-binding (CHD) family of proteins are ATP-dependent chromatin remodelers that contribute to the reorganization of chromatin structure and deposition of histone variants necessary to regulate gene expression. CHD proteins play an important role in neurodevelopment, as pathogenic variants in CHD1, CHD2, CHD4, CHD7 and CHD8 have been associated with a range of neurological phenotypes, including autism spectrum disorder (ASD), intellectual disability (ID) and epilepsy. Pathogenic variants in CHD2 are associated with developmental epileptic encephalopathy (DEE) in humans, however little is known about how these variants contribute to this disorder. Of the nine CHD family members, CHD2 is the only one that leads to a brain-restricted phenotype when disrupted in humans. This suggests that despite being expressed ubiquitously, CHD2 has a unique role in human brain development and function. In this review, we will discuss the phenotypic spectrum of patients with pathogenic variants in CHD2, current animal models of CHD2 deficiency, and the role of CHD2 in proliferation, neurogenesis, neuronal differentiation, chromatin remodeling and DNA-repair. We also consider how CHD2 depletion can affect each of these biological mechanisms and how these defects may underpin neurodevelopmental disorders including epilepsy.
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Affiliation(s)
- Kay-Marie J Lamar
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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35
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Ch’Ng SS, Lawrence AJ. Investigational drugs for alcohol use disorders: a review of preclinical data. Expert Opin Investig Drugs 2018; 27:459-474. [DOI: 10.1080/13543784.2018.1472763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Sarah S Ch’Ng
- Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
| | - Andrew J Lawrence
- Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
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36
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Manoli DS, Tollkuhn J. Gene regulatory mechanisms underlying sex differences in brain development and psychiatric disease. Ann N Y Acad Sci 2018; 1420:26-45. [PMID: 29363776 PMCID: PMC5991992 DOI: 10.1111/nyas.13564] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 10/26/2017] [Accepted: 11/01/2017] [Indexed: 12/12/2022]
Abstract
The sexual differentiation of the mammalian nervous system requires the precise coordination of the temporal and spatial regulation of gene expression in diverse cell types. Sex hormones act at multiple developmental time points to specify sex-typical differentiation during embryonic and early development and to coordinate subsequent responses to gonadal hormones later in life by establishing sex-typical patterns of epigenetic modifications across the genome. Thus, mutations associated with neuropsychiatric conditions may result in sexually dimorphic symptoms by acting on different neural substrates or chromatin landscapes in males and females. Finally, as stress hormone signaling may directly alter the molecular machinery that interacts with sex hormone receptors to regulate gene expression, the contribution of chronic stress to the pathogenesis or presentation of mental illness may be additionally different between the sexes. Here, we review the mechanisms that contribute to sexual differentiation in the mammalian nervous system and consider some of the implications of these processes for sex differences in neuropsychiatric conditions.
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Affiliation(s)
- Devanand S. Manoli
- Department of Psychiatry and Weill Institute for Neuroscience, University of California, San Francisco, San Francisco, California
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37
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Restoring Tip60 HAT/HDAC2 Balance in the Neurodegenerative Brain Relieves Epigenetic Transcriptional Repression and Reinstates Cognition. J Neurosci 2018; 38:4569-4583. [PMID: 29654189 DOI: 10.1523/jneurosci.2840-17.2018] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 03/26/2018] [Accepted: 04/06/2018] [Indexed: 12/16/2022] Open
Abstract
Cognitive decline is a debilitating hallmark during preclinical stages of Alzheimer's disease (AD), yet the causes remain unclear. Because histone acetylation homeostasis is critical for mediating epigenetic gene control throughout neuronal development, we postulated that its misregulation contributes to cognitive impairment preceding AD pathology. Here, we show that disruption of Tip60 histone acetlytransferase (HAT)/histone deacetylase 2 (HDAC2) homeostasis occurs early in the brain of an AD-associated amyloid precursor protein (APP) Drosophila model and triggers epigenetic repression of neuroplasticity genes well before Aβ plaques form in male and female larvae. Repressed genes display enhanced HDAC2 binding and reduced Tip60 and histone acetylation enrichment. Increasing Tip60 in the AD-associated APP brain restores Tip60 HAT/HDAC2 balance by decreasing HDAC2 levels, reverses neuroepigenetic alterations to activate synaptic plasticity genes, and reinstates brain morphology and cognition. Such Drosophila neuroplasticity gene epigenetic signatures are conserved in male and female mouse hippocampus and their expression and Tip60 function is compromised in hippocampus from AD patients. We suggest that Tip60 HAT/HDAC2-mediated epigenetic gene disruption is a critical initial step in AD that is reversed by restoring Tip60 in the brain.SIGNIFICANCE STATEMENT Mild cognitive impairment is a debilitating hallmark during preclinical stages of Alzheimer's disease (AD), yet its causes remain unclear. Although recent findings support elevated histone deacetylase 2 (HDAC2) as a cause for epigenetic repression of synaptic genes that contribute to cognitive deficits, whether alterations in histone acetlytransferase (HAT) levels that counterbalance HDAC2 repressor action occur and the identity of these HATs remain unknown. We demonstrate that disruption of Tip60 HAT/HDAC2 homeostasis occurs early in the AD Drosophila brain and triggers epigenetic repression of neuroplasticity genes before Aβ plaques form. Increasing Tip60 in the AD brain restores Tip60 HAT/HDAC2 balance, reverses neuroepigenetic alterations to activate synaptic genes, and reinstates brain morphology and cognition. Our data suggest that disruption of the Tip60 HAT/HDAC2 balance is a critical initial step in AD.
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38
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Legault LM, Bertrand-Lehouillier V, McGraw S. Pre-implantation alcohol exposure and developmental programming of FASD: an epigenetic perspective. Biochem Cell Biol 2018; 96:117-130. [DOI: 10.1139/bcb-2017-0141] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Exposure to alcohol during in-utero development can permanently change the developmental programming of physiological responses, thereby increasing the risk of neurological illnesses during childhood and later adverse health outcomes associated with fetal alcohol spectrum disorder (FASD). There is an increasing body of evidence indicating that exposure to alcohol during gestation triggers lasting epigenetic alterations in offspring, long after the initial insult; together, these studies support the role of epigenetics in FASD etiology. However, we still have little information about how ethanol interferes with the fundamental epigenetic reprogramming wave (e.g., erasure and re-establishment of DNA methylation marks) that characterizes pre-implantation embryo development. This review examines key epigenetic processes that occur during pre-implantation development and especially focus on the current knowledge regarding how prenatal exposure to alcohol during this period could affect the developmental programming of the early stage pre-implantation embryo. We will also outline the current limitations of studies examining the in-vivo and in-vitro effects of alcohol exposure on embryos and underline the next critical steps to be taken if we want to better understand the implicated mechanisms to strengthen the translational potential for epigenetic markers for non-invasive early detection, and the treatment of newborns that have higher risk of developing FASD.
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Affiliation(s)
- Lisa-Marie Legault
- Department of Biochemistry and Molecular Medicine, Université de Montreal, Research Center of the CHU Sainte-Justine, 3175 Côte Sainte-Catherine, Montreal, QC H3T 1C5, Canada
| | - Virginie Bertrand-Lehouillier
- Department of Biochemistry and Molecular Medicine, Université de Montreal, Research Center of the CHU Sainte-Justine, 3175 Côte Sainte-Catherine, Montreal, QC H3T 1C5, Canada
| | - Serge McGraw
- Department of Biochemistry and Molecular Medicine, Université de Montreal, Research Center of the CHU Sainte-Justine, 3175 Côte Sainte-Catherine, Montreal, QC H3T 1C5, Canada
- Obstetrics and Gynecology, Université de Montreal, Research Center of the CHU Sainte-Justine, Montreal, Canada
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39
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Negative regulation of REST on NR2B in spinal cord contributes to the development of bone cancer pain in mice. Oncotarget 2018; 7:85564-85572. [PMID: 27732941 PMCID: PMC5356758 DOI: 10.18632/oncotarget.9447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/15/2016] [Indexed: 11/25/2022] Open
Abstract
In this study, C3H/HeNCrlVr mice are implanted with sarcoma NCTC 2472 cells into the intramedullary space of the femur to induce ongoing bone cancer-related pain behaviors. During the progress of the bone cancer pain, the down-regulation in spinal REST (Neuron-restrictive silencer factor, NRSF/REST) with concomitant up-regulation in spinal NR2B (2B subunit of N-methyl-D-aspartate receptor, NR2B) protein expression are observed at days 5, 7, 10 and 14 post-inoculation. Immunofluorescence assay shows that almost all of REST and NR2B-positive signals encompass NeuN (neuron-specific nuclear protein, a neuronal marker)-positive signals in spinal cord of sham and tumor-bearing mice. Different from previous researches involved in the main distribution of REST in neural progenitors, the expression of REST in mature neurons in spinal cord of adult mice is observed. Intrathecal administration of AS-ODN of REST at days 0, 2, 4 and 6 post-inoculation further enhances expression of spinal NR2B at day 7 post-inoculation, which suggests the reduced suppression of spinal REST on NR2B during the development of bone cancer pain. In summary, our study provides the evidence that the negative regulation of REST on NR2B in spinal cord takes part in the exacerbation of bone cancer pain.
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Chronic treatment with fluoride affects the jejunum: insights from proteomics and enteric innervation analysis. Sci Rep 2018; 8:3180. [PMID: 29453425 PMCID: PMC5816638 DOI: 10.1038/s41598-018-21533-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 02/06/2018] [Indexed: 01/29/2023] Open
Abstract
Gastrointestinal symptoms are the first signs of fluoride (F) toxicity. In the present study, the jejunum of rats chronically exposed to F was evaluated by proteomics, as well as by morphological analysis. Wistar rats received water containing 0, 10 or 50 mgF/L during 30 days. HuC/D, neuronal Nitric Oxide (nNOS), Vasoactive Intestinal Peptide (VIP), Calcitonin Gene Related Peptide (CGRP), and Substance P (SP) were detected in the myenteric plexus of the jejunum by immunofluorescence. The density of nNOS-IR neurons was significantly decreased (compared to both control and 10 mgF/L groups), while the VIP-IR varicosities were significantly increased (compared to control) in the group treated with the highest F concentration. Significant morphological changes were seen observed in the density of HUC/D-IR neurons and in the area of SP-IR varicosities for F-treated groups compared to control. Changes in the abundance of various proteins correlated with relevant biological processes, such as protein synthesis, glucose homeostasis and energy metabolism were revealed by proteomics.
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Mito M, Kadota M, Tanaka K, Furuta Y, Abe K, Iwasaki S, Nakagawa S. Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing. Sci Rep 2018; 8:1143. [PMID: 29348483 PMCID: PMC5773701 DOI: 10.1038/s41598-018-19494-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/02/2018] [Indexed: 12/17/2022] Open
Abstract
The nervous system of higher eukaryotes is composed of numerous types of neurons and glia that together orchestrate complex neuronal responses. However, this complex pool of cells typically poses analytical challenges in investigating gene expression profiles and their epigenetic basis for specific cell types. Here, we developed a novel method that enables cell type-specific analyses of epigenetic modifications using tandem chromatin immunoprecipitation sequencing (tChIP-Seq). FLAG-tagged histone H2B, a constitutive chromatin component, was first expressed in Camk2a-positive pyramidal cortical neurons and used to purify chromatin in a cell type-specific manner. Subsequent chromatin immunoprecipitation using antibodies against H3K4me3-a chromatin modification mainly associated with active promoters-allowed us to survey the histone modifications in Camk2a-positive neurons. Indeed, tChIP-Seq identified hundreds of H3K4me3 modifications in promoter regions located upstream of genes associated with neuronal functions and genes with unknown functions in cortical neurons. tChIP-Seq provides a versatile approach to investigating the epigenetic modifications of particular cell types in vivo.
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Affiliation(s)
- Mari Mito
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan.,RNA Systems Biochemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan
| | - Mitsutaka Kadota
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-Minamimachi, Chuou-ku, Kobe, 650-0047, Japan
| | - Kaori Tanaka
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-Minamimachi, Chuou-ku, Kobe, 650-0047, Japan
| | - Yasuhide Furuta
- Animal Resource Development Unit and RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe, 650-0047, Japan.,Genetic Engineering Team, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe, 650-0047, Japan
| | - Kuniya Abe
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan. .,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 2-1 Hirosawa, Wako, 351-0198, Japan.
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan. .,RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan.
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Nitarska J, Smith JG, Sherlock WT, Hillege MMG, Nott A, Barshop WD, Vashisht AA, Wohlschlegel JA, Mitter R, Riccio A. A Functional Switch of NuRD Chromatin Remodeling Complex Subunits Regulates Mouse Cortical Development. Cell Rep 2017; 17:1683-1698. [PMID: 27806305 PMCID: PMC5149529 DOI: 10.1016/j.celrep.2016.10.022] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 08/03/2016] [Accepted: 10/07/2016] [Indexed: 12/31/2022] Open
Abstract
Histone modifications and chromatin remodeling represent universal mechanisms by which cells adapt their transcriptional response to rapidly changing environmental conditions. Extensive chromatin remodeling takes place during neuronal development, allowing the transition of pluripotent cells into differentiated neurons. Here, we report that the NuRD complex, which couples ATP-dependent chromatin remodeling with histone deacetylase activity, regulates mouse brain development. Subunit exchange of CHDs, the core ATPase subunits of the NuRD complex, is required for distinct aspects of cortical development. Whereas CHD4 promotes the early proliferation of progenitors, CHD5 facilitates neuronal migration and CHD3 ensures proper layer specification. Inhibition of each CHD leads to defects of neuronal differentiation and migration, which cannot be rescued by expressing heterologous CHDs. Finally, we demonstrate that NuRD complexes containing specific CHDs are recruited to regulatory elements and modulate the expression of genes essential for brain development. The ATPases CHD3, CHD4, and CHD5 are mutually exclusive subunits of the NuRD complex CHD3, CHD4, and CHD5 regulate distinct and non-redundant aspects of cortical development Loss of each CHD leads to specific defects of neuronal proliferation and migration CHD3, CHD4, and CHD5 regulate distinct set of genes essential for brain development
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Affiliation(s)
- Justyna Nitarska
- MRC Laboratory for Molecular and Cell Biology, University College London, London WC1E 6BT, UK
| | - Jacob G Smith
- MRC Laboratory for Molecular and Cell Biology, University College London, London WC1E 6BT, UK
| | - William T Sherlock
- MRC Laboratory for Molecular and Cell Biology, University College London, London WC1E 6BT, UK
| | - Michele M G Hillege
- MRC Laboratory for Molecular and Cell Biology, University College London, London WC1E 6BT, UK
| | - Alexi Nott
- MRC Laboratory for Molecular and Cell Biology, University College London, London WC1E 6BT, UK
| | - William D Barshop
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1737 USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1737 USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1737 USA
| | - Richard Mitter
- Lincoln's Inn Fields Laboratory, The Francis Crick Institute, London WC2A 3LY, UK
| | - Antonella Riccio
- MRC Laboratory for Molecular and Cell Biology, University College London, London WC1E 6BT, UK.
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CDYL suppresses epileptogenesis in mice through repression of axonal Nav1.6 sodium channel expression. Nat Commun 2017; 8:355. [PMID: 28842554 PMCID: PMC5572458 DOI: 10.1038/s41467-017-00368-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 06/25/2017] [Indexed: 12/27/2022] Open
Abstract
Impairment of intrinsic plasticity is involved in a range of neurological disorders such as epilepsy. However, how intrinsic excitability is regulated is still not fully understood. Here we report that the epigenetic factor Chromodomain Y-like (CDYL) protein is a critical regulator of the initiation and maintenance of intrinsic neuroplasticity by regulating voltage-gated ion channels in mouse brains. CDYL binds to a regulatory element in the intron region of SCN8A and mainly recruits H3K27me3 activity for transcriptional repression of the gene. Knockdown of CDYL in hippocampal neurons results in augmented Nav1.6 currents, lower neuronal threshold, and increased seizure susceptibility, whereas transgenic mice over-expressing CDYL exhibit higher neuronal threshold and are less prone to epileptogenesis. Finally, examination of human brain tissues reveals decreased CDYL and increased SCN8A in the temporal lobe epilepsy group. Together, our findings indicate CDYL is a critical player for experience-dependent gene regulation in controlling intrinsic excitability. Alterations in intrinsic plasticity are important in epilepsy. Here the authors show that the epigenetic factor CDYL regulates the gene expression of the voltage gated sodium channel, Nav1.6, which contributes to seizures in a rat model of epilepsy.
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Neuronal activity-regulated alternative mRNA splicing. Int J Biochem Cell Biol 2017; 91:184-193. [PMID: 28591617 DOI: 10.1016/j.biocel.2017.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/24/2017] [Accepted: 06/01/2017] [Indexed: 11/20/2022]
Abstract
Activity-regulated gene transcription underlies plasticity-dependent changes in the molecular composition and structure of neurons. Numerous genes whose expression is induced by different neuronal plasticity inducing pathways have been identified, but the alteration of gene expression levels represents only part of the complexity of the activity-regulated transcriptional program. Alternative splicing of precursor mRNA is an additional mechanism that modulates the activity-dependent transcriptional signature. Recently developed splicing sensitive transcriptome wide analyses improve our understanding of the underlying mechanisms and demonstrate to what extend the activity regulated transcriptome is alternatively spliced. So far, only for a small group of differentially spliced mRNAs of synaptic proteins, the functional implications have been studied in detail. These include examples in which differential exon usage can result in the expression of alternative proteins which interfere with or alter the function of preexisting proteins and cause a dominant negative functional block of constitutively expressed variants. Such altered proteins contribute to the structural and functional reorganization of pre- and postsynaptic terminals and to the maintenance and formation of synapses. In addition, activity-induced alternative splicing can affect the untranslated regions (UTRs) and generates mRNAs harboring different cis-regulatory elements. Such differential UTRs can influence mRNA stability, translation, and can change the targeting of mRNAs to subcellular compartments. Here, we summarize different categories of alternative splicing which are thought to contribute to synaptic remodeling, give an overview of activity-regulated alternatively spliced mRNAs of synaptic proteins that impact synaptic functions, and discuss splicing factors and epigenetic modifications as regulatory determinants.
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Baruteau J, Jameson E, Morris AA, Chakrapani A, Santra S, Vijay S, Kocadag H, Beesley CE, Grunewald S, Murphy E, Cleary M, Mundy H, Abulhoul L, Broomfield A, Lachmann R, Rahman Y, Robinson PH, MacPherson L, Foster K, Chong WK, Ridout DA, Bounford KM, Waddington SN, Mills PB, Gissen P, Davison JE. Expanding the phenotype in argininosuccinic aciduria: need for new therapies. J Inherit Metab Dis 2017; 40:357-368. [PMID: 28251416 PMCID: PMC5393288 DOI: 10.1007/s10545-017-0022-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/24/2017] [Accepted: 01/25/2017] [Indexed: 12/16/2022]
Abstract
OBJECTIVES This UK-wide study defines the natural history of argininosuccinic aciduria and compares long-term neurological outcomes in patients presenting clinically or treated prospectively from birth with ammonia-lowering drugs. METHODS Retrospective analysis of medical records prior to March 2013, then prospective analysis until December 2015. Blinded review of brain MRIs. ASL genotyping. RESULTS Fifty-six patients were defined as early-onset (n = 23) if symptomatic < 28 days of age, late-onset (n = 23) if symptomatic later, or selectively screened perinatally due to a familial proband (n = 10). The median follow-up was 12.4 years (range 0-53). Long-term outcomes in all groups showed a similar neurological phenotype including developmental delay (48/52), epilepsy (24/52), ataxia (9/52), myopathy-like symptoms (6/52) and abnormal neuroimaging (12/21). Neuroimaging findings included parenchymal infarcts (4/21), focal white matter hyperintensity (4/21), cortical or cerebral atrophy (4/21), nodular heterotopia (2/21) and reduced creatine levels in white matter (4/4). 4/21 adult patients went to mainstream school without the need of additional educational support and 1/21 lives independently. Early-onset patients had more severe involvement of visceral organs including liver, kidney and gut. All early-onset and half of late-onset patients presented with hyperammonaemia. Screened patients had normal ammonia at birth and received treatment preventing severe hyperammonaemia. ASL was sequenced (n = 19) and 20 mutations were found. Plasma argininosuccinate was higher in early-onset compared to late-onset patients. CONCLUSIONS Our study further defines the natural history of argininosuccinic aciduria and genotype-phenotype correlations. The neurological phenotype does not correlate with the severity of hyperammonaemia and plasma argininosuccinic acid levels. The disturbance in nitric oxide synthesis may be a contributor to the neurological disease. Clinical trials providing nitric oxide to the brain merit consideration.
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Affiliation(s)
- Julien Baruteau
- Gene Transfer Technology Group, Institute for Women’s Health, University College London, London, UK
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, WC1N 3JH London, UK
- Genetics and Genomic Medicine Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Elisabeth Jameson
- Metabolic Medicine Department, Royal Manchester Children Hospital NHS Foundation Trust, Manchester, UK
| | - Andrew A. Morris
- Metabolic Medicine Department, Royal Manchester Children Hospital NHS Foundation Trust, Manchester, UK
| | - Anupam Chakrapani
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, WC1N 3JH London, UK
- Metabolic Medicine Department, Birmingham Children’s Hospital NHS Foundation Trust, Birmingham, UK
| | - Saikat Santra
- Metabolic Medicine Department, Birmingham Children’s Hospital NHS Foundation Trust, Birmingham, UK
| | - Suresh Vijay
- Metabolic Medicine Department, Birmingham Children’s Hospital NHS Foundation Trust, Birmingham, UK
| | - Huriye Kocadag
- Gene Transfer Technology Group, Institute for Women’s Health, University College London, London, UK
| | - Clare E. Beesley
- North East Thames Regional Genetic Services, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Stephanie Grunewald
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, WC1N 3JH London, UK
| | - Elaine Murphy
- Charles Dent Metabolic Unit, National Hospital for Neurology and Neurosurgery, London, UK
| | - Maureen Cleary
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, WC1N 3JH London, UK
| | - Helen Mundy
- Metabolic Medicine Department, Evelina Children’s Hospital, London, UK
| | - Lara Abulhoul
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, WC1N 3JH London, UK
| | - Alexander Broomfield
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, WC1N 3JH London, UK
- Metabolic Medicine Department, Royal Manchester Children Hospital NHS Foundation Trust, Manchester, UK
| | - Robin Lachmann
- Charles Dent Metabolic Unit, National Hospital for Neurology and Neurosurgery, London, UK
| | - Yusof Rahman
- Metabolic Medicine Department, St Thomas Hospital, London, UK
| | - Peter H. Robinson
- Paediatric Metabolic Medicine, Royal Hospital for Sick Children, Glasgow, UK
| | - Lesley MacPherson
- Neuroradiology Department, Birmingham Children’s Hospital NHS Foundation Trust, Birmingham, UK
| | - Katharine Foster
- Neuroradiology Department, Birmingham Children’s Hospital NHS Foundation Trust, Birmingham, UK
| | - W. Kling Chong
- Neuroradiology Department, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Deborah A. Ridout
- Population, Policy and Practice Programme, UCL Institute of Child Health, London, UK
| | | | - Simon N. Waddington
- Gene Transfer Technology Group, Institute for Women’s Health, University College London, London, UK
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Philippa B. Mills
- Genetics and Genomic Medicine Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Paul Gissen
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, WC1N 3JH London, UK
- Genetics and Genomic Medicine Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - James E. Davison
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, WC1N 3JH London, UK
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Langie SAS, Cameron KM, Ficz G, Oxley D, Tomaszewski B, Gorniak JP, Maas LM, Godschalk RWL, van Schooten FJ, Reik W, von Zglinicki T, Mathers JC. The Ageing Brain: Effects on DNA Repair and DNA Methylation in Mice. Genes (Basel) 2017; 8:E75. [PMID: 28218666 PMCID: PMC5333064 DOI: 10.3390/genes8020075] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/02/2017] [Accepted: 02/07/2017] [Indexed: 12/15/2022] Open
Abstract
Base excision repair (BER) may become less effective with ageing resulting in accumulation of DNA lesions, genome instability and altered gene expression that contribute to age-related degenerative diseases. The brain is particularly vulnerable to the accumulation of DNA lesions; hence, proper functioning of DNA repair mechanisms is important for neuronal survival. Although the mechanism of age-related decline in DNA repair capacity is unknown, growing evidence suggests that epigenetic events (e.g., DNA methylation) contribute to the ageing process and may be functionally important through the regulation of the expression of DNA repair genes. We hypothesize that epigenetic mechanisms are involved in mediating the age-related decline in BER in the brain. Brains from male mice were isolated at 3-32 months of age. Pyrosequencing analyses revealed significantly increased Ogg1 methylation with ageing, which correlated inversely with Ogg1 expression. The reduced Ogg1 expression correlated with enhanced expression of methyl-CpG binding protein 2 and ten-eleven translocation enzyme 2. A significant inverse correlation between Neil1 methylation at CpG-site2 and expression was also observed. BER activity was significantly reduced and associated with increased 8-oxo-7,8-dihydro-2'-deoxyguanosine levels. These data indicate that Ogg1 and Neil1 expression can be epigenetically regulated, which may mediate the effects of ageing on DNA repair in the brain.
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Affiliation(s)
- Sabine A S Langie
- Centre for Ageing and Vitality, Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK.
| | - Kerry M Cameron
- The Ageing Biology Centre and Institute for Cell and Molecular Biology, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK.
| | - Gabriella Ficz
- Barts Cancer Institute, Queen Mary University, London EC1M 6BQ, UK.
| | - David Oxley
- Mass Spectrometry Laboratory, Babraham Institute, Cambridge CB22 3AT, UK.
| | - Bartłomiej Tomaszewski
- Centre for Ageing and Vitality, Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK.
| | - Joanna P Gorniak
- Centre for Ageing and Vitality, Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK.
| | - Lou M Maas
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands.
| | - Roger W L Godschalk
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands.
| | - Frederik J van Schooten
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands.
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK.
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
| | - Thomas von Zglinicki
- The Ageing Biology Centre and Institute for Cell and Molecular Biology, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK.
| | - John C Mathers
- Centre for Ageing and Vitality, Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK.
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Francelle L, Lotz C, Outeiro T, Brouillet E, Merienne K. Contribution of Neuroepigenetics to Huntington's Disease. Front Hum Neurosci 2017; 11:17. [PMID: 28194101 PMCID: PMC5276857 DOI: 10.3389/fnhum.2017.00017] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/10/2017] [Indexed: 12/29/2022] Open
Abstract
Unbalanced epigenetic regulation is thought to contribute to the progression of several neurodegenerative diseases, including Huntington’s disease (HD), a genetic disorder considered as a paradigm of epigenetic dysregulation. In this review, we attempt to address open questions regarding the role of epigenetic changes in HD, in the light of recent advances in neuroepigenetics. We particularly discuss studies using genome-wide scale approaches that provide insights into the relationship between epigenetic regulations, gene expression and neuronal activity in normal and diseased neurons, including HD neurons. We propose that cell-type specific techniques and 3D-based methods will advance knowledge of epigenome in the context of brain region vulnerability in neurodegenerative diseases. A better understanding of the mechanisms underlying epigenetic changes and of their consequences in neurodegenerative diseases is required to design therapeutic strategies more effective than current strategies based on histone deacetylase (HDAC) inhibitors. Researches in HD may play a driving role in this process.
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Affiliation(s)
- Laetitia Francelle
- Department of NeuroDegeneration and Restorative Research, University Medical Center Goettingen Goettingen, Germany
| | - Caroline Lotz
- CNRS UMR 7364, Laboratory of Cognitive and Adaptive Neurosciences, University of Strasbourg Strasbourg, France
| | - Tiago Outeiro
- Department of NeuroDegeneration and Restorative Research, University Medical Center Goettingen Goettingen, Germany
| | - Emmanuel Brouillet
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Département de Recherche Fondamentale, Institut d'Imagerie Biomédicale, Molecular Imaging Center, Neurodegenerative diseases Laboratory, UMR 9199, CNRS Université Paris-Sud, Université Paris-Saclay Fontenay-aux-Roses, France
| | - Karine Merienne
- CNRS UMR 7364, Laboratory of Cognitive and Adaptive Neurosciences, University of Strasbourg Strasbourg, France
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SFPQ associates to LSD1 and regulates the migration of newborn pyramidal neurons in the developing cerebral cortex. Int J Dev Neurosci 2016; 57:1-11. [PMID: 28034769 DOI: 10.1016/j.ijdevneu.2016.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/16/2016] [Accepted: 12/20/2016] [Indexed: 12/24/2022] Open
Abstract
The development of the cerebral cortex requires the coordination of multiple processes ranging from the proliferation of progenitors to the migration and establishment of connectivity of the newborn neurons. Epigenetic regulation carried out by the COREST/LSD1 complex has been identified as a mechanism that regulates the development of pyramidal neurons of the cerebral cortex. We now identify the association of the multifunctional RNA-binding protein SFPQ to LSD1 during the development of the cerebral cortex. In vivo reduction of SFPQ dosage by in utero electroporation of a shRNA results in impaired radial migration of newborn pyramidal neurons, in a similar way to that observed when COREST or LSD1 expressions are decreased. Diminished SFPQ expression also associates to decreased proliferation of progenitor cells, while it does not affect the acquisition of neuronal fate. These results are compatible with the idea that SFPQ, plays an important role regulating proliferation and migration during the development of the cerebral cortex.
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Grzybek M, Golonko A, Walczak M, Lisowski P. Epigenetics of cell fate reprogramming and its implications for neurological disorders modelling. Neurobiol Dis 2016; 99:84-120. [PMID: 27890672 DOI: 10.1016/j.nbd.2016.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 11/03/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
The reprogramming of human induced pluripotent stem cells (hiPSCs) proceeds in a stepwise manner with reprogramming factors binding and epigenetic composition changes during transition to maintain the epigenetic landscape, important for pluripotency. There arises a question as to whether the aberrant epigenetic state after reprogramming leads to epigenetic defects in induced stem cells causing unpredictable long term effects in differentiated cells. In this review, we present a comprehensive view of epigenetic alterations accompanying reprogramming, cell maintenance and differentiation as factors that influence applications of hiPSCs in stem cell based technologies. We conclude that sample heterogeneity masks DNA methylation signatures in subpopulations of cells and thus believe that beside a genetic evaluation, extensive epigenomic screening should become a standard procedure to ensure hiPSCs state before they are used for genome editing and differentiation into neurons of interest. In particular, we suggest that exploitation of the single-cell composition of the epigenome will provide important insights into heterogeneity within hiPSCs subpopulations to fast forward development of reliable hiPSC-based analytical platforms in neurological disorders modelling and before completed hiPSC technology will be implemented in clinical approaches.
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Affiliation(s)
- Maciej Grzybek
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-950 Lublin, Poland; Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland.
| | - Aleksandra Golonko
- Department of Biotechnology, Faculty of Civil and Environmental Engineering, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland.
| | - Marta Walczak
- Department of Animal Behavior, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland.
| | - Pawel Lisowski
- Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland; iPS Cell-Based Disease Modelling Group, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13092 Berlin, Germany.
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Gushchina SV, Balashov VP, Magoulas KB. Methodological Approaches to In Vitro Evaluation of Transcription Activity of Nuclear Factor Kappa B (NF-κB) in Sensory Neurons. Bull Exp Biol Med 2016; 161:736-740. [PMID: 27704345 DOI: 10.1007/s10517-016-3497-9] [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: 09/08/2015] [Indexed: 10/20/2022]
Abstract
Transcription activity of NF-κB in sensory neurons was analyzed in vitro using classical immunocytochemical methods and transgenic technologies. Activation of NF-κB in NIH3T3 cells and in murine sensory neurons after in vitro stimulation with TNF-α was demonstrated by the immunocytochemical method; however, the expression of the reporter NF-κB/LacZ transgene was detected only after addition of histon deacetylase inhibitor. Hence, formally contradictory conclusions from the results of immunocytochemical analysis and reporter transgene expression were in line with the hypothesis on epigenetic repression of NF-κB activity in sensory neurons mediated by histon deacetylases.
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Affiliation(s)
- S V Gushchina
- Department of Histology, Cytology, and Embryology, N. P. Ogarev Mordovia State University, Saransk, Republic of Mordovia, Russia. .,Molecular Neuroscience Group, Centre for Neuroscience and Trauma, Queen Mary University of London, London, UK.
| | - V P Balashov
- Department of Histology, Cytology, and Embryology, N. P. Ogarev Mordovia State University, Saransk, Republic of Mordovia, Russia
| | - K B Magoulas
- School of Science and Technology, Middlesex University, London, UK
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